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Almena Rodriguez L, Kallert E, Husmann JÅ, Schaubruch K, Meisel KIS, Schwickert M, Hoba SN, Heermann R, Kersten C. Electrostatic Anchoring in RNA-Ligand Design─Dissecting the Effects of Positive Charges on Affinity, Selectivity, Binding Kinetics, and Thermodynamics. J Med Chem 2025; 68:8659-8678. [PMID: 40191889 PMCID: PMC12035807 DOI: 10.1021/acs.jmedchem.5c00339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2025] [Revised: 03/23/2025] [Accepted: 03/31/2025] [Indexed: 04/25/2025]
Abstract
Targeting RNA with small molecules is an emerging field in medicinal chemistry. However, highly potent ligands are often challenging to achieve. One intuitive strategy to enhance ligand's potency is the implementation of positively charged moieties to interact with the negatively charged RNA phosphate backbone. We investigated the effect of such "electrostatic anchors" on binding affinity, kinetics, thermodynamics, and selectivity by MST, SPR, and ITC experiments, respectively, with the Ba SAM-VI riboswitch and the Tte preQ1 riboswitch aptamer model systems. RNA-ligand interactions were dominated by enthalpy, and electrostatic anchors had moderate effects on binding affinity driven by faster association rates for higher charged ligands. Despite the observations of loose binding interactions in SPR experiments with multibasic ligands, selectivity over structurally unrelated RNA off-targets was maintained. Therefore, the addition of positively charged moieties is no universal RNA-ligand design principle, but a purposefully implemented ionic RNA-ligand interaction can enhance potency without impairing selectivity.
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Affiliation(s)
- Laura Almena Rodriguez
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| | - Elisabeth Kallert
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| | - Jan-Åke Husmann
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| | - Kirsten Schaubruch
- Institute
of Molecular Physiology, Microbiology and Biotechnology, Johannes
Gutenberg-University, Hanns-DieterHüsch-Weg 17, 55128 Mainz, Germany
| | - Katherina I. S. Meisel
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| | - Marvin Schwickert
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| | - Sabrina N. Hoba
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| | - Ralf Heermann
- Institute
of Molecular Physiology, Microbiology and Biotechnology, Johannes
Gutenberg-University, Hanns-DieterHüsch-Weg 17, 55128 Mainz, Germany
| | - Christian Kersten
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
- Institute
for Quantitative and Computational Biosciences, Johannes Gutenberg-University, BioZentrum I, Hanns-Dieter-Hüsch
Weg 15, 55128 Mainz, Germany
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Lupidi G, Bassetti B, Ballini R, Petrini M, Palmieri A. A New and Effective One‐Pot Synthesis of Polysubstituted Carbazoles Starting from β‐Nitro‐β,γ‐Unsaturated‐Ketones and Indoles. ASIAN J ORG CHEM 2021. [DOI: 10.1002/ajoc.202100342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Gabriele Lupidi
- Green Chemistry Group School of Sciences and Technology Chemistry Division University of Camerino Via S. Agostino n. 1 MC 62032 Camerino Italy
| | - Benedetta Bassetti
- Green Chemistry Group School of Sciences and Technology Chemistry Division University of Camerino Via S. Agostino n. 1 MC 62032 Camerino Italy
| | - Roberto Ballini
- Green Chemistry Group School of Sciences and Technology Chemistry Division University of Camerino Via S. Agostino n. 1 MC 62032 Camerino Italy
| | - Marino Petrini
- Green Chemistry Group School of Sciences and Technology Chemistry Division University of Camerino Via S. Agostino n. 1 MC 62032 Camerino Italy
| | - Alessandro Palmieri
- Green Chemistry Group School of Sciences and Technology Chemistry Division University of Camerino Via S. Agostino n. 1 MC 62032 Camerino Italy
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Zhu P, Qian J, Xu Z, Meng C, Zhu W, Ran F, Zhang W, Zhang Y, Ling Y. Overview of piperlongumine analogues and their therapeutic potential. Eur J Med Chem 2021; 220:113471. [PMID: 33930801 DOI: 10.1016/j.ejmech.2021.113471] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/29/2021] [Accepted: 04/10/2021] [Indexed: 01/18/2023]
Abstract
Natural products have long been an important source for discovery of new drugs to treat human diseases. Piperlongumine (PL) is an amide alkaloid isolated from Piper longum L. (long piper) and other piper plants and has received widespread attention because of its diverse biological activities. A large number of PL derivatives have been designed, synthesized and assessed in many pharmacological functions, including antiplatelet aggregation, neuroprotective activities, anti-diabetic activities, anti-inflammatory activities, anti-senolytic activities, immune activities, and antitumor activities. Among them, the anti-tumor effects and application of PL and its derivatives are most extensively studied. We herein summarize the development of PL derivatives, the structure and activity relationships (SARs), and their therapeutic potential on the treatments of various diseases, especially against cancer. We also discussed the challenges and future directions associated with PL and its derivatives in these indications.
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Affiliation(s)
- Peng Zhu
- Medical School, Nantong University, Nantong, 226001, China; School of Pharmacy and Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong, 226001, China; State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau
| | - Jianqiang Qian
- Medical School, Nantong University, Nantong, 226001, China; School of Pharmacy and Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong, 226001, China
| | - Zhongyuan Xu
- Medical School, Nantong University, Nantong, 226001, China; School of Pharmacy and Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong, 226001, China
| | - Chi Meng
- School of Pharmacy and Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong, 226001, China
| | - Weizhong Zhu
- Medical School, Nantong University, Nantong, 226001, China; School of Pharmacy and Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong, 226001, China
| | - Fansheng Ran
- School of Pharmacy and Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong, 226001, China
| | - Wei Zhang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau.
| | - Yanan Zhang
- Medical School, Nantong University, Nantong, 226001, China; School of Pharmacy and Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong, 226001, China.
| | - Yong Ling
- Medical School, Nantong University, Nantong, 226001, China; School of Pharmacy and Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong, 226001, China.
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Zhao Z, Song H, Xie J, Liu T, Zhao X, Chen X, He X, Wu S, Zhang Y, Zheng X. Research progress in the biological activities of 3,4,5-trimethoxycinnamic acid (TMCA) derivatives. Eur J Med Chem 2019; 173:213-227. [PMID: 31009908 PMCID: PMC7115657 DOI: 10.1016/j.ejmech.2019.04.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 04/02/2019] [Accepted: 04/02/2019] [Indexed: 01/02/2023]
Abstract
TMCA (3,4,5-trimethoxycinnamic acid) ester and amide are privileged structural scaffolds in drug discovery which are widely distributed in natural products and consequently produced diverse therapeutically relevant pharmacological functions. Owing to the potential of TMCA ester and amide analogues as therapeutic agents, researches on chemical syntheses and modifications have been carried out to drug-like candidates with broad range of medicinal properties such as antitumor, antiviral, CNS (central nervous system) agents, antimicrobial, anti-inflammatory and hematologic agents for a long time. At the same time, SAR (structure-activity relationship) studies have draw greater attention among medicinal chemists, and many of the lead compounds were derived for various disease targets. However, there is an urgent need for the medicinal chemists to further exploit the precursor in developing chemical entities with promising bioactivity and druggability. This review concisely summarizes the synthesis and biological activity for TMCA ester and amide analogues. It also comprehensively reveals the relationship of significant biological activities along with SAR studies. 3,4,5-Trimethoxycinnamic acid (TMCA) derivatives show applications in different pathophysiological conditions due to its privileged structural scaffolds. Natural derived TMCA analogues and chemically modified TMCA ester and amide analogues and their bioactivities are focused in this review. Additionally, it also comprehensively summarized the relationship of significant biological activities along with SAR studies of synthetic TMCA derivatives.
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Affiliation(s)
- Zefeng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, 229 Taibai Road, Xi'an, 710069, China
| | - Huanhuan Song
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, 229 Taibai Road, Xi'an, 710069, China; Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Jing Xie
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, 229 Taibai Road, Xi'an, 710069, China
| | - Tian Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, 229 Taibai Road, Xi'an, 710069, China
| | - Xue Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, 229 Taibai Road, Xi'an, 710069, China
| | - Xufei Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, 229 Taibai Road, Xi'an, 710069, China
| | - Xirui He
- Honghui Hospital, Xi'an Jiaotong University, Xi'an, 710054, China
| | - Shaoping Wu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, 229 Taibai Road, Xi'an, 710069, China; Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, Shaanxi, 710069, China.
| | - Yongmin Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, 229 Taibai Road, Xi'an, 710069, China; Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, Shaanxi, 710069, China; Sorbonne Université, Institut Parisien de Chimie Moléculaire, CNRS UMR 8232, 4 place Jussieu, 75005, Paris, France
| | - Xiaohui Zheng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, 229 Taibai Road, Xi'an, 710069, China.
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