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Li A, Bouhss A, Clément MJ, Bauvais C, Taylor JP, Bollot G, Pastré D. Using the structural diversity of RNA: protein interfaces to selectively target RNA with small molecules in cells: methods and perspectives. Front Mol Biosci 2023; 10:1298441. [PMID: 38033386 PMCID: PMC10687564 DOI: 10.3389/fmolb.2023.1298441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023] Open
Abstract
In recent years, RNA has gained traction both as a therapeutic molecule and as a therapeutic target in several human pathologies. In this review, we consider the approach of targeting RNA using small molecules for both research and therapeutic purposes. Given the primary challenge presented by the low structural diversity of RNA, we discuss the potential for targeting RNA: protein interactions to enhance the structural and sequence specificity of drug candidates. We review available tools and inherent challenges in this approach, ranging from adapted bioinformatics tools to in vitro and cellular high-throughput screening and functional analysis. We further consider two critical steps in targeting RNA/protein interactions: first, the integration of in silico and structural analyses to improve the efficacy of molecules by identifying scaffolds with high affinity, and second, increasing the likelihood of identifying on-target compounds in cells through a combination of high-throughput approaches and functional assays. We anticipate that the development of a new class of molecules targeting RNA: protein interactions to prevent physio-pathological mechanisms could significantly expand the arsenal of effective therapeutic compounds.
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Affiliation(s)
- Aixiao Li
- Synsight, Genopole Entreprises, Evry, France
| | - Ahmed Bouhss
- Université Paris-Saclay, INSERM U1204, Université d’Évry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry, France
| | - Marie-Jeanne Clément
- Université Paris-Saclay, INSERM U1204, Université d’Évry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry, France
| | | | - J. Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | | | - David Pastré
- Université Paris-Saclay, INSERM U1204, Université d’Évry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry, France
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2
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Sun Y, Cheng L, Hong Y, Li Z, Li C, Ban X, Gu Z. Preparation and characterization of cationic hyperbranched maltodextrins as potential carrier for siRNA encapsulation. Int J Biol Macromol 2023; 225:786-794. [PMID: 36400207 DOI: 10.1016/j.ijbiomac.2022.11.142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/22/2022] [Accepted: 11/14/2022] [Indexed: 11/17/2022]
Abstract
The present study sought to investigate the physicochemical properties of cationic branched maltodextrins with similar degrees of substitution but different degrees of branching and their siRNA delivery capacity. The results showed that the ratio of α-1,6 glycosidic bonds was significantly increased in the sample treated with dual enzymes. The structural characterization results showed that abundant short chains reassembled by 1,4-α-glucan branching enzyme (GBEs) hydrolysis formed hyperbranched short clustered structure. The absorption peaks that appeared in the FT-IR spectrum confirmed the occurrence of quaternization. The complexes formed by self-assembly of cationic maltodextrins and siRNA were verified by the gel retardation assay and atomic force microscopy, demonstrating a uniform spherical structure with a size close to 300-350 nm. Meanwhile, cationic branched maltodextrins could effectively reduce the change of secondary structure of siRNA. Overall, the results suggested that branched maltodextrins with a cationic surface had significant potential as siRNA carriers.
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Affiliation(s)
- Yue Sun
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Li Cheng
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Wuxi 214122, Jiangsu Province, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, China.
| | - Yan Hong
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Wuxi 214122, Jiangsu Province, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, China
| | - Zhaofeng Li
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Wuxi 214122, Jiangsu Province, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, China
| | - Caiming Li
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Wuxi 214122, Jiangsu Province, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, China
| | - Xiaofeng Ban
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Wuxi 214122, Jiangsu Province, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, China
| | - Zhengbiao Gu
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Wuxi 214122, Jiangsu Province, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, China
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Ahamad S, Bhat SA. The Emerging Landscape of Small-Molecule Therapeutics for the Treatment of Huntington's Disease. J Med Chem 2022; 65:15993-16032. [PMID: 36490325 DOI: 10.1021/acs.jmedchem.2c00799] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Huntington's disease (HD) is a progressive neurodegenerative disorder caused by a CAG repeat expansion in the huntingtin gene (HTT). The new insights into HD's cellular and molecular pathways have led to the identification of numerous potent small-molecule therapeutics for HD therapy. The field of HD-targeting small-molecule therapeutics is accelerating, and the approval of these therapeutics to combat HD may be expected in the near future. For instance, preclinical candidates such as naphthyridine-azaquinolone, AN1, AN2, CHDI-00484077, PRE084, EVP4593, and LOC14 have shown promise for further optimization to enter into HD clinical trials. This perspective aims to summarize the advent of small-molecule therapeutics at various stages of clinical development for HD therapy, emphasizing their structure and design, therapeutic effects, and specific mechanisms of action. Further, we have highlighted the key drivers involved in HD pathogenesis to provide insights into the basic principle for designing promising anti-HD therapeutic leads.
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Affiliation(s)
- Shakir Ahamad
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh202002, India
| | - Shahnawaz A Bhat
- Department of Zoology, Aligarh Muslim University, Aligarh, Uttar Pradesh202002, India
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Wu J, Möhle L, Brüning T, Eiriz I, Rafehi M, Stefan K, Stefan SM, Pahnke J. A Novel Huntington's Disease Assessment Platform to Support Future Drug Discovery and Development. Int J Mol Sci 2022; 23:ijms232314763. [PMID: 36499090 PMCID: PMC9740291 DOI: 10.3390/ijms232314763] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Huntington's disease (HD) is a lethal neurodegenerative disorder without efficient therapeutic options. The inefficient translation from preclinical and clinical research into clinical use is mainly attributed to the lack of (i) understanding of disease initiation, progression, and involved molecular mechanisms; (ii) knowledge of the possible HD target space and general data awareness; (iii) detailed characterizations of available disease models; (iv) better suitable models; and (v) reliable and sensitive biomarkers. To generate robust HD-like symptoms in a mouse model, the neomycin resistance cassette was excised from zQ175 mice, generating a new line: zQ175Δneo. We entirely describe the dynamics of behavioral, neuropathological, and immunohistological changes from 15-57 weeks of age. Specifically, zQ175Δneo mice showed early astrogliosis from 15 weeks; growth retardation, body weight loss, and anxiety-like behaviors from 29 weeks; motor deficits and reduced muscular strength from 36 weeks; and finally slight microgliosis at 57 weeks of age. Additionally, we collected the entire bioactivity network of small-molecule HD modulators in a multitarget dataset (HD_MDS). Hereby, we uncovered 358 unique compounds addressing over 80 different pharmacological targets and pathways. Our data will support future drug discovery approaches and may serve as useful assessment platform for drug discovery and development against HD.
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Affiliation(s)
- Jingyun Wu
- Department of Pathology, Section of Neuropathology, Translational Neurodegeneration Research and Neuropathology Lab, University of Oslo and Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway; www.pahnkelab.eu
| | - Luisa Möhle
- Department of Pathology, Section of Neuropathology, Translational Neurodegeneration Research and Neuropathology Lab, University of Oslo and Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway; www.pahnkelab.eu
| | - Thomas Brüning
- Department of Pathology, Section of Neuropathology, Translational Neurodegeneration Research and Neuropathology Lab, University of Oslo and Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway; www.pahnkelab.eu
| | - Iván Eiriz
- Department of Pathology, Section of Neuropathology, Translational Neurodegeneration Research and Neuropathology Lab, University of Oslo and Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway; www.pahnkelab.eu
| | - Muhammad Rafehi
- Institute of Clinical Pharmacology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany
| | - Katja Stefan
- Department of Pathology, Section of Neuropathology, Translational Neurodegeneration Research and Neuropathology Lab, University of Oslo and Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway; www.pahnkelab.eu
| | - Sven Marcel Stefan
- Department of Pathology, Section of Neuropathology, Translational Neurodegeneration Research and Neuropathology Lab, University of Oslo and Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway; www.pahnkelab.eu
- Pahnke Lab (Drug Development and Chemical Biology), Lübeck Institute of Experimental Dermatology (LIED), University of Lübeck and University Medical Center Schleswig-Holstein, Ratzeburger Allee 160, 23538 Lübeck, Germany
- Correspondence: (J.P.); (S.M.S.); Tel.: +47-23-071-466 (J.P.)
| | - Jens Pahnke
- Department of Pathology, Section of Neuropathology, Translational Neurodegeneration Research and Neuropathology Lab, University of Oslo and Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway; www.pahnkelab.eu
- Pahnke Lab (Drug Development and Chemical Biology), Lübeck Institute of Experimental Dermatology (LIED), University of Lübeck and University Medical Center Schleswig-Holstein, Ratzeburger Allee 160, 23538 Lübeck, Germany
- Department of Pharmacology, Faculty of Medicine, University of Latvia, Jelgavas iela 4, 1004 Rīga, Latvia
- Department of Neurobiology, The Georg S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Correspondence: (J.P.); (S.M.S.); Tel.: +47-23-071-466 (J.P.)
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6
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Fisher E, Feng J. RNA splicing regulators play critical roles in neurogenesis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1728. [PMID: 35388651 DOI: 10.1002/wrna.1728] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Alternative RNA splicing increases transcript diversity in different cell types and under varying conditions. It is executed with the help of RNA splicing regulators (RSRs), which are operationally defined as RNA-binding proteins (RBPs) that regulate alternative splicing, but not directly catalyzing the chemical reactions of splicing. By systematically searching for RBPs and manually identifying those that regulate splicing, we curated 305 RSRs in the human genome. Surprisingly, most of the RSRs are involved in neurogenesis. Among these RSRs, we focus on nine families (PTBP, NOVA, RBFOX, ELAVL, CELF, DBHS, MSI, PCBP, and MBNL) that play essential roles in the neurogenic pathway. A better understanding of their functions will provide novel insights into the role of splicing in brain development, health, and disease. This comprehensive review serves as a stepping-stone to explore the diverse and complex set of RSRs as fundamental regulators of neural development. This article is categorized under: RNA-Based Catalysis > RNA Catalysis in Splicing and Translation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Emily Fisher
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
- Veterans Affairs Western New York Healthcare System, Buffalo, New York, USA
| | - Jian Feng
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
- Veterans Affairs Western New York Healthcare System, Buffalo, New York, USA
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Patel AK, Rathor SS, Samanta S. Regioselective access to di- and trisubstituted pyridines via a metal-oxidant-solvent-free domino reaction involving 3-chloropropiophenones. Org Biomol Chem 2022; 20:6759-6765. [PMID: 35972042 DOI: 10.1039/d2ob01193j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A remarkable metal-oxidant-solvent- and base-free domino route for regioselective access to a wide range of 2,4-di- and 2,3,4/6-trisubstituted pyridines including carbo- and heterocyclic fused pyridines is reported. This [3C + 2C + 1N] cyclization reaction occurs between 3-chloropropiophenones (3C units), enolizable acyclic/cyclic ketones (2C sources) and NH4OAc as a robust N source under neat conditions under an open atmosphere, producing new C=C and C=N-C bonds in highly chemo- and regioselective manners. Interestingly, this eco-friendly method has many positive features: excellent functional group tolerance, broad substrate scope, good to excellent regioselectivities, promising yields, no-unwanted products, neutral reaction conditions and appropriateness for large-scale synthesis. Mechanism studies reveal that the in situ generated β-amino ketone from 3-chloropropiophenone and an ammonium salt undergoes C=N bond formation with a ketone followed by an intramolecular cyclization process (C=C bond), which are the decisive steps for pyridine synthesis.
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Affiliation(s)
- Ashvani Kumar Patel
- Department of Chemistry, Indian Institute of Technology Indore, Simrol, 453552, India.
| | - Shikha Singh Rathor
- Department of Chemistry, Indian Institute of Technology Indore, Simrol, 453552, India.
| | - Sampak Samanta
- Department of Chemistry, Indian Institute of Technology Indore, Simrol, 453552, India.
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8
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Dolzhenko AV. Synthesis of Heterocycles in Nonconventional Bio‐based Reaction Media. HETEROCYCLES 2022. [DOI: 10.1002/9783527832002.ch9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Ferguson MW, Kennedy CJ, Palpagama TH, Waldvogel HJ, Faull RLM, Kwakowsky A. Current and Possible Future Therapeutic Options for Huntington’s Disease. J Cent Nerv Syst Dis 2022; 14:11795735221092517. [PMID: 35615642 PMCID: PMC9125092 DOI: 10.1177/11795735221092517] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 03/21/2022] [Indexed: 11/16/2022] Open
Abstract
Huntington’s disease (HD) is an autosomal neurodegenerative disease that is characterized by an excessive number of CAG trinucleotide repeats within the huntingtin gene ( HTT). HD patients can present with a variety of symptoms including chorea, behavioural and psychiatric abnormalities and cognitive decline. Each patient has a unique combination of symptoms, and although these can be managed using a range of medications and non-drug treatments there is currently no cure for the disease. Current therapies prescribed for HD can be categorized by the symptom they treat. These categories include chorea medication, antipsychotic medication, antidepressants, mood stabilizing medication as well as non-drug therapies. Fortunately, there are also many new HD therapeutics currently undergoing clinical trials that target the disease at its origin; lowering the levels of mutant huntingtin protein (mHTT). Currently, much attention is being directed to antisense oligonucleotide (ASO) therapies, which bind to pre-RNA or mRNA and can alter protein expression via RNA degradation, blocking translation or splice modulation. Other potential therapies in clinical development include RNA interference (RNAi) therapies, RNA targeting small molecule therapies, stem cell therapies, antibody therapies, non-RNA targeting small molecule therapies and neuroinflammation targeted therapies. Potential therapies in pre-clinical development include Zinc-Finger Protein (ZFP) therapies, transcription activator-like effector nuclease (TALEN) therapies and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated system (Cas) therapies. This comprehensive review aims to discuss the efficacy of current HD treatments and explore the clinical trial progress of emerging potential HD therapeutics.
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Affiliation(s)
- Mackenzie W. Ferguson
- Centre for Brain Research, Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Connor J. Kennedy
- Centre for Brain Research, Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Thulani H. Palpagama
- Centre for Brain Research, Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Henry J. Waldvogel
- Centre for Brain Research, Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Richard L. M. Faull
- Centre for Brain Research, Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Andrea Kwakowsky
- Centre for Brain Research, Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Pharmacology and Therapeutics, School of Medicine, Galway Neuroscience Centre, National University of Ireland Galway, Galway, Ireland
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Small Molecule Screening Discovers Compounds that Reduce FMRpolyG Protein Aggregates and Splicing Defect Toxicity in Fragile X-Associated Tremor/Ataxia Syndrome. Mol Neurobiol 2022; 59:1992-2007. [PMID: 35040038 DOI: 10.1007/s12035-021-02697-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 12/10/2021] [Indexed: 12/20/2022]
Abstract
Expansion of CGG trinucleotide repeats in 5' untranslated region of the FMR1 gene is the causative mutation of neurological diseases such as fragile X syndrome (FXS), fragile X-associated tremor/ataxia syndrome (FXTAS), and ovarian disorder such as fragile X-associated primary ovarian insufficiency (FXPOI). CGG repeats containing FMR1 transcripts form the toxic ribonuclear aggregates, abrupt pre-mRNA splicing, and cause repeat-associated non-AUG translation, leading to the disease symptoms. Here, we utilized a small molecule library of ~ 250,000 members obtained from the National Cancer Institute (NCI) and implemented a shape-based screening approach to identify the candidate small molecules that mitigate toxic CGG RNA-mediated pathogenesis. The compounds obtained from screening were further assessed for their affinity and selectivity towards toxic CGG repeat RNA by employing fluorescence-binding experiment and isothermal calorimetry titration assay. Three candidate molecules B1, B4, and B11 showed high affinity and selectivity for expanded CGG repeats RNA. Further, NMR spectroscopy, gel mobility shift assay, CD spectroscopy, UV-thermal denaturation assay, and molecular docking affirmed their high affinity and selectivity for toxic CGG RNAs. Next, these lead compounds selectively improved the pre-mRNA alternative splicing defects with no perturbation in global splicing efficacy and simultaneously reduced the FMR1polyG protein aggregate formation without affecting the downstream expression of the gene. Taken together these findings, we addressed compound B1, B4, and B11 as potential lead molecules for developing promising therapeutics against FXTAS. Herein, this study, we have utilized shape similarity approach to screen the NCI library and found out the potential candidate which improves the pre-mRNA splicing defects and reduces FMR1polyG aggregations.
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Goud SB, Guin S, Prakash M, Samanta S. Cu(OAc) 2/DABCO-mediated domino reaction of vinyl malononitriles with cyclic sulfamidate imines: access to 6-hydroxyaryl-2-aminonicotinonitriles. Org Biomol Chem 2022; 20:352-357. [PMID: 34931209 DOI: 10.1039/d1ob02095a] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A novel Cu(II)-salt/DABCO-mediated one-pot access to a myriad of highly substituted biologically relevant 2-aminonicotinonitriles possessing a resourceful phenolic moiety with satisfactory yields is reported. This method involves cyclic sulfamidate imines as 1C1N sources and different kinds of acyclic/cyclic vinyl malononitriles as 4C sources for pyridine synthesis via a vinylogous Mannich-cycloaromatization sequence process, creating two new C-N bonds under mild conditions. Importantly, this de novo strategy is applicable to gram-scale syntheses, underlining the method's practicability and allowing for a wide range of substrates with excellent functional group tolerance.
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Affiliation(s)
- S Banuprakash Goud
- Department of Chemistry, Indian Institute of Technology Indore, Simrol, 453552 India.
| | - Soumitra Guin
- Department of Chemistry, Indian Institute of Technology Indore, Simrol, 453552 India.
| | - Meher Prakash
- Department of Chemistry, Indian Institute of Technology Indore, Simrol, 453552 India.
| | - Sampak Samanta
- Department of Chemistry, Indian Institute of Technology Indore, Simrol, 453552 India.
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12
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Piperine analogs arrest c-myc gene leading to downregulation of transcription for targeting cancer. Sci Rep 2021; 11:22909. [PMID: 34824301 PMCID: PMC8617303 DOI: 10.1038/s41598-021-01529-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/28/2021] [Indexed: 11/08/2022] Open
Abstract
G-quadruplex (G4) structures are considered a promising therapeutic target in cancer. Since Ayurveda, Piperine has been known for its medicinal properties. Piperine shows anticancer properties by stabilizing the G4 motif present upstream of the c-myc gene. This gene belongs to a group of proto-oncogenes, and its aberrant transcription drives tumorigenesis. The transcriptional regulation of the c-myc gene is an interesting approach for anticancer drug design. The present study employed a chemical similarity approach to identify Piperine similar compounds and analyzed their interaction with cancer-associated G-quadruplex motifs. Among all Piperine analogs, PIP-2 exhibited strong selectivity, specificity, and affinity towards c-myc G4 DNA as elaborated through biophysical studies such as fluorescence emission, isothermal calorimetry, and circular dichroism. Moreover, our biophysical observations are supported by molecular dynamics analysis and cellular-based studies. Our study showed that PIP-2 showed higher toxicity against the A549 lung cancer cell line but lower toxicity towards normal HEK 293 cells, indicating increased efficacy of the drug at the cellular level. Biological evaluation assays such as TFP reporter assay, quantitative real-time PCR (qRT- PCR), and western blotting suggest that the Piperine analog-2 (PIP-2) stabilizes the G-quadruplex motif located at the promoter site of c-myc oncogene and downregulates its expression. In conclusion, Piperine analog PIP-2 may be used as anticancer therapeutics as it affects the c-myc oncogene expression via G-quadruplex mediated mechanism.
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Patra P, Kar GK. The synthesis, biological evaluation and fluorescence study of chromeno[4,3- b]pyridin/quinolin-one derivatives, the backbone of natural product polyneomarline C scaffolds: a brief review. NEW J CHEM 2021. [DOI: 10.1039/d0nj04761a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This review presents the synthesis, biological and fluorescence study of chromeno[4,3-b]pyridin/quinolin-ones via classical reactions including metal-catalyzed and green reaction protocols.
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Affiliation(s)
- Prasanta Patra
- Department of Chemistry
- Jhargram Raj College
- Jhargram 721507
- India
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14
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Patra P. 4-Chloro-3-formylcoumarin as a multifaceted building block for the development of various bio-active substituted and fused coumarin heterocycles: a brief review. NEW J CHEM 2021. [DOI: 10.1039/d1nj02755g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This review presents the diverse synthesis of 3,4-substituted coumarins and 5-, 6- and 7-membered ring fused coumarins using 4-chloro-3-formylcoumarin as the precursor via classical reactions including metal-catalyzed and green reaction protocols.
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Affiliation(s)
- Prasanta Patra
- Department of Chemistry
- Jhargram Raj College
- Jhargram 721507
- India
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Chatterjee B, Kalyani N, Anand A, Khan E, Das S, Bansal V, Kumar A, Sharma TK. GOLD SELEX: a novel SELEX approach for the development of high-affinity aptamers against small molecules without residual activity. Mikrochim Acta 2020; 187:618. [PMID: 33074441 DOI: 10.1007/s00604-020-04577-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 09/29/2020] [Indexed: 12/17/2022]
Abstract
GOLD SELEX, a novel SELEX approach has been developed that obviates the need for target immobilization for aptamer development. The approach purely relies on the affinity of the aptamers towards its target, to get detached from the gold nanoparticle (GNP) surface (weak attraction) after binding with its target. Thus, only the completely detached aptamers are selected for the next round of SELEX. This, in-process, also addresses the issue of residual binding and thus improves the sensitivity of the developed aptamers. As a proof of concept for establishing the utility of the approach for small molecules, we have developed aptamers against dichlorvos (DV), a pesticide in just 8 rounds. Using these aptamer candidates, we have developed an aptamer-NanoZyme (GNP having peroxidase mimic activity) based colorimetric assay. The developed aptamer displayed high affinity (Kd in sub micromolar range) and selectivity for DV. The developed assay could detect as low as 15 μM DV. The best-performing aptamer was also able to work in real samples like river water and commercial apple juice. The GOLD SELEX approach developed in this study, we believe, can act as a template for future SELEX strategy development and can replace the conventional SELEX strategy.
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Affiliation(s)
- Bandhan Chatterjee
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, 121001, India
| | - Neeti Kalyani
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, 121001, India
| | - Anjali Anand
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, 121001, India
| | - Eshan Khan
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Soonjyoti Das
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, 121001, India
| | - Vipul Bansal
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Lab (NBRL), School of Science, RMIT University, GPO Box 2476, Melbourne, Victoria, 3001, Australia
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Tarun Kumar Sharma
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, 121001, India.
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16
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Jamwal S, Elsworth JD, Rahi V, Kumar P. Gene therapy and immunotherapy as promising strategies to combat Huntington's disease-associated neurodegeneration: emphasis on recent updates and future perspectives. Expert Rev Neurother 2020; 20:1123-1141. [PMID: 32720531 DOI: 10.1080/14737175.2020.1801424] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Modulation of gene expression using gene therapy as well as modulation of immune activation using immunotherapy has attracted considerable attention as rapidly emerging potential therapeutic intervention for the treatment of HD. Several preclinical and clinical trials for gene-based therapy and immunotherapy/antibody-based have been conducted. AREAS COVERED This review focused on the potential use of gene therapy and immuno-based therapies to treat HD, including the current status, the rationale for these approaches as well as preclinical and clinical data supporting it. Growing knowledge of HD pathogenesis has resulted in the discovery of new therapeutic targets, some of which are now in clinical trials. Focus has been allocated to RNA and DNA-based gene therapies for the reduction of mutant huntingtin (mHTT), using Immuno/antibody-based therapies. EXPERT OPINION While safety and efficacy of gene therapy and immunotherapy has been well demonstrated for HD, therefore much focus has now been shifted to disease-modifying therapies. This review defines the current status and future directions of gene therapy and immunotherapies. The review summarizes by what means HD genetic root cause modification and functional restoration of mHtt protein could be achieved by using targeted multimodality gene therapy and immunotherapy to target intracellular and extracellular mHtt.
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Affiliation(s)
- Sumit Jamwal
- Department of Psychiatry, Yale University School of Medicine , New Haven, CT, USA
| | - John D Elsworth
- Department of Psychiatry, Yale University School of Medicine , New Haven, CT, USA
| | - Vikrant Rahi
- Department of Pharmaceutical Sciences and Technology, Maharaja Ranjit Singh Punjab Technical University , Bathinda, India
| | - Puneet Kumar
- Department of Pharmacology, School of Basic and Applied Sciences, Central University of Punjab , Bathinda, India
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17
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Gudimella SK, Kaur A, Kumar R, Samanta S. CuCl2-catalyzed N O bond cleavage of oxime esters: Approach to imidazoheterocycles and furo[3,2-c]chromenyl fused imidazoles. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.152147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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18
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Palomino‐Hernandez O, Margreiter MA, Rossetti G. Challenges in RNA Regulation in Huntington's Disease: Insights from Computational Studies. Isr J Chem 2020. [DOI: 10.1002/ijch.202000021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Oscar Palomino‐Hernandez
- Computational Biomedicine, Institute of Neuroscience and Medicine (INM-9)/Instute for advanced simulations (IAS-5)Forschungszentrum Juelich 52425 Jülich Germany
- Faculty 1RWTH Aachen 52425 Aachen Germany
- Computation-based Science and Technology Research CenterThe Cyprus Institute Nicosia 2121 Cyprus
- Institute of Life ScienceThe Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Michael A. Margreiter
- Computational Biomedicine, Institute of Neuroscience and Medicine (INM-9)/Instute for advanced simulations (IAS-5)Forschungszentrum Juelich 52425 Jülich Germany
- Faculty 1RWTH Aachen 52425 Aachen Germany
| | - Giulia Rossetti
- Computational Biomedicine, Institute of Neuroscience and Medicine (INM-9)/Instute for advanced simulations (IAS-5)Forschungszentrum Juelich 52425 Jülich Germany
- Jülich Supercomputing Centre (JSC)Forschungszentrum Jülich 52425 Jülich Germany
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation University Hospital AachenRWTH Aachen University Pauwelsstraße 30 52074 Aachen Germany
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19
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Padroni G, Patwardhan NN, Schapira M, Hargrove AE. Systematic analysis of the interactions driving small molecule-RNA recognition. RSC Med Chem 2020; 11:802-813. [PMID: 33479676 DOI: 10.1039/d0md00167h] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 05/20/2020] [Indexed: 12/14/2022] Open
Abstract
RNA molecules are becoming an important target class in drug discovery. However, the principles for designing RNA-binding small molecules are yet to be fully uncovered. In this study, we examined the Protein Data Bank (PDB) to highlight privileged interactions underlying small molecule-RNA recognition. By comparing this analysis with previously determined small molecule-protein interactions, we find that RNA recognition is driven mostly by stacking and hydrogen bonding interactions, while protein recognition is instead driven by hydrophobic effects. Furthermore, we analyze patterns of interactions to highlight potential strategies to tune RNA recognition, such as stacking and cation-π interactions that favor purine and guanine recognition, and note an unexpected paucity of backbone interactions, even for cationic ligands. Collectively, this work provides further understanding of RNA-small molecule interactions that may inform the design of small molecules targeting RNA.
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Affiliation(s)
- G Padroni
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA .
| | - N N Patwardhan
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA .
| | - M Schapira
- Structural Genomics Consortium , University of Toronto , Toronto , ON M5G 1L7 , Canada.,Department of Pharmacology and Toxicology , University of Toronto , Toronto , ON M5S 1A8 , Canada
| | - A E Hargrove
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA .
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20
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Verma AK, Khan E, Mishra SK, Mishra A, Charlet-Berguerand N, Kumar A. Curcumin Regulates the r(CGG) exp RNA Hairpin Structure and Ameliorate Defects in Fragile X-Associated Tremor Ataxia Syndrome. Front Neurosci 2020; 14:295. [PMID: 32317919 PMCID: PMC7155420 DOI: 10.3389/fnins.2020.00295] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/16/2020] [Indexed: 12/21/2022] Open
Abstract
Fragile X-associated tremor ataxia syndrome is an untreatable neurological and neuromuscular disorder caused by unstable expansion of 55–200 CGG nucleotide repeats in 5′ UTR of Fragile X intellectual disability 1 (FMR1) gene. The expansion of CGG repeats in the FMR1 mRNA elicits neuronal cell toxicity through two main pathogenic mechanisms. First, mRNA with CGG expanded repeats sequester specific RNA regulatory proteins resulting in splicing alterations and formation of ribonuclear inclusions. Second, repeat-associated non-canonical translation (RANT) of the CGG expansion produces a toxic homopolymeric protein, FMRpolyG. Very few small molecules are known to modulate these pathogenic events, limiting the therapeutic possibilities for FXTAS. Here, we found that a naturally available biologically active small molecule, Curcumin, selectively binds to CGG RNA repeats. Interestingly, Curcumin improves FXTAS associated alternative splicing defects and decreases the production and accumulation of FMRpolyG protein inclusion. Furthermore, Curcumin decreases cell cytotoxicity promptly by expression of CGG RNA in FXTAS cell models. In conclusion, our data suggest that small molecules like Curcumin and its derivatives may be explored as a potential therapeutic strategy against the debilitating repeats associated neurodegenerative disorders.
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Affiliation(s)
- Arun Kumar Verma
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Eshan Khan
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Subodh Kumar Mishra
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India
| | - Nicolas Charlet-Berguerand
- Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, University of Strasbourg, Strasbourg, France
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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21
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Khristich AN, Mirkin SM. On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability. J Biol Chem 2020; 295:4134-4170. [PMID: 32060097 PMCID: PMC7105313 DOI: 10.1074/jbc.rev119.007678] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Expansions of simple tandem repeats are responsible for almost 50 human diseases, the majority of which are severe, degenerative, and not currently treatable or preventable. In this review, we first describe the molecular mechanisms of repeat-induced toxicity, which is the connecting link between repeat expansions and pathology. We then survey alternative DNA structures that are formed by expandable repeats and review the evidence that formation of these structures is at the core of repeat instability. Next, we describe the consequences of the presence of long structure-forming repeats at the molecular level: somatic and intergenerational instability, fragility, and repeat-induced mutagenesis. We discuss the reasons for gender bias in intergenerational repeat instability and the tissue specificity of somatic repeat instability. We also review the known pathways in which DNA replication, transcription, DNA repair, and chromatin state interact and thereby promote repeat instability. We then discuss possible reasons for the persistence of disease-causing DNA repeats in the genome. We describe evidence suggesting that these repeats are a payoff for the advantages of having abundant simple-sequence repeats for eukaryotic genome function and evolvability. Finally, we discuss two unresolved fundamental questions: (i) why does repeat behavior differ between model systems and human pedigrees, and (ii) can we use current knowledge on repeat instability mechanisms to cure repeat expansion diseases?
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Affiliation(s)
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, Massachusetts 02155.
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22
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Abstract
Huntington's disease is a dominantly inherited neurodegenerative disease caused by an unstable expanded trinucleotide repeat at the short end of the fourth chromosome. Central nervous system pathology begins in the striatum, eventually affecting the entire brain and occurs consequent to multiple intracellular derangements. The proximate cause is a mutant protein with an elongated polyglutamine tract. Pharmacological approaches targeting multiple domains of intracellular functions have universally been disappointing. However, recent developments in gene therapy, including antisense oligonucleotides, small interfering RNAs, and gene editing are bringing new hope to the Huntington's community. This review discusses the promises and challenges of these new potential treatments.
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Affiliation(s)
- Kathleen M Shannon
- Department of Neurology, University of Wisconsin School of Medicine and Public Health, 1685 Highland Avenue #7158, Madison, WI, 53705, USA.
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23
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Yadav A, Gudimella SK, Samanta S. An Expedient Lewis‐Acid‐Catalyzed Microwave‐Assisted Domino Approach to Coumarin‐Fused Pyrroles and Related Heterocycles under Neat Conditions. ChemistrySelect 2019. [DOI: 10.1002/slct.201903711] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Anubha Yadav
- Discipline of ChemistryIndian Institute of Technology Indore, Simrol, Indore 453552 Madhya Pradesh India
| | - Santosh K. Gudimella
- Discipline of ChemistryIndian Institute of Technology Indore, Simrol, Indore 453552 Madhya Pradesh India
| | - Sampak Samanta
- Discipline of ChemistryIndian Institute of Technology Indore, Simrol, Indore 453552 Madhya Pradesh India
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24
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Discovery of a potent small molecule inhibiting Huntington's disease (HD) pathogenesis via targeting CAG repeats RNA and Poly Q protein. Sci Rep 2019; 9:16872. [PMID: 31728006 PMCID: PMC6856162 DOI: 10.1038/s41598-019-53410-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 10/23/2019] [Indexed: 02/07/2023] Open
Abstract
CAG repeats RNA causes various fatal neurodegenerative diseases exemplified by Huntington's disease (HD) and several spinocerebellar ataxias (SCAs). Although there are differences in the pathogenic mechanisms, these diseases share the common cause, i.e., expansion of CAG repeats. The shared cause of these diseases raises the possibility for the exploiting the common target as a potential therapeutic approach. Oligonucleotide-based therapeutics are designed earlier with the help of the base pairing rule but are not very promiscuous, considering the nonspecific stimulation of the immune system and the poor cellular delivery. Therefore, small molecules-based therapeutics are preferred for targeting the repeats expansion disorders. Here, we have used the chemical similarity search approach to discern the small molecules that selectively target toxic CAG RNA. The lead compounds showed the specificity towards AA mismatch in biophysical studies including CD, ITC, and NMR spectroscopy and thus aided to forestall the polyQ mediated pathogenicity. Furthermore, the lead compounds also explicitly alleviate the polyQ mediated toxicity in HD cell models and patient-derived cells. These findings suggest that the lead compound could act as a chemical probe for AA mismatch containing RNA as well as plays a neuroprotective role in fatal neurodegenerative diseases like HD and SCAs.
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Verma AK, Khan E, Mishra SK, Jain N, Kumar A. Piperine Modulates Protein Mediated Toxicity in Fragile X-Associated Tremor/Ataxia Syndrome through Interacting Expanded CGG Repeat (r(CGG) exp) RNA. ACS Chem Neurosci 2019; 10:3778-3788. [PMID: 31264835 DOI: 10.1021/acschemneuro.9b00282] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
An expansion of CGG tandem repeats in the 5' untranslated region (5'-UTR) of fragile X mental retardation 1 (FMR1) gene causes fragile X-associated tremor/ataxia syndrome (FXTAS). The transcripts of these expanded repeats r(CGG)exp either form RNA foci or undergo the repeat-associated non-ATG (RAN) translation that produces toxic homopolymeric proteins in neuronal cells. The discovery of small molecule modulators that possess a strong binding affinity and high selectivity to these toxic expanded repeats RNA could be a promising therapeutic approach to cure the expanded repeat-associated neurological diseases. Therefore, here we sought to test the therapeutic potential of a natural alkaloid, piperine, by assessing its ability to bind and neutralize the toxicity of r(CGG)exp RNA motif. To accomplish this first, we have determined the affinity of piperine to r(CGG)exp RNA using fluorescence-based binding assay and isothermal titration calorimetry assay. These assays showed that piperine forms a thermodynamically favorable interaction with r(CGG)exp RNA with high selectivity to the G-rich RNA motif. Interaction of piperine with r(CGG)exp motif was further validated using several biophysical techniques such as CD, CD melting, NMR spectroscopy, and gel retardation assay. Moreover, piperine was also found to be effective for improving the r(CGG)exp associated splicing defects and RAN translation in a FXTAS cell model system. Our results effectively provided the evidence that piperine strongly interacts with r(CGG)exp RNA and could be used as a suitable candidate for therapeutic development against FXTAS.
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Affiliation(s)
- Arun Kumar Verma
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Eshan Khan
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Subodh Kumar Mishra
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Neha Jain
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
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26
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Verma AK, Khan E, Bhagwat SR, Kumar A. Exploring the Potential of Small Molecule-Based Therapeutic Approaches for Targeting Trinucleotide Repeat Disorders. Mol Neurobiol 2019; 57:566-584. [DOI: 10.1007/s12035-019-01724-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/29/2019] [Indexed: 12/18/2022]
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