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Galal KA, Obeng S, Pallares VLC, Senetra A, Seabra MABL, Awad A, McCurdy CR. Guanidine-to-piperidine switch affords high affinity small molecule NPFF ligands with preference for NPFF1-R and NPFF2-R subtypes. Eur J Med Chem 2024; 269:116330. [PMID: 38522114 DOI: 10.1016/j.ejmech.2024.116330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 03/03/2024] [Accepted: 03/11/2024] [Indexed: 03/26/2024]
Abstract
The Neuropeptide FF (NPFF) receptor system is known to modulate opioid actions and has been shown to mediate opioid-induced hyperalgesia and tolerance. The lack of subtype selective small molecule compounds has hampered further exploration of the pharmacology of this receptor system. The vast majority of available NPFF ligands possess a highly basic guanidine group, including our lead small molecule, MES304. Despite providing strong receptor binding, the guanidine group presents a potential pharmacokinetic liability for in vivo pharmacological tool development. Through structure-activity relationship exploration, we were able to modify our lead molecule MES304 to arrive at guanidine-free NPFF ligands. The novel piperidine analogues 8b and 16a are among the few non-guanidine based NPFF ligands known in literature. Both compounds displayed nanomolar NPFF-R binding affinity approaching that of the parent molecule. Moreover, while MES304 was non-subtype selective, these two analogues presented new starting points for subtype selective scaffolds, whereby 8b displayed a 15-fold preference for NPFF1-R, and 16a demonstrated an 8-fold preference for NPFF2-R. Both analogues showed no agonist activity on either receptor subtype in the in vitro functional activity assay, while 8b displayed antagonistic properties at NPFF1-R. The calculated physicochemical properties of 8b and 16a were also shown to be more favorable for in vivo tool design. These results indicate the possibility of developing potent, subtype selective NPFF ligands devoid of a guanidine functionality.
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Affiliation(s)
- Kareem A Galal
- Department of Medicinal Chemistry, College of Pharmacy, The University of Florida, Gainesville, FL, 32610, USA.
| | - Samuel Obeng
- Department of Medicinal Chemistry, College of Pharmacy, The University of Florida, Gainesville, FL, 32610, USA; Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, 79106, USA
| | - Victoria L C Pallares
- Department of Medicinal Chemistry, College of Pharmacy, The University of Florida, Gainesville, FL, 32610, USA
| | - Alexandria Senetra
- Department of Pharmaceutics, College of Pharmacy, The University of Florida, Gainesville, FL, 32610, USA
| | - Maria A B L Seabra
- Department of Medicinal Chemistry, College of Pharmacy, The University of Florida, Gainesville, FL, 32610, USA
| | - Ahmed Awad
- Department of Medicinal Chemistry, College of Pharmacy, The University of Florida, Gainesville, FL, 32610, USA
| | - Christopher R McCurdy
- Department of Medicinal Chemistry, College of Pharmacy, The University of Florida, Gainesville, FL, 32610, USA; Department of Pharmaceutics, College of Pharmacy, The University of Florida, Gainesville, FL, 32610, USA; UF Translational Drug Development Core, The University of Florida, Gainesville, FL, 32610, USA
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2
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Ratto A, Honek JF. Oxocarbon Acids and their Derivatives in Biological and Medicinal Chemistry. Curr Med Chem 2024; 31:1172-1213. [PMID: 36915986 DOI: 10.2174/0929867330666230313141452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 03/15/2023]
Abstract
The biological and medicinal chemistry of the oxocarbon acids 2,3- dihydroxycycloprop-2-en-1-one (deltic acid), 3,4-dihydroxycyclobut-3-ene-1,2-dione (squaric acid), 4,5-dihydroxy-4-cyclopentene-1,2,3-trione (croconic acid), 5,6-dihydroxycyclohex- 5-ene-1,2,3,4-tetrone (rhodizonic acid) and their derivatives is reviewed and their key chemical properties and reactions are discussed. Applications of these compounds as potential bioisosteres in biological and medicinal chemistry are examined. Reviewed areas include cell imaging, bioconjugation reactions, antiviral, antibacterial, anticancer, enzyme inhibition, and receptor pharmacology.
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Affiliation(s)
- Amanda Ratto
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - John F Honek
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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3
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Bourgard C, Rodríguez-Hernández D, Rudenko A, Rutgersson C, Palm M, Larsson DGJ, Farewell A, Grøtli M, Sunnerhagen P. Development of Dicationic Bisguanidine-Arylfuran Derivatives as Potent Agents against Gram-Negative Bacteria. Antibiotics (Basel) 2022; 11:antibiotics11081115. [PMID: 36009984 PMCID: PMC9404985 DOI: 10.3390/antibiotics11081115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022] Open
Abstract
Antibiotic resistance among bacteria is a growing global challenge. A major reason for this is the limited progress in developing new classes of antibiotics active against Gram-negative bacteria. Here, we investigate the antibacterial activity of a dicationic bisguanidine-arylfuran, originally developed as an antitrypanosomal agent, and new derivatives thereof. The compounds showed good activity (EC50 2–20 µM) against antibiotic-resistant isolates of the Gram-negative members of the ESKAPE group (Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp.) and Escherichia coli with different antibiotic susceptibility patterns, including ESBL isolates. Cytotoxicity was moderate, and several of the new derivatives were less cytotoxic than the lead molecule, offering better selectivity indices (40–80 for several ESKAPE isolates). The molecular mechanism for the antibacterial activity of these molecules is unknown, but sensitivity profiling against human ESKAPE isolates and E. coli collections with known susceptibility patterns against established antibiotics indicates that it is distinct from lactam and quinolone antibiotics.
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Affiliation(s)
- Catarina Bourgard
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, S-405 30 Gothenburg, Sweden
| | - Diego Rodríguez-Hernández
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Gothenburg, Sweden
| | - Anastasia Rudenko
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, S-405 30 Gothenburg, Sweden
| | - Carolin Rutgersson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, S-405 30 Gothenburg, Sweden
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, S-413 46 Gothenburg, Sweden
| | - Martin Palm
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, S-405 30 Gothenburg, Sweden
| | - D. G. Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, S-405 30 Gothenburg, Sweden
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, S-413 46 Gothenburg, Sweden
| | - Anne Farewell
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, S-405 30 Gothenburg, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Gothenburg, Sweden
- Correspondence: (M.G.); (P.S.)
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, S-405 30 Gothenburg, Sweden
- Correspondence: (M.G.); (P.S.)
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4
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Chasák J, Šlachtová V, Urban M, Brulíková L. Squaric acid analogues in medicinal chemistry. Eur J Med Chem 2020; 209:112872. [PMID: 33035923 DOI: 10.1016/j.ejmech.2020.112872] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/12/2020] [Accepted: 09/21/2020] [Indexed: 12/16/2022]
Abstract
In this review, we summarize the published data on squaric acid analogues with a special focus on their use in medicinal chemistry and as potential drugs. Squaric acid is an interesting small molecule with an almost perfectly square shape, and its analogues have a variety of biological activities that are enabled by the presence of significant H-bond donors and acceptors. Unfortunately, most of these compounds also exhibit reactive functionalities, and this deters the majority of medicinal chemists and pharmacologists from trying to use them in drug development. However, this group of compounds is experiencing a renaissance, and large numbers of them are being tested for antiprotozoal, antibacterial, antifungal, and antiviral activities. The most useful of these compounds exhibited IC50 values in the nanomolar range, which makes them promising drug candidates. In addition to these activities, their interactions with living systems were intensively explored, revealing that squaric acid analogues inhibit various enzymes and often serve as receptor antagonists and that the squaric acid moiety may be used as a non-classical isosteric replacement for other functional groups such as carboxylate. In summary, this review is focused on squaric acid and its analogues and their use in medicinal chemistry and should serve as a guide for other researchers in the field to demonstrate the potential of these compounds based on previous research.
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Affiliation(s)
- Jan Chasák
- Department of Organic Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Veronika Šlachtová
- Department of Organic Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Milan Urban
- Medicinal Chemistry, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University in Olomouc, Hněvotínská 5, 779 00, Olomouc, Czech Republic
| | - Lucie Brulíková
- Department of Organic Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46, Olomouc, Czech Republic.
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Greifenstein L, Engelbogen N, Lahnif H, Sinnes JP, Bergmann R, Bachmann M, Rösch F. Synthesis, Labeling and Preclinical Evaluation of a Squaric Acid Containing PSMA Inhibitor Labeled with 68 Ga: A Comparison with PSMA-11 and PSMA-617. ChemMedChem 2020; 15:695-704. [PMID: 32057189 DOI: 10.1002/cmdc.201900559] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/19/2019] [Indexed: 02/06/2023]
Abstract
The L-lysine urea-L-glutamate (KuE) represents a key motif in recent diagnostic and therapeutic radiopharmaceuticals targeting the prostate specific membrane antigen (PSMA). Using a squaric acid moiety for coupling of KuE with a radioactive label, the squaric acid as a linker in the PSMA ligand seems to mimic the aromatic structure of the naphthylalanine unit on PSMA-617. In this work, we investigate the influence of squaric acid moiety on the biological activity of the compound carrying a KuE motif and three typical chelates. The derivatives TRAM.SA.KuE, DOTAGA.SA.KuE and NODAGA.SA.KuE were all synthesized in straightforward organic reactions and purified by HPLC afterward. Different amounts of tracer were labeled at different temperatures with 68 Ga. PET examinations were performed on NMRInu/nu nude mice with an LNCaP tumor on the right hind leg including ex vivo investigations of the organs. For comparison, 68 Ga-derivatives of PSMA-11 and PSMA-617, the derivatives most commonly used in clinics, were investigated in the same animal model.
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Affiliation(s)
- Lukas Greifenstein
- Institute of Nuclear Chemistry, Johannes Gutenberg University, Fritz-Strassmann-Weg 2, 55128, Mainz, Germany
| | - Nils Engelbogen
- Institute of Nuclear Chemistry, Johannes Gutenberg University, Fritz-Strassmann-Weg 2, 55128, Mainz, Germany
| | - Hanane Lahnif
- Institute of Nuclear Chemistry, Johannes Gutenberg University, Fritz-Strassmann-Weg 2, 55128, Mainz, Germany
| | - Jean-Philippe Sinnes
- Institute of Nuclear Chemistry, Johannes Gutenberg University, Fritz-Strassmann-Weg 2, 55128, Mainz, Germany
| | - Ralf Bergmann
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany.,Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, 1094, Budapest, Hungary
| | - Michael Bachmann
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Frank Rösch
- Institute of Nuclear Chemistry, Johannes Gutenberg University, Fritz-Strassmann-Weg 2, 55128, Mainz, Germany
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6
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Dick A, Cocklin S. Bioisosteric Replacement as a Tool in Anti-HIV Drug Design. Pharmaceuticals (Basel) 2020; 13:ph13030036. [PMID: 32121077 PMCID: PMC7151723 DOI: 10.3390/ph13030036] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 12/22/2022] Open
Abstract
Bioisosteric replacement is a powerful tool for modulating the drug-like properties, toxicity, and chemical space of experimental therapeutics. In this review, we focus on selected cases where bioisosteric replacement and scaffold hopping have been used in the development of new anti-HIV-1 therapeutics. Moreover, we cover field-based, computational methodologies for bioisosteric replacement, using studies from our group as an example. It is our hope that this review will serve to highlight the utility and potential of bioisosteric replacement in the continuing search for new and improved anti-HIV drugs.
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Affiliation(s)
| | - Simon Cocklin
- Correspondence: ; Tel.: +215-762-7234 or +215-762-4979
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7
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8
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Park S, Uchida J, Urushibara K, Kagechika H, Kato T, Tanatani A. Self-assembly of Liquid-crystalline Squaramides. CHEM LETT 2018. [DOI: 10.1246/cl.171208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Soyoung Park
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Junya Uchida
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ko Urushibara
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Hiroyuki Kagechika
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takashi Kato
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Aya Tanatani
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
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9
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Ximenis M, Bustelo E, Algarra AG, Vega M, Rotger C, Basallote MG, Costa A. Kinetic Analysis and Mechanism of the Hydrolytic Degradation of Squaramides and Squaramic Acids. J Org Chem 2017; 82:2160-2170. [PMID: 28107005 DOI: 10.1021/acs.joc.6b02963] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The hydrolytic degradation of squaramides and squaramic acids, the product of partial hydrolysis of squaramides, has been evaluated by UV spectroscopy at 37 °C in the pH range 3-10. Under these conditions, the compounds are kinetically stable over long time periods (>100 days). At pH >10, the hydrolysis of the squaramate anions shows first-order dependence on both squaramate and OH-. At the same temperature and [OH-], the hydrolysis of squaramides usually displays biphasic spectral changes (A → B → C kinetic model) with formation of squaramates as detectable reaction intermediates. The measured rates for the first step (k1 ≈ 10-4 M-1 s-1) are 2-3 orders of magnitude faster than those for the second step (k2 ≈ 10-6 M-1 s-1). Experiments at different temperatures provide activation parameters with values of ΔH⧧ ≈ 9-18 kcal mol-1 and ΔS⧧ ≈ -5 to -30 cal K-1 mol-1. DFT calculations show that the mechanism for the alkaline hydrolysis of squaramic acids is quite similar to that of amides.
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Affiliation(s)
- Marta Ximenis
- Department of Chemistry, Universitat de les Illes Balears , Palma 07122, Spain
| | - Emilio Bustelo
- Department of Materials Scientist, Metallurgic Engineering and Inorganic Chemistry, Universidad de Cádiz , Puerto Real, 11510 Cádiz, Spain
| | - Andrés G Algarra
- Department of Materials Scientist, Metallurgic Engineering and Inorganic Chemistry, Universidad de Cádiz , Puerto Real, 11510 Cádiz, Spain
| | - Manel Vega
- Department of Chemistry, Universitat de les Illes Balears , Palma 07122, Spain
| | - Carmen Rotger
- Department of Chemistry, Universitat de les Illes Balears , Palma 07122, Spain
| | - Manuel G Basallote
- Department of Materials Scientist, Metallurgic Engineering and Inorganic Chemistry, Universidad de Cádiz , Puerto Real, 11510 Cádiz, Spain
| | - Antonio Costa
- Department of Chemistry, Universitat de les Illes Balears , Palma 07122, Spain
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10
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Lu M, Lu QB, Honek JF. Squarate-based carbocyclic nucleosides: Syntheses, computational analyses and anticancer/antiviral evaluation. Bioorg Med Chem Lett 2017; 27:282-287. [DOI: 10.1016/j.bmcl.2016.11.058] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/20/2016] [Accepted: 11/21/2016] [Indexed: 12/31/2022]
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11
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Le Douce V, Ait-Amar A, Forouzan Far F, Fahmi F, Quiel J, El Mekdad H, Daouad F, Marban C, Rohr O, Schwartz C. Improving combination antiretroviral therapy by targeting HIV-1 gene transcription. Expert Opin Ther Targets 2016; 20:1311-1324. [PMID: 27266557 DOI: 10.1080/14728222.2016.1198777] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Combination Antiretroviral Therapy (cART) has not allowed the cure of HIV. The main obstacle to HIV eradication is the existence of quiescent reservoirs. Several other limitations of cART have been described, such as strict life-long treatment and high costs, restricting it to Western countries, as well as the development of multidrug resistance. Given these limitations and the impetus to find a cure, the development of new treatments is necessary. Areas covered: In this review, we discuss the current status of several efficient molecules able to suppress HIV gene transcription, including NF-kB and Tat inhibitors. We also assess the potential of new proteins belonging to the intriguing DING family, which have been reported to have potential anti-HIV-1 activity by inhibiting HIV gene transcription. Expert opinion: Targeting HIV-1 gene transcription is an alternative approach, which could overcome cART-related issues, such as the emergence of multidrug resistance. Improving cART will rely on the identification and characterization of new actors inhibiting HIV-1 transcription. Combining such efforts with the use of new technologies, the development of new models for preclinical studies, and improvement in drug delivery will considerably reduce drug toxicity and thus increase patient adherence.
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Affiliation(s)
- Valentin Le Douce
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France.,b IUT de Schiltigheim , Schiltigheim , France.,c UCD Centre for Research in Infectious Diseases (CRID) School of Medicine and Medical Science , University College Dublin , Dublin 4 , Ireland
| | - Amina Ait-Amar
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France
| | - Faezeh Forouzan Far
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France
| | - Faiza Fahmi
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France
| | - Jose Quiel
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France
| | - Hala El Mekdad
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France
| | - Fadoua Daouad
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France
| | - Céline Marban
- d Faculté de Chirurgie Dentaire , Inserm UMR 1121 , Strasbourg , France
| | - Olivier Rohr
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France.,b IUT de Schiltigheim , Schiltigheim , France.,e Institut Universitaire de France , Paris , France
| | - Christian Schwartz
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France.,b IUT de Schiltigheim , Schiltigheim , France
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Mishiro K, Hu F, Paley DW, Min W, Lambert TH. Macrosteres: The Deltic Guanidinium Ion. European J Org Chem 2016; 2016:1655-1659. [PMID: 27790071 PMCID: PMC5079176 DOI: 10.1002/ejoc.201600137] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Indexed: 11/12/2022]
Abstract
The "deltic guanidinium" ion is described here as a "macrostere" of the guanidinium ion. The use of the 2,4-dimethoxybenzyl protecting group allows for the synthesis of the fully unsubstituted parent compound and a variety of derivatives bearing multiple N-H functions for the first time. Deltic urea, deltic thiourea, and deltic benzamidine are also synthesized. A comparison of the physical properties of guanidinium and deltic guanidinium ions is provided. The use of a deltic guanidinium dendrimer for cell transport is demonstrated.
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Affiliation(s)
- Kenji Mishiro
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027 USA, Fax: (+) 212-932-1289, http://www.columbia.edu/cu/chemistry/groups/lambert/
| | - Fanghao Hu
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027 USA, Fax: (+) 212-932-1289, http://www.columbia.edu/cu/chemistry/groups/lambert/
| | - Daniel W. Paley
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027 USA, Fax: (+) 212-932-1289, http://www.columbia.edu/cu/chemistry/groups/lambert/
| | - Wei Min
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027 USA, Fax: (+) 212-932-1289, http://www.columbia.edu/cu/chemistry/groups/lambert/
| | - Tristan H. Lambert
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027 USA, Fax: (+) 212-932-1289, http://www.columbia.edu/cu/chemistry/groups/lambert/
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13
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Le Grice SFJ. Targeting the HIV RNA genome: high-hanging fruit only needs a longer ladder. Curr Top Microbiol Immunol 2015; 389:147-69. [PMID: 25735922 PMCID: PMC7120518 DOI: 10.1007/82_2015_434] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Small molecules targeting the enzymes responsible for human immunodeficiency virus (HIV) maturation, DNA synthesis and its subsequent chromosomal integration as ribonucleotide-free double-stranded DNA remain the mainstay of combination antiretroviral therapy. For infected individuals harboring drug-susceptible virus, this approach has afforded complete or near-complete viral suppression. However, in the absence of a curative strategy, the predictable emergence of drug-resistant variants requires continued development of improved antiviral strategies, inherent to which is the necessity of identifying novel targets. Regulatory elements that mediate transcription, translation, nucleocytoplasmic transport, dimerization, packaging and reverse transcription of the (+) strand RNA genome should now be considered viable targets for small molecule, peptide- and oligonucleotide-based therapeutics. Where target specificity and cellular penetration and toxicity have been the primary obstacle to successful “macromolecule therapeutics”, this chapter summarizes (a) novel approaches targeting RNA motifs whose three-dimensional structure is critical for biological function and consequently may be less prone to resistance-conferring mutations and (b) improved methods for delivery.
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Affiliation(s)
- Stuart F J Le Grice
- RT Biochemistry Section, Basic Research Laboratory, National Cancer Institute, Frederick, MD, 21702, USA,
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14
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Sampedro A, Villalonga-Planells R, Vega M, Ramis G, Fernández de Mattos S, Villalonga P, Costa A, Rotger C. Cell uptake and localization studies of squaramide based fluorescent probes. Bioconjug Chem 2014; 25:1537-46. [PMID: 25036647 DOI: 10.1021/bc500258b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cell internalization is a major issue in drug design. Although squaramide-based compounds are receiving much attention because of their interesting bioactivity, cell uptake and trafficking within cells of this type of compounds are still unknown. In order to monitor the cell internalization process of cyclosquaramide compounds we have prepared two fluorescent probes by covalently linking a fluorescent dye (BODIPY derivative or fluorescein) to a noncytotoxic cyclosquaramide framework. These two probes (C2-BDP and C2-FITC) rapidly internalize across live cell membranes through endocytic receptor-mediated mechanisms. Due to its higher fluorescence and photochemical stability, C2-BDP is a superior dye than C2-FITC. C2-BDP remains sequestered in late endosomes allowing their fast and selective imaging in various live cell types. Cyclosquaramide-cell membrane interactions facilitate cell uptake and have been investigated by binding studies in solution as well as in live cells. Cyclosquaramide 1 (C2-BDP) can be used as a highly fluorescent probe for the rapid and selective imaging of late endosomes in live cells.
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Affiliation(s)
- Angel Sampedro
- Departament de Química, ‡Departament de Biologia Fonamental, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS) and Instituto de Investigación Sanitaria de Palma (IdISPa), Illes Balears, Spain, Universitat de les Illes Balears , Ctra. Valldemossa km 7.5, 07122 Palma, Spain
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Mehrabi H, Anary-Abbasinejad M, Pour SA. The Formation of Squaramic Acids and Squaryl Diamides by the Reaction of Squaric Acid with Alkyl Isocyanides. JOURNAL OF CHEMICAL RESEARCH 2013. [DOI: 10.3184/174751913x13677757448841] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The reaction between squaric acid with one equivalent of alkyl isocyanides such as t-butyl isocyanide, cyclohexyl isocyanide and n-butyl isocyanide in ethanol at room temperature after 3h afforded the corresponding squaramic acid derivatives. Symmetric 2,4-squaryl diamides were obtained when the reaction of squaric acid was carried out with two equivalents of alkyl isocyanides under the same conditions. Asymmetric 2,4-squaryl diamides were obtained by reaction of squaramic acids with one equivalent of alkyl isocyanides.
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Affiliation(s)
- Hossein Mehrabi
- Department of Chemistry, Vali-e-Asr University of Rafsanjan, Rafsanjan 77176, Iran
| | | | - Sajjad Abbasi Pour
- Department of Chemistry, Vali-e-Asr University of Rafsanjan, Rafsanjan 77176, Iran
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16
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Li CH, Zuo ZC, Su JG, Xu XJ, Wang CX. The interactions and recognition of cyclic peptide mimetics of Tat with HIV-1 TAR RNA: a molecular dynamics simulation study. J Biomol Struct Dyn 2012; 31:276-87. [PMID: 22943434 DOI: 10.1080/07391102.2012.698248] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The interaction of HIV-1 trans-activator protein Tat with its cognate trans-activation response element (TAR) RNA is critical for viral transcription and replication. Therefore, it has long been considered as an attractive target for the development of antiviral compounds. Recently, the conformationally constrained cyclic peptide mimetics of Tat have been tested to be a promising family of lead peptides. Here, we focused on two representative cyclic peptides termed as L-22 and KP-Z-41, both of which exhibit excellent inhibitory potency against Tat and TAR interaction. By means of molecular dynamics simulations, we obtained a detailed picture of the interactions between them and HIV-1 TAR RNA. In results, it is found that the binding modes of the two cyclic peptides to TAR RNA are almost identical at or near the bulge regions, whereas the binding interfaces at the apical loop exhibit large conformational heterogeneity. In addition, it is revealed that electrostatic interaction energy contributes much more to KP-Z-41 complex formation than to L-22 complex, which is the main source of energy that results in a higher binding affinity of KP-Z-41 over-22 for TAR RNA. Furthermore, we identified a conserved motif RRK (Arg-Arg-Lys) that is shown to be essential for specific binding of this class of cyclic peptides to TAR RNA. This work can provide a useful insight into the design and modification of cyclic peptide inhibitors targeting the association of HIV-1 Tat and TAR RNA.
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Affiliation(s)
- Chun Hua Li
- College of Life Science and Bioengineering, Beijing University of Technology, Pingleyuan 100, Chaoyang District, Beijing 100124, China.
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17
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Villalonga P, Fernández de Mattos S, Ramis G, Obrador-Hevia A, Sampedro A, Rotger C, Costa A. Cyclosquaramides as Kinase Inhibitors with Anticancer Activity. ChemMedChem 2012; 7:1472-80. [DOI: 10.1002/cmdc.201200157] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 06/15/2012] [Indexed: 11/11/2022]
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18
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Giner-Casares JJ, Keller J, Rotger C, Costa A, Brezesinski G. Mechanism of Action of Cyclic Oligosquaramides on DPPC Phospholipid Monolayers. Chemphyschem 2011; 13:453-8. [DOI: 10.1002/cphc.201100666] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 12/02/2011] [Indexed: 11/06/2022]
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19
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Süleymanoğlu N, Ustabaş R, Alpaslan YB, Eyduran F, Ozyürek C, Iskeleli NO. Experimental (13C NMR, 1H NMR, FT-IR, single-crystal X-ray diffraction) and DFT studies on 3,4-bis(isoproylamino)cyclobut-3-ene-1,2-dione. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 83:472-477. [PMID: 21963193 DOI: 10.1016/j.saa.2011.08.068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 08/23/2011] [Accepted: 08/29/2011] [Indexed: 05/31/2023]
Abstract
In this work, 3,4-bis(isoproylamino)cyclobut-3-ene-1,2-dione C(10)H(16)N(2)O(2) (I), was synthesized and characterized by (13)C NMR, (1)H NMR, FT-IR, UV-vis spectroscopy and single-crystal X-ray diffraction. DFT method with 6-31G(d,p) basis set has been used to calculate the optimized geometrical parameters, atomic charges, vibrational frequencies and chemical shift values. The calculated vibrational frequencies and chemical shift values are compared with experimental FT-IR and NMR spectra. The results of the calculation shows good agreement between experimental and calculated values of the compound I. The existence of N-H⋯O type intermolecular ve C-H⋯O type intramolecular hydrogen bonds can be deduced from differences between experimental and calculated results of FT-IR and NMR. In addition, the molecular electrostatic potential map and frontier molecular orbitals and electronic absorption spectra were performed at B3LYP/6-31G(d,p) level of theory. HOMO-LUMO electronic transition of 4.90 eV are derived from the contribution of the bands π→π* and n→π* The spectral results obtained from FT-IR, NMR and X-ray of I revealed that the compound I is in predominantly enamine tautomeric form, which was supported by DFT calculations.
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20
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Nilson KA, Price DH. The Role of RNA Polymerase II Elongation Control in HIV-1 Gene Expression, Replication, and Latency. GENETICS RESEARCH INTERNATIONAL 2011; 2011:726901. [PMID: 22567366 PMCID: PMC3335632 DOI: 10.4061/2011/726901] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 07/22/2011] [Indexed: 11/20/2022]
Abstract
HIV-1 usurps the RNA polymerase II elongation control machinery to regulate the expression of its genome during lytic and latent viral stages. After integration into the host genome, the HIV promoter within the long terminal repeat (LTR) is subject to potent downregulation in a postinitiation step of transcription. Once produced, the viral protein Tat commandeers the positive transcription elongation factor, P-TEFb, and brings it to the engaged RNA polymerase II (Pol II), leading to the production of viral proteins and genomic RNA. HIV can also enter a latent phase during which factors that regulate Pol II elongation may play a role in keeping the virus silent. HIV, the causative agent of AIDS, is a worldwide health concern. It is hoped that knowledge of the mechanisms regulating the expression of the HIV genome will lead to treatments and ultimately a cure.
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Affiliation(s)
- Kyle A Nilson
- Molecular and Cellular Biology Program, The University of Iowa, Iowa City, IA 52242, USA
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21
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Lalonde MS, Lobritz MA, Ratcliff A, Chamanian M, Athanassiou Z, Tyagi M, Wong J, Robinson JA, Karn J, Varani G, Arts EJ. Inhibition of both HIV-1 reverse transcription and gene expression by a cyclic peptide that binds the Tat-transactivating response element (TAR) RNA. PLoS Pathog 2011; 7:e1002038. [PMID: 21625572 PMCID: PMC3098202 DOI: 10.1371/journal.ppat.1002038] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 03/04/2011] [Indexed: 11/18/2022] Open
Abstract
The RNA response element TAR plays a critical role in HIV replication by
providing a binding site for the recruitment of the viral transactivator protein
Tat. Using a structure-guided approach, we have developed a series of
conformationally-constrained cyclic peptides that act as structural mimics of
the Tat RNA binding region and block Tat-TAR interactions at nanomolar
concentrations in vitro. Here we show that these compounds
block Tat-dependent transcription in cell-free systems and in cell-based
reporter assays. The compounds are also cell permeable, have low toxicity, and
inhibit replication of diverse HIV-1 strains, including both CXCR4-tropic and
CCR5-tropic primary HIV-1 isolates of the divergent subtypes A, B, C, D and
CRF01_AE. In human peripheral blood mononuclear cells, the cyclic peptidomimetic
L50 exhibited an IC50 ∼250 nM. Surprisingly, inhibition of
LTR-driven HIV-1 transcription could not account for the full antiviral
activity. Timed drug-addition experiments revealed that L-50 has a bi-phasic
inhibition curve with the first phase occurring after HIV-1 entry into the host
cell and during the initiation of HIV-1 reverse transcription. The second phase
coincides with inhibition of HIV-1 transcription. Reconstituted reverse
transcription assays confirm that HIV-1 (−) strand strong stop DNA
synthesis is blocked by L50-TAR RNA interactions in-vitro.
These findings are consistent with genetic evidence that TAR plays critical
roles both during reverse transcription and during HIV gene expression. Our
results suggest that antiviral drugs targeting TAR RNA might be highly effective
due to a dual inhibitory mechanism. The HIV-1 transactivator protein (Tat), together with the elongation factor
P-TEFb binds to an HIV-1 RNA secondary structure in the 5′-UTRs of nascent
viral mRNAs (TAR) and promotes transcription elongation. This process has been
an attractive target for drug development but previous inhibitors that bind
either Tat or TAR have been plagued by poor inhibition of virus replication,
limited cell penetration, and off-target effects. In this article, we describe a
series of rationally designed cyclic peptides that block Tat-TAR interactions.
L50, the most potent of these compounds, inhibits a wide range of HIV-1 strains
from around the world. Remarkably, L50 inhibits two distinct steps in the HIV-1
lifecycle. As expected, L50 inhibits Tat-dependent HIV-1 transcription, but the
majority of its anti-HIV activity is due to a block in reverse transcription,
i.e. synthesis of the proviral DNA from the RNA genome. L50 inhibition of
reverse transcription reveals an important role for TAR RNA during reverse
transcription as well as providing one of first examples of a drug with a dual
mechanism of action.
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Affiliation(s)
- Matthew S. Lalonde
- Department of Biochemistry, Case Western
Reserve University, Cleveland, Ohio, United States of America
| | - Michael A. Lobritz
- Department of Molecular Biology and
Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of
America
| | - Annette Ratcliff
- Department of Molecular Biology and
Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of
America
| | - Mastooreh Chamanian
- Department of Molecular Biology and
Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of
America
| | - Zafiria Athanassiou
- Department of Chemistry and Department of
Biochemistry, University of Washington, Seattle, Washington, United States of
America
| | - Mudit Tyagi
- Department of Molecular Biology and
Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of
America
| | - Julian Wong
- Department of Molecular Biology and
Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of
America
| | - John A. Robinson
- Department of Chemistry, University of Zurich,
Zurich, Switzerland
| | - Jonathan Karn
- Department of Molecular Biology and
Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of
America
| | - Gabriele Varani
- Department of Chemistry and Department of
Biochemistry, University of Washington, Seattle, Washington, United States of
America
| | - Eric J. Arts
- Department of Molecular Biology and
Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of
America
- Division of Infectious Diseases, Department of
Medicine, Case Western Reserve University, Cleveland, Ohio, United States of
America
- * E-mail:
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22
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Meanwell NA. Synopsis of Some Recent Tactical Application of Bioisosteres in Drug Design. J Med Chem 2011; 54:2529-91. [DOI: 10.1021/jm1013693] [Citation(s) in RCA: 1876] [Impact Index Per Article: 144.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nicholas A. Meanwell
- Department of Medicinal Chemistry, Bristol-Myers Squibb Pharmaceutical Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
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Storer RI, Aciro C, Jones LH. Squaramides: physical properties, synthesis and applications. Chem Soc Rev 2011; 40:2330-46. [PMID: 21399835 DOI: 10.1039/c0cs00200c] [Citation(s) in RCA: 409] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Squaramides are remarkable four-membered ring systems derived from squaric acid that are able to form up to four hydrogen bonds. A high affinity for hydrogen bonding is driven through a concomitant increase in aromaticity of the ring. This hydrogen bonding and aromatic switching, in combination with structural rigidity, have been exploited in many of the applications of squaramides. Substituted squaramides can be accessed via modular synthesis under relatively mild or aqueous conditions, making them ideal units for bioconjugation and supramolecular chemistry. In this tutorial review the fundamental electronic and structural properties of squaramides are explored to rationalise the geometry, conformation, reactivity and biological activity.
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Affiliation(s)
- R Ian Storer
- Worldwide Medicinal Chemistry, Pfizer Global Research and Development, Ramsgate Road, Sandwich, Kent, CT13 9NJ, UK.
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24
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Role of Tat protein in HIV neuropathogenesis. Neurotox Res 2009; 16:205-20. [PMID: 19526283 DOI: 10.1007/s12640-009-9047-8] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 03/09/2009] [Accepted: 03/09/2009] [Indexed: 12/13/2022]
Abstract
The Tat protein of the human immunodeficiency virus (HIV) has been implicated in the pathophysiology of the neurocognitive deficits associated with HIV infection. This is the earliest protein to be produced by the proviral DNA in the infected cell. The protein not only drives the regulatory regions of the virus but may also be actively released from the cell and then interact with the cell surface receptors of other uninfected cells in the brain leading to cellular dysfunction. It may also be taken up by these cells and can then activate a number of host genes. The Tat protein is highly potent and has the unique ability to travel along neuronal pathways. Importantly, its production is not impacted by the use of antiretroviral drugs once the proviral DNA has been formed. This article reviews the pleomorphic actions of Tat protein and the evidence supporting its central role in the neuropathogenesis of the HIV infection.
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Bonnard V, Azoulay S, Di Giorgio A, Patino N. Polyamide amino acids: a new class of RNA ligands. Chem Commun (Camb) 2009:2302-4. [DOI: 10.1039/b815324h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ludwig V, Krebs A, Stoll M, Dietrich U, Ferner J, Schwalbe H, Scheffer U, Dürner G, Göbel MW. Tripeptides from synthetic amino acids block the Tat-TAR association and slow down HIV spread in cell cultures. Chembiochem 2008; 8:1850-6. [PMID: 17886825 DOI: 10.1002/cbic.200700232] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Non-natural amino acids with aromatic or heteroaromatic side chains were incorporated into tripeptides of the general structure Arg-X-Arg and tested as ligands of the HIV RNA element TAR. Some of these compounds could compete efficiently with the association of TAR and Tat and downregulated a TAR-controlled reporter gene in HeLa cells. Peptide 7, which contains a 2-pyrimidinyl-alkyl chain, also inhibited the spread of HIV-1 in cell cultures. NMR studies of 7 bound to HIV-2-TAR gave evidence for contacts in the bulge region.
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Affiliation(s)
- Verena Ludwig
- Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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28
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Ivanovsky SA, Dorogov MV, Kravchenko DV, Ivachtchenko AV. Synthesis of the Substituted 3‐Cyclobutene‐1,2‐diones. SYNTHETIC COMMUN 2007. [DOI: 10.1080/00397910701462716] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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29
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Ramalingam V, Bhagirath N, Muthyala RS. Copper-Mediated Synthesis of Tertiary Diaryl Squaramides. J Org Chem 2007; 72:3976-9. [PMID: 17419651 DOI: 10.1021/jo070393l] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tertiary aryl squaramides were synthesized by using copper catalyzed C-N bond-formation with L-proline as the ligand. Symmetrical diaryl squaramides could be prepared in a one-pot reaction by using excess aryl bromide with varying yields. Unsymmetrical derivatives were prepared by sequential arylation. Yields of the diarylated products were highly sensitive to steric effects.
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Affiliation(s)
- Vijayakumar Ramalingam
- Department of Chemistry and Biochemistry, Queens College and the Graduate Center of the City University of New York, Flushing, New York 11367-1597, USA
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