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Deng H, Li Y, Li J, Shen W, Chen Q, Weng S, He J, Xu X. Neomycin inhibits Megalocytivirus infection in fish by antagonizing the increase of intracellular reduced glutathione. FISH & SHELLFISH IMMUNOLOGY 2022; 127:148-154. [PMID: 35714896 DOI: 10.1016/j.fsi.2022.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/04/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Infectious spleen and kidney necrosis virus (ISKNV) is the type species of the Megalocytivirus genus that infects a number of marine and freshwater fishes, causing huge economic losses in aquaculture. The ISKNV infection leads to increase of reducing power in cells. As the antibiotic neomycin can promote the production of reactive oxygen species (ROS) in animal cells, in the current study, the potential therapeutic effect of neomycin on ISKNV infection was explored. We showed that neomycin could decrease the reducing power in cultured MFF-1 cells and inhibit ISKNV infection by antagonizing the shift of the cellular redox balance toward reduction. In vivo experiments further demonstrated that neomycin treatment significantly suppresses ISKNV infection in mandarin fish. Expression of the major capsid protein (MCP) and the proportion of infected cells in tissues were down-regulated after neomycin treatment. Furthermore, neomycin showed complex effects on expression of a set of antiviral related genes of the host. Taking together, the current study suggested that the viral-induced redox imbalance in the infected cells could be used as a target for suppressing ISKNV infection. Neomycin can be potentially utilized for therapeutic treatment of Megalocytivirus diseases by antagonizing intracellular redox changes.
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Affiliation(s)
- Hengwei Deng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Yeyu Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - Jinling Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - Wenjie Shen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - Qiankang Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Jianguo He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Xiaopeng Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China.
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2
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fingeRNAt—A novel tool for high-throughput analysis of nucleic acid-ligand interactions. PLoS Comput Biol 2022; 18:e1009783. [PMID: 35653385 PMCID: PMC9197077 DOI: 10.1371/journal.pcbi.1009783] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 06/14/2022] [Accepted: 05/06/2022] [Indexed: 11/19/2022] Open
Abstract
Computational methods play a pivotal role in drug discovery and are widely applied in virtual screening, structure optimization, and compound activity profiling. Over the last decades, almost all the attention in medicinal chemistry has been directed to protein-ligand binding, and computational tools have been created with this target in mind. With novel discoveries of functional RNAs and their possible applications, RNAs have gained considerable attention as potential drug targets. However, the availability of bioinformatics tools for nucleic acids is limited. Here, we introduce fingeRNAt—a software tool for detecting non-covalent interactions formed in complexes of nucleic acids with ligands. The program detects nine types of interactions: (i) hydrogen and (ii) halogen bonds, (iii) cation-anion, (iv) pi-cation, (v) pi-anion, (vi) pi-stacking, (vii) inorganic ion-mediated, (viii) water-mediated, and (ix) lipophilic interactions. However, the scope of detected interactions can be easily expanded using a simple plugin system. In addition, detected interactions can be visualized using the associated PyMOL plugin, which facilitates the analysis of medium-throughput molecular complexes. Interactions are also encoded and stored as a bioinformatics-friendly Structural Interaction Fingerprint (SIFt)—a binary string where the respective bit in the fingerprint is set to 1 if a particular interaction is present and to 0 otherwise. This output format, in turn, enables high-throughput analysis of interaction data using data analysis techniques. We present applications of fingeRNAt-generated interaction fingerprints for visual and computational analysis of RNA-ligand complexes, including analysis of interactions formed in experimentally determined RNA-small molecule ligand complexes deposited in the Protein Data Bank. We propose interaction fingerprint-based similarity as an alternative measure to RMSD to recapitulate complexes with similar interactions but different folding. We present an application of interaction fingerprints for the clustering of molecular complexes. This approach can be used to group ligands that form similar binding networks and thus have similar biological properties. The fingeRNAt software is freely available at https://github.com/n-szulc/fingeRNAt.
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Emerging impact of triazoles as anti-tubercular agent. Eur J Med Chem 2022; 238:114454. [PMID: 35597009 DOI: 10.1016/j.ejmech.2022.114454] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 05/04/2022] [Accepted: 05/08/2022] [Indexed: 01/08/2023]
Abstract
Tuberculosis, a disease of poverty is a communicable infection with a reasonably high mortality rate worldwide. 10 Million new cases of TB were reported with approx 1.4 million deaths in the year 2019. Due to the growing number of drug-sensitive and drug-resistant tuberculosis cases, there is a vital need to develop new and effective candidates useful to combat this deadly disease. Despite tremendous efforts to identify a mechanism-based novel antitubercular agent, only a few have entered into clinical trials in the last six decades. In recent years, triazoles have been well explored as the most valuable scaffolds in drug discovery and development. Triazole framework possesses favorable properties like hydrogen bonding, moderate dipole moment, enhanced water solubility, and also the ability to bind effectively with biomolecular targets of M. tuberculosis and therefore this scaffold displayed excellent potency against TB. This review is an endeavor to summarize an up-to-date innovation of triazole-appended hybrids during the last 10 years having potential in vitro and in vivo antitubercular activity with structure activity relationship analysis. This review may help medicinal chemists to explore the triazole scaffolds for the rational design of potent drug candidates having better efficacy, improved selectivity and minimal toxicity so that these hybrid NCEs can effectively be explored as potential lead to fight against M. tuberculosis.
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Obszynski J, Loidon H, Blanc A, Weibel JM, Pale P. Targeted modifications of neomycin and paromomycin: Towards resistance-free antibiotics? Bioorg Chem 2022; 126:105824. [DOI: 10.1016/j.bioorg.2022.105824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 04/10/2022] [Accepted: 04/19/2022] [Indexed: 12/01/2022]
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5
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Agrahari AK, Bose P, Jaiswal MK, Rajkhowa S, Singh AS, Hotha S, Mishra N, Tiwari VK. Cu(I)-Catalyzed Click Chemistry in Glycoscience and Their Diverse Applications. Chem Rev 2021; 121:7638-7956. [PMID: 34165284 DOI: 10.1021/acs.chemrev.0c00920] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Copper(I)-catalyzed 1,3-dipolar cycloaddition between organic azides and terminal alkynes, commonly known as CuAAC or click chemistry, has been identified as one of the most successful, versatile, reliable, and modular strategies for the rapid and regioselective construction of 1,4-disubstituted 1,2,3-triazoles as diversely functionalized molecules. Carbohydrates, an integral part of living cells, have several fascinating features, including their structural diversity, biocompatibility, bioavailability, hydrophilicity, and superior ADME properties with minimal toxicity, which support increased demand to explore them as versatile scaffolds for easy access to diverse glycohybrids and well-defined glycoconjugates for complete chemical, biochemical, and pharmacological investigations. This review highlights the successful development of CuAAC or click chemistry in emerging areas of glycoscience, including the synthesis of triazole appended carbohydrate-containing molecular architectures (mainly glycohybrids, glycoconjugates, glycopolymers, glycopeptides, glycoproteins, glycolipids, glycoclusters, and glycodendrimers through regioselective triazole forming modular and bio-orthogonal coupling protocols). It discusses the widespread applications of these glycoproducts as enzyme inhibitors in drug discovery and development, sensing, gelation, chelation, glycosylation, and catalysis. This review also covers the impact of click chemistry and provides future perspectives on its role in various emerging disciplines of science and technology.
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Affiliation(s)
- Anand K Agrahari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Priyanka Bose
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Manoj K Jaiswal
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Sanchayita Rajkhowa
- Department of Chemistry, Jorhat Institute of Science and Technology (JIST), Jorhat, Assam 785010, India
| | - Anoop S Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Srinivas Hotha
- Department of Chemistry, Indian Institute of Science and Engineering Research (IISER), Pune, Maharashtra 411021, India
| | - Nidhi Mishra
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Vinod K Tiwari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
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Deshmukh TR, Khedkar VM, Jadhav RG, Sarkate AP, Sangshetti JN, Tiwari SV, Shingate BB. A copper-catalyzed synthesis of aryloxy-tethered symmetrical 1,2,3-triazoles as potential antifungal agents targeting 14 α-demethylase. NEW J CHEM 2021. [DOI: 10.1039/d1nj01759d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The search for potent therapeutic agents has prompted the design and synthesis of a library of twenty-six aryloxy-tethered and amide-linked symmetrical 1,2,3-triazoles (8a–z) using a copper(i)-catalyzed click chemistry approach.
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Affiliation(s)
- Tejshri R. Deshmukh
- Department of Chemistry
- Dr. Babasaheb Ambedkar Marathwada University
- Aurangabad-431004
- India
| | - Vijay M. Khedkar
- Department of Pharmaceutical Chemistry
- School of Pharmacy
- Vishwakarma University
- Pune-411048
- India
| | - Rohit G. Jadhav
- Department of Chemistry
- Indian Institute of Technology
- Indore-453552
- India
| | - Aniket P. Sarkate
- Department of Chemical Technology
- Dr. Babasaheb Ambedkar Marathwada University
- Aurangabad-431004
- India
| | | | - Shailee V. Tiwari
- Department of Pharmaceutical Chemistry
- Durgamata Institute of Pharmacy
- Dharmapuri, Parbhani-431401
- India
| | - Bapurao B. Shingate
- Department of Chemistry
- Dr. Babasaheb Ambedkar Marathwada University
- Aurangabad-431004
- India
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Feng LS, Zheng MJ, Zhao F, Liu D. 1,2,3-Triazole hybrids with anti-HIV-1 activity. Arch Pharm (Weinheim) 2020; 354:e2000163. [PMID: 32960467 DOI: 10.1002/ardp.202000163] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/04/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022]
Abstract
The human immunodeficiency virus type 1 (HIV-1) is the major etiological agent responsible for the acquired immunodeficiency syndrome (AIDS), which is a serious infectious disease and remains one of the most prevalent problems at present. Currently, combined antiretroviral therapy is the primary modality for the treatment and management of HIV/AIDS, but the long-term use can result in major drawbacks such as the development of multidrug-resistant viruses and multiple side effects. 1,2,3-Triazole is the common framework in the development of new drugs, and its derivatives have the potential to inhibit various HIV-1 enzymes such as reverse transcriptase, integrase, and protease, consequently possessing a potential anti-HIV-1 activity. This review covers the recent advances regarding the 1,2,3-triazole hybrids with potential anti-HIV-1 activity; it focuses on the chemical structures, structure-activity relationship, and mechanisms of action, covering articles published from 2010 to 2020.
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Affiliation(s)
| | | | | | - Duan Liu
- WuXi AppTec Co., Ltd., Wuhan, China
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8
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Aradi K, Di Giorgio A, Duca M. Aminoglycoside Conjugation for RNA Targeting: Antimicrobials and Beyond. Chemistry 2020; 26:12273-12309. [PMID: 32539167 DOI: 10.1002/chem.202002258] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/11/2020] [Indexed: 01/04/2023]
Abstract
Natural aminoglycosides are therapeutically useful antibiotics and very efficient RNA ligands. They are oligosaccharides that contain several ammonium groups able to interfere with the translation process in prokaryotes upon binding to bacterial ribosomal RNA (rRNA), and thus, impairing protein synthesis. Even if aminoglycosides are commonly used in therapy, these RNA binders lack selectivity and are able to bind to a wide number of RNA sequences/structures. This is one of the reasons for their toxicity and limited applications in therapy. At the same time, the ability of aminoglycosides to bind to various RNAs renders them a great source of inspiration for the synthesis of new binders with improved affinity and specificity toward several therapeutically relevant RNA targets. Thus, a number of studies have been performed on these complex and highly functionalized compounds, leading to the development of various synthetic methodologies toward the synthesis of conjugated aminoglycosides. The aim of this review is to highlight recent progress in the field of aminoglycoside conjugation, paying particular attention to modifications performed toward the improvement of affinity and especially to the selectivity of the resulting compounds. This will help readers to understand how to introduce a desired chemical modification for future developments of RNA ligands as antibiotics, antiviral, and anticancer compounds.
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Affiliation(s)
- Klara Aradi
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice (ICN), 06100, Nice, France
| | - Audrey Di Giorgio
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice (ICN), 06100, Nice, France
| | - Maria Duca
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice (ICN), 06100, Nice, France
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9
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Ranjan N, Andreasen KF, Arora Y, Xue L, Arya DP. Surface Dependent Dual Recognition of a G-quadruplex DNA With Neomycin-Intercalator Conjugates. Front Chem 2020; 8:60. [PMID: 32117884 PMCID: PMC7028757 DOI: 10.3389/fchem.2020.00060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 01/20/2020] [Indexed: 01/17/2023] Open
Abstract
G-quadruplexes have been characterized as structures of vital importance in the cellular functioning of several life forms. They have subsequently been established to serve as a therapeutic target of several diseases including cancer, HIV, tuberculosis and malaria. In this paper, we report the binding of aminosugar-intercalator conjugates with a well-studied anti-parallel G-quadruplex derived from Oxytricha Nova G-quadruplex DNA. Of the four neomycin-intercalator conjugates studied with varying surface areas, BQQ-neomycin conjugate displayed the best binding to this DNA G-quadruplex structure with an association constant of Ka = (1.01 ±0.03) × 107 M−1 which is nearly 100-fold higher than the binding of neomycin to this quadruplex. The binding of BQQ-neomycin displays a binding stoichiometry of 1:1 indicating the presence of a single and unique binding site for this G-quadruplex. In contrast, the BQQ-neomycin displays very weak binding to the bacterial A-site rRNA sequence showing that BQQ-does not enhance the neomycin binding to its natural target, the bacterial rRNA A-site. The BQQ-neomycin conjugate is prone to aggregation even at low micromolar concentrations (4 μM) leading to some ambiguities in the analysis of thermal denaturation profiles. Circular dichroism experiments showed that binding of BQQ-neomycin conjugate causes some structural changes in the quadruplex while still maintaining the overall anti-parallel structure. Finally, the molecular docking experiments suggest that molecular surface plays an important role in the recognition of a second site on the G-quadruplex. Overall, these results show that molecules with more than one binding moieties can be made to specifically recognize G-quadruplexes with high affinities. The dual binding molecules comprise of quadruplex groove binding and intercalator units, and the molecular surface of the intercalator plays an important part in enhancing binding interaction to the G-quadruplex structure.
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Affiliation(s)
- Nihar Ranjan
- Laboratory for Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC, United States.,Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Raebareli, India
| | - Katrine F Andreasen
- Laboratory for Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC, United States
| | - Yashaswina Arora
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Raebareli, India
| | - Liang Xue
- Laboratory for Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC, United States
| | - Dev P Arya
- Laboratory for Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC, United States
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Deshmukh TR, Khare SP, Krishna VS, Sriram D, Sangshetti JN, Khedkar VM, Shingate BB. Synthesis, bioevaluation and molecular docking study of new piperazine and amide linked dimeric 1,2,3-triazoles. SYNTHETIC COMMUN 2019. [DOI: 10.1080/00397911.2019.1695275] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Tejshri R. Deshmukh
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, Maharashtra, India
| | - Smita P. Khare
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, Maharashtra, India
| | - Vagolu S. Krishna
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad, Telangana, India
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad, Telangana, India
| | - Jaiprakash N. Sangshetti
- Department of Pharmaceutical Chemistry, Y. B. Chavan College of Pharmacy, Aurangabad, Maharashtra, India
| | - Vijay M. Khedkar
- Department of Pharmaceutical Chemistry, Shri Vile Parle Kelavani Mandal's Institute of Pharmacy, Dhule, Maharashtra, India
| | - Bapurao B. Shingate
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, Maharashtra, India
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11
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Deshmukh TR, Khare SP, Krishna VS, Sriram D, Sangshetti JN, Bhusnure O, Khedkar VM, Shingate BB. Design and Synthesis of New Aryloxy‐linked Dimeric 1,2,3‐TriazolesviaClick Chemistry Approach: Biological Evaluation and Molecular Docking Study. J Heterocycl Chem 2019. [DOI: 10.1002/jhet.3608] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Tejshri R. Deshmukh
- Department of ChemistryDr. Babasaheb Ambedkar Marathwada University Aurangabad 431 004 Maharashtra India
| | - Smita P. Khare
- Department of ChemistryDr. Babasaheb Ambedkar Marathwada University Aurangabad 431 004 Maharashtra India
| | - Vagolu S. Krishna
- Department of PharmacyBirla Institute of Technology and Science‐Pilani Hyderabad Campus, Jawahar Nagar Hyderabad 500 078 Telangana India
| | - Dharmarajan Sriram
- Department of PharmacyBirla Institute of Technology and Science‐Pilani Hyderabad Campus, Jawahar Nagar Hyderabad 500 078 Telangana India
| | - Jaiprakash N. Sangshetti
- Department of Pharmaceutical ChemistryY. B. Chavan College of Pharmacy, Dr. Rafiq Zakaria Campus Aurangabad 431 001 Maharashtra India
| | - Omprakash Bhusnure
- Department of Pharmaceutical ChemistryChannabasweshwar College of Pharmacy Latur Maharashtra India
| | - Vijay M. Khedkar
- Department of Pharmaceutical ChemistryShri Vile Parle Kelavani Mandal's Institute of Pharmacy Dhule 424 001 Maharashtra India
| | - Bapurao B. Shingate
- Department of ChemistryDr. Babasaheb Ambedkar Marathwada University Aurangabad 431 004 Maharashtra India
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12
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Watkins D, Maiti K, Arya DP. Aminoglycoside Functionalization as a Tool for Targeting Nucleic Acids. Methods Mol Biol 2019; 1973:147-162. [PMID: 31016700 DOI: 10.1007/978-1-4939-9216-4_9] [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] [Indexed: 01/19/2023]
Abstract
Aminoglycoside functionalization as a tool for targeting natural and unnatural nucleic acids holds great promise in their development as diagnostic probes and medicinally relevant compounds. Simple synthetic procedures designed to easily and quickly manipulate amino sugar (neomycin, kanamycin) to more powerful and selective ligands are presented in this chapter. We describe representative procedures for (a) aminoglycoside conjugation and (b) preliminary screening for their nucleic acid binding and selectivity.
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Affiliation(s)
- Derrick Watkins
- Department of Chemistry, Clemson University, Clemson, SC, USA
| | | | - Dev P Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC, USA.
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13
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Kukielski C, Maiti K, Bhaduri S, Story S, Arya DP. Rapid solid-phase syntheses of a peptidic-aminoglycoside library. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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14
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Bhaduri S, Ranjan N, Arya DP. An overview of recent advances in duplex DNA recognition by small molecules. Beilstein J Org Chem 2018; 14:1051-1086. [PMID: 29977379 PMCID: PMC6009268 DOI: 10.3762/bjoc.14.93] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 04/06/2018] [Indexed: 12/13/2022] Open
Abstract
As the carrier of genetic information, the DNA double helix interacts with many natural ligands during the cell cycle, and is amenable to such intervention in diseases such as cancer biogenesis. Proteins bind DNA in a site-specific manner, not only distinguishing between the geometry of the major and minor grooves, but also by making close contacts with individual bases within the local helix architecture. Over the last four decades, much research has been reported on the development of small non-natural ligands as therapeutics to either block, or in some cases, mimic a DNA–protein interaction of interest. This review presents the latest findings in the pursuit of novel synthetic DNA binders. This article provides recent coverage of major strategies (such as groove recognition, intercalation and cross-linking) adopted in the duplex DNA recognition by small molecules, with an emphasis on major works of the past few years.
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Affiliation(s)
| | - Nihar Ranjan
- National Institute of Pharmaceutical Education and Research (NIPER), Raebareli 122003, India
| | - Dev P Arya
- NUBAD, LLC, 900B West Faris Rd., Greenville 29605, SC, USA.,Clemson University, Hunter Laboratory, Clemson 29634, SC, USA
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Thamban Chandrika N, Garneau-Tsodikova S. Comprehensive review of chemical strategies for the preparation of new aminoglycosides and their biological activities. Chem Soc Rev 2018; 47:1189-1249. [PMID: 29296992 PMCID: PMC5818290 DOI: 10.1039/c7cs00407a] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A systematic analysis of all synthetic and chemoenzymatic methodologies for the preparation of aminoglycosides for a variety of applications (therapeutic and agricultural) reported in the scientific literature up to 2017 is presented. This comprehensive analysis of derivatization/generation of novel aminoglycosides and their conjugates is divided based on the types of modifications used to make the new derivatives. Both the chemical strategies utilized and the biological results observed are covered. Structure-activity relationships based on different synthetic modifications along with their implications for activity and ability to avoid resistance against different microorganisms are also presented.
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Affiliation(s)
- Nishad Thamban Chandrika
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA.
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16
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Bhosle GS, Kharche S, Kumar S, Sengupta D, Maiti S, Fernandes M. Superior HIV-1 TAR Binders with Conformationally Constrained R52 Arginine Mimics in the Tat(48-57) Peptide. ChemMedChem 2018; 13:220-226. [PMID: 29314706 DOI: 10.1002/cmdc.201700653] [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: 10/17/2017] [Revised: 12/18/2017] [Indexed: 02/05/2023]
Abstract
We report a 100-fold increase in binding affinity of the Tat(48-57) peptide to HIV-1 transcriptional activator-responsive element (TAR) RNA by replacing Arg52, an essential and critical residue for Tat's specific binding, with (2S,4S)-4-guanidinoproline. The resulting αTat1M peptide is a far superior binder than γTat1M, a peptide containing another conformationally constrained arginine mimic, (2S,4S)-4-amino-N-(3-guanidinopropyl)proline, or even the control Tat peptide (CtrlTat) itself. Our observations are supported by circular dichroism (CD), isothermal titration calorimetry (ITC), gel electrophoresis and UV spectroscopy studies. Molecular dynamics simulations suggest increased interactions between the more compact αTat1M and TAR RNA, relative to CtrlTat. The CD signature of the RNA itself remains largely unchanged upon binding of the peptides. The Tat mimetics further have better cell uptake properties than the control Tat peptide, thus increasing their potential application as specific TAR-binding molecules.
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Affiliation(s)
- Govind S Bhosle
- Organic Chemistry Division, CSIR - National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NCL Campus, Pune, India
| | - Shalmali Kharche
- Physical and Materials Chemistry Division, CSIR - National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NCL Campus, Pune, India
| | - Santosh Kumar
- Structural Biology Unit, CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Durba Sengupta
- Physical and Materials Chemistry Division, CSIR - National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NCL Campus, Pune, India
| | - Souvik Maiti
- Structural Biology Unit, CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB Campus, Delhi, India
| | - Moneesha Fernandes
- Organic Chemistry Division, CSIR - National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NCL Campus, Pune, India
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17
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Ranjan N, Kellish P, King A, Arya DP. Impact of Linker Length and Composition on Fragment Binding and Cell Permeation: Story of a Bisbenzimidazole Dye Fragment. Biochemistry 2017; 56:6434-6447. [PMID: 29131946 DOI: 10.1021/acs.biochem.7b00929] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Small molecules that modulate biological functions are targets of modern day drug discovery efforts. In a common platform fragment-based drug discovery, two fragments that bind to adjacent sites on a target are identified and are then linked together using different linkers to identify the linkage for optimum activity. What are not known from these studies are the effects these linkers, which typically contain C, H, and O atoms, have on the properties of the individual fragment. Herein, we investigate such effects in a bisbenzimidazole fragment whose derivatives have a wide range of therapeutic applications in nucleic acid recognition, sensing, and photodynamic therapy and as cellular probes. We report a dramatic effect of linker length and composition of alkynyl (clickable) Hoechst 33258 derivatives in target binding and cell uptake. We show that the binding of Hoechst 33258-modeled bisbenzimidazoles (1-9) that contain linkers of varying lengths (3-21 atoms) display length- and composition-dependent variation in B-DNA stabilization using a variety of spectroscopic methods. For a dodecamer DNA duplex, the thermal stabilization varied from 0.3 to 9.0 °C as the linker length increased from 3 to 21 atoms, respectively. Compounds with linker lengths of ≤11 atoms (such as compounds 1 and 5) are localized in the nucleus, while compounds with long linkers (such as compounds 8 and 9) are distributed in the extranuclear space, as well, with possible interactions with extranuclear targets. These findings provide insights into future drug design by revealing how linkers can influence the biophysical and cellular properties of individual drug fragments.
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Affiliation(s)
- Nihar Ranjan
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University , Clemson, South Carolina 29634, United States
| | - Patrick Kellish
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University , Clemson, South Carolina 29634, United States
| | - Ada King
- NUBAD LLC , 900 B West Faris Road, Greenville, South Carolina 29605, United States
| | - Dev P Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University , Clemson, South Carolina 29634, United States.,NUBAD LLC , 900 B West Faris Road, Greenville, South Carolina 29605, United States
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18
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Kamphan A, Gong C, Maiti K, Sur S, Traiphol R, Arya DP. Utilization of chromic polydiacetylene assemblies as a platform to probe specific binding between drug and RNA. RSC Adv 2017; 7:41435-41443. [PMID: 29276583 PMCID: PMC5739335 DOI: 10.1039/c7ra07178g] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Recognition of nucleic acids remains an important endeavor in biology. Nucleic acids adopt shapes ranging from A-form (RNA and GC rich DNA) to B-form (AT rich DNA). We show, in this contribution, shape-specific recognition of A-U rich RNA duplex by a neomycin (Neo)-polydiacetylene (PDA) complex. PDA assemblies are fabricated by using a well-known diacetylene (DA) monomer, 10,12-pentacosadiynoic acid (PCDA). The response of poly(PCDA) assemblies is generated by mixing with a modified neomycin-PCDA monomer (Neo-PCDA). The functionalization by neomycin moiety provides specific binding with homopolyribonucleotide poly (rA) - poly (rU) stimulus. Various types of alcohols are utilized as additives to enhance the sensitivity of poly(PCDA)/Neo-PCDA assemblies. A change of absorption spectra is clearly observed when a relatively low concentration of poly (rA)-poly (rU) is added into the system. Furthermore, poly(PCDA)/Neo-PCDA shows a clear specificity for poly (rA)-poly (rU) over the corresponding DNA duplex. The variation of linker between neomycin moiety and conjugated PDA backbone is found to significantly affect its sensitivity. We also investigate other parameters including the concentration of Neo-PCDA and the DA monomer structure. Our results provide here preliminary data for an alternative approach to improve the sensitivity of PDA utilized in biosensing and diagnostic applications.
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Affiliation(s)
- Anothai Kamphan
- Department of Chemistry, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
- Laboratory of Advanced Polymers and Nanomaterials, School of Materials Science and Engineering and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University at Salaya, Phuttamonthon 4 Road, Salaya, Nakhon Pathom 73170, Thailand
| | - Changjun Gong
- Laboratories of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Krishnagopal Maiti
- Laboratories of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Souvik Sur
- Laboratories of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Rakchart Traiphol
- Department of Chemistry, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
- Laboratory of Advanced Polymers and Nanomaterials, School of Materials Science and Engineering and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University at Salaya, Phuttamonthon 4 Road, Salaya, Nakhon Pathom 73170, Thailand
- NANOTEC-MU Excellence Center on Intelligent Materials and Systems, Faculty of Science, Mahidol University, Rama 6 Road, Ratchathewi, Bangkok 10400,Thailand
| | - Dev P. Arya
- Laboratories of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
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19
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Patwardhan NN, Ganser LR, Kapral GJ, Eubanks CS, Lee J, Sathyamoorthy B, Al-Hashimi HM, Hargrove AE. Amiloride as a new RNA-binding scaffold with activity against HIV-1 TAR. MEDCHEMCOMM 2017; 8:1022-1036. [PMID: 28798862 PMCID: PMC5546750 DOI: 10.1039/c6md00729e] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 03/14/2017] [Indexed: 12/23/2022]
Abstract
Diversification of RNA-targeted scaffolds offers great promise in the search for selective ligands of therapeutically relevant RNA such as HIV-1 TAR. We herein report the establishment of amiloride as a novel RNA-binding scaffold along with synthetic routes for combinatorial C(5)- and C(6)-diversification. Iterative modifications at the C(5)- and C(6)- positions yielded derivative 24, which demonstrated a 100-fold increase in activity over the parent dimethylamiloride in peptide displacement assays. NMR chemical shift mapping was performed using the 2D SOFAST- [1H-13C] HMQC NMR method, which allowed for facile and rapid evaluation of binding modes for all library members. Cheminformatic analysis revealed distinct differences between selective and non-selective ligands. In this study, we evolved dimethylamiloride from a weak TAR ligand to one of the tightest binding selective TAR ligands reported to date through a novel combination of synthetic methods and analytical techniques. We expect these methods to allow for rapid library expansion and tuning of the amiloride scaffold for a range of RNA targets and for SOFAST NMR to allow unprecedented evaluation of small molecule:RNA interactions.
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Affiliation(s)
- Neeraj N. Patwardhan
- Department of Chemistry
, Duke University
,
Durham
, North Carolina 27708
, USA
.
; Tel: +1 919 660 1522
| | - Laura R. Ganser
- Department of Biochemistry
, Duke University Medical Center
,
Durham
, North Carolina 27708
, USA
| | - Gary J. Kapral
- Department of Chemistry
, Duke University
,
Durham
, North Carolina 27708
, USA
.
; Tel: +1 919 660 1522
| | - Christopher S. Eubanks
- Department of Chemistry
, Duke University
,
Durham
, North Carolina 27708
, USA
.
; Tel: +1 919 660 1522
| | - Janghyun Lee
- Department of Biochemistry
, Duke University Medical Center
,
Durham
, North Carolina 27708
, USA
| | - Bharathwaj Sathyamoorthy
- Department of Biochemistry
, Duke University Medical Center
,
Durham
, North Carolina 27708
, USA
| | - Hashim M. Al-Hashimi
- Department of Chemistry
, Duke University
,
Durham
, North Carolina 27708
, USA
.
; Tel: +1 919 660 1522
- Department of Biochemistry
, Duke University Medical Center
,
Durham
, North Carolina 27708
, USA
| | - Amanda E. Hargrove
- Department of Chemistry
, Duke University
,
Durham
, North Carolina 27708
, USA
.
; Tel: +1 919 660 1522
- Department of Biochemistry
, Duke University Medical Center
,
Durham
, North Carolina 27708
, USA
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20
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Probing A-form DNA: A fluorescent aminosugar probe and dual recognition by anthraquinone-neomycin conjugates. Bioorg Med Chem 2016; 25:1309-1319. [PMID: 28129992 DOI: 10.1016/j.bmc.2016.11.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/30/2016] [Accepted: 11/01/2016] [Indexed: 12/19/2022]
Abstract
Nucleic acids adopt a broad array of hydrogen-bonded structures that enable their diverse roles in the cell; even the familiar DNA double helix displays subtle architectural nuances that are sequence dependent. While there have been many approaches for recognition of B-form nucleic acids, A-form DNA recognition has lagged behind. Here, using a tight binding fluorescein-neomycin (F-neo) conjugate that can probe the electrostatic environment of A-form DNA major groove, we developed a fluorescent displacement assay to be used as a screen for DNA duplex-binding compounds. As opposed to intercalating dyes that can significantly perturb DNA structure, the groove binding F-neo allows the probing of native DNA conformation. In combination with the assay development and probing of DNA grooves, we also report the synthesis and binding of a series of neomycin-anthraquinone conjugates, two units with a known preference for binding GC rich DNA. The assay can be used to identify duplex DNA-binding compounds, as well as probe structural features of a target DNA duplex, and can easily be scaled up for high throughput screening of compound libraries.
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21
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Kumar S, Ranjan N, Kellish P, Gong C, Watkins D, Arya DP. Multivalency in the recognition and antagonism of a HIV TAR RNA-TAT assembly using an aminoglycoside benzimidazole scaffold. Org Biomol Chem 2016; 14:2052-6. [PMID: 26765486 DOI: 10.1039/c5ob02016f] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recognition of RNA by high-affinity binding small molecules is crucial for expanding existing approaches in RNA recognition, and for the development of novel RNA binding drugs. A novel neomycin dimer benzimidazole conjugate 5 (DPA 83) was synthesized by conjugating a neomycin-dimer with a benzimidazole alkyne using click chemistry to target multiple binding sites on HIV TAR RNA. Ligand 5 significantly enhances the thermal stability of HIV TAR RNA and interacts stoichiometrically with HIV TAR RNA with a low nanomolar affinity. 5 displayed enhanced binding compared to its individual building blocks including the neomycin dimer azide and benzimidazole alkyne. In essence, a high affinity multivalent ligand was designed and synthesized to target HIV TAR RNA.
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Affiliation(s)
- Sunil Kumar
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA.
| | - Nihar Ranjan
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA. and Nubad LLC, 900 B West Faris Road, Greenville, SC 29630, USA
| | - Patrick Kellish
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA.
| | - Changjun Gong
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA.
| | | | - Dev P Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA.
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22
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Gao P, Sun L, Zhou J, Li X, Zhan P, Liu X. Discovery of novel anti-HIV agents via Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry-based approach. Expert Opin Drug Discov 2016; 11:857-71. [PMID: 27400283 DOI: 10.1080/17460441.2016.1210125] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION In recent years, a variety of new synthetic methodologies and concepts have been proposed in the search for new pharmaceutical lead structures and optimization. Notably, the Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry approach has drawn great attention and has become a powerful tool for the generation of privileged medicinal skeletons in the discovery of anti-HIV agents. This is due to the high degree of reliability, complete specificity (chemoselectivity and regioselectivity), mild conditions, and the biocompatibility of the reactants. AREAS COVERED Herein, the authors describe the progress thus far on the discovery of novel anti-HIV agents via the CuAAC click chemistry-based approach. EXPERT OPINION CuAAC click chemistry is a proven protocol for synthesizing triazole products which could serve as basic pharmacophores, act as replacements of traditional scaffold or substituent modification, be a linker of dual-target or dual-site inhibitors and more for the discovery of novel anti-HIV agents. What's more, it also provides convenience and feasibility for dynamic combinatorial chemistry and in situ screening. It is envisioned that click chemistry will draw more attention and make more contributions in anti-HIV drug discovery in the future.
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Affiliation(s)
- Ping Gao
- a Department of Medicinal Chemistry, Key laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
| | - Lin Sun
- a Department of Medicinal Chemistry, Key laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
| | - Junsu Zhou
- a Department of Medicinal Chemistry, Key laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
| | - Xiao Li
- a Department of Medicinal Chemistry, Key laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
| | - Peng Zhan
- a Department of Medicinal Chemistry, Key laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
| | - Xinyong Liu
- a Department of Medicinal Chemistry, Key laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
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23
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Kumar S, Newby Spano M, Arya DP. Shape readout of AT-rich DNA by carbohydrates. Biopolymers 2016; 101:720-32. [PMID: 24281844 DOI: 10.1002/bip.22448] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 11/10/2013] [Accepted: 11/23/2013] [Indexed: 12/16/2022]
Abstract
Gene expression can be altered by small molecules that target DNA; sequence as well as shape selectivities are both extremely important for DNA recognition by intercalating and groove-binding ligands. We have characterized a carbohydrate scaffold (1) exhibiting DNA "shape readout" properties. Thermodynamic studies with 1 and model duplex DNAs demonstrate the molecule's high affinity and selectivity towards B* form (continuous AT-rich) DNA. Isothermal titration calorimetry (ITC), circular dichroism (CD) titration, ultraviolet (UV) thermal denaturation, and Differential Scanning Calorimetry were used to characterize the binding of 1 with a B* form AT-rich DNA duplex d[5'-G2 A6 T6 C2 -3']. The binding constant was determined using ITC at various temperatures, salt concentrations, and pH. ITC titrations were fit using a two-binding site model. The first binding event was shown to have a 1:1 binding stoichiometry and was predominantly entropy-driven with a binding constant of approximately 10(8) M(-1) . ITC-derived binding enthalpies were used to obtain the binding-induced change in heat capacity (ΔCp ) of -225 ± 19 cal/mol·K. The ionic strength dependence of the binding constant indicated a significant electrolytic contribution in ligand:DNA binding, with approximately four to five ion pairs involved in binding. Ligand 1 displayed a significantly higher affinity towards AT-tract DNA over sequences containing GC inserts, and binding experiments revealed the order of binding affinity for 1 with DNA duplexes: contiguous B* form AT-rich DNA (d[5'-G2 A6 T6 C2 -3']) >B form alternate AT-rich DNA (d[5'-G2 (AT)6 C2- 3']) > A form GC-rich DNA (d[5'-A2 G6 C6 T2 -3']), demonstrating the preference of ligand 1 for B* form DNA.
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Affiliation(s)
- Sunil Kumar
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC, 29634
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24
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Yanagi M, Ninomiya R, Ueda Y, Furuta T, Yamada T, Sunazuka T, Kawabata T. Organocatalytic Site-Selective Acylation of 10-Deacetylbaccatin III. Chem Pharm Bull (Tokyo) 2016; 64:907-12. [PMID: 26903156 DOI: 10.1248/cpb.c16-00037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Organocatalytic site-selective diversification of 10-deacetylbaccatin III, a key natural product for the semisynthesis of taxol, has been achieved. Various acyl groups were selectively introduced into the C(10)-OH of 10-deacetylbaccatin III. The C(10)-OH selective acylation was also applied to acylative site-selective dimerization of 10-deacetylbaccatin III to provide the structurally defined dimer.
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25
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Jiang L, Watkins D, Jin Y, Gong C, King A, Washington AZ, Green KD, Garneau-Tsodikova S, Oyelere AK, Arya DP. Rapid synthesis, RNA binding, and antibacterial screening of a peptidic-aminosugar (PA) library. ACS Chem Biol 2015; 10:1278-89. [PMID: 25706406 DOI: 10.1021/cb5010367] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A 215-member mono- and diamino acid peptidic-aminosugar (PA) library, with neomycin as the model aminosugar, was systematically and rapidly synthesized via solid phase synthesis. Antibacterial activities of the PA library, on 13 bacterial strains (seven Gram-positive and six Gram-negative bacterial strains), and binding affinities of the PA library for a 27-base model of the bacterial 16S ribosomal A-site RNA were evaluated using high-throughput screening. The results of the two assays were correlated using Ribosomal Binding-Bacterial Inhibition Plot (RB-BIP) analysis to provide structure-activity relationship (SAR) information. From this work, we have identified PAs that can discriminate the E. coli A-site from the human A-site by up to a 28-fold difference in binding affinity. Aminoglycoside-modifying enzyme activity studies indicate that APH(2″)-Ia showed nearly complete removal of activity with a number of PAs. The synthesis of the compound library and screening can both be performed rapidly, allowing for an iterative process of aminoglycoside synthesis and screening of PA libraries for optimal binding and antibacterial activity for lead identification.
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Affiliation(s)
- Liuwei Jiang
- Laboratory
of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | | | - Yi Jin
- Laboratory
of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Changjun Gong
- Laboratory
of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Ada King
- NUBAD, LLC, Greenville, South Carolina 29605, United States
| | - Arren Z. Washington
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Keith D. Green
- College
of Pharmacy, Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- College
of Pharmacy, Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Adegboyega K. Oyelere
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Dev P. Arya
- Laboratory
of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
- NUBAD, LLC, Greenville, South Carolina 29605, United States
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26
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Influence of linker length and composition on enzymatic activity and ribosomal binding of neomycin dimers. Antimicrob Agents Chemother 2015; 59:3899-905. [PMID: 25896697 DOI: 10.1128/aac.00861-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 04/10/2015] [Indexed: 12/16/2022] Open
Abstract
The human and bacterial A site rRNA binding as well as the aminoglycoside-modifying enzyme (AME) activity against a series of neomycin B (NEO) dimers is presented. The data indicate that by simple modifications of linker length and composition, substantial differences in rRNA selectivity and AME activity can be obtained. We tested five different AMEs with dimeric NEO dimers that were tethered via triazole, urea, and thiourea linkages. We show that triazole-linked dimers were the worst substrates for most AMEs, with those containing the longer linkers showing the largest decrease in activity. Thiourea-linked dimers that showed a decrease in activity by AMEs also showed increased bacterial A site binding, with one compound (compound 14) even showing substantially reduced human A site binding. The urea-linked dimers showed a substantial decrease in activity by AMEs when a conformationally restrictive phenyl linker was introduced. The information learned herein advances our understanding of the importance of the linker length and composition for the generation of dimeric aminoglycoside antibiotics capable of avoiding the action of AMEs and selective binding to the bacterial rRNA over binding to the human rRNA.
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27
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Dickson A, Mustoe AM, Salmon L, Brooks CL. Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore. Nucleic Acids Res 2014; 42:12126-37. [PMID: 25294827 PMCID: PMC4231733 DOI: 10.1093/nar/gku799] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/04/2014] [Accepted: 08/25/2014] [Indexed: 12/20/2022] Open
Abstract
HIV-1 TAR RNA is a two-helix bulge motif that plays a critical role in HIV viral replication and is an important drug target. However, efforts at designing TAR inhibitors have been challenged by its high degree of structural flexibility, which includes slow large-amplitude reorientations of its helices with respect to one another. Here, we use the recently introduced algorithm WExplore in combination with Euler angles to achieve unprecedented sampling of the TAR conformational ensemble. Our ensemble achieves similar agreement with experimental NMR data when compared with previous TAR computational studies, and is generated at a fraction of the computational cost. It clearly emerges from configuration space network analysis that the intermittent formation of the A22-U40 base pair acts as a reversible switch that enables sampling of interhelical conformations that would otherwise be topologically disallowed. We find that most previously determined ligand-bound structures are found in similar location in the network, and we use a sample-and-select approach to guide the construction of a set of novel conformations which can serve as the basis for future drug development efforts. Collectively, our findings demonstrate the utility of WExplore in combination with suitable order parameters as a method for exploring RNA conformational space.
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Affiliation(s)
- Alex Dickson
- Department of Chemistry, University of Michigan, 930 N University, Ann Arbor, MI 48109, USA
| | - Anthony M Mustoe
- Department of Biophysics, University of Michigan, 930 N University, Ann Arbor, MI 48109, USA
| | - Loïc Salmon
- Department of Biophysics, University of Michigan, 930 N University, Ann Arbor, MI 48109, USA
| | - Charles L Brooks
- Department of Chemistry, University of Michigan, 930 N University, Ann Arbor, MI 48109, USA Department of Biophysics, University of Michigan, 930 N University, Ann Arbor, MI 48109, USA
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28
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Willis B, Arya DP. Recognition of RNA duplex by a neomycin–Hoechst 33258 conjugate. Bioorg Med Chem 2014; 22:2327-32. [DOI: 10.1016/j.bmc.2014.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/27/2014] [Accepted: 02/06/2014] [Indexed: 01/01/2023]
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29
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Targeting C-myc G-quadruplex: dual recognition by aminosugar-bisbenzimidazoles with varying linker lengths. Molecules 2013; 18:14228-40. [PMID: 24252993 PMCID: PMC6270413 DOI: 10.3390/molecules181114228] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 11/04/2013] [Accepted: 11/08/2013] [Indexed: 12/01/2022] Open
Abstract
G-quadruplexes are therapeutically important biological targets. In this report, we present biophysical studies of neomycin-Hoechst 33258 conjugates binding to a G-quadruplex derived from the C-myc promoter sequence. Our studies indicate that conjugation of neomycin to a G-quadruplex binder, Hoechst 33258, enhances its binding. The enhancement in G-quadruplex binding of these conjugates varies with the length and composition of the linkers joining the neomycin and Hoechst 33258 units.
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30
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Ranjan N, Kumar S, Watkins D, Wang D, Appella DH, Arya DP. Recognition of HIV-TAR RNA using neomycin-benzimidazole conjugates. Bioorg Med Chem Lett 2013; 23:5689-93. [PMID: 24012122 PMCID: PMC4048829 DOI: 10.1016/j.bmcl.2013.08.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 07/30/2013] [Accepted: 08/05/2013] [Indexed: 10/26/2022]
Abstract
Synthesis of a novel class of compounds and their biophysical studies with TAR-RNA are presented. The synthesis of these compounds was achieved by conjugating neomycin, an aminoglycoside, with benzimidazoles modeled from a B-DNA minor groove binder, Hoechst 33258. The neomycin-benzimidazole conjugates have varying linkers that connect the benzimidazole and neomycin units. The linkers of varying length (5-23 atoms) in these conjugates contain one to three triazole units. The UV thermal denaturation experiments showed that the conjugates resulted in greater stabilization of the TAR-RNA than either neomycin or benzimidazole used in the synthesis of conjugates. These results were corroborated by the FID displacement and tat-TAR inhibition assays. The binding of ligands to the TAR-RNA is affected by the length and composition of the linker. Our results show that increasing the number of triazole groups and the linker length in these compounds have diminishing effect on the binding to TAR-RNA. Compounds that have shorter linker length and fewer triazole units in the linker displayed increased affinity towards the TAR RNA.
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Affiliation(s)
- Nihar Ranjan
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina , United States 29634
| | - Sunil Kumar
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina , United States 29634
| | - Derrick Watkins
- NUBAD LLC, 900 B West Faris Road, Greenville, SC 29630, United States
| | - Deyun Wang
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health,Bethesda, Maryland 20892, United States
| | - Daniel H. Appella
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health,Bethesda, Maryland 20892, United States
| | - Dev P. Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina , United States 29634
- NUBAD LLC, 900 B West Faris Road, Greenville, SC 29630, United States
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31
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Characterization of ribosomal binding and antibacterial activities using two orthogonal high-throughput screens. Antimicrob Agents Chemother 2013; 57:4717-26. [PMID: 23856777 DOI: 10.1128/aac.00671-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We report here the affinity and antibacterial activity of a structurally similar class of neomycin dimers. The affinity of the dimer library for rRNA was established by using a screen that measures the displacement of fluorescein-neomycin (F-neo) probe from RNA. A rapid growth inhibition assay using a single drug concentration was used to examine the antibacterial activity. The structure-activity relationship data were then rapidly analyzed using a two-dimensional ribosomal binding-bacterial inhibition plot analysis.
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Berkov-Zrihen Y, Green KD, Labby KJ, Feldman M, Garneau-Tsodikova S, Fridman M. Synthesis and evaluation of hetero- and homodimers of ribosome-targeting antibiotics: antimicrobial activity, in vitro inhibition of translation, and drug resistance. J Med Chem 2013; 56:5613-25. [PMID: 23786357 PMCID: PMC3823688 DOI: 10.1021/jm400707f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, we describe the synthesis of a full set of homo- and heterodimers of three intact structures of different ribosome-targeting antibiotics: tobramycin, clindamycin, and chloramphenicol. Several aspects of the biological activity of the dimeric structures were evaluated including antimicrobial activity, inhibition of in vitro bacterial protein translation, and the effect of dimerization on the action of several bacterial resistance mechanisms that deactivate tobramycin and chloramphenicol. This study demonstrates that covalently linking two identical or different ribosome-targeting antibiotics may lead to (i) a broader spectrum of antimicrobial activity, (ii) improved inhibition of bacterial translation properties compared to that of the parent antibiotics, and (iii) reduction in the efficacy of some drug-modifying enzymes that confer high levels of resistance to the parent antibiotics from which the dimers were derived.
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Affiliation(s)
| | - Keith D. Green
- Department of Medicinal Chemistry and the Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Kristin J. Labby
- Department of Medicinal Chemistry and the Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Mark Feldman
- School of Chemistry, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Sylvie Garneau-Tsodikova
- Department of Medicinal Chemistry and the Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Micha Fridman
- School of Chemistry, Tel Aviv University, Tel Aviv, 6997801, Israel
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Penchovsky R, Stoilova CC. Riboswitch-based antibacterial drug discovery using high-throughput screening methods. Expert Opin Drug Discov 2012; 8:65-82. [DOI: 10.1517/17460441.2013.740455] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Robert Penchovsky
- Sofia University “St. Kliment Ohridski”, Department of Genetics, Faculty of Biology,
8 Dragan Tzankov Blvd, 1164 Sofia, Bulgaria ;
| | - Cvetelina C Stoilova
- Sofia University “St. Kliment Ohridski”, Department of Genetics, Faculty of Biology,
8 Dragan Tzankov Blvd, 1164 Sofia, Bulgaria ;
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3,6-bis(3-alkylguanidino)acridines as DNA-intercalating antitumor agents. Eur J Med Chem 2012; 57:283-95. [PMID: 23072739 DOI: 10.1016/j.ejmech.2012.09.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 09/12/2012] [Accepted: 09/13/2012] [Indexed: 11/20/2022]
Abstract
A series of 3,6-bis(3-alkylguanidino) acridines was prepared and the interaction of these novel compounds with calf thymus DNA was investigated with UV-vis, fluorescence and circular dichroism spectroscopy, in addition to DNA melting techniques. The binding constants K were estimated to range from 1.25 to 5.26 × 10(5) M(-1), and the percentage of hypochromism was found to be 17-42% (from spectral titration). UV-vis, fluorescence and circular dichroism measurements indicated that the compounds act as effective DNA-intercalating agents. Electrophoretic separation proved that ligands 6a-e relaxed topoisomerase I at a concentration of 60 μM, although only those with longer alkyl chains were able to penetrate cell membranes and suppress cell proliferation effectively. The biological activity of novel compounds was assessed using different techniques (cell cycle distribution, phosphatidylserine externalization, caspase-3 activation, changes in mitochondrial membrane potential) and demonstrated mostly transient cytostatic action of the ethyl 6c and pentyl 6d derivatives. The hexyl derivative 6e proved to be the most cytotoxic. Different patterns of cell penetration were also observed for individual derivatives. Principles of molecular dynamics were applied to explore DNA-ligand interactions at the molecular level.
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Charles I, Davis E, Arya DP. Efficient stabilization of phosphodiester (PO), phosphorothioate (PS), and 2'-O-methoxy (2'-OMe) DNA·RNA hybrid duplexes by amino sugars. Biochemistry 2012; 51:5496-505. [PMID: 22639785 DOI: 10.1021/bi3004507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Antisense strategies that target DNA·RNA hybrid structures offer potential for the development of new therapeutic drugs. The α-sarcin loop region of the 23S [corrected] rRNA domain has been shown to be a high value target for such strategies. Herein, aminoglycoside interaction with three RNA·DNA α-sarcin targeted duplexes (rR·dY, rR·S-dY, and rR·2'OMe-rY) have been investigated to determine the overall effect of aminoglycoside interaction on the stability, affinity, and conformation of these hybrid duplexes. To this end, UV thermal denaturation, circular dichroism spectroscopy, fluorescence intercalator displacement, and ITC as well as DSC calorimetry experiments were carried out. The results suggest the following. (1) Of all the aminoglycosides studied, neomycin confers the highest thermal stability on all three hybrid duplexes studied. (2) There is no appreciable difference in aminoglycoside-induced thermal stability between the unmodified rR·dY and phophorothioate modified rR·S-dY duplexes. (3) The rR·2'OMe-rY duplexes thermal stability is slightly less than the other two hybrids. (4) In all three duplexes, aminoglycoside-induced thermal stability decreased as the number of amino groups decreased. (5) CD scans revealed similar spectra for the rR·dY and rR·S-dY duplexes as well as a more pronounced A-form signal for the rR·2'OMe-rY duplex. (6) FID assays paralleled the CD results, yielding similar affinity values between the rR·dY and rR·S-dY duplexes and higher affinities with the rR·2'OMe-rY duplex. (7) The overall affinity trend between aminoglycosides and the three duplexes was determined to be neomycin > paromomycin > neamine > ribostamycin. (8) ITC K(a) values revealed similar binding constants for the rR·dY and rR·S-dY duplexes with rR·dY having a K(1) of (1.03 ± 0.58) × 10(7) M(-1) and K(2) of (1.13 ± 0.07) × 10(5) M(-1) while rR·S-dY produced a K(1) of (1.17 ± 0.54) × 10(7) M(-1) and K(2) of (1.27 ± 0.69) × 10(5) M(-1). (8) The rR·2'OMe-rY produced a slightly higher binding constant values with a K(1) of (1.25 ± 0.24) × 10(7) M(-1) and K(2) of (3.62 ± 0.18) × 10(5) M(-1). (9) The ΔT(m)-derived K(Tm) of 3.81 × 10(7) M(-1) for rR·S-dY was in relative agreement with the corresponding K(1) of 1.17 × 10(7) M(-1) derived constant from the fitted ITC. These results illustrate that the increased DNA·RNA hybrid duplex stability in the presence of aminoglycosides can help extend the roles of aminoglycosides in designing modified ODNs for targeting RNA.
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Affiliation(s)
- I Charles
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, South Carolina 29634, United States
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Kumar S, Kellish P, Robinson WE, Wang D, Appella DH, Arya DP. Click dimers to target HIV TAR RNA conformation. Biochemistry 2012; 51:2331-47. [PMID: 22339203 DOI: 10.1021/bi201657k] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of neomycin dimers have been synthesized using "click chemistry" with varying functionality and length in the linker region to target the human immunodeficiency virus type 1 (HIV-1) TAR RNA region of the HIV virus. The TAR (Trans-Activation Responsive) RNA region, a 59 bp stem-loop structure located at the 5'-end of all nascent viral transcripts, interacts with its target, a key regulatory protein, Tat, and necessitates the replication of HIV-1. Neomycin, an aminosugar, has been shown to exhibit multiple binding sites on TAR RNA. This observation prompted us to design and synthesize a library of triazole-linked neomycin dimers using click chemistry. The binding between neomycin dimers and TAR RNA was characterized using spectroscopic techniques, including FID (fluorescent intercalator displacement), a FRET (fluorescence resonance energy transfer) competitive assay, circular dichroism (CD), and UV thermal denaturation. UV thermal denaturation studies demonstrate that binding of neomycin dimers increases the melting temperature (T(m)) of the HIV TAR RNA up to 10 °C. Ethidium bromide displacement (FID) and a FRET competition assay revealed nanomolar binding affinity between neomycin dimers and HIV TAR RNA, while in case of neomycin, only weak binding was detected. More importantly, most of the dimers exhibited lower IC(50) values toward HIV TAR RNA, when compared to the fluorescent Tat peptide, and show increased selectivity over mutant TAR RNA. Cytopathic effects investigated using MT-2 cells indicate a number of the dimers with high affinity toward TAR show promising anti-HIV activity.
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Affiliation(s)
- Sunil Kumar
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
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Abstract
RNAs are underexploited targets for small molecule drugs or chemical probes of function. This may be due, in part, to a fundamental lack of understanding of the types of small molecules that bind RNA specifically and the types of RNA motifs that specifically bind small molecules. In this review, we describe recent advances in the development and design of small molecules that bind to RNA and modulate function that aim to fill this void.
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Affiliation(s)
- Lirui Guan
- Department of Chemistry, The Kellogg School of Science
and Technology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #3A1, Jupiter, Florida 33458,
United States
| | - Matthew D. Disney
- Department of Chemistry, The Kellogg School of Science
and Technology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #3A1, Jupiter, Florida 33458,
United States
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