1
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Basagni F, Marotta G, Rosini M, Minarini A. Polyamine-Drug Conjugates: Do They Boost Drug Activity? Molecules 2023; 28:molecules28114518. [PMID: 37298993 DOI: 10.3390/molecules28114518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
Over the past two decades, the strategy of conjugating polyamine tails with bioactive molecules such as anticancer and antimicrobial agents, as well as antioxidant and neuroprotective scaffolds, has been widely exploited to enhance their pharmacological profile. Polyamine transport is elevated in many pathological conditions, suggesting that the polyamine portion could improve cellular and subcellular uptake of the conjugate via the polyamine transporter system. In this review, we have presented a glimpse on the polyamine conjugate scenario, classified by therapeutic area, of the last decade with the aim of highlighting achievements and fostering future developments.
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Affiliation(s)
- Filippo Basagni
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Giambattista Marotta
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Michela Rosini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Anna Minarini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
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2
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Munafò F, Donati E, Brindani N, Ottonello G, Armirotti A, De Vivo M. Quercetin and luteolin are single-digit micromolar inhibitors of the SARS-CoV-2 RNA-dependent RNA polymerase. Sci Rep 2022; 12:10571. [PMID: 35732785 PMCID: PMC9216299 DOI: 10.1038/s41598-022-14664-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 06/10/2022] [Indexed: 01/18/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a global health pandemic. Among the viral proteins, RNA-dependent RNA polymerase (RdRp) is responsible for viral genome replication and has emerged as one of the most promising targets for pharmacological intervention against SARS-CoV-2. To this end, we experimentally tested luteolin and quercetin for their ability to inhibit the RdRp enzyme. These two compounds are ancestors of flavonoid natural compounds known for a variety of basal pharmacological activities. Luteolin and quercetin returned a single-digit IC50 of 4.6 µM and 6.9 µM, respectively. Then, through dynamic docking simulations, we identified possible binding modes of these compounds to a recently published cryo-EM structure of RdRp. Collectively, these data indicate that these two compounds are a valid starting point for further optimization and development of a new class of RdRp inhibitors to treat SARS-CoV-2 and potentially other viral infections.
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Affiliation(s)
- Federico Munafò
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano Di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Elisa Donati
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano Di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Nicoletta Brindani
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano Di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Giuliana Ottonello
- Analytical Chemistry Facility, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genoa, Italy
| | - Andrea Armirotti
- Analytical Chemistry Facility, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genoa, Italy
| | - Marco De Vivo
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano Di Tecnologia, via Morego 30, 16163, Genoa, Italy.
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3
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Ortega JA, Arencibia JM, Minniti E, Byl JAW, Franco-Ulloa S, Borgogno M, Genna V, Summa M, Bertozzi SM, Bertorelli R, Armirotti A, Minarini A, Sissi C, Osheroff N, De Vivo M. Novel, Potent, and Druglike Tetrahydroquinazoline Inhibitor That Is Highly Selective for Human Topoisomerase II α over β. J Med Chem 2020; 63:12873-12886. [PMID: 33079544 PMCID: PMC7668297 DOI: 10.1021/acs.jmedchem.0c00774] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
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We disclose a novel
class of 6-amino-tetrahydroquinazoline derivatives
that inhibit human topoisomerase II (topoII), a validated target of
anticancer drugs. In contrast to topoII-targeted drugs currently in
clinical use, these compounds do not act as topoII poisons that enhance
enzyme-mediated DNA cleavage, a mechanism that is linked to the development
of secondary leukemias. Instead, these tetrahydroquinazolines block
the topoII function with no evidence of DNA intercalation. We identified
a potent lead compound [compound 14 (ARN-21934) IC50 = 2 μM for inhibition of DNA relaxation, as compared
to an IC50 = 120 μM for the anticancer drug etoposide]
with excellent metabolic stability and solubility. This new compound
also shows ~100-fold selectivity for topoIIα over topoβ,
a broad antiproliferative activity toward cultured human cancer cells,
a favorable in vivo pharmacokinetic profile, and the ability to penetrate
the blood–brain barrier. Thus, ARN-21934 is a highly promising
lead for the development of novel and potentially safer topoII-targeted
anticancer drugs.
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Affiliation(s)
- Jose Antonio Ortega
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Jose M Arencibia
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Elirosa Minniti
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy.,Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Sebastian Franco-Ulloa
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Marco Borgogno
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Vito Genna
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Maria Summa
- Analytical Chemistry & Translational Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Sine Mandrup Bertozzi
- Analytical Chemistry & Translational Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Rosalia Bertorelli
- Analytical Chemistry & Translational Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Andrea Armirotti
- Analytical Chemistry & Translational Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Anna Minarini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States.,Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, Tennessee 37232-6307, United States.,VA Tennessee Valley Healthcare System, Nashville, Tennessee 37212, United States
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
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4
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Tiwari PB, Chapagain PP, Seddek A, Annamalai T, Üren A, Tse-Dinh YC. Covalent Complex of DNA and Bacterial Topoisomerase: Implications in Antibacterial Drug Development. ChemMedChem 2020; 15:623-631. [PMID: 32043806 PMCID: PMC7133791 DOI: 10.1002/cmdc.201900721] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Indexed: 12/11/2022]
Abstract
A topoisomerase-DNA transient covalent complex can be a druggable target for novel topoisomerase poison inhibitors that represent a new class of antibacterial or anticancer drugs. Herein, we have investigated molecular features of the functionally important Escherichia coli topoisomerase I (EctopoI)-DNA covalent complex (EctopoIcc) for molecular simulations, which is very useful in the development of new antibacterial drugs. To demonstrate the usefulness of our approach, we used a model small molecule (SM), NSC76027, obtained from virtual screening. We examined the direct binding of NSC76027 to EctopoI as well as inhibition of EctopoI relaxation activity of this SM via experimental techniques. We then performed molecular dynamics (MD) simulations to investigate the dynamics and stability of EctopoIcc and EctopoI-NSC76027-DNA ternary complex. Our simulation results show that NSC76027 forms a stable ternary complex with EctopoIcc. EctopoI investigated here also serves as a model system for investigating a complex of topoisomerase and DNA in which DNA is covalently attached to the protein.
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Affiliation(s)
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular sciences institute, Florida International University, Miami, FL 33199, USA
| | - Ahmed Seddek
- Biomolecular sciences institute, Florida International University, Miami, FL 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Thirunavukkarasu Annamalai
- Biomolecular sciences institute, Florida International University, Miami, FL 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Aykut Üren
- Department of Oncology, Georgetown University, Washington, DC 20057, USA
| | - Yuk-Ching Tse-Dinh
- Biomolecular sciences institute, Florida International University, Miami, FL 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
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5
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Arencibia JM, Brindani N, Franco-Ulloa S, Nigro M, Kuriappan JA, Ottonello G, Bertozzi SM, Summa M, Girotto S, Bertorelli R, Armirotti A, De Vivo M. Design, Synthesis, Dynamic Docking, Biochemical Characterization, and in Vivo Pharmacokinetics Studies of Novel Topoisomerase II Poisons with Promising Antiproliferative Activity. J Med Chem 2020; 63:3508-3521. [PMID: 32196342 PMCID: PMC7997578 DOI: 10.1021/acs.jmedchem.9b01760] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
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We
previously reported a first set of hybrid topoisomerase II (topoII)
poisons whose chemical core merges key pharmacophoric elements of
etoposide and merbarone, which are two well-known topoII blockers.
Here, we report on the expansion of this hybrid molecular scaffold
and present 16 more hybrid derivatives that have been designed, synthesized,
and characterized for their ability to block topoII and for their
overall drug-like profile. Some of these compounds act as topoII poison
and exhibit good solubility, metabolic (microsomal) stability, and
promising cytotoxicity in three cancer cell lines (DU145, HeLa, A549).
Compound 3f (ARN24139) is the most promising drug-like
candidate, with a good pharmacokinetics profile in vivo. Our results indicate that this hybrid new chemical class of topoII
poisons deserves further exploration and that 3f is a
favorable lead candidate as a topoII poison, meriting future studies
to test its efficacy in in vivo tumor models.
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Affiliation(s)
- Jose M Arencibia
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Nicoletta Brindani
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Sebastian Franco-Ulloa
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Michela Nigro
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | | | - Giuliana Ottonello
- Analytical Chemistry and in Vivo Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Sine Mandrup Bertozzi
- Analytical Chemistry and in Vivo Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Maria Summa
- Analytical Chemistry and in Vivo Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Stefania Girotto
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Rosalia Bertorelli
- Analytical Chemistry and in Vivo Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Andrea Armirotti
- Analytical Chemistry and in Vivo Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Marco De Vivo
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
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6
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Limongelli V. Ligand binding free energy and kinetics calculation in 2020. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1455] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Vittorio Limongelli
- Faculty of Biomedical Sciences, Institute of Computational Science – Center for Computational Medicine in Cardiology Università della Svizzera italiana (USI) Lugano Switzerland
- Department of Pharmacy University of Naples “Federico II” Naples Italy
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7
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Tomaselli D, Lucidi A, Rotili D, Mai A. Epigenetic polypharmacology: A new frontier for epi-drug discovery. Med Res Rev 2020; 40:190-244. [PMID: 31218726 PMCID: PMC6917854 DOI: 10.1002/med.21600] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 05/10/2019] [Accepted: 05/14/2019] [Indexed: 12/11/2022]
Abstract
Recently, despite the great success achieved by the so-called "magic bullets" in the treatment of different diseases through a marked and specific interaction with the target of interest, the pharmacological research is moving toward the development of "molecular network active compounds," embracing the related polypharmacology approach. This strategy was born to overcome the main limitations of the single target therapy leading to a superior therapeutic effect, a decrease of adverse reactions, and a reduction of potential mechanism(s) of drug resistance caused by robustness and redundancy of biological pathways. It has become clear that multifactorial diseases such as cancer, neurological, and inflammatory disorders, may require more complex therapeutic approaches hitting a certain biological system as a whole. Concerning epigenetics, the goal of the multi-epi-target approach consists in the development of small molecules able to simultaneously and (often) reversibly bind different specific epi-targets. To date, two dual histone deacetylase/kinase inhibitors (CUDC-101 and CUDC-907) are in an advanced stage of clinical trials. In the last years, the growing interest in polypharmacology encouraged the publication of high-quality reviews on combination therapy and hybrid molecules. Hence, to update the state-of-the-art of these therapeutic approaches avoiding redundancy, herein we focused only on multiple medication therapies and multitargeting compounds exploiting epigenetic plus nonepigenetic drugs reported in the literature in 2018. In addition, all the multi-epi-target inhibitors known in literature so far, hitting two or more epigenetic targets, have been included.
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Affiliation(s)
- Daniela Tomaselli
- Department of Chemistry and Technologies of Drugs,
“Sapienza” University of Rome, P.le A. Moro 5, 00185 Roma, Italy
| | - Alessia Lucidi
- Department of Chemistry and Technologies of Drugs,
“Sapienza” University of Rome, P.le A. Moro 5, 00185 Roma, Italy
| | - Dante Rotili
- Department of Chemistry and Technologies of Drugs,
“Sapienza” University of Rome, P.le A. Moro 5, 00185 Roma, Italy
| | - Antonello Mai
- Department of Chemistry and Technologies of Drugs,
“Sapienza” University of Rome, P.le A. Moro 5, 00185 Roma, Italy
- Pasteur Institute - Cenci Bolognetti Foundation, Viale
Regina Elena 291, 00161 Roma, Italy
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8
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Rosini M, Simoni E, Caporaso R, Basagni F, Catanzaro M, Abu IF, Fagiani F, Fusco F, Masuzzo S, Albani D, Lanni C, Mellor IR, Minarini A. Merging memantine and ferulic acid to probe connections between NMDA receptors, oxidative stress and amyloid-β peptide in Alzheimer's disease. Eur J Med Chem 2019; 180:111-120. [DOI: 10.1016/j.ejmech.2019.07.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 12/21/2022]
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9
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Kuriappan JA, Osheroff N, De Vivo M. Smoothed Potential MD Simulations for Dissociation Kinetics of Etoposide To Unravel Isoform Specificity in Targeting Human Topoisomerase II. J Chem Inf Model 2019; 59:4007-4017. [PMID: 31449404 PMCID: PMC6800198 DOI: 10.1021/acs.jcim.9b00605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Human
type II topoisomerases (TopoII) are essential for controlling
DNA topology within the cell. For this reason, there are a number
of TopoII-targeted anticancer drugs that act by inducing DNA cleavage
mediated by both TopoII isoforms (TopoIIα and TopoIIβ)
in cells. However, recent studies suggest that specific poisoning
of TopoIIα may be a safer strategy for treating cancer. This
is because poisoning of TopoIIβ appears to be linked to the
generation of secondary leukemia in patients. We recently reported
that enzyme-mediated DNA cleavage complexes (in which TopoII is covalently
linked to the cleaved DNA during catalysis) formed in the presence
of the anticancer drug etoposide persisted approximately 3-fold longer
with TopoIIα than TopoIIβ. Notably, enhanced drug-target
residence time may reduce the adverse effects of specific TopoIIα
poisons. However, it is still not clear how to design drugs that are
specific for the α isoform. In this study, we report the results
of classical molecular dynamics (MD) simulations to comparatively
analyze the molecular interactions formed within the TopoII/DNA/etoposide
complex with both isoforms. We also used smoothed potential MD to
estimate etoposide dissociation kinetics from the two isoform complexes.
These extensive classical and enhanced sampling simulations revealed
stabilizing interactions of etoposide with two serine residues (Ser763
and Ser800) in TopoIIα. These interactions are missing in TopoIIβ,
where both amino acids are alanine residues. This may explain the
greater persistence of etoposide-stabilized cleavage complexes formed
with Topo TopoIIα. These findings could be useful for the rational
design of specific TopoIIα poisons.
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Affiliation(s)
- Jissy A Kuriappan
- Laboratory of Molecular Modeling and Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 Genova , Italy
| | - Neil Osheroff
- Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , Tennessee 37232-0146 , United States.,Department of Medicine (Hematology/Oncology) , Vanderbilt University School of Medicine , Nashville , Tennessee 37232-6307 , United States.,VA Tennessee Valley Healthcare System , Nashville , Tennessee 37212 , United States
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 Genova , Italy
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10
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Athanasiou C, Cournia Z. From Computers to Bedside: Computational Chemistry Contributing to FDA Approval. BIOMOLECULAR SIMULATIONS IN STRUCTURE-BASED DRUG DISCOVERY 2018. [DOI: 10.1002/9783527806836.ch7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Christina Athanasiou
- Biomedical Research Foundation; Academy of Athens; 4 Soranou Ephessiou 11527 Athens Greece
| | - Zoe Cournia
- Biomedical Research Foundation; Academy of Athens; 4 Soranou Ephessiou 11527 Athens Greece
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11
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Rocha-Roa C, Cossio-Pérez R, Molina D, Patiño J, Cardona N. In silico study of Moxifloxacin derivatives with possible antibacterial activity against a resistant form of DNA gyrase from Porphyromonas gingivalis. Arch Oral Biol 2018; 95:30-39. [DOI: 10.1016/j.archoralbio.2018.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 07/18/2018] [Accepted: 07/18/2018] [Indexed: 11/24/2022]
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12
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Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate. Nat Commun 2018; 9:3085. [PMID: 30082834 PMCID: PMC6078968 DOI: 10.1038/s41467-018-05406-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/05/2018] [Indexed: 12/11/2022] Open
Abstract
Type IIA topoisomerases (Top2s) manipulate the handedness of DNA crossovers by introducing a transient and protein-linked double-strand break in one DNA duplex, termed the DNA-gate, whose opening allows another DNA segment to be transported through to change the DNA topology. Despite the central importance of this gate-opening event to Top2 function, the DNA-gate in all reported structures of Top2-DNA complexes is in the closed state. Here we present the crystal structure of a human Top2 DNA-gate in an open conformation, which not only reveals structural characteristics of its DNA-conducting path, but also uncovers unexpected yet functionally significant conformational changes associated with gate-opening. This structure further implicates Top2’s preference for a left-handed DNA braid and allows the construction of a model representing the initial entry of another DNA duplex into the DNA-gate. Steered molecular dynamics calculations suggests the Top2-catalyzed DNA passage may be achieved by a rocker-switch-type movement of the DNA-gate. Type II DNA topoisomerases (Top2s) direct the passage of one DNA duplex through another, which is important for resolving DNA entanglements. Here the authors combine X-ray crystallography and MD simulations and present the structure of the human Top2 DNA-gate in an open conformation and discuss mechanistic implications.
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13
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Li J, Tian R, Ge C, Chen Y, liu X, Wang Y, Yang Y, Luo W, Dai F, Wang S, Chen S, Xie S, Wang C. Discovery of the Polyamine Conjugate with Benzo[cd]indol-2(1H)-one as a Lysosome-Targeted Antimetastatic Agent. J Med Chem 2018; 61:6814-6829. [DOI: 10.1021/acs.jmedchem.8b00694] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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14
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Oviatt AA, Kuriappan JA, Minniti E, Vann KR, Onuorah P, Minarini A, De Vivo M, Osheroff N. Polyamine-containing etoposide derivatives as poisons of human type II topoisomerases: Differential effects on topoisomerase IIα and IIβ. Bioorg Med Chem Lett 2018; 28:2961-2968. [PMID: 30006062 DOI: 10.1016/j.bmcl.2018.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/21/2018] [Accepted: 07/03/2018] [Indexed: 01/19/2023]
Abstract
Etoposide is an anticancer drug that acts by inducing topoisomerase II-mediated DNA cleavage. Despite its wide use, etoposide is associated with some very serious side-effects including the development of treatment-related acute myelogenous leukemias. Etoposide targets both human topoisomerase IIα and IIβ. However, the contributions of the two enzyme isoforms to the therapeutic vs. leukemogenic properties of the drug are unclear. In order to develop an etoposide-based drug with specificity for cancer cells that express an active polyamine transport system, the sugar moiety of the drug has been replaced with a polyamine tail. To analyze the effects of this substitution on the specificity of hybrid molecules toward the two enzyme isoforms, we analyzed the activity of a series of etoposide-polyamine hybrids toward human topoisomerase IIα and IIβ. All of the compounds displayed an ability to induce enzyme-mediated DNA cleavage that was comparable to or higher than that of etoposide. Relative to the parent drug, the hybrid compounds displayed substantially higher activity toward topoisomerase IIβ than IIα. Modeling studies suggest that the enhanced specificity may result from interactions with Gln778 in topoisomerase IIβ. The corresponding residue in the α isoform is a methionine.
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Affiliation(s)
- Alexandria A Oviatt
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Jissy A Kuriappan
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Elirosa Minniti
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy; Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Kendra R Vann
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Princess Onuorah
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Anna Minarini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy.
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, TN 37232-6307, USA; VA Tennessee Valley Healthcare System, Nashville, TN 37212, USA.
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15
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Milelli A, Marchetti C, Turrini E, Catanzaro E, Mazzone R, Tomaselli D, Fimognari C, Tumiatti V, Minarini A. Novel polyamine-based Histone deacetylases-Lysine demethylase 1 dual binding inhibitors. Bioorg Med Chem Lett 2018; 28:1001-1004. [DOI: 10.1016/j.bmcl.2018.02.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/15/2018] [Accepted: 02/16/2018] [Indexed: 11/30/2022]
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16
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Franco-Ulloa S, La Sala G, Miscione GP, De Vivo M. Novel Bacterial Topoisomerase Inhibitors Exploit Asp83 and the Intrinsic Flexibility of the DNA Gyrase Binding Site. Int J Mol Sci 2018; 19:ijms19020453. [PMID: 29401640 PMCID: PMC5855675 DOI: 10.3390/ijms19020453] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 11/19/2022] Open
Abstract
DNA gyrases are enzymes that control the topology of DNA in bacteria cells. This is a vital function for bacteria. For this reason, DNA gyrases are targeted by widely used antibiotics such as quinolones. Recently, structural and biochemical investigations identified a new class of DNA gyrase inhibitors called NBTIs (i.e., novel bacterial topoisomerase inhibitors). NBTIs are particularly promising because they are active against multi-drug resistant bacteria, an alarming clinical issue. Structural data recently demonstrated that these NBTIs bind tightly to a newly identified pocket at the dimer interface of the DNA–protein complex. In the present study, we used molecular dynamics (MD) simulations and docking calculations to shed new light on the binding of NBTIs to this site. Interestingly, our MD simulations demonstrate the intrinsic flexibility of this binding site, which allows the pocket to adapt its conformation and form optimal interactions with the ligand. In particular, we examined two ligands, AM8085 and AM8191, which induced a repositioning of a key aspartate (Asp83B), whose side chain can rotate within the binding site. The conformational rearrangement of Asp83B allows the formation of a newly identified H-bond interaction with an NH on the bound NBTI, which seems important for the binding of NBTIs having such functionality. We validated these findings through docking calculations using an extended set of cognate oxabicyclooctane-linked NBTIs derivatives (~150, in total), screened against multiple target conformations. The newly identified H-bond interaction significantly improves the docking enrichment. These insights could be helpful for future virtual screening campaigns against DNA gyrase.
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Affiliation(s)
- Sebastian Franco-Ulloa
- COBO Computational Bio-Organic Chemistry Bogotá, Chemistry Department, Universidad de los Andes, Cra 1 No 18A-12, 111711 Bogotá, Colombia.
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
| | - Giuseppina La Sala
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
| | - Gian Pietro Miscione
- COBO Computational Bio-Organic Chemistry Bogotá, Chemistry Department, Universidad de los Andes, Cra 1 No 18A-12, 111711 Bogotá, Colombia.
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
- IAS-5/INM-9 Computational Biomedicine Forschungszentrum Jülich Wilhelm-Johnen-Straße, 52428 Jülich, Germany.
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17
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Pasini A, Marchetti C, Sissi C, Cortesi M, Giordano E, Minarini A, Milelli A. Novel Polyamine-Naphthalene Diimide Conjugates Targeting Histone Deacetylases and DNA for Cancer Phenotype Reprogramming. ACS Med Chem Lett 2017; 8:1218-1223. [PMID: 29259737 PMCID: PMC5733267 DOI: 10.1021/acsmedchemlett.7b00289] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/24/2017] [Indexed: 01/02/2023] Open
Abstract
A series of hybrid compounds was designed to target histone deacetylases and ds-/G-quadruplex DNAs by merging structural features deriving from Scriptaid and compound 1. Compound 6 binds different DNA arrangements, inhibits HDACs both in vitro and in cells, and is able to induce a reduction of cell proliferation. Moreover, compound 6 displays cell phenotype-reprogramming properties since it prevents the epithelial to mesenchymal transition in cancer cells, inducing a less aggressive and migratory phenotype, which is one of the goals of present innovative strategies in cancer therapies.
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Affiliation(s)
- Alice Pasini
- Department of Electrical,
Electronic and Information Engineering “Guglielmo Marconi”
(DEI), Alma Mater Studiorum-University of Bologna, Via Venezia
52, 47521 Cesena
(FC), Italy
| | - Chiara Marchetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum−University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131 Padova, Italy
| | - Marilisa Cortesi
- Department of Electrical,
Electronic and Information Engineering “Guglielmo Marconi”
(DEI), Alma Mater Studiorum-University of Bologna, Via Venezia
52, 47521 Cesena
(FC), Italy
| | - Emanuele Giordano
- Department of Electrical,
Electronic and Information Engineering “Guglielmo Marconi”
(DEI), Alma Mater Studiorum-University of Bologna, Via Venezia
52, 47521 Cesena
(FC), Italy
- Health Sciences
and Technologies−Interdepartmental Center for Industrial Research
(HST-ICIR), Alma Mater Studiorum−University of Bologna, Via Tolara
di Sopra 41/E, 40064 Ozzano dell’Emilia (BO), Italy
- Advanced
Research Center on Electronic Systems (ARCES), Alma Mater Studiorum−University of Bologna, Via Vincenzo Toffano 2/2, 40125 Bologna, Italy
| | - Anna Minarini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum−University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Andrea Milelli
- Department
for Life Quality Studies, Alma Mater Studiorum−University of Bologna, Corso d’Augusto
237, 47921 Rimini, Italy
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18
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Ortega JA, Riccardi L, Minniti E, Borgogno M, Arencibia JM, Greco ML, Minarini A, Sissi C, De Vivo M. Pharmacophore Hybridization To Discover Novel Topoisomerase II Poisons with Promising Antiproliferative Activity. J Med Chem 2017; 61:1375-1379. [DOI: 10.1021/acs.jmedchem.7b01388] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Jose Antonio Ortega
- Laboratory
of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Laura Riccardi
- Laboratory
of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Elirosa Minniti
- Laboratory
of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- Department
of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Marco Borgogno
- Laboratory
of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Jose M. Arencibia
- Laboratory
of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Maria L. Greco
- Department
of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Anna Minarini
- Department
of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Claudia Sissi
- Department
of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Marco De Vivo
- Laboratory
of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- IAS-5/INM-9 Computational Biomedicine Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
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19
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Novel xanthone-polyamine conjugates as catalytic inhibitors of human topoisomerase IIα. Bioorg Med Chem Lett 2017; 27:4687-4693. [PMID: 28919339 DOI: 10.1016/j.bmcl.2017.09.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 08/31/2017] [Accepted: 09/04/2017] [Indexed: 01/03/2023]
Abstract
It has been proposed that xanthone derivatives with anticancer potential act as topoisomerase II inhibitors because they interfere with the ability of the enzyme to bind its ATP cofactor. In order to further characterize xanthone mechanism and generate compounds with potential as anticancer drugs, we synthesized a series of derivatives in which position 3 was substituted with different polyamine chains. As determined by DNA relaxation and decatenation assays, the resulting compounds are potent topoisomerase IIα inhibitors. Although xanthone derivatives inhibit topoisomerase IIα-catalyzed ATP hydrolysis, mechanistic studies indicate that they do not act at the ATPase site. Rather, they appear to function by blocking the ability of DNA to stimulate ATP hydrolysis. On the basis of activity, competition, and modeling studies, we propose that xanthones interact with the DNA cleavage/ligation active site of topoisomerase IIα and inhibit the catalytic activity of the enzyme by interfering with the DNA strand passage step.
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20
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Bombarde O, Larminat F, Gomez D, Frit P, Racca C, Gomes B, Guilbaud N, Calsou P. The DNA-Binding Polyamine Moiety in the Vectorized DNA Topoisomerase II Inhibitor F14512 Alters Reparability of the Consequent Enzyme-Linked DNA Double-Strand Breaks. Mol Cancer Ther 2017; 16:2166-2177. [PMID: 28611105 DOI: 10.1158/1535-7163.mct-16-0767] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 04/18/2017] [Accepted: 05/24/2017] [Indexed: 11/16/2022]
Abstract
Poisons of topoisomerase II (TOP2) kill cancer cells by preventing religation of intermediate DNA breaks during the enzymatic process and thus by accumulating enzyme-drug-DNA complexes called TOP2 cleavage-complex (TOP2cc). F14512 is a highly cytotoxic polyamine-vectorized TOP2 inhibitor derived from etoposide and currently in clinical trials. It was shown in vitro that F14512 has acquired DNA-binding properties and that the stability of TOP2cc was strongly increased. Paradoxically, at equitoxic concentrations in cells, F14512 induced less DNA breaks than etoposide. Here, we directly compared etoposide and F14512 for their rates of TOP2cc production and resolution in human cells. We report that targeting of TOP2α and not TOP2β impacts cell killing by F14512, contrary to etoposide that kills cells through targeting both isoforms. Then, we show that despite being more cytotoxic, F14512 is less efficient than etoposide at producing TOP2α cleavage-complex (TOP2αcc) in cells. Finally, we report that compared with TOP2αcc mediated by etoposide, those generated by F14512 persist longer in the genome, are not dependent on TDP2 for cleaning break ends from TOP2α, are channeled to a larger extent to resection-based repair processes relying on CtIP and BRCA1 and promote RAD51 recruitment to damaged chromatin. In addition to the addressing of F14512 to the polyamine transport system, the properties uncovered here would be particularly valuable for a therapeutic usage of this new anticancer compound. More generally, the concept of increasing drug cytotoxicity by switching the repair mode of the induced DNA lesions via addition of a DNA-binding moiety deserves further developments. Mol Cancer Ther; 16(10); 2166-77. ©2017 AACR.
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Affiliation(s)
- Oriane Bombarde
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Florence Larminat
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Dennis Gomez
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Philippe Frit
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Carine Racca
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Bruno Gomes
- Pierre Fabre Research Institute, CRDPF, Toulouse Cedex, France
| | | | - Patrick Calsou
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France. .,Equipe labellisée Ligue Nationale Contre le Cancer 2013
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21
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De Vivo M, Cavalli A. Recent advances in dynamic docking for drug discovery. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1320] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Marco De Vivo
- Laboratory of Molecular Modeling and Drug DiscoveryIstituto Italiano di TecnologiaGenoaItaly
- IAS‐S/INM‐9 Computational BiomedicineForschungszentrum JülichJülichGermany
| | - Andrea Cavalli
- CompunetIstituto Italiano di TecnologiaGenoaItaly
- Department of Pharmacy and Biotechnology, Alma Mater StudiorumUniversity of BolognaBolognaItaly
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22
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Estimation of kinetic and thermodynamic ligand-binding parameters using computational strategies. Future Med Chem 2017; 9:507-523. [DOI: 10.4155/fmc-2016-0224] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Kinetic and thermodynamic ligand–protein binding parameters are gaining growing importance as key information to consider in drug discovery. The determination of the molecular structures, using particularly x-ray and NMR techniques, is crucial for understanding how a ligand recognizes its target in the final binding complex. However, for a better understanding of the recognition processes, experimental studies of ligand–protein interactions are needed. Even though several techniques can be used to investigate both thermodynamic and kinetic profiles for a ligand–protein complex, these procedures are very often laborious, time consuming and expensive. In the last 10 years, computational approaches have enormous potential in providing insights into each of the above effects and in parsing their contributions to the changes in both kinetic and thermodynamic binding parameters. The main purpose of this review is to summarize the state of the art of computational strategies for estimating the kinetic and thermodynamic parameters of a ligand–protein binding.
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23
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Dai F, Li Q, Wang Y, Ge C, Feng C, Xie S, He H, Xu X, Wang C. Design, Synthesis, and Biological Evaluation of Mitochondria-Targeted Flavone–Naphthalimide–Polyamine Conjugates with Antimetastatic Activity. J Med Chem 2017; 60:2071-2083. [DOI: 10.1021/acs.jmedchem.6b01846] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Fujun Dai
- Key
Laboratory of Natural Medicine and Immuno-Engineering, ‡College of Chemistry
and Chemical Engineering, and §Pharmaceutical College, Henan University, Kaifeng 475004, Henan, China
| | - Qian Li
- Key
Laboratory of Natural Medicine and Immuno-Engineering, ‡College of Chemistry
and Chemical Engineering, and §Pharmaceutical College, Henan University, Kaifeng 475004, Henan, China
| | - Yuxia Wang
- Key
Laboratory of Natural Medicine and Immuno-Engineering, ‡College of Chemistry
and Chemical Engineering, and §Pharmaceutical College, Henan University, Kaifeng 475004, Henan, China
| | - Chaochao Ge
- Key
Laboratory of Natural Medicine and Immuno-Engineering, ‡College of Chemistry
and Chemical Engineering, and §Pharmaceutical College, Henan University, Kaifeng 475004, Henan, China
| | - Chenyang Feng
- Key
Laboratory of Natural Medicine and Immuno-Engineering, ‡College of Chemistry
and Chemical Engineering, and §Pharmaceutical College, Henan University, Kaifeng 475004, Henan, China
| | - Songqiang Xie
- Key
Laboratory of Natural Medicine and Immuno-Engineering, ‡College of Chemistry
and Chemical Engineering, and §Pharmaceutical College, Henan University, Kaifeng 475004, Henan, China
| | - Haoying He
- Key
Laboratory of Natural Medicine and Immuno-Engineering, ‡College of Chemistry
and Chemical Engineering, and §Pharmaceutical College, Henan University, Kaifeng 475004, Henan, China
| | - Xiaojuan Xu
- Key
Laboratory of Natural Medicine and Immuno-Engineering, ‡College of Chemistry
and Chemical Engineering, and §Pharmaceutical College, Henan University, Kaifeng 475004, Henan, China
| | - Chaojie Wang
- Key
Laboratory of Natural Medicine and Immuno-Engineering, ‡College of Chemistry
and Chemical Engineering, and §Pharmaceutical College, Henan University, Kaifeng 475004, Henan, China
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24
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Incerti M, Russo S, Callegari D, Pala D, Giorgio C, Zanotti I, Barocelli E, Vicini P, Vacondio F, Rivara S, Castelli R, Tognolini M, Lodola A. Metadynamics for Perspective Drug Design: Computationally Driven Synthesis of New Protein-Protein Interaction Inhibitors Targeting the EphA2 Receptor. J Med Chem 2017; 60:787-796. [PMID: 28005388 DOI: 10.1021/acs.jmedchem.6b01642] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Metadynamics (META-D) is emerging as a powerful method for the computation of the multidimensional free-energy surface (FES) describing the protein-ligand binding process. Herein, the FES of unbinding of the antagonist N-(3α-hydroxy-5β-cholan-24-oyl)-l-β-homotryptophan (UniPR129) from its EphA2 receptor was reconstructed by META-D simulations. The characterization of the free-energy minima identified on this FES proposes a binding mode fully consistent with previously reported and new structure-activity relationship data. To validate this binding mode, new N-(3α-hydroxy-5β-cholan-24-oyl)-l-β-homotryptophan derivatives were designed, synthesized, and tested for their ability to displace ephrin-A1 from the EphA2 receptor. Among them, two antagonists, namely compounds 21 and 22, displayed high affinity versus the EphA2 receptor and resulted endowed with better physicochemical and pharmacokinetic properties than the parent compound. These findings highlight the importance of free-energy calculations in drug design, confirming that META-D simulations can be used to successfully design novel bioactive compounds.
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Affiliation(s)
- Matteo Incerti
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Simonetta Russo
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Donatella Callegari
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Daniele Pala
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Carmine Giorgio
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Ilaria Zanotti
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Elisabetta Barocelli
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Paola Vicini
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Federica Vacondio
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Silvia Rivara
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Riccardo Castelli
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Massimiliano Tognolini
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Alessio Lodola
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy.,Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University , Newcastle upon Tyne NE1 8ST, United Kingdom
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25
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26
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Advances in the Chemistry of Natural and Semisynthetic Topoisomerase I/II Inhibitors. STUDIES IN NATURAL PRODUCTS CHEMISTRY 2017. [DOI: 10.1016/b978-0-444-63929-5.00002-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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27
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Li M, Wang Y, Zhang J, Xie S, Wang C, Wu Y. Synthesis and Biological Evaluation of Novel Aromatic Imide-Polyamine Conjugates. Molecules 2016; 21:molecules21121637. [PMID: 27916902 PMCID: PMC6273765 DOI: 10.3390/molecules21121637] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 11/17/2016] [Accepted: 11/23/2016] [Indexed: 11/16/2022] Open
Abstract
Three types of conjugates in which aromatic imide scaffolds were coupled to diverse amine/polyamine motifs were synthesized, and their antitumor activities were evaluated in vitro and in vivo. Results showed that the conjugate 11e of 1,8-naphthilimide with spermine had pronounced effects on inhibiting tumor cell proliferation and inducing tumor cell apoptosis via ROS-mediated mitochondrial pathway. The in vivo assays on three H22 tumor transplant models revealed that compound 11e exerted potent ability in preventing lung cancer metastasis and extending lifespan. Furthermore, the efficacy of 11e in inhibiting tumor growth and improving body weight index were better than that of positive control, amonafide. Our study demonstrates that compound 11e is a valuable lead compound for further investigation.
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Affiliation(s)
- Ming Li
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China.
- Pharmaceutical College, Henan University, Kaifeng 475001, China.
| | - Yuxia Wang
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475001, China.
| | - Jianying Zhang
- Pharmaceutical College, Henan University, Kaifeng 475001, China.
| | - Songqiang Xie
- Pharmaceutical College, Henan University, Kaifeng 475001, China.
| | - Chaojie Wang
- Key Laboratory of Natural Medicine and Immuno-Engineering, Kaifeng 475001, China.
| | - Yingliang Wu
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China.
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28
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La Sala G, Riccardi L, Gaspari R, Cavalli A, Hantschel O, De Vivo M. HRD Motif as the Central Hub of the Signaling Network for Activation Loop Autophosphorylation in Abl Kinase. J Chem Theory Comput 2016; 12:5563-5574. [DOI: 10.1021/acs.jctc.6b00600] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | | | - Andrea Cavalli
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Oliver Hantschel
- Swiss
Institute for Experimental Cancer Research (ISREC), School of Life
Sciences, École polytechnique fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- ISREC Foundation Chair in Translational Oncology, 1015 Lausanne, Switzerland
| | - Marco De Vivo
- IAS-S/INM-9 Computational Biomedicine Forschungszentrum, Jülich Wilhelm-Johnen-Staße, 52428 Jülich, Germany
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29
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Li Q, Zhai Y, Luo W, Zhu Z, Zhang X, Xie S, Hong C, Wang Y, Su Y, Zhao J, Wang C. Synthesis and biological properties of polyamine modified flavonoids as hepatocellular carcinoma inhibitors. Eur J Med Chem 2016; 121:110-119. [DOI: 10.1016/j.ejmech.2016.04.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/15/2016] [Accepted: 04/11/2016] [Indexed: 02/03/2023]
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30
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De Vivo M, Masetti M, Bottegoni G, Cavalli A. Role of Molecular Dynamics and Related Methods in Drug Discovery. J Med Chem 2016; 59:4035-61. [DOI: 10.1021/acs.jmedchem.5b01684] [Citation(s) in RCA: 538] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Marco De Vivo
- Laboratory
of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- IAS-5/INM-9 Computational
Biomedicine Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Matteo Masetti
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
6, I-40126 Bologna, Italy
| | - Giovanni Bottegoni
- CompuNet, Istituto
Italiano di Tecnologia, Via Morego
30, 16163 Genova, Italy
- BiKi Technologies
srl, Via XX Settembre 33/10, 16121 Genova, Italy
| | - Andrea Cavalli
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
6, I-40126 Bologna, Italy
- CompuNet, Istituto
Italiano di Tecnologia, Via Morego
30, 16163 Genova, Italy
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31
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Palermo G, Favia AD, Convertino M, De Vivo M. The Molecular Basis for Dual Fatty Acid Amide Hydrolase (FAAH)/Cyclooxygenase (COX) Inhibition. ChemMedChem 2015; 11:1252-8. [PMID: 26593700 PMCID: PMC5063142 DOI: 10.1002/cmdc.201500507] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Indexed: 12/20/2022]
Abstract
The design of multitarget‐directed ligands is a promising strategy for discovering innovative drugs. Here, we report a mechanistic study that clarifies key aspects of the dual inhibition of the fatty acid amide hydrolase (FAAH) and the cyclooxygenase (COX) enzymes by a new multitarget‐directed ligand named ARN2508 (2‐[3‐fluoro‐4‐[3‐(hexylcarbamoyloxy)phenyl]phenyl]propanoic acid). This potent dual inhibitor combines, in a single scaffold, the pharmacophoric elements often needed to block FAAH and COX, that is, a carbamate moiety and the 2‐arylpropionic acid functionality, respectively. Molecular modeling and molecular dynamics simulations suggest that ARN2508 uses a noncovalent mechanism of inhibition to block COXs, while inhibiting FAAH via the acetylation of the catalytic Ser241, in line with previous experimental evidence for covalent FAAH inhibition. This study proposes the molecular basis for the dual FAAH/COX inhibition by this novel hybrid scaffold, stimulating further experimental studies and offering new insights for the rational design of novel anti‐inflammatory agents that simultaneously act on FAAH and COX.
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Affiliation(s)
- Giulia Palermo
- Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Angelo D Favia
- Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Marino Convertino
- Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy. .,Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428, Jülich, Germany.
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