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Fanfrlík J, Řezáč J, Hnyk D, Holub J. Heats of formation on the way from B 2H 6 to B 20H 16: thermochemical consequences of multicenter bonding in ab initio and DFT methods. Dalton Trans 2024; 54:239-246. [PMID: 39530746 DOI: 10.1039/d4dt02589j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2024]
Abstract
The objective of this study is to evaluate the effectiveness of various computational methods in reproducing the experimental heats of formation of boron hydrides using the atomization energy approach. The results have demonstrated that the empirical dispersion combined with the BJ damping function provided too large intramolecular dispersion energies, thereby compromising the accuracy of the outcomes produced by the DFT-D3 methods. Additionally, the CCSD(T) method has reproduced the experimental values only when combined with a basis set optimized for an accurate description of the core-valence correlation effect. Furthermore, the number of multicenter bonds present in the molecules under examination has also reflected their stability, as indicated by the heats of formation. Finally, a five-center two-electron (5c-2e) bond has emerged in B5H9, by applying the intrinsic bond orbital (IBO) method.
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Affiliation(s)
- Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic.
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic.
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, Husinec-Řež 250 68, Czech Republic
| | - Josef Holub
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, Husinec-Řež 250 68, Czech Republic
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2
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Giugliano G, Gajo M, Marforio TD, Zerbetto F, Mattioli EJ, Calvaresi M. Identification of Potential Drug Targets of Calix[4]arene by Reverse Docking. Chemistry 2024; 30:e202400871. [PMID: 38777795 DOI: 10.1002/chem.202400871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 05/25/2024]
Abstract
Calixarenes are displaying great potential for the development of new drug delivery systems, diagnostic imaging, biosensing devices and inhibitors of biological processes. In particular, calixarene derivatives are able to interact with many different enzymes and function as inhibitors. By screening of the potential drug target database (PDTD) with a reverse docking procedure, we identify and discuss a selection of 100 proteins that interact strongly with calix[4]arene. We also discover that leucine (23.5 %), isoleucine (11.3 %), phenylalanines (11.3 %) and valine (9.5 %) are the most frequent binding residues followed by hydrophobic cysteines and methionines and aromatic histidines, tyrosines and tryptophanes. Top binders are peroxisome proliferator-activated receptors that already are targeted by commercial drugs, demonstrating the practical interest in calix[4]arene. Nuclear receptors, potassium channel, several carrier proteins, a variety of cancer-related proteins and viral proteins are prominent in the list. It is concluded that calix[4]arene, which is characterized by facile access, well-defined conformational characteristics, and ease of functionalization at both the lower and higher rims, could be a potential lead compound for the development of enzyme inhibitors and theranostic platforms.
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Affiliation(s)
- Giulia Giugliano
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Margherita Gajo
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Tainah Dorina Marforio
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Francesco Zerbetto
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Edoardo Jun Mattioli
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Matteo Calvaresi
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
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3
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Selg C, Grell T, Brakel A, Andrews PC, Hoffmann R, Hey-Hawkins E. Fusing Bismuth and Mercaptocarboranes: Design and Biological Evaluation of Low-Toxicity Antimicrobial Thiolato Complexes. Chempluschem 2024; 89:e202300759. [PMID: 38263504 DOI: 10.1002/cplu.202300759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 01/25/2024]
Abstract
This study proposes an innovative strategy to enhance the pharmacophore model of antimicrobial bismuth thiolato complex drugs by substituting hydrocarbon ligand structures with boron clusters, particularly icosahedral closo-dicarbadodecaborane (C2B10H12, carboranes). The hetero- and homoleptic mercaptocarborane complexes BiPh2L (1) and BiL3 (2) (L=9-S-1,2-C2B10H11) were prepared from 9-mercaptocarborane (HL) and triphenylbismuth. Comprehensive characterization using NMR, IR, MS, and XRD techniques confirmed their successful synthesis. Evaluation of antimicrobial activity in a liquid broth microdilution assay demonstrated micromolar to submicromolar minimum inhibitory concentrations (MIC) suggesting high effectiveness against S. aureus and limited efficacy against E. coli. This study highlights the potential of boron-containing bismuth complexes as promising antimicrobial agents, especially targeting Gram-positive bacteria, thus contributing to the advancement of novel therapeutic approaches.
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Affiliation(s)
- Christoph Selg
- Institute of Bioanalytical Chemistry, Centre for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103, Leipzig, Germany
| | - Toni Grell
- Department of Chemistry, University of Milano, Via Camillo Golgi 19, 20133, Milano, Italy
| | - Alexandra Brakel
- Institute of Bioanalytical Chemistry, Centre for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103, Leipzig, Germany
| | - Philip C Andrews
- School of Chemistry, Monash University, Clayton, 3800, Melbourne, VIC, Australia
| | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, Centre for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103, Leipzig, Germany
| | - Evamarie Hey-Hawkins
- Institute of Bioanalytical Chemistry, Centre for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103, Leipzig, Germany
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Grams RJ, Santos WL, Scorei IR, Abad-García A, Rosenblum CA, Bita A, Cerecetto H, Viñas C, Soriano-Ursúa MA. The Rise of Boron-Containing Compounds: Advancements in Synthesis, Medicinal Chemistry, and Emerging Pharmacology. Chem Rev 2024; 124:2441-2511. [PMID: 38382032 DOI: 10.1021/acs.chemrev.3c00663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Boron-containing compounds (BCC) have emerged as important pharmacophores. To date, five BCC drugs (including boronic acids and boroles) have been approved by the FDA for the treatment of cancer, infections, and atopic dermatitis, while some natural BCC are included in dietary supplements. Boron's Lewis acidity facilitates a mechanism of action via formation of reversible covalent bonds within the active site of target proteins. Boron has also been employed in the development of fluorophores, such as BODIPY for imaging, and in carboranes that are potential neutron capture therapy agents as well as novel agents in diagnostics and therapy. The utility of natural and synthetic BCC has become multifaceted, and the breadth of their applications continues to expand. This review covers the many uses and targets of boron in medicinal chemistry.
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Affiliation(s)
- R Justin Grams
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 900 West Campus Drive, Blacksburg, Virginia 24061, United States
| | - Webster L Santos
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 900 West Campus Drive, Blacksburg, Virginia 24061, United States
| | | | - Antonio Abad-García
- Academia de Fisiología y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, 11340 Mexico City, Mexico
| | - Carol Ann Rosenblum
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 900 West Campus Drive, Blacksburg, Virginia 24061, United States
| | - Andrei Bita
- Department of Pharmacognosy & Phytotherapy, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - Hugo Cerecetto
- Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Mataojo 2055, 11400 Montevideo, Uruguay
| | - Clara Viñas
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Bellaterra, Spain
| | - Marvin A Soriano-Ursúa
- Academia de Fisiología y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, 11340 Mexico City, Mexico
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Marforio TD, Carboni A, Calvaresi M. In Vivo Application of Carboranes for Boron Neutron Capture Therapy (BNCT): Structure, Formulation and Analytical Methods for Detection. Cancers (Basel) 2023; 15:4944. [PMID: 37894311 PMCID: PMC10605826 DOI: 10.3390/cancers15204944] [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: 07/31/2023] [Revised: 09/22/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Carboranes have emerged as one of the most promising boron agents in boron neutron capture therapy (BNCT). In this context, in vivo studies are particularly relevant, since they provide qualitative and quantitative information about the biodistribution of these molecules, which is of the utmost importance to determine the efficacy of BNCT, defining their localization and (bio)accumulation, as well as their pharmacokinetics and pharmacodynamics. First, we gathered a detailed list of the carboranes used for in vivo studies, considering the synthesis of carborane derivatives or the use of delivery system such as liposomes, micelles and nanoparticles. Then, the formulation employed and the cancer model used in each of these studies were identified. Finally, we examined the analytical aspects concerning carborane detection, identifying the main methodologies applied in the literature for ex vivo and in vivo analysis. The present work aims to identify the current strengths and weakness of the use of carboranes in BNCT, establishing the bottlenecks and the best strategies for future applications.
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Affiliation(s)
| | - Andrea Carboni
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum—Università di Bologna, Via Francesco Selmi 2, 40126 Bologna, Italy;
| | - Matteo Calvaresi
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum—Università di Bologna, Via Francesco Selmi 2, 40126 Bologna, Italy;
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Shukla S, Jakowski J, Kadian S, Narayan RJ. Computational approaches to delivery of anticancer drugs with multidimensional nanomaterials. Comput Struct Biotechnol J 2023; 21:4149-4158. [PMID: 37675288 PMCID: PMC10477808 DOI: 10.1016/j.csbj.2023.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 09/08/2023] Open
Abstract
Functionalized nanotubes (NTs), nanosheets, nanorods, and porous organometallic scaffolds are potential in vivo carriers for cancer therapeutics. Precise delivery through these agents depends on factors like hydrophobicity, payload capacity, bulk/surface adsorption, orientation of molecules inside the host matrix, bonding, and nonbonding interactions. Herein, we summarize advances in simulation techniques, which are extremely valuable in initial geometry optimization and evaluation of the loading and unloading behavior of encapsulated drug molecules. Computational methods broadly involve the use of quantum and classical mechanics for studying the behavior of molecular properties. Combining theoretical processes with experimental techniques, such as X-ray crystallography, NMR spectroscopy, and bioassays, can provide a more comprehensive understanding of the structure and function of biological molecules. This integrated approach has led to numerous breakthroughs in drug discovery, enzyme design, and the study of complex biological processes. This short review provides an overview of results and challenges described from erstwhile investigations on the molecular interaction of anticancer drugs with nanocarriers of different aspect ratios.
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Affiliation(s)
- Shubhangi Shukla
- Joint Department of Biomedical Engineering, North Carolina State University, Raleigh, NC 27695-7907, United States
| | - Jacek Jakowski
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Sachin Kadian
- Joint Department of Biomedical Engineering, North Carolina State University, Raleigh, NC 27695-7907, United States
| | - Roger J. Narayan
- Joint Department of Biomedical Engineering, North Carolina State University, Raleigh, NC 27695-7907, United States
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Marforio TD, Mattioli EJ, Zerbetto F, Calvaresi M. Exploiting Blood Transport Proteins as Carborane Supramolecular Vehicles for Boron Neutron Capture Therapy. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:nano13111770. [PMID: 37299673 DOI: 10.3390/nano13111770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/26/2023] [Accepted: 05/28/2023] [Indexed: 06/12/2023]
Abstract
Carboranes are promising agents for applications in boron neutron capture therapy (BNCT), but their hydrophobicity prevents their use in physiological environments. Here, by using reverse docking and molecular dynamics (MD) simulations, we identified blood transport proteins as candidate carriers of carboranes. Hemoglobin showed a higher binding affinity for carboranes than transthyretin and human serum albumin (HSA), which are well-known carborane-binding proteins. Myoglobin, ceruloplasmin, sex hormone-binding protein, lactoferrin, plasma retinol-binding protein, thyroxine-binding globulin, corticosteroid-binding globulin and afamin have a binding affinity comparable to transthyretin/HSA. The carborane@protein complexes are stable in water and characterized by favorable binding energy. The driving force in the carborane binding is represented by the formation of hydrophobic interactions with aliphatic amino acids and BH-π and CH-π interactions with aromatic amino acids. Dihydrogen bonds, classical hydrogen bonds and surfactant-like interactions also assist the binding. These results (i) identify the plasma proteins responsible for binding carborane upon their intravenous administration, and (ii) suggest an innovative formulation for carboranes based on the formation of a carborane@protein complex prior to the administration.
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Affiliation(s)
- Tainah Dorina Marforio
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum-Università di Bologna, Via Francesco Selmi 2, 40126 Bologna, Italy
| | - Edoardo Jun Mattioli
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum-Università di Bologna, Via Francesco Selmi 2, 40126 Bologna, Italy
| | - Francesco Zerbetto
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum-Università di Bologna, Via Francesco Selmi 2, 40126 Bologna, Italy
| | - Matteo Calvaresi
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum-Università di Bologna, Via Francesco Selmi 2, 40126 Bologna, Italy
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Dissecting the Interactions between Chlorin e6 and Human Serum Albumin. Molecules 2023; 28:molecules28052348. [PMID: 36903592 PMCID: PMC10005744 DOI: 10.3390/molecules28052348] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Chlorin e6 (Ce6) is among the most used sensitizers in photodynamic (PDT) and sonodynamic (SDT) therapy; its low solubility in water, however, hampers its clinical exploitation. Ce6 has a strong tendency to aggregate in physiological environments, reducing its performance as a photo/sono-sensitizer, as well as yielding poor pharmacokinetic and pharmacodynamic properties. The interaction of Ce6 with human serum albumin (HSA) (i) governs its biodistribution and (ii) can be used to improve its water solubility by encapsulation. Here, using ensemble docking and microsecond molecular dynamics simulations, we identified the two Ce6 binding pockets in HSA, i.e., the Sudlow I site and the heme binding pocket, providing an atomistic description of the binding. Comparing the photophysical and photosensitizing properties of Ce6@HSA with respect to the same properties regarding the free Ce6, it was observed that (i) a red-shift occurred in both the absorption and emission spectra, (ii) a maintaining of the fluorescence quantum yield and an increase of the excited state lifetime was detected, and (iii) a switch from the type II to the type I mechanism in a reactive oxygen species (ROS) production, upon irradiation, took place.
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Smith N, Quan D, Nagalingam G, Triccas JA, Rendina LM, Rutledge PJ. Carborane clusters increase the potency of bis-substituted cyclam derivatives against Mycobacterium tuberculosis. RSC Med Chem 2022; 13:1234-1238. [PMID: 36325397 PMCID: PMC9579921 DOI: 10.1039/d2md00150k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/28/2022] [Indexed: 08/04/2023] Open
Abstract
Bis-substituted cyclam derivatives have recently emerged as a promising new class of antibacterial agents, displaying excellent activity against drug-resistant Mycobacterium tuberculosis (Mtb) and in vivo efficacy in a zebrafish assay. Herein we report the synthesis and biological activity of new carborane derivatives within this class of antitubercular compounds. The resulting carborane-cyclam conjugates incorporating either hydrophobic closo-1,2-carborane or anionic, hydrophilic nido-7,8-carborane clusters display promising activity in an antibacterial assay employing the virulent Mtb strain H37Rv. The most active of these carborane derivatives exhibit MIC50 values of <1 μM, making them the most active compounds in this unique class of antibacterial cyclams reported to date.
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Affiliation(s)
- Nicholas Smith
- School of Chemistry, The University of Sydney Sydney NSW 2006 Australia +61 2 9351 5020 +61 2 9351 4781
| | - Diana Quan
- Sydney Institute of Infectious Diseases and Charles Perkins Centre, The University of Sydney Sydney NSW 2006 Australia
- School of Medical Sciences, The University of Sydney Sydney NSW 2006 Australia
| | - Gayathri Nagalingam
- Sydney Institute of Infectious Diseases and Charles Perkins Centre, The University of Sydney Sydney NSW 2006 Australia
- School of Medical Sciences, The University of Sydney Sydney NSW 2006 Australia
| | - James A Triccas
- Sydney Institute of Infectious Diseases and Charles Perkins Centre, The University of Sydney Sydney NSW 2006 Australia
- School of Medical Sciences, The University of Sydney Sydney NSW 2006 Australia
| | - Louis M Rendina
- School of Chemistry, The University of Sydney Sydney NSW 2006 Australia +61 2 9351 5020 +61 2 9351 4781
- The University of Sydney Nano Institute (Sydney Nano), The University of Sydney Sydney NSW 2006 Australia
| | - Peter J Rutledge
- School of Chemistry, The University of Sydney Sydney NSW 2006 Australia +61 2 9351 5020 +61 2 9351 4781
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El Azab EF, Saleh AM, Yousif SO, Mazhari BBZ, Abu Alrub H, Elfaki EM, Hamza A, Abdulmalek S. New insights into geraniol's antihemolytic, anti-inflammatory, antioxidant, and anticoagulant potentials using a combined biological and in silico screening strategy. Inflammopharmacology 2022; 30:1811-1833. [PMID: 35932440 DOI: 10.1007/s10787-022-01039-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 07/15/2022] [Indexed: 11/05/2022]
Abstract
The study aims to assess the antihemolytic and antioxidant activities of geraniol versus 2, 2'-azobis, 2-amidinopropane dihydro-chloride- (AAPH-) induced oxidative damage and hemolysis to erythrocytes and its anti-inflammatory potential against lipopolysaccharide- (LPS-) induced inflammation in white blood cells (WBCs) with a focus on its integrated computational strategies against different targeted receptors participating in inflammation and coagulation. The rats' erythrocyte suspension was incubated with different geraniol concentrations. Molecular docking and simulation were used to explore the possible interaction patterns of geraniol against the potential targeted proteins for therapeutic screening. The results displayed that geraniol had a prolonged noteworthy effect on activated partial thromboplastin time and thromboplastin time. Geraniol displayed strong antioxidant effects via reduced malondialdehyde (MDA) formation and increased GSH level and SOD activity. We observed dose-dependent prevention of K+ ion leakage along with a remarkable decline of hemolysis in erythrocytes pretreated with geraniol. Geraniol 100 µg/mL and diclofenac 100 µM were nontoxic to WBCs. Geraniol significantly reduces the expression and release of cellular pro-inflammatory factors TNF-α, IL-1β, IL-8, and nitric oxide, accompanied by a significant upregulation of gene expression of anti-inflammatory cytokine IL-10 in LPS-induced WBCs compared to nontreated cells. It demonstrates a much stronger inhibition potential than diclofenac in terms of inflammation inhibition. When comparing molecular docking and simulation data, current work showed that geraniol has a good affinity toward apoptosis signal-regulating kinase 1 (ASK1) and human P2Y12 receptors and could be developed as an antioxidant, anti-inflammatory, and anticoagulant medication in the future. Consequently, geraniol is recommended to have a defensive influence against oxidative stress, and hemolysis also could be developed as a promising anti-inflammatory, antioxidant, and anticoagulant medication.
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Affiliation(s)
- Eman Fawzy El Azab
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences at Al-Qurayyat, Jouf University, Al-Qurayyat, 77454, Saudi Arabia. .,Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, 21511, Egypt.
| | - Abdulrahman M Saleh
- Pharmaceutical Medicinal Chemistry and Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, 11884, Egypt
| | - Sara Osman Yousif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences at Al-Qurayyat, Jouf University, Al-Qurayyat, 77454, Saudi Arabia.,Department of Clinical Chemistry, Faculty of Medical Laboratory Sciences, Sudan University of Science and Technology, Khartoum, Sudan
| | - Bi Bi Zainab Mazhari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences at Al-Qurayyat, Jouf University, Al-Qurayyat, 77454, Saudi Arabia
| | - Heba Abu Alrub
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences at Al-Qurayyat, Jouf University, Al-Qurayyat, 77454, Saudi Arabia
| | - Elyasa Mustafa Elfaki
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences at Al-Qurayyat, Jouf University, Al-Qurayyat, 77454, Saudi Arabia
| | - Alneil Hamza
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences at Al-Qurayyat, Jouf University, Al-Qurayyat, 77454, Saudi Arabia
| | - Shaymaa Abdulmalek
- Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, 21511, Egypt
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11
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Carboranes in drug discovery, chemical biology and molecular imaging. Nat Rev Chem 2022; 6:486-504. [PMID: 37117309 DOI: 10.1038/s41570-022-00400-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2022] [Indexed: 11/08/2022]
Abstract
There exists a paucity of structural innovation and limited molecular diversity associated with molecular frameworks in drug discovery and biomolecular imaging/chemical probe design. The discovery and exploitation of new molecular entities for medical and biological applications will necessarily involve voyaging into previously unexplored regions of chemical space. Boron clusters, notably the carboranes, offer an alternative to conventional (poly)cyclic organic frameworks that may address some of the limitations associated with the use of novel molecular frameworks in chemical biology or medicine. The high thermal stability, unique 3D structure and aromaticity, kinetic inertness to metabolism and ability to engage in unusual types of intermolecular interactions, such as dihydrogen bonds, with biological receptors make carboranes exquisite frameworks in the design of probes for chemical biology, novel drug candidates and biomolecular imaging agents. This Review highlights the key developments of carborane derivatives made over the last decade as new design tools in medicinal chemistry and chemical biology, showcasing the versatility of this unique family of boron compounds.
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Selg C, Schöler A, Schliehe-Diecks J, Hanl M, Sinatra L, Borkhardt A, Sárosi MB, Bhatia S, Hey-Hawkins E, Hansen FK. Borinostats: solid-phase synthesis of carborane-capped histone deacetylase inhibitors with a tailor-made selectivity profile. Chem Sci 2021; 12:11873-11881. [PMID: 34659728 PMCID: PMC8442681 DOI: 10.1039/d1sc02268g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/28/2021] [Indexed: 12/27/2022] Open
Abstract
The elevated expression of histone deacetylases (HDACs) in various tumor types renders their inhibition an attractive strategy for epigenetic therapeutics. One key issue in the development of improved HDAC inhibitors (HDACis) is the selectivity for single HDAC isoforms over unspecific pan inhibition to minimize off-target toxicity. Utilizing the carborane moiety as a fine-tuning pharmacophore, we herein present a robust solid phase synthetic approach towards tailor-made HDACis meeting both ends of the selectivity spectrum, namely pan inhibition and highly selective HDAC6 inhibition.
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Affiliation(s)
- Christoph Selg
- Institute for Drug Discovery, Medical Faculty, Leipzig University Brüderstraße 34 04103 Leipzig Germany
| | - Andrea Schöler
- Institute for Drug Discovery, Medical Faculty, Leipzig University Brüderstraße 34 04103 Leipzig Germany
| | - Julian Schliehe-Diecks
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University Düsseldorf Düsseldorf Germany
| | - Maria Hanl
- Pharmaceutical Institute, Department of Pharmaceutical and Cell Biological Chemistry, University of Bonn An der Immenburg 4 53121 Bonn Germany
| | - Laura Sinatra
- Institute for Drug Discovery, Medical Faculty, Leipzig University Brüderstraße 34 04103 Leipzig Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University Düsseldorf Düsseldorf Germany
| | - Menyhárt B Sárosi
- Institute of Inorganic Chemistry, Faculty of Chemistry and Mineralogy, Leipzig University Johannisallee 29 04103 Leipzig Germany
| | - Sanil Bhatia
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University Düsseldorf Düsseldorf Germany
| | - Evamarie Hey-Hawkins
- Institute of Inorganic Chemistry, Faculty of Chemistry and Mineralogy, Leipzig University Johannisallee 29 04103 Leipzig Germany
| | - Finn K Hansen
- Pharmaceutical Institute, Department of Pharmaceutical and Cell Biological Chemistry, University of Bonn An der Immenburg 4 53121 Bonn Germany
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Fanfrlík J, Pecina A, Řezáč J, Lepšík M, Sárosi MB, Hnyk D, Hobza P. Benchmark Data Sets of Boron Cluster Dihydrogen Bonding for the Validation of Approximate Computational Methods. Chemphyschem 2020; 21:2599-2604. [PMID: 33179424 DOI: 10.1002/cphc.202000729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/16/2020] [Indexed: 12/31/2022]
Abstract
The success of approximate computational methods, such as molecular mechanics, or dispersion-corrected density functional theory, in the description of non-covalent interactions relies on accurate parameterizations. Benchmark data sets are thus required. This area is well developed for organic molecules and biomolecules but practically non-existent for boron clusters, which have been gaining in importance in modern drug as well as material design. To fill this gap, we have introduced two data sets featuring the most common non-covalent interaction of boron clusters, the dihydrogen bond, and calculated reference interaction energies at the "golden standard" CCSD(T)/CBS level. The boron clusters studied interact with formamide, methanol, water and methane at various distances and in two geometrical arrangements. The performance of the tested approximate methods is variable and recommendations for further use are given.
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Affiliation(s)
- Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Adam Pecina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Current address: Istituto Italiano di Tecnologia, Molecular Modeling and Drug Discovery, Via Morego 30, 161 63, Genoa, Italy
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Menyhárt B Sárosi
- Leipzig University, Faculty of Chemistry and Mineralogy, Institute of Inorganic Chemistry, Johannisallee 29, 04103, Leipzig, Germany
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 25068, Husinec-Řež, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 77146, Olomouc, Czech Republic
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14
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Di Giosia M, Marforio TD, Cantelli A, Valle F, Zerbetto F, Su Q, Wang H, Calvaresi M. Inhibition of α-chymotrypsin by pristine single-wall carbon nanotubes: Clogging up the active site. J Colloid Interface Sci 2020; 571:174-184. [DOI: 10.1016/j.jcis.2020.03.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/26/2020] [Accepted: 03/08/2020] [Indexed: 10/24/2022]
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15
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Di Giosia M, Genovese D, Cantelli A, Cingolani M, Rampazzo E, Strever G, Tavoni M, Zaccheroni N, Calvaresi M, Prodi L. Synthesis and characterization of a reconstituted myoglobin-chlorin e6 adduct for theranostic applications. J PORPHYR PHTHALOCYA 2020. [DOI: 10.1142/s108842461950202x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chlorin e6 (Ce6) and its derivatives are among the most important photosensitizers in photodynamic therapy. Due to their intense fluorescence, chlorins may also be used for diagnostics. However, low solubility in water and high tendency to aggregation restrict their medical use. Here we demonstrate that apo-myoglobin, by reinserting Ce6 in its heme binding pocket, can be used to monomolecularly disperse it. The reconstructed myoglobin-Ce6 adduct presents noticeable changes in the photophysical properties of the chromophore. A red-shift, in particular in the transparency window, can be observed in the absorption and in the emission spectra of the adduct compared to the spectra of the free chlorin in PBS. The adduct presents a higher quantum yield and an increased excited-state lifetime with respect to the free Ce6. The binding of Ce6 to apo-myoglobin determines a decrease of the 1O2 generation but a three-fold increase of peroxides production, determining globally an increase in the performance of Ce6 as a photosensitizer and imaging agent.
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Affiliation(s)
- Matteo Di Giosia
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
| | - Damiano Genovese
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
| | - Andrea Cantelli
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
| | - Matteo Cingolani
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
| | - Enrico Rampazzo
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
| | - Giulia Strever
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
| | - Marta Tavoni
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
| | - Nelsi Zaccheroni
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
| | - Matteo Calvaresi
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
- CIRI Scienze Della Vita e Tecnologie per la Salute, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
| | - Luca Prodi
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
- CIRI Scienze Della Vita e Tecnologie per la Salute, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
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16
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Ali F, S Hosmane N, Zhu Y. Boron Chemistry for Medical Applications. Molecules 2020; 25:E828. [PMID: 32070043 PMCID: PMC7071021 DOI: 10.3390/molecules25040828] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/07/2020] [Accepted: 02/11/2020] [Indexed: 12/13/2022] Open
Abstract
Boron compounds now have many applications in a number of fields, including Medicinal Chemistry. Although the uses of boron compounds in pharmacological science have been recognized several decades ago, surprisingly few are found in pharmaceutical drugs. The boron-containing compounds epitomize a new class for medicinal chemists to use in their drug designs. Carboranes are a class of organometallic compounds containing carbon (C), boron (B), and hydrogen (H) and are the most widely studied boron compounds in medicinal chemistry. Additionally, other boron-based compounds are of great interest, such as dodecaborate anions, metallacarboranes and metallaboranes. The boron neutron capture therapy (BNCT) has been utilized for cancer treatment from last decade, where chemotherapy and radiation have their own shortcomings. However, the improvement in the already existing (BPA and/or BSH) localized delivery agents or new tumor-targeted compounds are required before realizing the full clinical potential of BNCT. The work outlined in this short review addresses the advancements in boron containing compounds. Here, we have focused on the possible clinical implications of the new and improved boron-based biologically active compounds for BNCT that are reported to have in vivo and/or in vitro efficacy.
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Affiliation(s)
- Fayaz Ali
- School of Pharmacy, Macau university of Science and Technology, Avenida Wai Long Taipa, Macau 999078, China;
| | - Narayan S Hosmane
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Yinghuai Zhu
- School of Pharmacy, Macau university of Science and Technology, Avenida Wai Long Taipa, Macau 999078, China;
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17
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Demianenko E, Rayevsky A, Soriano-Ursúa MA, Trujillo-Ferrara JG. Theoretical Coupling and Stability of Boronic Acid Adducts with Catecholamines. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180815666180710101604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Background:
Catecholamines combined with boric/boronic acids are attractive chemical
agents in drug design because some of their adducts have shown interesting biological activity.
Scant information exists about their stability.
Objective:
The aim of the present theoretical study was to explore the role of boron in molecules
that combine catecholamines and boric/boronic acids, with a particular interest in examining
stability.
Method:
The methodology was based on the US GAMESS program using DFT with the B3LYP
exchange-correlation functional and the 6-31G (d,p) split-valence basis set.
Results:
According to the current findings, the boron-containing compounds (BCCs) exhibit weaker
bonding to the hydroxyls on the ethylamine moiety than to those in the aromatic ring. The strongest
binding site of a hydroxyl group was often found to be in meta-position (relative to ethylamine
moiety) for boron-free compounds and in para-position for BCCs. Nonetheless, the methyl substituent
in the amino group was able to induce changes in this pattern. We analyzed feasible boronsubstituted
structures and assessed the relative strength of the respective C-B bonds, which allowed
for the identification of the favorable points for reaction and stability.
Conclusion:
It is feasible to form adducts by bonding on the amine and catechol sides of catecholamines.
The presence of boron stabilizes the adducts in para-position. Since some of these BCCs
are promising therapeutic agents, understanding the mechanisms of reaction is relevant for drug
design.
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Affiliation(s)
- Eugeniy Demianenko
- Chuiko Institute of Surface Chemistry, National Academy of Sciences of Ukraine, 17 General Naumov Str., Kyiv, 03164, Ukraine
| | - Alexey Rayevsky
- Chuiko Institute of Surface Chemistry, National Academy of Sciences of Ukraine, 17 General Naumov Str., Kyiv, 03164, Ukraine
| | - Marvin A. Soriano-Ursúa
- Seccion de Estudios de Posgrado e Investigacion, Escuela Superior de Medicina, Instituto Politecnico Nacional, Plan de San Luis y Diaz Miron s/n, Mexico City, 11340, Mexico
| | - José G. Trujillo-Ferrara
- Seccion de Estudios de Posgrado e Investigacion, Escuela Superior de Medicina, Instituto Politecnico Nacional, Plan de San Luis y Diaz Miron s/n, Mexico City, 11340, Mexico
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18
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Frontera A, Bauzá A. closo-Carboranes as dual CH⋯π and BH⋯π donors: theoretical study and biological significance. Phys Chem Chem Phys 2019; 21:19944-19950. [DOI: 10.1039/c9cp03858b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this manuscript the ability ofcloso-carboranes to establish CH⋯π and BH⋯π interactions with several aromatic moieties exhibiting different electronic natures has been evaluated at the PBE0-D3/def2-TZVP level of theory.
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Affiliation(s)
- Antonio Frontera
- Department of Chemistry Universitat de les Illes Balears
- Crta. de Valldemossa km 7.5
- 07122 Palma (Baleares)
- Spain
| | - Antonio Bauzá
- Department of Chemistry University of Florida
- Gainesville
- USA
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19
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Bologna F, Mattioli EJ, Bottoni A, Zerbetto F, Calvaresi M. Interactions between Endohedral Metallofullerenes and Proteins: The Gd@C 60-Lysozyme Model. ACS OMEGA 2018; 3:13782-13789. [PMID: 31458078 PMCID: PMC6644377 DOI: 10.1021/acsomega.8b01888] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/09/2018] [Indexed: 06/10/2023]
Abstract
Endohedral metallofullerenes (EMFs) have great potential as radioisotope carriers for nuclear medicine and as contrast agents for X-ray and magnetic resonance imaging. EMFs have still important restrictions for their use due to low solubility in physiological environments, low biocompatibility, nonspecific cellular uptake, and a strong dependence of their peculiar properties on physiological parameters, such as pH and salt content. Conjugation of the EMFs with proteins can overcome many of these limitations. Here we investigated the thermodynamics of binding of a model EMF (Gd@C60) with a protein (lysozyme) that is known to act as a host for the empty fullerene. As a rule, even if the shape of an EMF is exactly the same as that of the related fullerene, the interactions with a protein are significantly different. The estimated interaction energy (ΔG binding) between Gd@C60 and lysozyme is -18.7 kcal mol-1, suggesting the possibility of using proteins as supramolecular carriers for EMFs. π-π stacking, hydrophobic interactions, surfactant-like interactions, and electrostatic interactions govern the formation of the hybrid between Gd@C60 and lysozyme. The comparison of the energy contributions to the binding between C60 or Gd@C60 and lysozyme suggests that, although shape complementarity remains the driving force of the binding, the presence of electron transfer from the gadolinium atom to the carbon cage induces a charge distribution on the fullerene cage that strongly affects its interaction with the protein.
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Affiliation(s)
- Fabio Bologna
- Dipartimento di Chimica “Giacomo
Ciamician”, Alma Mater Studiorum—Università
di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Edoardo Jun Mattioli
- Dipartimento di Chimica “Giacomo
Ciamician”, Alma Mater Studiorum—Università
di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Andrea Bottoni
- Dipartimento di Chimica “Giacomo
Ciamician”, Alma Mater Studiorum—Università
di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Francesco Zerbetto
- Dipartimento di Chimica “Giacomo
Ciamician”, Alma Mater Studiorum—Università
di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Matteo Calvaresi
- Dipartimento di Chimica “Giacomo
Ciamician”, Alma Mater Studiorum—Università
di Bologna, via F. Selmi 2, 40126 Bologna, Italy
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20
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Nekvinda J, Grüner B, Gabel D, Nau WM, Assaf KI. Host-Guest Chemistry of Carboranes: Synthesis of Carboxylate Derivatives and Their Binding to Cyclodextrins. Chemistry 2018; 24:12970-12975. [DOI: 10.1002/chem.201802134] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/06/2018] [Indexed: 01/13/2023]
Affiliation(s)
- Jan Nekvinda
- Institute of Inorganic Chemistry; Academy of Sciences of the Czech Republic; v.v.i., Hlavní 1001 250 68 Řež Czech Republic
- Department of Organic Chemistry, Faculty of Science; Charles University; Hlavova 2030 128 42 Prague 2 Czech Republic
| | - Bohumír Grüner
- Institute of Inorganic Chemistry; Academy of Sciences of the Czech Republic; v.v.i., Hlavní 1001 250 68 Řež Czech Republic
| | - Detlef Gabel
- Jacobs University Bremen; Department of Life Sciences and Chemistry; Campus Ring 1 28759 Bremen Germany
| | - Werner M. Nau
- Jacobs University Bremen; Department of Life Sciences and Chemistry; Campus Ring 1 28759 Bremen Germany
| | - Khaleel I. Assaf
- Jacobs University Bremen; Department of Life Sciences and Chemistry; Campus Ring 1 28759 Bremen Germany
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21
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Ocampo-Néstor AL, Trujillo-Ferrara JG, Abad-García A, Reyes-López C, Geninatti-Crich S, Soriano-Ursúa MA. Boron's journey: advances in the study and application of pharmacokinetics. Expert Opin Ther Pat 2017; 27:203-215. [PMID: 27788608 DOI: 10.1080/13543776.2017.1252750] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Boron-containing compounds (BCCs) are attractive chemical entities in drug development. Some of these compounds have been used in the treatment of human disease, and studies on their pharmacodynamics suggest that they employ multiple forms of activity. However, less is known about the pharmacokinetic profile of these molecules. Areas covered: The herein compiled reported data is presented in accordance with the classical 'ADME' system for identifying the scope of BCCs in the respective fields. Our analysis suggests that these compounds have several distinct ways to move within the human body, and that the specific structural features of each molecule account for its distinct pharmacokinetic profile. These insights should be useful for designing BCCs with a desired effect. Expert opinion: Increasing knowledge about the pharmacokinetics of BCCs is providing a broader understanding about the design of new release systems and potential drugs, as well as probable protein transporters that could be related to key roles in physiological processes. These transporters may be involved in sodium transport, hormone release and regulation of the cell cycle. The shared features among groups of BCCs are being identified in order to apply these insights to the design of advantageous compounds.
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Affiliation(s)
- Ana L Ocampo-Néstor
- a Departamentos de Fisiología y Bioquímica , Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n , México City , Del. Miguel Hidalgo , México
| | - José G Trujillo-Ferrara
- a Departamentos de Fisiología y Bioquímica , Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n , México City , Del. Miguel Hidalgo , México
| | - Antonio Abad-García
- a Departamentos de Fisiología y Bioquímica , Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n , México City , Del. Miguel Hidalgo , México
| | - Cynthia Reyes-López
- a Departamentos de Fisiología y Bioquímica , Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n , México City , Del. Miguel Hidalgo , México
| | - Simonetta Geninatti-Crich
- b Dipartimento di Biotecnologie Molecolari e Scienze per la Salute , Centro Imaging Molecolare. Università di Torino , Torino , Italy
| | - Marvin A Soriano-Ursúa
- a Departamentos de Fisiología y Bioquímica , Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n , México City , Del. Miguel Hidalgo , México
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22
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Trozzi F, Marforio TD, Bottoni A, Zerbetto F, Calvaresi M. Engineering the Fullerene-protein Interface by Computational Design: The Sum is More than its Parts. Isr J Chem 2016. [DOI: 10.1002/ijch.201600127] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Francesco Trozzi
- Dipartimento di Chimica “G. Ciamician”; Alma Mater Studiorum; Università di Bologna; via F. Selmi 2 40126 Bologna Italy
| | - Tainah Dorina Marforio
- Dipartimento di Chimica “G. Ciamician”; Alma Mater Studiorum; Università di Bologna; via F. Selmi 2 40126 Bologna Italy
| | - Andrea Bottoni
- Dipartimento di Chimica “G. Ciamician”; Alma Mater Studiorum; Università di Bologna; via F. Selmi 2 40126 Bologna Italy
| | - Francesco Zerbetto
- Dipartimento di Chimica “G. Ciamician”; Alma Mater Studiorum; Università di Bologna; via F. Selmi 2 40126 Bologna Italy
| | - Matteo Calvaresi
- Dipartimento di Chimica “G. Ciamician”; Alma Mater Studiorum; Università di Bologna; via F. Selmi 2 40126 Bologna Italy
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23
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Calvaresi M, Eckhart L, Alibardi L. The molecular organization of the beta-sheet region in Corneous beta-proteins (beta-keratins) of sauropsids explains its stability and polymerization into filaments. J Struct Biol 2016; 194:282-91. [DOI: 10.1016/j.jsb.2016.03.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 02/29/2016] [Accepted: 03/05/2016] [Indexed: 11/17/2022]
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Abstract
AbstractBoron clusters have been employed successfully as constituents in bioactive substances. In this review, the perspectives of boron clusters for drug design and problems to be solved for a broader application are discussed, and a list of actions is given for overcoming the problems.
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Affiliation(s)
- Detlef Gabel
- 1Life Science and Health, Jacobs University Bremen, Bremen, Germany
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25
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Goszczyński TM, Kowalski K, Leśnikowski ZJ, Boratyński J. Solid state, thermal synthesis of site-specific protein-boron cluster conjugates and their physicochemical and biochemical properties. Biochim Biophys Acta Gen Subj 2014; 1850:411-8. [PMID: 25445715 DOI: 10.1016/j.bbagen.2014.11.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 11/07/2014] [Accepted: 11/14/2014] [Indexed: 12/25/2022]
Abstract
BACKGROUND Boron clusters represent a vast family of boron-rich compounds with extraordinary properties that provide the opportunity of exploitation in different areas of chemistry and biology. In addition, boron clusters are clinically used in boron neutron capture therapy (BNCT) of tumors. In this paper, a novel, in solid state (solvent free), thermal method for protein modification with boron clusters has been proposed. METHODS The method is based on a cyclic ether ring opening in oxonium adduct of cyclic ether and a boron cluster with nucleophilic centers of the protein. Lysozyme was used as the model protein, and the physicochemical and biological properties of the obtained conjugates were characterized. RESULTS The main residues of modification were identified as arginine-128 and threonine-51. No significant changes in the secondary or tertiary structures of the protein after tethering of the boron cluster were found using mass spectrometry and circular dichroism measurements. However, some changes in the intermolecular interactions and hydrodynamic and catalytic properties were observed. CONCLUSIONS To the best of our knowledge, we have described the first example of an application of cyclic ether ring opening in the oxonium adducts of a boron cluster for protein modification. In addition, a distinctive feature of the proposed approach is performing the reaction in solid state and at elevated temperature. GENERAL SIGNIFICANCE The proposed methodology provides a new route to protein modification with boron clusters and extends the range of innovative molecules available for biological and medical testing.
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Affiliation(s)
- Tomasz M Goszczyński
- "Neolek" Laboratory of Biomedical Chemistry, Department of Experimental Oncology, Institute of Immunology and Experimental Therapy, PAS, 12 Rudolf Weigl St., 53-114 Wrocław, Poland.
| | - Konrad Kowalski
- "Neolek" Laboratory of Biomedical Chemistry, Department of Experimental Oncology, Institute of Immunology and Experimental Therapy, PAS, 12 Rudolf Weigl St., 53-114 Wrocław, Poland
| | - Zbigniew J Leśnikowski
- Laboratory of Molecular Virology and Biological Chemistry, Institute of Medical Biology, PAS, 106 Lodowa St., 93-232 Łódź, Poland.
| | - Janusz Boratyński
- "Neolek" Laboratory of Biomedical Chemistry, Department of Experimental Oncology, Institute of Immunology and Experimental Therapy, PAS, 12 Rudolf Weigl St., 53-114 Wrocław, Poland
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26
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Utilization of Boron Compounds for the Modification of Suberoyl Anilide Hydroxamic Acid as Inhibitor of Histone Deacetylase Class II Homo sapiens. Adv Bioinformatics 2014; 2014:104823. [PMID: 25214833 PMCID: PMC4158260 DOI: 10.1155/2014/104823] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/12/2014] [Accepted: 08/12/2014] [Indexed: 01/26/2023] Open
Abstract
Histone deacetylase (HDAC) has a critical function in regulating gene expression. The inhibition of HDAC has developed as an interesting anticancer research area that targets biological processes such as cell cycle, apoptosis, and cell differentiation. In this study, an HDAC inhibitor that is available commercially, suberoyl anilide hydroxamic acid (SAHA), has been modified to improve its efficacy and reduce the side effects of the compound. Hydrophobic cap and zinc-binding group of these compounds were substituted with boron-based compounds, whereas the linker region was substituted with p-aminobenzoic acid. The molecular docking analysis resulted in 8 ligands with ΔGbinding value more negative than the standards, SAHA and trichostatin A (TSA). That ligands were analyzed based on the nature of QSAR, pharmacological properties, and ADME-Tox. It is conducted to obtain a potent inhibitor of HDAC class II Homo sapiens. The screening process result gave one best ligand, Nova2 (513246-99-6), which was then further studied by molecular dynamics simulations.
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27
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Soriano-Ursúa MA, Das BC, Trujillo-Ferrara JG. Boron-containing compounds: chemico-biological properties and expanding medicinal potential in prevention, diagnosis and therapy. Expert Opin Ther Pat 2014; 24:485-500. [PMID: 24456081 DOI: 10.1517/13543776.2014.881472] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Although the medicinal use of boron-containing compounds (BCCs) had long been limited to antiseptics, in the last few decades, these compounds have been used as antibiotics or chemotherapeutic agents. In the last few years, boron has been included in the moieties of many known drugs to improve their capacity in binding to their respective target receptors. AREAS COVERED The current review focuses on research and patent literature of the last decade related to the development of BCCs as preventive, diagnostic and therapeutic tools. It explores the possible mechanisms of action of these compounds as well as the advantageous features of their structure and chemico-pharmacological properties. EXPERT OPINION Although uncertainties exist about the mechanism of action of BCCs, increasing evidence about their toxicological profile strongly suggests that many can be safely administered to humans. Even stronger evidence exists regarding the capacity of BCCs to reach multiple targets that are involved in the treatment of common diseases. It seems fair to say that some BCCs will reach the market for medicinal use in the near future, not only for targeting microbial or neoplastic systems but also for acting on cell-signaling processes involved in many other disorders.
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Affiliation(s)
- Marvin A Soriano-Ursúa
- Departamento de Fisiología and Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional , Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Del. Miguel Hidalgo, México City, D.F, 11340 , México +52 555 7296000 ; +52 555 7296000-Ext 62751 ;
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Sedlák D, Eignerová B, Dračínský M, Janoušek Z, Bartůněk P, Kotora M. Synthesis and evaluation of 17α-(carboranylalkyl)estradiols as ligands for estrogen receptors α and β. J Organomet Chem 2013. [DOI: 10.1016/j.jorganchem.2013.06.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Barry NPE, Sadler PJ. Exploration of the medical periodic table: towards new targets. Chem Commun (Camb) 2013; 49:5106-5131. [PMID: 23636600 DOI: 10.1039/c3cc41143e] [Citation(s) in RCA: 573] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
Abstract
Metallodrugs offer potential for unique mechanisms of drug action based on the choice of the metal, its oxidation state, the types and number of coordinated ligands and the coordination geometry. We discuss recent progress in identifying new target sites and elucidating the mechanisms of action of anti-cancer, anti-bacterial, anti-viral, anti-parasitic, anti-inflammatory, and anti-neurodegenerative agents, as well as in the design of metal-based diagnostic agents. Progress in identifying and defining target sites has been accelerated recently by advances in proteomics, genomics and metal speciation analysis. Examples of metal compounds and chelating agents (enzyme inhibitors) currently in clinical use, clinical trials or preclinical development are highlighted.
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Affiliation(s)
- Nicolas P E Barry
- University of Warwick, Department of Chemistry, Gibbet Hill Road, Warwick, UK.
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Ok K, Jung YW, Jee JG, Byun Y. Facile Docking and Scoring Studies of Carborane Ligands with Estrogen Receptor. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.4.1051] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
INTRODUCTION Boron lies on the borderline between metals and non-metals in the periodic table. As such, it possesses peculiarities which render it suitable for a variety of applications in chemistry, technology and medicine. However, boron's peculiarities have been exploited only partially so far. AREAS COVERED In this review, the authors highlight selected areas of research which have witnessed new uses of boron compounds in recent times. The examples reported illustrate how difficulties in the synthesis and physicochemical characterization of boronated molecules, encountered in past years, can be overcome with positive effects in different fields. EXPERT OPINION Many potentialities of boron-based systems reside in the peculiar properties of both boron atoms (the ability to replace carbon atoms, electron deficiency) and of boronated compounds (hydrophobicity, lipophilicity, versatile stereochemistry). Taken in conjunction, these properties can provide innovative drugs. The authors highlight the need to further investigate the assembly of boronated compounds, in terms of drug design, since the mechanisms required to obtain supramolecular structures may be unconventional compared with the more standard molecules used. Furthermore, the authors propose that computational methods are a valuable tool for assessing the role of multicenter, quasi-aromatic bonds and its peculiar geometries.
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Affiliation(s)
- Laura Ciani
- University of Florence, Department of Chemistry & CSGI, Sesto Fiorentino, Italy.
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Calvaresi M, Hoefinger S, Zerbetto F. Probing the Structure of Lysozyme-Carbon-Nanotube Hybrids with Molecular Dynamics. Chemistry 2012; 18:4308-13. [DOI: 10.1002/chem.201102703] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Indexed: 11/09/2022]
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Barry NPE, Sadler PJ. Dicarba-closo-dodecarborane-containing half-sandwich complexes of ruthenium, osmium, rhodium and iridium: biological relevance and synthetic strategies. Chem Soc Rev 2012; 41:3264-79. [PMID: 22307021 DOI: 10.1039/c2cs15300a] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This review describes how the incorporation of dicarba-closo-dodecarboranes into half-sandwich complexes of ruthenium, osmium, rhodium and iridium might lead to the development of a new class of compounds with applications in medicine. Such a combination not only has unexplored potential in traditional areas such as Boron Neutron Capture Therapy agents, but also as pharmacophores for the targeting of biologically important proteins and the development of targeted drugs. The synthetic pathways used for the syntheses of dicarba-closo-dodecarboranes-containing half-sandwich complexes of ruthenium, osmium, rhodium and iridium are also reviewed. Complexes with a wide variety of geometries and characteristics can be prepared. Examples of addition reactions on the metal centre, B-H activation, transmetalation reactions and/or direct formation of metal-metal bonds are discussed (103 references).
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Affiliation(s)
- Nicolas P E Barry
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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