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Huang S, Zuo L, Zhang L, Guo X, Cheng C, He Y, Cheng G, Yu J, Liu Y, Chen R, Tang G, Fan Y, Feng L. Design, Synthesis, and Mode of Action of Thioacetamide Derivatives as the Algicide Candidate Based on Active Substructure Splicing Strategy. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7021-7032. [PMID: 38501582 DOI: 10.1021/acs.jafc.4c00912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Lakes and reservoirs worldwide are experiencing a growing problem with harmful cyanobacterial blooms (HCBs), which have significant implications for ecosystem health and water quality. Algaecide is an effective way to control HCBs effectively. In this study, we applied an active substructure splicing strategy for rapid discovery of algicides. Through this strategy, we first optimized the structure of the lead compound S5, designed and synthesized three series of thioacetamide derivatives (series A, B, C), and then evaluated their algicidal activities. Finally, compound A3 with excellent performance was found, which accelerated the process of discovering and developing new algicides. The biological activity assay data showed that A3 had a significant inhibitory effect on M. aeruginosa. FACHB905 (EC50 = 0.46 μM) and Synechocystis sp. PCC6803 (EC50 = 0.95 μM), which was better than the commercial algicide prometryn (M. aeruginosa. FACHB905, EC50 = 6.52 μM; Synechocystis sp. PCC6803, EC50 = 4.64 μM) as well as better than lead compound S5 (M. aeruginosa. FACHB905, EC50 = 8.80 μM; Synechocystis sp. PCC6803, EC50 = 7.70 μM). The relationship between the surface electrostatic potential, chemical reactivity, and global electrophilicity of the compounds and their activities was discussed by density functional theory (DFT). Physiological and biochemical studies have shown that A3 might affect the photosynthesis pathway and antioxidant system in cyanobacteria, resulting in the morphological changes of cyanobacterial cells. Our work demonstrated that A3 might be a promising candidate for the development of novel algicides and provided a new active skeleton for the development of subsequent chemical algicides.
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Affiliation(s)
- Shi Huang
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Lingzi Zuo
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Liexiong Zhang
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Xiaoliang Guo
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Cai Cheng
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Yanlin He
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Guonian Cheng
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Jie Yu
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Yanyang Liu
- Wuhan Institute of Photochemistry and Technology, 7 North Bingang Road, Wuhan, Hubei 430083, China
| | - Ruiqing Chen
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Guangmei Tang
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Yuxuan Fan
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Lingling Feng
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, China
- Wuhan Institute of Photochemistry and Technology, 7 North Bingang Road, Wuhan, Hubei 430083, China
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2
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Liu L, Malagu K, Haughan AF, Khetarpal V, Stott AJ, Esmieu W, Vater HD, Webster SJ, Van de Poël AJ, Clissold C, Cosgrove B, Sutton B, Spencer JA, Breccia P, Gancia E, Bonomo S, Ladduwahetty T, Lazari O, Patel H, Atton HC, Clifton S, Mota DM, Magnani D, O'Neill A, Stebbeds M, Macabuag N, Todd D, Herva ME, Mitchell P, Visser M, Compte Sancerni S, Grand Moursel L, da Silva M, Kritikou E, Heikkinen TT, Bolkvadze T, Fodale V, Spadafora D, Daldin M, Bresciani A, Mangette JE, Doherty EM, Lee MR, Herbst T, Monteagudo E, Macdonald D, Plotnikov NV, Chambers M, McAllister G, Muňoz-Sanjuan I, Dominguez C. Identification and Optimization of RNA-Splicing Modulators as Huntingtin Protein-Lowering Agents for the Treatment of Huntington's Disease. J Med Chem 2023; 66:13205-13246. [PMID: 37712656 DOI: 10.1021/acs.jmedchem.3c01173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Huntington's disease (HD) is caused by an expanded CAG trinucleotide repeat in exon 1 of the huntingtin (HTT) gene. We report the design of a series of HTT pre-mRNA splicing modulators that lower huntingtin (HTT) protein, including the toxic mutant huntingtin (mHTT), by promoting insertion of a pseudoexon containing a premature termination codon at the exon 49-50 junction. The resulting transcript undergoes nonsense-mediated decay, leading to a reduction of HTT mRNA transcripts and protein levels. The starting benzamide core was modified to pyrazine amide and further optimized to give a potent, CNS-penetrant, and orally bioavailable HTT-splicing modulator 27. This compound reduced canonical splicing of the HTT RNA exon 49-50 and demonstrated significant HTT-lowering in both human HD stem cells and mouse BACHD models. Compound 27 is a structurally diverse HTT-splicing modulator that may help understand the mechanism of adverse effects such as peripheral neuropathy associated with branaplam.
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Affiliation(s)
- Longbin Liu
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Karine Malagu
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Alan F Haughan
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Vinod Khetarpal
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Andrew J Stott
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - William Esmieu
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Huw D Vater
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Stephen J Webster
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Amanda J Van de Poël
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Cole Clissold
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Brett Cosgrove
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Benjamin Sutton
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Jonathan A Spencer
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Perla Breccia
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Emanuela Gancia
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Silvia Bonomo
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Tammy Ladduwahetty
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Ovadia Lazari
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Hiral Patel
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Helen C Atton
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Steve Clifton
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Daniel M Mota
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Dario Magnani
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Amy O'Neill
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Marta Stebbeds
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Natsuko Macabuag
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Daniel Todd
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Maria E Herva
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Philip Mitchell
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Mijke Visser
- Charles River, Darwinweg 24, 2333 CR Leiden, The Netherlands
| | | | | | - Marta da Silva
- Charles River, Darwinweg 24, 2333 CR Leiden, The Netherlands
| | - Eva Kritikou
- Charles River, Darwinweg 24, 2333 CR Leiden, The Netherlands
| | | | | | | | | | | | | | | | - Elizabeth M Doherty
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Matthew R Lee
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Todd Herbst
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Edith Monteagudo
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Douglas Macdonald
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Nikolay V Plotnikov
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Mark Chambers
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - George McAllister
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Ignacio Muňoz-Sanjuan
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Celia Dominguez
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
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3
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Ottesen EW, Singh NN, Luo D, Kaas B, Gillette B, Seo J, Jorgensen H, Singh RN. Diverse targets of SMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy. Nucleic Acids Res 2023; 51:5948-5980. [PMID: 37026480 PMCID: PMC10325915 DOI: 10.1093/nar/gkad259] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 03/13/2023] [Accepted: 03/28/2023] [Indexed: 04/08/2023] Open
Abstract
Designing an RNA-interacting molecule that displays high therapeutic efficacy while retaining specificity within a broad concentration range remains a challenging task. Risdiplam is an FDA-approved small molecule for the treatment of spinal muscular atrophy (SMA), the leading genetic cause of infant mortality. Branaplam is another small molecule which has undergone clinical trials. The therapeutic merit of both compounds is based on their ability to restore body-wide inclusion of Survival Motor Neuron 2 (SMN2) exon 7 upon oral administration. Here we compare the transcriptome-wide off-target effects of these compounds in SMA patient cells. We captured concentration-dependent compound-specific changes, including aberrant expression of genes associated with DNA replication, cell cycle, RNA metabolism, cell signaling and metabolic pathways. Both compounds triggered massive perturbations of splicing events, inducing off-target exon inclusion, exon skipping, intron retention, intron removal and alternative splice site usage. Our results of minigenes expressed in HeLa cells provide mechanistic insights into how these molecules targeted towards a single gene produce different off-target effects. We show the advantages of combined treatments with low doses of risdiplam and branaplam. Our findings are instructive for devising better dosing regimens as well as for developing the next generation of small molecule therapeutics aimed at splicing modulation.
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Affiliation(s)
- Eric W Ottesen
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Natalia N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Diou Luo
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Bailey Kaas
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Benjamin J Gillette
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Joonbae Seo
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Hannah J Jorgensen
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Ravindra N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
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5
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Yaragani M, Yadlapalli P, Raghavan S, Giridhar T, Mandava VBR, Singh RV, Kottapalli RP, Chinnusamy S. Electronic effect-dependent intramolecular non-covalent interactions on the activity of 4,4-dimethylimidazolidin-2-one pharmacophore-based androgen receptor antagonists. Chem Biol Drug Des 2023; 101:614-625. [PMID: 36198102 DOI: 10.1111/cbdd.14151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 09/15/2022] [Accepted: 09/30/2022] [Indexed: 11/30/2022]
Abstract
Because androgen receptor (AR) signalling is important for the development and progression of prostate cancer (PC), AR antagonists are utilized in clinical practices to treat PC and are referred to as androgen deprivation therapy (ADT). However, continued administration of AR antagonists often results in the development of resistance, known as castration-resistant prostate cancer (CRPC). Despite castration, it has been demonstrated that AR signalling continues to be fundamental to tumour growth. In this regard, a series of readily synthesizable 4,4-dimethylimidazolidine-2-one pharmacophore-based AR antagonists (FAR01-FAR11) were designed and synthesized. Androgen-dependent LNCaP PC cell line was used to test the AR-antagonist activity of these compounds in vitro and compared with the U.S. Food and Drug Administration (FDA) approved second-generation enzalutamide. In our previous work, rigid thiohydantoin pharmacophore in enzalutamide is replaced by the flexible 4,4-dimethylimidazolidin-2-one. In order to improve the flexibility further, one methylene group is introduced between the pharmacophore and one of the aromatic ring. Despite the fact that the amide functional group is a crucial characteristic for building AR antagonists, this class of molecules lacks one. FAR06 has the exact same activity as enzalutamide (IC50 : 0.782 μM) with an IC50 value of 0.801 μM among the series of compounds.
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Affiliation(s)
- Muralikrishna Yaragani
- Department of Chemistry, Koneru Lakshmaiah Education Foundation, Guntur, Andhra Pradesh, India
| | | | - Sriram Raghavan
- CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu, India
| | - Thota Giridhar
- Sigma-Aldrich Chemicals Pvt. Ltd, Bangalure, Karnataka, India
| | | | | | | | - Saravanan Chinnusamy
- Center for Advanced Organic Materials (Sona-AROMA), Department of Chemistry, Sona College of Technology, Salem, Tamil Nadu, India
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