1
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Singha K, Habib I, Hossain M. Quinoline N‐Oxide: A Versatile Precursor in Organic Transformations. ChemistrySelect 2022. [DOI: 10.1002/slct.202203537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Koustav Singha
- Synthetic Organic Research Laboratory UGC-Human Resource Development Centre (Chemistry) University of North Bengal Siliguri Darjeeling 734013 India
| | - Imran Habib
- Synthetic Organic Research Laboratory UGC-Human Resource Development Centre (Chemistry) University of North Bengal Siliguri Darjeeling 734013 India
| | - Mossaraf Hossain
- Synthetic Organic Research Laboratory UGC-Human Resource Development Centre (Chemistry) University of North Bengal Siliguri Darjeeling 734013 India
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2
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Sarmah BK, Konwar M, Das A. Copper-Catalyzed Oxidative Dehydrogenative Reaction of Quinoline- N-Oxides with Donor-Acceptor Cyclopropanes: Installation of a Tertiary Alkyl Motif at C2 Position. Org Lett 2021; 23:8390-8395. [PMID: 34633204 DOI: 10.1021/acs.orglett.1c03115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A copper-catalyzed oxidative dehydrogenative reaction of quinoline N-oxides with donor-acceptor cyclopropanes has been demonstrated to construct C2-alkylated quinolines containing a γ-keto diester motif. The use of molecular oxygen as an oxidant, excellent site-selectivity, and good functional group tolerance are the important features in this process. The preliminary mechanistic studies demonstrate that the catalyst plays a dual role as a Lewis acid and a redox catalyst.
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Affiliation(s)
- Bikash Kumar Sarmah
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Monuranjan Konwar
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Animesh Das
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
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3
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Inhibitory Effect of Lithospermic Acid on the HIV-1 Nucleocapsid Protein. Molecules 2020; 25:molecules25225434. [PMID: 33233563 PMCID: PMC7699738 DOI: 10.3390/molecules25225434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/10/2020] [Accepted: 11/18/2020] [Indexed: 02/06/2023] Open
Abstract
The HIV-1 nucleocapsid protein (NC) is a desirable target in antiretroviral therapy due to its high conservation among HIV-1 strains, and to its multiple and crucial roles in the HIV-1 replication cycle. Natural products represent a valuable source of NC inhibitors, with the catechol group being a privileged scaffold in NC inhibition. By coupling molecular modeling with NMR spectroscopy and fluorescence-based assays, we disclosed lithospermic acid, a catechol derivative extracted from Salvia miltiorrhizza, as a potent and chemically stable non-covalent inhibitor of the NC. Being different from other catechol derivative reported so far, lithospermic acid does not undergo spontaneous oxidation in physiological conditions, thus becoming a profitable starting point for the development of efficient NC inhibitors.
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4
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Malancona S, Mori M, Fezzardi P, Santoriello M, Basta A, Nibbio M, Kovalenko L, Speziale R, Battista MR, Cellucci A, Gennari N, Monteagudo E, Di Marco A, Giannini A, Sharma R, Pires M, Real E, Zazzi M, Dasso Lang MC, De Forni D, Saladini F, Mely Y, Summa V, Harper S, Botta M. 5,6-Dihydroxypyrimidine Scaffold to Target HIV-1 Nucleocapsid Protein. ACS Med Chem Lett 2020; 11:766-772. [PMID: 32435383 DOI: 10.1021/acsmedchemlett.9b00608] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/19/2020] [Indexed: 01/27/2023] Open
Abstract
The HIV-1 nucleocapsid (NC) protein is a small basic DNA and RNA binding protein that is absolutely necessary for viral replication and thus represents a target of great interest to develop new anti-HIV agents. Moreover, the highly conserved sequence offers the opportunity to escape the drug resistance (DR) that emerged following the highly active antiretroviral therapy (HAART) treatment. On the basis of our previous research, nordihydroguaiaretic acid 1 acts as a NC inhibitor showing moderate antiviral activity and suboptimal drug-like properties due to the presence of the catechol moieties. A bioisosteric catechol replacement approach led us to identify the 5-dihydroxypyrimidine-6-carboxamide substructure as a privileged scaffold of a new class of HIV-1 NC inhibitors. Hit validation efforts led to the identification of optimized analogs, as represented by compound 28, showing improved NC inhibition and antiviral activity as well as good ADME and PK properties.
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Affiliation(s)
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Paola Fezzardi
- IRBM S.p.A., Via Pontina Km 30.600, 00071 Pomezia, Rome, Italy
| | | | - Andreina Basta
- IRBM S.p.A., Via Pontina Km 30.600, 00071 Pomezia, Rome, Italy
| | - Martina Nibbio
- IRBM S.p.A., Via Pontina Km 30.600, 00071 Pomezia, Rome, Italy
| | - Lesia Kovalenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | | | | | | | - Nadia Gennari
- IRBM S.p.A., Via Pontina Km 30.600, 00071 Pomezia, Rome, Italy
| | | | | | - Alessia Giannini
- Department of Medical Biotechnologies, University of Siena, Viale Mario Bracci, 16, 50100 Siena, Italy
| | - Rajhans Sharma
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Manuel Pires
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Eleonore Real
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Viale Mario Bracci, 16, 50100 Siena, Italy
| | - Maria Chiara Dasso Lang
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | | | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, Viale Mario Bracci, 16, 50100 Siena, Italy
| | - Yves Mely
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Vincenzo Summa
- IRBM S.p.A., Via Pontina Km 30.600, 00071 Pomezia, Rome, Italy
| | - Steven Harper
- IRBM S.p.A., Via Pontina Km 30.600, 00071 Pomezia, Rome, Italy
| | - Maurizio Botta
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
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5
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Humbert N, Kovalenko L, Saladini F, Giannini A, Pires M, Botzanowski T, Cherenok S, Boudier C, Sharma KK, Real E, Zaporozhets OA, Cianférani S, Seguin-Devaux C, Poggialini F, Botta M, Zazzi M, Kalchenko VI, Mori M, Mély Y. (Thia)calixarenephosphonic Acids as Potent Inhibitors of the Nucleic Acid Chaperone Activity of the HIV-1 Nucleocapsid Protein with a New Binding Mode and Multitarget Antiviral Activity. ACS Infect Dis 2020; 6:687-702. [PMID: 32045204 DOI: 10.1021/acsinfecdis.9b00290] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nucleocapsid protein (NC) is a highly conserved protein that plays key roles in HIV-1 replication through its nucleic acid chaperone properties mediated by its two zinc fingers and basic residues. NC is a promising target for antiviral therapy, particularly to control viral strains resistant to currently available drugs. Since calixarenes with antiviral properties have been described, we explored the ability of calixarene hydroxymethylphosphonic or sulfonic acids to inhibit NC chaperone properties and exhibit antiviral activity. By using fluorescence-based assays, we selected four calixarenes inhibiting NC chaperone activity with submicromolar IC50 values. These compounds were further shown by mass spectrometry, isothermal titration calorimetry, and fluorescence anisotropy to bind NC with no zinc ejection and to compete with nucleic acids for the binding to NC. Molecular dynamic simulations further indicated that these compounds interact via their phosphonate or sulfonate groups with the basic surface of NC but not with the hydrophobic plateau at the top of the folded fingers. Cellular studies showed that the most soluble compound CIP201 inhibited the infectivity of wild-type and drug-resistant HIV-1 strains at low micromolar concentrations, primarily targeting the early steps of HIV-1 replication. Moreover, CIP201 was also found to inhibit the flipping and polymerization activity of reverse transcriptase. Calixarenes thus form a class of noncovalent NC inhibitors, endowed with a new binding mode and multitarget antiviral activity.
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Affiliation(s)
- Nicolas Humbert
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Lesia Kovalenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
- Department of Chemistry, Taras Shevchenko National University of Kyiv, 01601 Kyiv, Ukraine
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, viale Mario Bracci no. 16, 53100 Siena, Italy
| | - Alessia Giannini
- Department of Medical Biotechnologies, University of Siena, viale Mario Bracci no. 16, 53100 Siena, Italy
| | - Manuel Pires
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Sergiy Cherenok
- Institute of Organic Chemistry, National Academy of Science of Ukraine, Murmanska str. 5, Kyiv 02660, Ukraine
| | - Christian Boudier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Kamal K. Sharma
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Eleonore Real
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Olga A. Zaporozhets
- Department of Chemistry, Taras Shevchenko National University of Kyiv, 01601 Kyiv, Ukraine
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Carole Seguin-Devaux
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg
| | - Federica Poggialini
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 Università degli Studi di Siena, via Aldo Moro 2, I-53019 Siena, Italy
| | - Maurizio Botta
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 Università degli Studi di Siena, via Aldo Moro 2, I-53019 Siena, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, viale Mario Bracci no. 16, 53100 Siena, Italy
| | - Vitaly I. Kalchenko
- Institute of Organic Chemistry, National Academy of Science of Ukraine, Murmanska str. 5, Kyiv 02660, Ukraine
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 Università degli Studi di Siena, via Aldo Moro 2, I-53019 Siena, Italy
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
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6
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Mori M, Manetti F, Botta B, Tafi A. In Memory of Maurizio Botta: His Contribution to the Development of Computer-Aided Drug Design. J Chem Inf Model 2019; 59:4961-4967. [PMID: 31804073 DOI: 10.1021/acs.jcim.9b01043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 , University of Siena , via Aldo Moro 2 , 53100 Siena , Italy
| | - Fabrizio Manetti
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 , University of Siena , via Aldo Moro 2 , 53100 Siena , Italy
| | - Bruno Botta
- Department of Chemistry and Technology of Drugs, Department of Excellence 2018-2022 , Sapienza University of Rome , Piazzale Aldo Moro 5 , 00185 Rome , Italy
| | - Andrea Tafi
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 , University of Siena , via Aldo Moro 2 , 53100 Siena , Italy
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7
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Ku T, Lopresti N, Shirley M, Mori M, Marchant J, Heng X, Botta M, Summers MF, Seley-Radtke KL. Synthesis of distal and proximal fleximer base analogues and evaluation in the nucleocapsid protein of HIV-1. Bioorg Med Chem 2019; 27:2883-2892. [PMID: 31126822 PMCID: PMC6556414 DOI: 10.1016/j.bmc.2019.05.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/01/2019] [Accepted: 05/11/2019] [Indexed: 11/29/2022]
Abstract
Anti-HIV-1 drug design has been notably challenging due to the virus’ ability to mutate and develop immunity against commercially available drugs. The aims of this project were to develop a series of fleximer base analogues that not only possess inherent flexibility that can remain active when faced with binding site mutations, but also target a non-canonical, highly conserved target: the nucleocapsid protein of HIV (NC). The compounds were predicted by computational studies not to function via zinc ejection, which would endow them with significant advantages over non-specific and thus toxic zinc-ejectors. The target fleximer bases were synthesized using palladium-catalyzed cross-coupling techniques and subsequently tested against NC and HIV-1. The results of those studies are described herein.
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Affiliation(s)
- Therese Ku
- University of Maryland, Baltimore County, Department of Chemistry and Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Natalie Lopresti
- University of Maryland, Baltimore County, Department of Chemistry and Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Matthew Shirley
- University of Maryland, Baltimore County, Department of Chemistry and Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Mattia Mori
- University of Siena, Department of Biotechnology, Chemistry and Pharmacy, via Aldo Moro 2, 53100 Siena, Italy
| | - Jan Marchant
- University of Maryland, Baltimore County, Department of Chemistry and Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Xiao Heng
- University of Maryland, Baltimore County, Department of Chemistry and Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Maurizio Botta
- University of Siena, Department of Biotechnology, Chemistry and Pharmacy, via Aldo Moro 2, 53100 Siena, Italy; Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, BioLife Science Bldg., Suite 333, 1900 N 12th Street, Philadelphia, PA 19122, USA
| | - Michael F Summers
- University of Maryland, Baltimore County, Department of Chemistry and Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21250, USA; Howard Hughes Medical Institute, USA
| | - Katherine L Seley-Radtke
- University of Maryland, Baltimore County, Department of Chemistry and Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
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8
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Mori M, Dasso Lang MC, Saladini F, Palombi N, Kovalenko L, De Forni D, Poddesu B, Friggeri L, Giannini A, Malancona S, Summa V, Zazzi M, Mely Y, Botta M. Synthesis and Evaluation of Bifunctional Aminothiazoles as Antiretrovirals Targeting the HIV-1 Nucleocapsid Protein. ACS Med Chem Lett 2019; 10:463-468. [PMID: 30996780 DOI: 10.1021/acsmedchemlett.8b00506] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/07/2018] [Indexed: 02/07/2023] Open
Abstract
Small molecule inhibitors of the HIV-1 nucleocapsid protein (NC) are considered as promising agents in the treatment of HIV/AIDS. In an effort to exploit the privileged 2-amino-4-phenylthiazole moiety in NC inhibition, here we conceived, synthesized, and tested in vitro 18 NC inhibitors (NCIs) bearing a double functionalization. In these NCIs, one part of the molecule is deputed to interact noncovalently with the NC hydrophobic pocket, while the second portion is designed to interact with the N-terminal domain of NC. This binding hypothesis was verified by molecular dynamics simulations, while the linkage between these two pharmacophores was found to enhance antiretroviral activity both on the wild-type virus and on HIV-1 strains with resistance to currently licensed drugs. The two most interesting compounds 6 and 13 showed no cytotoxicity, thus becoming valuable leads for further investigations.
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Affiliation(s)
- Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, “Department of Excellence 2018-2022”, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Maria Chiara Dasso Lang
- Department of Biotechnology, Chemistry and Pharmacy, “Department of Excellence 2018-2022”, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, Viale Mario Bracci, 16, 53100 Siena, Italy
| | - Nastasja Palombi
- Department of Biotechnology, Chemistry and Pharmacy, “Department of Excellence 2018-2022”, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Lesia Kovalenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Faculté
de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Davide De Forni
- ViroStatics S.r.l., Viale Umberto I 46, 07100 Sassari, Italy
| | - Barbara Poddesu
- ViroStatics S.r.l., Viale Umberto I 46, 07100 Sassari, Italy
| | - Laura Friggeri
- Department of Biotechnology, Chemistry and Pharmacy, “Department of Excellence 2018-2022”, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Alessia Giannini
- Department of Medical Biotechnologies, University of Siena, Viale Mario Bracci, 16, 53100 Siena, Italy
| | - Savina Malancona
- IRBM Science Park S.p.A., Via Pontina Km 30.600, 00071 Pomezia (RM), Italy
| | - Vincenzo Summa
- IRBM Science Park S.p.A., Via Pontina Km 30.600, 00071 Pomezia (RM), Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Viale Mario Bracci, 16, 53100 Siena, Italy
| | - Yves Mely
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Faculté
de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Maurizio Botta
- Department of Biotechnology, Chemistry and Pharmacy, “Department of Excellence 2018-2022”, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, BioLife Science Bldg., Suite
333, 1900 N 12th Street, Philadelphia, Pennsylvania 19122, United States
- Lead Discovery Siena s.r.l., Via Vittorio Alfieri 31, 53019 Castelnuovo, Berardenga, Italy
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9
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Fratev F, Steinbrecher T, Jónsdóttir SÓ. Prediction of Accurate Binding Modes Using Combination of Classical and Accelerated Molecular Dynamics and Free-Energy Perturbation Calculations: An Application to Toxicity Studies. ACS OMEGA 2018; 3:4357-4371. [PMID: 31458661 PMCID: PMC6641415 DOI: 10.1021/acsomega.8b00123] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 04/04/2018] [Indexed: 05/30/2023]
Abstract
Estimating the correct binding modes of ligands in protein-ligand complexes is crucial not only in the drug discovery process but also for elucidating potential toxicity mechanisms. In the current paper, we propose a computational modeling workflow using the combination of docking, classical molecular dynamics (cMD), accelerated molecular dynamics (aMD) and free-energy perturbation (FEP+ protocol) for identification of possible ligand binding modes. It was applied for investigation of selected perfluorocarboxyl acids (PFCAs) in the PPARγ nuclear receptor. Although both regular and induced fit docking failed to reproduce the experimentally determined binding mode of the ligands when docked into a non-native X-ray structure, cMD and aMD simulations successfully identified the most probable binding conformations. Moreover, multiple binding modes were identified for all of these compounds and the shorter-chain PFCAs continuously moved between a few energetically favorable binding conformations. On the basis of MD predictions of binding conformations, we applied the default and also redesigned FEP+ sampling protocols, which accurately reproduced experimental differences in the binding energies. Thus, the preliminary MD simulations can also provide helpful information about correct setup of the FEP+ calculations. These results show that the PFCA binding modes were accurately predicted and that the FEP+ protocol can be used to estimate free energies of binding of flexible ligands that are not typical druglike compounds. Our in silico workflow revealed the specific ligand-residue interactions within the ligand binding domain and the main characteristics of the PFCAs, and it was concluded that these compounds are week PPARγ partial agonists. This work also suggests a common pipeline for identification of ligand binding modes, ligand-protein dynamics description, and relative free-energy calculations.
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Affiliation(s)
- Filip Fratev
- Department
of Pharmaceutical Sciences, School of Pharmacy, The University of Texas at El Paso, 1101 N Campbell Street, El Paso, Texas 79902, United
States
- Micar21
Ltd., Persenk 34B, 1407 Sofia, Bulgaria
| | - Thomas Steinbrecher
- Schrödinger
GmbH, Dynamostrasse 13, 68165 Mannheim, Baden-Württemberg, Germany
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10
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Calcaterra A, Iovine V, Botta B, Quaglio D, D'Acquarica I, Ciogli A, Iazzetti A, Alfonsi R, Lospinoso Severini L, Infante P, Di Marcotullio L, Mori M, Ghirga F. Chemical, computational and functional insights into the chemical stability of the Hedgehog pathway inhibitor GANT61. J Enzyme Inhib Med Chem 2018; 33:349-358. [PMID: 29338454 PMCID: PMC6009951 DOI: 10.1080/14756366.2017.1419221] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
This work aims at elucidating the mechanism and kinetics of hydrolysis of GANT61, the first and most-widely used inhibitor of the Hedgehog (Hh) signalling pathway that targets Glioma-associated oncogene homologue (Gli) proteins, and at confirming the chemical nature of its bioactive form. GANT61 is poorly stable under physiological conditions and rapidly hydrolyses into an aldehyde species (GANT61-A), which is devoid of the biological activity against Hh signalling, and a diamine derivative (GANT61-D), which has shown inhibition of Gli-mediated transcription. Here, we combined chemical synthesis, NMR spectroscopy, analytical studies, molecular modelling and functional cell assays to characterise the GANT61 hydrolysis pathway. Our results show that GANT61-D is the bioactive form of GANT61 in NIH3T3 Shh-Light II cells and SuFu−/− mouse embryonic fibroblasts, and clarify the structural requirements for GANT61-D binding to Gli1. This study paves the way to the design of GANT61 derivatives with improved potency and chemical stability.
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Affiliation(s)
- Andrea Calcaterra
- a Department of Chemistry and Technology of Drugs , Sapienza University of Rome , Rome , Italy
| | - Valentina Iovine
- a Department of Chemistry and Technology of Drugs , Sapienza University of Rome , Rome , Italy
| | - Bruno Botta
- a Department of Chemistry and Technology of Drugs , Sapienza University of Rome , Rome , Italy
| | - Deborah Quaglio
- a Department of Chemistry and Technology of Drugs , Sapienza University of Rome , Rome , Italy
| | - Ilaria D'Acquarica
- a Department of Chemistry and Technology of Drugs , Sapienza University of Rome , Rome , Italy
| | - Alessia Ciogli
- a Department of Chemistry and Technology of Drugs , Sapienza University of Rome , Rome , Italy
| | - Antonia Iazzetti
- a Department of Chemistry and Technology of Drugs , Sapienza University of Rome , Rome , Italy
| | - Romina Alfonsi
- b Department of Molecular Medicine , Sapienza University of Rome , Rome , Italy
| | | | - Paola Infante
- c Center for Life Nano Science@Sapienza , Istituto Italiano di Tecnologia , Rome , Italy
| | - Lucia Di Marcotullio
- b Department of Molecular Medicine , Sapienza University of Rome , Rome , Italy.,d Pasteur Institute/Cenci Bolognetti Foundation , Sapienza University of Rome , Rome , Italy
| | - Mattia Mori
- c Center for Life Nano Science@Sapienza , Istituto Italiano di Tecnologia , Rome , Italy
| | - Francesca Ghirga
- c Center for Life Nano Science@Sapienza , Istituto Italiano di Tecnologia , Rome , Italy
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11
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Mori M, Kovalenko L, Malancona S, Saladini F, De Forni D, Pires M, Humbert N, Real E, Botzanowski T, Cianférani S, Giannini A, Dasso Lang MC, Cugia G, Poddesu B, Lori F, Zazzi M, Harper S, Summa V, Mely Y, Botta M. Structure-Based Identification of HIV-1 Nucleocapsid Protein Inhibitors Active against Wild-Type and Drug-Resistant HIV-1 Strains. ACS Chem Biol 2018; 13:253-266. [PMID: 29235845 DOI: 10.1021/acschembio.7b00907] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
HIV/AIDS is still one of the leading causes of death worldwide. Current drugs that target the canonical steps of the HIV-1 life cycle are efficient in blocking viral replication but are unable to eradicate HIV-1 from infected patients. Moreover, drug resistance (DR) is often associated with the clinical use of these molecules, thus raising the need for novel drug candidates as well as novel putative drug targets. In this respect, pharmacological inhibition of the highly conserved and multifunctional nucleocapsid protein (NC) of HIV-1 is considered a promising alternative to current drugs, particularly to overcome DR. Here, using a multidisciplinary approach combining in silico screening, fluorescence-based molecular assays, and cellular antiviral assays, we identified nordihydroguaiaretic acid (6), as a novel natural product inhibitor of NC. By using NMR, mass spectrometry, fluorescence spectroscopy, and molecular modeling, 6 was found to act through a dual mechanism of action never highlighted before for NC inhibitors (NCIs). First, the molecule recognizes and binds NC noncovalently, which results in the inhibition of the nucleic acid chaperone properties of NC. In a second step, chemical oxidation of 6 induces a potent chemical inactivation of the protein. Overall, 6 inhibits NC and the replication of wild-type and drug-resistant HIV-1 strains in the low micromolar range with moderate cytotoxicity that makes it a profitable tool compound as well as a good starting point for the development of pharmacologically relevant NCIs.
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Affiliation(s)
- Mattia Mori
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Lesia Kovalenko
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213, Faculté de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
- Department
of Chemistry, Kyiv National Taras Shevchenko University, 01033 Kyiv, Ukraine
| | - Savina Malancona
- IRBM Science Park S.p.A., Via Pontina Km 30.600, 00071 Pomezia (RM), Italy
| | - Francesco Saladini
- Department
of Medical Biotechnologies, University of Siena, Viale Mario Bracci,
16, 50100 Siena, Italy
| | | | - Manuel Pires
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213, Faculté de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Nicolas Humbert
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213, Faculté de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Eleonore Real
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213, Faculté de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Thomas Botzanowski
- Laboratoire
de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
| | - Sarah Cianférani
- Laboratoire
de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
| | - Alessia Giannini
- Department
of Medical Biotechnologies, University of Siena, Viale Mario Bracci,
16, 50100 Siena, Italy
| | - Maria Chiara Dasso Lang
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Giulia Cugia
- ViroStatics S.r.l, Viale Umberto
I 46, 07100 Sassari, Italy
| | | | - Franco Lori
- ViroStatics S.r.l, Viale Umberto
I 46, 07100 Sassari, Italy
| | - Maurizio Zazzi
- Department
of Medical Biotechnologies, University of Siena, Viale Mario Bracci,
16, 50100 Siena, Italy
| | - Steven Harper
- IRBM Science Park S.p.A., Via Pontina Km 30.600, 00071 Pomezia (RM), Italy
| | - Vincenzo Summa
- IRBM Science Park S.p.A., Via Pontina Km 30.600, 00071 Pomezia (RM), Italy
| | - Yves Mely
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213, Faculté de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Maurizio Botta
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
- Sbarro
Institute for Cancer Research and Molecular Medicine, Center for Biotechnology,
College of Science and Technology, Temple University, BioLife Science
Bldg., Suite 333, 1900 N 12th Street, Philadelphia, Pennsylvania 19122, United States
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12
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Iraci N, Tabarrini O, Santi C, Sancineto L. NCp7: targeting a multitask protein for next-generation anti-HIV drug development part 2. Noncovalent inhibitors and nucleic acid binders. Drug Discov Today 2018; 23:687-695. [PMID: 29326078 DOI: 10.1016/j.drudis.2018.01.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 10/25/2017] [Accepted: 01/04/2018] [Indexed: 02/06/2023]
Abstract
Nucleocapsid protein 7 (NCp7) represents a viable target not yet reached by the currently available antiretrovirals. It is a small and highly basic protein, which is essential for multiple stages of the viral replicative cycle, with its structure preserved in all viral strains, including clinical isolates. NCp7 can be inhibited covalently, noncovalently and by shielding the nucleic acid (NA) substrates of its chaperone activity. Although covalent NCp7 inhibitors have already been detailed in the first part of this review series, the focus here is based on noncovalent and NA-binder inhibitors and on the analysis of the NCp7 3D structure to deliver fruitful insights for future drug design strategies.
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Affiliation(s)
- Nunzio Iraci
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Claudio Santi
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Luca Sancineto
- Department of Heterorganic Chemistry, Centre of Molecular and Macromulecular Studies, Lodz, Poland.
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13
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Identification of novel 2-benzoxazolinone derivatives with specific inhibitory activity against the HIV-1 nucleocapsid protein. Eur J Med Chem 2017; 145:154-164. [PMID: 29324338 DOI: 10.1016/j.ejmech.2017.12.073] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/16/2017] [Accepted: 12/20/2017] [Indexed: 11/23/2022]
Abstract
In this report, we present a new benzoxazole derivative endowed with inhibitory activity against the HIV-1 nucleocapsid protein (NC). NC is a 55-residue basic protein with nucleic acid chaperone properties, which has emerged as a novel and potential pharmacological target against HIV-1. In the pursuit of novel NC-inhibitor chemotypes, we performed virtual screening and in vitro biological evaluation of a large library of chemical entities. We found that compounds sharing a benzoxazolinone moiety displayed putative inhibitory properties, which we further investigated by considering a series of chemical analogues. This approach provided valuable information on the structure-activity relationships of these compounds and, in the process, demonstrated that their anti-NC activity could be finely tuned by the addition of specific substituents to the initial benzoxazolinone scaffold. This study represents the starting point for the possible development of a new class of antiretroviral agents targeting the HIV-1 NC protein.
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14
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Piras M, Testa A, Fleming IN, Dall'Angelo S, Andriu A, Menta S, Mori M, Brown GD, Forster D, Williams KJ, Zanda M. High-Affinity “Click” RGD Peptidomimetics as Radiolabeled Probes for Imaging αv
β3
Integrin. ChemMedChem 2017; 12:1142-1151. [DOI: 10.1002/cmdc.201700328] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Monica Piras
- Institute of Medical Sciences and Kosterlitz Centre for Therapeutics, School of Medicine, Medical Sciences and Nutrition; University of Aberdeen, Foresterhill; Aberdeen AB25 2ZD Scotland UK
| | - Andrea Testa
- Institute of Medical Sciences and Kosterlitz Centre for Therapeutics, School of Medicine, Medical Sciences and Nutrition; University of Aberdeen, Foresterhill; Aberdeen AB25 2ZD Scotland UK
| | - Ian N. Fleming
- Institute of Medical Sciences and Kosterlitz Centre for Therapeutics, School of Medicine, Medical Sciences and Nutrition; University of Aberdeen, Foresterhill; Aberdeen AB25 2ZD Scotland UK
| | - Sergio Dall'Angelo
- Institute of Medical Sciences and Kosterlitz Centre for Therapeutics, School of Medicine, Medical Sciences and Nutrition; University of Aberdeen, Foresterhill; Aberdeen AB25 2ZD Scotland UK
| | - Alexandra Andriu
- Institute of Medical Sciences and Kosterlitz Centre for Therapeutics, School of Medicine, Medical Sciences and Nutrition; University of Aberdeen, Foresterhill; Aberdeen AB25 2ZD Scotland UK
| | - Sergio Menta
- Dipartimento di Chimica e Tecnologie del Farmaco; “Sapienza” Università di Roma; P.le A. Moro 5 00185 Rome Italy
- Current affiliation: IRBM Science Park SpA; Via Pontina km 30 600 00071 Pomezia RM Italy
| | - Mattia Mori
- Center for Life Nano Science@Sapienza; Istituto Italiano di Tecnologia; Viale Regina Elena 291 00161 Roma RM Italy
| | - Gavin D. Brown
- Manchester Cancer Research Centre and Wolfson Molecular Imaging Centre; The University of Manchester; Palatine Road Manchester M20 3JJ UK
| | - Duncan Forster
- Manchester Cancer Research Centre and Wolfson Molecular Imaging Centre; The University of Manchester; Palatine Road Manchester M20 3JJ UK
| | - Kaye J. Williams
- CRUK-EPSRC Cancer Imaging Centre in Cambridge and Manchester, Manchester Cancer Research Centre, Division of Pharmacy and Optometry; The University of Manchester; Oxford Road Manchester M13 9PT UK
| | - Matteo Zanda
- Institute of Medical Sciences and Kosterlitz Centre for Therapeutics, School of Medicine, Medical Sciences and Nutrition; University of Aberdeen, Foresterhill; Aberdeen AB25 2ZD Scotland UK
- C.N.R.-I.C.R.M.; via Mancinelli 7 20131 Milan Italy
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15
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Evain-Bana E, Schiavo L, Bour C, Lanfranchi DA, Berardozzi S, Ghirga F, Bagrel D, Botta B, Hanquet G, Mori M. Synthesis, biological evaluation and molecular modeling studies on novel quinonoid inhibitors of CDC25 phosphatases. J Enzyme Inhib Med Chem 2016; 32:113-118. [PMID: 27774816 PMCID: PMC6010111 DOI: 10.1080/14756366.2016.1238364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The cell division cycle 25 phosphatases (CDC25A, B, and C; E.C. 3.1.3.48) are key regulator of the cell cycle in human cells. Their aberrant expression has been associated with the insurgence and development of various types of cancer, and with a poor clinical prognosis. Therefore, CDC25 phosphatases are a valuable target for the development of small molecule inhibitors of therapeutic relevance. Here, we used an integrated strategy mixing organic chemistry with biological investigation and molecular modeling to study novel quinonoid derivatives as CDC25 inhibitors. The most promising molecules proved to inhibit CDC25 isoforms at single digit micromolar concentration, becoming valuable tools in chemical biology investigations and profitable leads for further optimization.
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Affiliation(s)
- Emilie Evain-Bana
- a Pôle Chimie Et Physique Moléculaire, UMR CNRS 7565, Laboratoire Structure et Réactivite des Systèmes Moléculaires Complexes , Université de Lorraine , Metz , France
| | - Lucie Schiavo
- b Ecole Européenne de Chimie, Polymères et Matériaux (ECPM), Laboratoire de Synthèse et Catalyze (UMR CNRS 7509) , Université de Strasbourg , Strasbourg , France
| | | | - Don Antoine Lanfranchi
- b Ecole Européenne de Chimie, Polymères et Matériaux (ECPM), Laboratoire de Synthèse et Catalyze (UMR CNRS 7509) , Université de Strasbourg , Strasbourg , France
| | - Simone Berardozzi
- d Dipartimento di Chimica e Tecnologie del Farmaco , Sapienza University of Roma , Rome , Italy.,e Istituto Italiano di Tecnologia , Center for Life Nano Science@Sapienza , Rome , Italy
| | - Francesca Ghirga
- e Istituto Italiano di Tecnologia , Center for Life Nano Science@Sapienza , Rome , Italy
| | - Denyse Bagrel
- a Pôle Chimie Et Physique Moléculaire, UMR CNRS 7565, Laboratoire Structure et Réactivite des Systèmes Moléculaires Complexes , Université de Lorraine , Metz , France
| | - Bruno Botta
- d Dipartimento di Chimica e Tecnologie del Farmaco , Sapienza University of Roma , Rome , Italy
| | - Gilles Hanquet
- b Ecole Européenne de Chimie, Polymères et Matériaux (ECPM), Laboratoire de Synthèse et Catalyze (UMR CNRS 7509) , Université de Strasbourg , Strasbourg , France
| | - Mattia Mori
- e Istituto Italiano di Tecnologia , Center for Life Nano Science@Sapienza , Rome , Italy
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16
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Infante P, Alfonsi R, Ingallina C, Quaglio D, Ghirga F, D'Acquarica I, Bernardi F, Di Magno L, Canettieri G, Screpanti I, Gulino A, Botta B, Mori M, Di Marcotullio L. Inhibition of Hedgehog-dependent tumors and cancer stem cells by a newly identified naturally occurring chemotype. Cell Death Dis 2016; 7:e2376. [PMID: 27899820 PMCID: PMC5059851 DOI: 10.1038/cddis.2016.195] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/24/2016] [Accepted: 06/08/2016] [Indexed: 12/11/2022]
Abstract
Hedgehog (Hh) inhibitors have emerged as valid tools in the treatment of a wide range of cancers. Indeed, aberrant activation of the Hh pathway occurring either by ligand-dependent or -independent mechanisms is a key driver in tumorigenesis. The smoothened (Smo) receptor is one of the main upstream transducers of the Hh signaling and is a validated target for the development of anticancer compounds, as underlined by the FDA-approved Smo antagonist Vismodegib (GDC-0449/Erivedge) for the treatment of basal cell carcinoma. However, Smo mutations that confer constitutive activity and drug resistance have emerged during treatment with Vismodegib. For this reason, the development of new effective Hh inhibitors represents a major challenge for cancer therapy. Natural products have always represented a unique source of lead structures in drug discovery, and in recent years have been used to modulate the Hh pathway at multiple levels. Here, starting from an in house library of natural compounds and their derivatives, we discovered novel chemotypes of Hh inhibitors by mean of virtual screening against the crystallographic structure of Smo. Hh functional based assay identified the chalcone derivative 12 as the most effective Hh inhibitor within the test set. The chalcone 12 binds the Smo receptor and promotes the displacement of Bodipy-Cyclopamine in both Smo WT and drug-resistant Smo mutant. Our molecule stands as a promising Smo antagonist able to specifically impair the growth of Hh-dependent tumor cells in vitro and in vivo and medulloblastoma stem-like cells and potentially overcome the associated drug resistance.
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Affiliation(s)
- Paola Infante
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291 Rome, Italy
| | - Romina Alfonsi
- Department of Molecular Medicine, Sapienza Università di Roma, Viale Regina Elena 291, Rome, Italy
| | - Cinzia Ingallina
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291 Rome, Italy
| | - Deborah Quaglio
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, Rome, Italy
| | - Francesca Ghirga
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291 Rome, Italy
| | - Ilaria D'Acquarica
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, Rome, Italy
| | - Flavia Bernardi
- Department of Molecular Medicine, Sapienza Università di Roma, Viale Regina Elena 291, Rome, Italy
| | - Laura Di Magno
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291 Rome, Italy
| | - Gianluca Canettieri
- Department of Molecular Medicine, Sapienza Università di Roma, Viale Regina Elena 291, Rome, Italy
| | - Isabella Screpanti
- Department of Molecular Medicine, Sapienza Università di Roma, Viale Regina Elena 291, Rome, Italy
- Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza Università di Roma, Viale Regina Elena 291, Rome, Italy
| | - Alberto Gulino
- Department of Molecular Medicine, Sapienza Università di Roma, Viale Regina Elena 291, Rome, Italy
| | - Bruno Botta
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, Rome, Italy
| | - Mattia Mori
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291 Rome, Italy
| | - Lucia Di Marcotullio
- Department of Molecular Medicine, Sapienza Università di Roma, Viale Regina Elena 291, Rome, Italy
- Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza Università di Roma, Viale Regina Elena 291, Rome, Italy
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17
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Cau Y, Mori M, Supuran CT, Botta M. Mycobacterial carbonic anhydrase inhibition with phenolic acids and esters: kinetic and computational investigations. Org Biomol Chem 2016; 14:8322-30. [DOI: 10.1039/c6ob01477a] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Phenolic acids and their ester derivatives show specific inhibition of beta-carbonic anhydrases from Mycobacterium tuberculosis, and are interesting anti-mycobacterial leads.
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Affiliation(s)
- Ylenia Cau
- Department of Biotechnology
- Chemistry and Pharmacy
- University of Siena
- I-53100 Siena
- Italy
| | - Mattia Mori
- Department of Biotechnology
- Chemistry and Pharmacy
- University of Siena
- I-53100 Siena
- Italy
| | - Claudiu T. Supuran
- Dipartimento NEUROFARBA
- Sezione di Scienze Farmaceutiche
- Università degli Studi di Firenze
- 50019 Sesto Fiorentino (Firenze)
- Italy
| | - Maurizio Botta
- Department of Biotechnology
- Chemistry and Pharmacy
- University of Siena
- I-53100 Siena
- Italy
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18
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Cau Y, Fiorillo A, Mori M, Ilari A, Botta M, Lalle M. Molecular Dynamics Simulations and Structural Analysis of Giardia duodenalis 14-3-3 Protein-Protein Interactions. J Chem Inf Model 2015; 55:2611-22. [PMID: 26551337 DOI: 10.1021/acs.jcim.5b00452] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Giardiasis is a gastrointestinal diarrheal illness caused by the protozoan parasite Giardia duodenalis, which affects annually over 200 million people worldwide. The limited antigiardial drug arsenal and the emergence of clinical cases refractory to standard treatments dictate the need for new chemotherapeutics. The 14-3-3 family of regulatory proteins, extensively involved in protein-protein interactions (PPIs) with pSer/pThr clients, represents a highly promising target. Despite homology with human counterparts, the single 14-3-3 of G. duodenalis (g14-3-3) is characterized by a constitutive phosphorylation in a region critical for target binding, thus affecting the function and the conformation of g14-3-3/clients interaction. However, to approach the design of specific small molecule modulators of g14-3-3 PPIs, structural elucidations are required. Here, we present a detailed computational and crystallographic study exploring the implications of g14-3-3 phosphorylation on protein structure and target binding. Self-Guided Langevin Dynamics and classical molecular dynamics simulations show that phosphorylation affects locally and globally g14-3-3 conformation, inducing a structural rearrangement more suitable for target binding. Profitable features for g14-3-3/clients interaction were highlighted using a hydrophobicity-based descriptor to characterize g14-3-3 client peptides. Finally, the X-ray structure of g14-3-3 in complex with a mode-1 prototype phosphopeptide was solved and combined with structure-based simulations to identify molecular features relevant for clients binding to g14-3-3. The data presented herein provide a further and structural understanding of g14-3-3 features and set the basis for drug design studies.
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Affiliation(s)
- Ylenia Cau
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena , via Aldo Moro 2, 53019 Siena, Italy
| | - Annarita Fiorillo
- Dipartimento di Scienze Biochimiche, Sapienza Università di Roma , Piazzale A. Moro 5, 00185 Roma, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena , via Aldo Moro 2, 53019 Siena, Italy.,Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia , Viale Regina Elena 291, 00161 Roma, Italy
| | - Andrea Ilari
- CNR-Institute of Molecular Biology and Pathology (IBPM), c/o Department Biochemical Sciences "A. Rossi Fanelli", University Sapienza , P.le A. Moro 5, 00185 Roma, Italy
| | - Maurizo Botta
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena , via Aldo Moro 2, 53019 Siena, Italy.,Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University , BioLife Science Building, Suite 333, 1900 North 12th Street, Philadelphia, Pennsylvania 19122, United States
| | - Marco Lalle
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità , Viale Regina Elena 299, 00161 Roma, Italy
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19
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Mori M, Kovalenko L, Lyonnais S, Antaki D, Torbett BE, Botta M, Mirambeau G, Mély Y. Nucleocapsid Protein: A Desirable Target for Future Therapies Against HIV-1. Curr Top Microbiol Immunol 2015; 389:53-92. [PMID: 25749978 PMCID: PMC7122173 DOI: 10.1007/82_2015_433] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The currently available anti-HIV-1 therapeutics is highly beneficial to infected patients. However, clinical failures occur as a result of the ability of HIV-1 to rapidly mutate. One approach to overcome drug resistance is to target HIV-1 proteins that are highly conserved among phylogenetically distant viral strains and currently not targeted by available therapies. In this respect, the nucleocapsid (NC) protein, a zinc finger protein, is particularly attractive, as it is highly conserved and plays a central role in virus replication, mainly by interacting with nucleic acids. The compelling rationale for considering NC as a viable drug target is illustrated by the fact that point mutants of this protein lead to noninfectious viruses and by the inability to select viruses resistant to a first generation of anti-NC drugs. In our review, we discuss the most relevant properties and functions of NC, as well as recent developments of small molecules targeting NC. Zinc ejectors show strong antiviral activity, but are endowed with a low therapeutic index due to their lack of specificity, which has resulted in toxicity. Currently, they are mainly being investigated for use as topical microbicides. Greater specificity may be achieved by using non-covalent NC inhibitors (NCIs) targeting the hydrophobic platform at the top of the zinc fingers or key nucleic acid partners of NC. Within the last few years, innovative methodologies have been developed to identify NCIs. Though the antiviral activity of the identified NCIs needs still to be improved, these compounds strongly support the druggability of NC and pave the way for future structure-based design and optimization of efficient NCIs.
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Affiliation(s)
- Mattia Mori
- Dipartimento di Biotecnologie Chimica e Farmacia, Università degli Studi di Siena, via A. Moro 2, 53100, Siena, Italy
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20
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Infante P, Mori M, Alfonsi R, Ghirga F, Aiello F, Toscano S, Ingallina C, Siler M, Cucchi D, Po A, Miele E, D'Amico D, Canettieri G, De Smaele E, Ferretti E, Screpanti I, Uccello Barretta G, Botta M, Botta B, Gulino A, Di Marcotullio L. Gli1/DNA interaction is a druggable target for Hedgehog-dependent tumors. EMBO J 2014; 34:200-17. [PMID: 25476449 PMCID: PMC4298015 DOI: 10.15252/embj.201489213] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Hedgehog signaling is essential for tissue development and stemness, and its deregulation has been observed in many tumors. Aberrant activation of Hedgehog signaling is the result of genetic mutations of pathway components or other Smo-dependent or independent mechanisms, all triggering the downstream effector Gli1. For this reason, understanding the poorly elucidated mechanism of Gli1-mediated transcription allows to identify novel molecules blocking the pathway at a downstream level, representing a critical goal in tumor biology. Here, we clarify the structural requirements of the pathway effector Gli1 for binding to DNA and identify Glabrescione B as the first small molecule binding to Gli1 zinc finger and impairing Gli1 activity by interfering with its interaction with DNA. Remarkably, as a consequence of its robust inhibitory effect on Gli1 activity, Glabrescione B inhibited the growth of Hedgehog-dependent tumor cells in vitro and in vivo as well as the self-renewal ability and clonogenicity of tumor-derived stem cells. The identification of the structural requirements of Gli1/DNA interaction highlights their relevance for pharmacologic interference of Gli signaling.
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Affiliation(s)
- Paola Infante
- Center for Life NanoScience@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Mattia Mori
- Center for Life NanoScience@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Romina Alfonsi
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Francesca Ghirga
- Dipartimento di Chimica e Tecnologie del Farmaco, University La Sapienza, Rome, Italy
| | - Federica Aiello
- Department of Chemistry and Industrial Chemistry, University of Pisa, Pisa, Italy
| | - Sara Toscano
- Center for Life NanoScience@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Cinzia Ingallina
- Center for Life NanoScience@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Mariangela Siler
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Danilo Cucchi
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Agnese Po
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Evelina Miele
- Center for Life NanoScience@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Davide D'Amico
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | | | - Enrico De Smaele
- Department of Experimental Medicine, University La Sapienza, Rome, Italy
| | | | | | | | - Maurizio Botta
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA, USA
| | - Bruno Botta
- Dipartimento di Chimica e Tecnologie del Farmaco, University La Sapienza, Rome, Italy
| | - Alberto Gulino
- Center for Life NanoScience@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy Department of Molecular Medicine, University La Sapienza, Rome, Italy Istituto Pasteur, Fondazione Cenci-Bolognetti - University La Sapienza, Rome, Italy IRCCS Neuromed, Pozzilli, Italy
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21
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Garg D, Torbett BE. Advances in targeting nucleocapsid-nucleic acid interactions in HIV-1 therapy. Virus Res 2014; 193:135-43. [PMID: 25026536 PMCID: PMC4252855 DOI: 10.1016/j.virusres.2014.07.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 07/02/2014] [Accepted: 07/03/2014] [Indexed: 11/16/2022]
Abstract
The continuing challenge of HIV-1 treatment resistance in patients creates a need for the development of new antiretroviral inhibitors. The HIV nucleocapsid (NC) protein is a potential therapeutic target. NC is necessary for viral RNA packaging and in the early stages of viral infection. The high level of NC amino acid conservation among all HIV-1 clades suggests a low tolerance for mutations. Thus, NC mutations that could arise during inhibitor treatment to provide resistance may render the virus less fit. Disruption of NC function provides a unique opportunity to strongly dampen replication at multiple points during the viral life cycle with a single inhibitor. Although NC exhibits desirable features for a potential antiviral target, the structural flexibility, size, and the presence of two zinc fingers makes small molecule targeting of NC a challenging task. In this review, we discuss the recent advances in strategies to develop inhibitors of NC function and present a perspective on potential novel approaches that may help to overcome some of the current challenges in the field.
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Affiliation(s)
- Divita Garg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bruce E Torbett
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
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22
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Mori M, Nucci A, Lang MCD, Humbert N, Boudier C, Debaene F, Sanglier-Cianferani S, Catala M, Schult-Dietrich P, Dietrich U, Tisné C, Mely Y, Botta M. Functional and structural characterization of 2-amino-4-phenylthiazole inhibitors of the HIV-1 nucleocapsid protein with antiviral activity. ACS Chem Biol 2014; 9:1950-5. [PMID: 24988251 DOI: 10.1021/cb500316h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nucleocapsid protein (NC) is a highly conserved protein in diverse HIV-1 subtypes that plays a central role in virus replication, mainly by interacting with conserved nucleic acid sequences. NC is considered a highly profitable drug target to inhibit multiple steps in the HIV-1 life cycle with just one compound, a unique property not shown by any of the other antiretroviral classes. However, most of NC inhibitors developed so far act through an unspecific and potentially toxic mechanism (zinc ejection) and are mainly being investigated as topical microbicides. In an effort to provide specific NC inhibitors that compete for the binding of nucleic acids to NC, here we combined molecular modeling, organic synthesis, biophysical studies, NMR spectroscopy, and antiviral assays to design, synthesize, and characterize an efficient NC inhibitor endowed with antiviral activity in vitro, a desirable property for the development of efficient antiretroviral lead compounds.
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Affiliation(s)
- Mattia Mori
- Department
of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, via Aldo Moro 2, I-53019 Siena, Italy
| | - Alessandro Nucci
- Department
of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, via Aldo Moro 2, I-53019 Siena, Italy
| | - Maria Chiara Dasso Lang
- Department
of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, via Aldo Moro 2, I-53019 Siena, Italy
| | - Nicolas Humbert
- Laboratoire
de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213 CNRS, 74 route du Rhin, F-67401 Illkirch, France
| | - Christian Boudier
- Laboratoire
de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213 CNRS, 74 route du Rhin, F-67401 Illkirch, France
| | - Francois Debaene
- Laboratoire
de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213 CNRS, 74 route du Rhin, F-67401 Illkirch, France
| | - Sarah Sanglier-Cianferani
- Laboratoire
de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213 CNRS, 74 route du Rhin, F-67401 Illkirch, France
| | - Marjorie Catala
- Laboratoire
de Cristallographie et RMN Biologiques, CNRS, Paris Sorbonne Cité, 4 avenue de l’Observatoire, F-75006 Paris, France
| | - Patricia Schult-Dietrich
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Paul-Ehrlich-Str. 42-44, D-60596 Frankfurt, Germany
| | - Ursula Dietrich
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Paul-Ehrlich-Str. 42-44, D-60596 Frankfurt, Germany
| | - Carine Tisné
- Laboratoire
de Cristallographie et RMN Biologiques, CNRS, Paris Sorbonne Cité, 4 avenue de l’Observatoire, F-75006 Paris, France
| | - Yves Mely
- Laboratoire
de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213 CNRS, 74 route du Rhin, F-67401 Illkirch, France
| | - Maurizio Botta
- Department
of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, via Aldo Moro 2, I-53019 Siena, Italy
- Sbarro
Institute for Cancer Research and Molecular Medicine, Temple University, BioLife Science Bldg.,
Suite 333, 1900 N. 12th Street, Philadelphia, Pennsylvania 19122, United States
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23
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Discovery of the first potent and selective Mycobacterium tuberculosis Zmp1 inhibitor. Bioorg Med Chem Lett 2014; 24:2508-11. [DOI: 10.1016/j.bmcl.2014.04.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 03/31/2014] [Accepted: 04/02/2014] [Indexed: 11/24/2022]
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24
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Pawar R, Das T, Mishra S, Nutan, Pancholi B, Gupta SK, Bhat SV. Synthesis, anti-HIV activity, integrase enzyme inhibition and molecular modeling of catechol, hydroquinone and quinol labdane analogs. Bioorg Med Chem Lett 2014; 24:302-7. [DOI: 10.1016/j.bmcl.2013.11.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/11/2013] [Accepted: 11/09/2013] [Indexed: 10/26/2022]
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25
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Mascarello A, Mori M, Chiaradia-Delatorre LD, Menegatti ACO, Monache FD, Ferrari F, Yunes RA, Nunes RJ, Terenzi H, Botta B, Botta M. Discovery of Mycobacterium tuberculosis protein tyrosine phosphatase B (PtpB) inhibitors from natural products. PLoS One 2013; 8:e77081. [PMID: 24155919 PMCID: PMC3796549 DOI: 10.1371/journal.pone.0077081] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 09/05/2013] [Indexed: 11/18/2022] Open
Abstract
Protein tyrosine phosphatase B (PtpB) is one of the virulence factors secreted into the host cell by Mycobacterium tuberculosis. PtpB attenuates host immune defenses by interfering with signal transduction pathways in macrophages and, therefore, it is considered a promising target for the development of novel anti-tuberculosis drugs. Here we report the discovery of natural compound inhibitors of PtpB among an in house library of more than 800 natural substances by means of a multidisciplinary approach, mixing in silico screening with enzymatic and kinetics studies and MS assays. Six natural compounds proved to inhibit PtpB at low micromolar concentrations (< 30 µM) with Kuwanol E being the most potent with Ki = 1.6 ± 0.1 µM. To the best of our knowledge, Kuwanol E is the most potent natural compound PtpB inhibitor reported so far, as well as it is the first non-peptidic PtpB inhibitor discovered from natural sources. Compounds herein identified may inspire the design of novel specific PtpB inhibitors.
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Affiliation(s)
- Alessandra Mascarello
- Laboratório Estrutura e Atividade, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Mattia Mori
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma La Sapienza, Roma, Italy
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Siena, Italy
| | - Louise Domeneghini Chiaradia-Delatorre
- Laboratório Estrutura e Atividade, Universidade Federal de Santa Catarina, Florianópolis, Brazil
- Centro de Biologia Molecular Estrutural, Universidade Federal de Santa Catarina, Florianopolis, Brazil
| | | | - Franco Delle Monache
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma La Sapienza, Roma, Italy
| | - Franco Ferrari
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma La Sapienza, Roma, Italy
| | - Rosendo Augusto Yunes
- Laboratório Estrutura e Atividade, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Ricardo José Nunes
- Laboratório Estrutura e Atividade, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Hernán Terenzi
- Centro de Biologia Molecular Estrutural, Universidade Federal de Santa Catarina, Florianopolis, Brazil
- * E-mail: (BB); (HT); (MB)
| | - Bruno Botta
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma La Sapienza, Roma, Italy
- * E-mail: (BB); (HT); (MB)
| | - Maurizio Botta
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Siena, Italy
- Center for Biotechnology, Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- * E-mail: (BB); (HT); (MB)
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26
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Mori M, Massaro A, Calderone V, Fragai M, Luchinat C, Mordini A. Discovery of a New Class of Potent MMP Inhibitors by Structure-Based Optimization of the Arylsulfonamide Scaffold. ACS Med Chem Lett 2013; 4:565-9. [PMID: 24900710 DOI: 10.1021/ml300446a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 03/13/2013] [Indexed: 01/29/2023] Open
Abstract
A new class of potent matrix metalloproteinase (MMP) inhibitors designed by structure-based optimization of the well-known arylsulfonamide scaffold is presented. Molecules show an ethylene linker connecting the sulfonamide group with the P1' aromatic portion and a d-proline residue bearing the zinc-binding group. The affinity improvement provided by these modifications led us to discover a nanomolar MMP inhibitor bearing a carboxylate moiety as zinc-binding group, which might be a promising lead molecule. Notably, a significant selectivity for MMP-8, MMP-12, and MMP-13 was observed with respect to MMP-1 and MMP-7.
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Affiliation(s)
- Mattia Mori
- ProtEra Srl, Scientific Campus, University of Florence, viale delle idee 22, I-50019
Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, I-50019 Sesto
Fiorentino, Italy
| | - Assunta Massaro
- ProtEra Srl, Scientific Campus, University of Florence, viale delle idee 22, I-50019
Sesto Fiorentino, Italy
| | - Vito Calderone
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, I-50019 Sesto
Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, I-50019 Sesto
Fiorentino, Italy
- Department
of Chemistry “Ugo
Shiff”, University of Florence,
via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, I-50019 Sesto
Fiorentino, Italy
- Department
of Chemistry “Ugo
Shiff”, University of Florence,
via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Alessandro Mordini
- ICCOM-CNR, Dipartimento
di Chimica “U. Schiff”, via della Lastruccia
13, I-50019 Sesto Fiorentino, Italy
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27
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Baiocco P, Poce G, Alfonso S, Cocozza M, Porretta GC, Colotti G, Biava M, Moraca F, Botta M, Yardley V, Fiorillo A, Lantella A, Malatesta F, Ilari A. Inhibition of Leishmania infantum trypanothione reductase by azole-based compounds: a comparative analysis with its physiological substrate by X-ray crystallography. ChemMedChem 2013; 8:1175-83. [PMID: 23733388 DOI: 10.1002/cmdc.201300176] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Indexed: 11/11/2022]
Abstract
Herein we report a study aimed at discovering a new class of compounds that are able to inhibit Leishmania donovani cell growth. Evaluation of an in-house library of compounds in a whole-cell screening assay highlighted 4-((1-(4-ethylphenyl)-2-methyl-5-(4-(methylthio)phenyl)-1H-pyrrol-3-yl)methyl)thiomorpholine (compound 1) as the most active. Enzymatic assays on Leishmania infantum trypanothione reductase (LiTR, belonging to the Leishmania donovani complex) shed light on both the interaction with, and the nature of inhibition by, compound 1. A molecular modeling approach based on docking studies and on the estimation of the binding free energy aided our rationalization of the biological data. Moreover, X-ray crystal structure determination of LiTR in complex with compound 1 confirmed all our results: compound 1 binds to the T(SH)2 binding site, lined by hydrophobic residues such as Trp21 and Met113, as well as residues Glu18 and Tyr110. Analysis of the structure of LiTR in complex with trypanothione shows that Glu18 and Tyr110 are also involved in substrate binding, according to a competitive inhibition mechanism.
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Affiliation(s)
- Paola Baiocco
- Dipartimento di Scienze Biochimiche, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Roma, Italy
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28
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Mori M, Schult-Dietrich P, Szafarowicz B, Humbert N, Debaene F, Sanglier-Cianferani S, Dietrich U, Mély Y, Botta M. Use of virtual screening for discovering antiretroviral compounds interacting with the HIV-1 nucleocapsid protein. Virus Res 2012; 169:377-87. [PMID: 22634301 DOI: 10.1016/j.virusres.2012.05.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 05/14/2012] [Accepted: 05/16/2012] [Indexed: 12/16/2022]
Abstract
The HIV-1 nucleocapsid protein (NC) is considered as an emerging drug target for the therapy of AIDS. Several studies have highlighted the crucial role of NC within the viral replication cycle. However, although NC inhibition has provided in vitro and in vivo antiretroviral activity, drug-candidates which interfere with NC functions are still missing in the therapeutic arsenal against HIV. Based on previous studies, where the dynamic behavior of NC and its ligand binding properties have been investigated by means of computational methods, here we used a virtual screening protocol for discovering novel antiretroviral compounds which interact with NC. The antiretroviral activity of virtual hits was tested in vitro, whereas biophysical studies elucidated the direct interaction of most active compounds with NC(11-55), a peptide corresponding to the zinc finger domain of NC. Two novel antiretroviral small molecules capable of interacting with NC are presented here.
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Affiliation(s)
- Mattia Mori
- Università di Roma La Sapienza, Dipartimento di Chimica e Tecnologie del Farmaco, piazzale A. Moro 5, I-00185 Roma, Italy
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29
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Do TN, Ippoliti E, Carloni P, Varani G, Parrinello M. Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA. J Chem Theory Comput 2012; 8:688-94. [PMID: 26596616 DOI: 10.1021/ct2005769] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Binding of proteins and small molecules to RNA involves many electrostatic interactions, which may alter the distribution of ions around the RNA molecule. Here, we use molecular dynamics simulations to investigate how binding of a cyclic peptide mimic of the HIV-1 Tat protein affects the ionic distribution around the HIV-1 TAR RNA element. The calculations reproduce the structural properties observed in NMR studies of TAR and its complex. They also provide insight into the rearrangement of counterions during the molecular recognition events leading to the formation of the protein/RNA complex.
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Affiliation(s)
- Trang N Do
- SISSA/ISAS-International School for Advanced Studies, Trieste 34136, Italy.,Department of Physics, University of Science, Hochiminh City 70000, Vietnam
| | - Emiliano Ippoliti
- German Research School for Simulation Sciences GmbH, Jülich 52425, Germany
| | - Paolo Carloni
- German Research School for Simulation Sciences GmbH, Jülich 52425, Germany
| | - Gabriele Varani
- Department of Chemistry and Department of Biochemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences, ETH Zurich, Lugano 6900, Switzerland
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30
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Whalen KL, Chang KM, Spies MA. Hybrid Steered Molecular Dynamics-Docking: An Efficient Solution to the Problem of Ranking Inhibitor Affinities Against a Flexible Drug Target. Mol Inform 2011; 30:459-471. [PMID: 21738559 PMCID: PMC3129543 DOI: 10.1002/minf.201100014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Existing techniques which attempt to predict the affinity of protein-ligand interactions have demonstrated a direct relationship between computational cost and prediction accuracy. We present here the first application of a hybrid ensemble docking and steered molecular dynamics scheme (with a minimized computational cost), which achieves a binding affinity rank-ordering of ligands with a Spearman correlation coefficient of 0.79 and an RMS error of 0.7 kcal/mol. The scheme, termed Flexible Enzyme Receptor Method by Steered Molecular Dynamics (FERM-SMD), is applied to an in-house collection of 17 validated ligands of glutamate racemase. The resulting improved accuracy in affinity prediction allows elucidation of the key structural components of a heretofore unreported glutamate racemase inhibitor (K(i) = 9 µM), a promising new lead in the development of antibacterial therapeutics.
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Affiliation(s)
- Katie L. Whalen
- Roger Adams Laboratory, Department of Biochemistry, University of Illinois, 600 S. Mathews Ave., Urbana, IL 61801, USA
| | - Kevin M. Chang
- Roger Adams Laboratory, Department of Biochemistry, University of Illinois, 600 S. Mathews Ave., Urbana, IL 61801, USA
| | - M. Ashley Spies
- Roger Adams Laboratory, Department of Biochemistry, University of Illinois, 600 S. Mathews Ave., Urbana, IL 61801, USA
- Institute of Genomic Biology, University of Illinois 600 S. Mathews Ave., Urbana, IL 61801, USA
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