1
|
Li C, Du H, Zhang C, Huang W, Zhang X, Wang T, Jiang D, Hou T, Wang E. Comprehensive Evaluation of End-Point Free Energy Methods in DNA-Ligand Interaction Predictions. J Chem Inf Model 2025; 65:2014-2025. [PMID: 39888349 DOI: 10.1021/acs.jcim.4c01947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2025]
Abstract
Deoxyribonucleic acid (DNA) serves as a repository of genetic information in cells and is a critical molecular target for various antibiotics and anticancer drugs. A profound understanding of small molecule interaction with DNA is crucial for the rational design of DNA-targeted therapies. While the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) and molecular mechanics/generalized Born surface area (MM/GBSA) approaches have been well established for predicting protein-ligand binding, their application to DNA-ligand interactions has been less explored. In this study, we systematically investigated the binding of 13 diverse small molecules to DNA, evaluating the accuracy of DNA-ligand interaction predictions across different solvation approaches, interior dielectric constants (εin), and molecular force fields. Our results demonstrate that MM/PBSA, using energy-minimized structures (the bsc1 force field and εin = 20), provides the best correlation (Rp = -0.742) with experimental binding affinities, surpassing the performance of rDock scoring functions (best Rp = -0.481). Notably, the interior dielectric constant was found to significantly impact DNA-ligand binding free energy predictions, especially for MM/PBSA. Moreover, both MM/PBSA and MM/GBSA predictions (εin = 16 or 20) exhibited superior performance in distinguishing native-like binding modes within the top-10 poses from decoys, compared to the molecular docking tools used in this study. However, the popular docking software PLANTS demonstrates notable efficacy in predicting the top-1 binding pose. Given the considerably higher computational cost of MM/PBSA, MM/GBSA rescoring with higher εin = 16 or 20 is more efficient for recognizing the native-like binding poses for DNA-ligand systems. This study presents the first detailed exploration of end-point free energy calculations in the context of DNA-ligand interactions and offers valuable insights for the application of the MM/PB(GB)SA methods in this domain.
Collapse
Affiliation(s)
- Cuiyu Li
- Zhejiang Laboratory, Hangzhou 311100, Zhejiang, China
| | - Hongyan Du
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | | | - Wanying Huang
- Zhejiang Laboratory, Hangzhou 311100, Zhejiang, China
| | - Xujun Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Tianyue Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Dejun Jiang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410004, Hunan, China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Ercheng Wang
- Zhejiang Laboratory, Hangzhou 311100, Zhejiang, China
| |
Collapse
|
2
|
Metangle S, Ranjan N. Preferential Binding of a Red Emissive Julolidine Derivative to a Promoter G-Quadruplex. Chembiochem 2024; 25:e202300527. [PMID: 37926689 DOI: 10.1002/cbic.202300527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/23/2023] [Accepted: 11/02/2023] [Indexed: 11/07/2023]
Abstract
The therapeutic potential of G-quadruplexes has increased significantly with the growing understanding of their functional roles in pathogens apart from human diseases such as cancer. Here, we report the synthesis of three julolidine-based molecules and their binding to nucleic acids. Among the synthesized molecules, compound 1 exhibited red emissive fluorescence with a distinct preference for Pu22 G-quadruplex. The binding of compound 1 to Pu22 G-quadruplex, initially identified through a fluorescence-based screening, was further confirmed by UV-vis, fluorescence spectroscopy, and circular dichroism-based experiments. Thermal denaturation of compound 1 in the presence of Pu22 G-quadruplex revealed a concentration-dependent stabilization (~10.0 °C at 1 : 3 stoichiometry). Fluorescence-based experiments revealed 1 : 1 stoichiometry of the interaction and an association constant (Ka ) of 5.67×106 M-1 . CD experiments displayed that the parallel conformation of the G-quadruplex was retained on compound 1's binding and signs of higher order binding/complex formation were observed at high compound 1 to DNA ratio. Molecular docking studies revealed the dominance of stacking and van der Waals interactions in the molecular recognition which was aided by some close-distance interactions involving the quinolinium nitrogen atom.
Collapse
Affiliation(s)
- Sachin Metangle
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, 226002, India
| | - Nihar Ranjan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, 226002, India
| |
Collapse
|
3
|
Tian Y, Huang X, Li H, Chen Q, Gong X, Chen H, Fan M, Gong Z. Highly sensitive and selective off-on fluorescent platform for tricresyl phosphate flame retardant based on twisted intramolecular charge transfer probe. Anal Chim Acta 2024; 1285:342009. [PMID: 38057048 DOI: 10.1016/j.aca.2023.342009] [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: 08/15/2023] [Revised: 10/20/2023] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND Tricresyl phosphate (TCP), a typical organic phosphorus flame retardant (OPFR), is an emerging pollutant that causes great concern in recent years due to its high neurotoxicity and reproductive toxicity, etc. Conventional analysis methods for TCP such as gas chromatography and liquid chromatography-tandem mass spectrometry exhibit high sensitivity and accuracy. However, these techniques generally suffer from certain limitations, such as high cost, bulky equipment, time-consuming and operator-dependent properties. Therefore, the establishment of fast and efficient analytical methods for TCP still remains a great challenge. RESULT A "turn on" fluorescence sensing strategy for the efficient detection of TCP was established, based on a unique molecular rotor probe of 9-(2,2-dicyanovinyl)-julolidine (DCVJ). The introduction of TCP led to a significant enhancement of the fluorescence intensity of DCVJ. The results show that twisted intramolecular charge transfer (TICT) process might play an important role for this enhancement of fluorescence response via dynamic light scattering measurements and fluorescence lifetime analysis. Further investigations demonstrate that the hydrophobic interaction and conjugation effect between DCVJ and TCP constrain the molecular rotation and vibration of DCVJ, thereby regulating the TICT process, which contribute to this intriguing "turn on" behavior. In view of this, a new sensing platform with excellent performance for TCP was established, which offers quick response time, high selectivity, wide linear range (20-1200 ng mL-1, 1600-8000 ng mL-1), and low detection limit (4.82 ng mL-1). SIGNIFICANCE The established new sensing platform for TCP demonstrates the advantages of simplicity, high efficiency, excellent sensitivity and selectivity. The obtained results are also superior to some other previously reported fluorescence methods. This work opens up a new perspective for the efficient detection of emerging OPFRs pollutants.
Collapse
Affiliation(s)
- Yulu Tian
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu 611756, China
| | - Xiaoying Huang
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu 611756, China
| | - Hangzhou Li
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu 611756, China
| | - Qiumeng Chen
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu 611756, China
| | - Xinying Gong
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu 611756, China
| | - Huan Chen
- Biogeochemistry & Environmental Quality Research Group, Clemson University, South Carolina 29442, United States
| | - Meikun Fan
- State-province Joint Engineering Laboratory of Spatial Information Technology of High-Speed Rail Safety, Chengdu 611756, China
| | - Zhengjun Gong
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu 611756, China; State-province Joint Engineering Laboratory of Spatial Information Technology of High-Speed Rail Safety, Chengdu 611756, China.
| |
Collapse
|
4
|
Kumagai T, Kinoshita B, Hirashima S, Sugiyama H, Park S. Thiophene-Extended Fluorescent Nucleosides as Molecular Rotor-Type Fluorogenic Sensors for Biomolecular Interactions. ACS Sens 2023; 8:923-932. [PMID: 36740828 DOI: 10.1021/acssensors.2c02617] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluorescent molecular rotors are versatile tools for the investigation of biomolecular interactions and the monitoring of microenvironmental changes in biological systems. They can transform invisible information into a fluorescence signal as a straightforward response. Their utility is synergistically amplified when they are merged with biomolecules. Despite the tremendous significance and superior programmability of nucleic acids, there are very few reports on the development of molecular rotor-type isomorphic nucleosides. Here, we report the synthesis and characterization of a highly emissive molecular rotor-containing thymine nucleoside (ThexT) and its 2'-O-methyluridine analogue (2'-OMe-ThexU) as fluorogenic microenvironment-sensitive sensors that emit vivid fluorescence via an interaction with the target proteins. ThexT and 2'-OMe-ThexU may potentially serve as robust probes for a broad range of applications, such as fluorescence mapping, to monitor viscosity changes and specific protein-binding interactions in biological systems.
Collapse
Affiliation(s)
- Tomotaka Kumagai
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ban Kinoshita
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shingo Hirashima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Soyoung Park
- Immunology Frontier Research Center, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
5
|
Mini-review on a polymers film detector for chloroform vapour: julolidine as fluorescent molecular rotors (JCFMRs). CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02567-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
6
|
Kalel RA, Gaikwad DS. Cooperative catalysis: Condensation-aromatization for synthesis of 2-(4-nitrophenyl)-1H-benzimidazole by silica immobilized Brønsted-Lewis acidic ionic liquid (Si-BLAIL). J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
7
|
Nandy A, Shekhar S, Paul BK, Mukherjee S. Exploring the Nucleobase-Specific Hydrophobic Interaction of Cryptolepine Hydrate with RNA and Its Subsequent Sequestration. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11176-11187. [PMID: 34499515 DOI: 10.1021/acs.langmuir.1c02123] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The study of the interactions of drug molecules with genetic materials plays a key role underlying the development of new drugs for many life-threatening diseases in pharmaceutical industries. Understanding their fundamental base-specific and/or groove-binding interaction is crucial to target the genetic material with an external drug, which can pave the way to curing diseases related to the genetic material. Here, we studied the interaction of cryptolepine hydrate (CRYP) with RNA under physiological conditions knowing the antimalarial and anticancer activities of the drug. Our experiments explicitly demonstrate that CRYP interacts with the guanine- and adenine-rich region within the RNA duplex. The pivotal role of the hydrophobic interaction governing the interaction is substantiated by temperature-dependent isothermal titration calorimetry experiments and spectroscopic studies. Circular dichroism study underpins a principally intercalative mode of binding of CRYP with RNA. This interaction is found to be drastically affected in the presence of magnesium salt, which has a strong propensity to coordinate with RNA nucleobases, which can in turn modulate the interaction of the drug with RNA. The temperature-dependent calorimetric results substantiate the occurrence of entropy-enthalpy compensation, which enabled us to rule out the possibility of groove binding of the drug with RNA. Furthermore, our results also show the application of host-guest chemistry in sequestering the RNA-bound drug, which is crucial to the development of safer therapeutic applications.
Collapse
Affiliation(s)
- Atanu Nandy
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Shashi Shekhar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Bijan K Paul
- Department of Chemistry, Mahadevananda Mahavidyalaya, Barrackpore, Kolkata 700120, India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| |
Collapse
|
8
|
Zhang J, He Y, Zhang K, Liang X, Bance‐Soualhi R, Zhu Y, Ge X, Shehzad MA, Yu W, Ge Z, Wu L, Varcoe JR, Xu T. Cation–dipole interaction that creates ordered ion channels in an anion exchange membrane for fast
OH
−
conduction. AIChE J 2021. [DOI: 10.1002/aic.17133] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Jianjun Zhang
- CAS Key Laboratory of Soft Matter Chemistry Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science, University of Science and Technology of China Hefei China
| | - Yubin He
- CAS Key Laboratory of Soft Matter Chemistry Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science, University of Science and Technology of China Hefei China
| | - Kaiyu Zhang
- CAS Key Laboratory of Soft Matter Chemistry Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science, University of Science and Technology of China Hefei China
| | - Xian Liang
- CAS Key Laboratory of Soft Matter Chemistry Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science, University of Science and Technology of China Hefei China
| | | | - Yuan Zhu
- CAS Key Laboratory of Soft Matter Chemistry Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science, University of Science and Technology of China Hefei China
| | - Xiaolin Ge
- CAS Key Laboratory of Soft Matter Chemistry Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science, University of Science and Technology of China Hefei China
| | - Muhammad A. Shehzad
- CAS Key Laboratory of Soft Matter Chemistry Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science, University of Science and Technology of China Hefei China
| | - Weisheng Yu
- CAS Key Laboratory of Soft Matter Chemistry Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science, University of Science and Technology of China Hefei China
| | - Zijuan Ge
- CAS Key Laboratory of Soft Matter Chemistry Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science, University of Science and Technology of China Hefei China
| | - Liang Wu
- CAS Key Laboratory of Soft Matter Chemistry Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science, University of Science and Technology of China Hefei China
| | | | - Tongwen Xu
- CAS Key Laboratory of Soft Matter Chemistry Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science, University of Science and Technology of China Hefei China
| |
Collapse
|
9
|
Wang X, Xing Y, Su J, Wang C, Wang Z, Yu Y, Xu H, Ma D. Synthesis of two new naphthalene-containing compounds and their bindings to human serum albumin. J Biomol Struct Dyn 2020; 39:3435-3448. [DOI: 10.1080/07391102.2020.1764867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Xia Wang
- School of Chemistry and Materials Science, Heilongjiang University, Harbin, China
| | - Yue Xing
- School of Agricultural Resources and Environment, Heilongjiang University, Harbin, China
| | - Jing Su
- School of Agricultural Resources and Environment, Heilongjiang University, Harbin, China
| | - Changsheng Wang
- School of Chemistry and Materials Science, Heilongjiang University, Harbin, China
| | - Zishi Wang
- School of Agricultural Resources and Environment, Heilongjiang University, Harbin, China
| | - Yinghui Yu
- School of Chemistry and Materials Science, Heilongjiang University, Harbin, China
| | - Hongliang Xu
- School of Agricultural Resources and Environment, Heilongjiang University, Harbin, China
| | - DongSheng Ma
- School of Chemistry and Materials Science, Heilongjiang University, Harbin, China
| |
Collapse
|
10
|
Exploring the interaction of copper-esculetin complex with ct-DNA: Insight from spectroscopic and docking studies. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127901] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
11
|
Kumar B, Ghosh R, Mora AK, Nath S. Anthryl Benzothiazolium Molecular Rotor-Based Turn-On DNA Probe: Detailed Mechanistic Studies. J Phys Chem B 2019; 123:7518-7527. [DOI: 10.1021/acs.jpcb.9b05570] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Bhupesh Kumar
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Rajib Ghosh
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400085, India
| | - Aruna K. Mora
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400085, India
| | - Sukhendu Nath
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400085, India
| |
Collapse
|
12
|
Varejão JOS, Varejão EVV, Fernandes SA. Synthesis and Derivatization of Julolidine: A Powerful Heterocyclic Structure. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900398] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Jodieh Oliveira Santana Varejão
- Grupo de Química Supramolecular e Biomimética (GQSB); Departamento de Química; Universidade Federal de Viçosa; 36570-900 Brazil
| | - Eduardo Vinícius Vieira Varejão
- Grupo de Química Supramolecular e Biomimética (GQSB); Departamento de Química; Universidade Federal de Viçosa; 36570-900 Brazil
| | - Sergio Antonio Fernandes
- Grupo de Química Supramolecular e Biomimética (GQSB); Departamento de Química; Universidade Federal de Viçosa; 36570-900 Brazil
| |
Collapse
|
13
|
Mora AK, Basu A, Kalel R, Nath S. Polymer-assisted drug sequestration from plasma protein by a surfactant with curtailed denaturing capacity. Phys Chem Chem Phys 2019; 21:7127-7136. [PMID: 30887975 DOI: 10.1039/c8cp03576h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The capability of a surfactant to sequester a drug bound to plasma protein was investigated using steady-state and time-resolved spectroscopic techniques. Surfactants are known to denature protein, and hence are not suitable for the sequestration of a drug from protein. Herein, we show that the denaturing capacity of a surfactant is curtailed completely and its drug sequestration power is enhanced in the presence of biocompatible Pluronic micelles due to the formation of unique supramolecular assemblies. Further, our detailed studies indicate that the concentration of surfactant required for the sequestration of a drug is less than its critical micellar concentration (CMC). The extent of sequestration of drug by polymer-surfactant supramolecular assemblies can be tuned finely by controlling the concentration of surfactant. Detailed analysis showed that up to ∼85% sequestration of a drug from plasma protein could be achieved using a sub-CMC concentration of surfactant. Our results clearly show that controlled sequestration of a drug from plasma protein can be achieved with a reduction in the protein denaturing properties of surfactants.
Collapse
Affiliation(s)
- Aruna K Mora
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India.
| | | | | | | |
Collapse
|
14
|
Kuang G, Murugan NA, Ågren H. Mechanistic Insight into the Binding Profile of DCVJ and α-Synuclein Fibril Revealed by Multiscale Simulations. ACS Chem Neurosci 2019; 10:610-617. [PMID: 30277753 DOI: 10.1021/acschemneuro.8b00465] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Parkinson's disease (PD) is a serious neurodegenerative disease and is characterized by abnormal α-synuclein (α-syn) accumulation in Lewy bodies (LB) and Lewy neurites (LN), which makes α-syn an important imaging target for PD. An imaging probe that quantifies fibrillar α-syn can enhance the clinical diagnosis of PD and can also be used to evaluate the efficacy of therapeutics aimed at reducing the abnormal aggregation of the α-syn fibril in the brain. In this paper, we study the binding profile of fibrillar α-syn with a fluorescent probe 4-(dicyanovinyl)julolidine (DCVJ), which is being explored for identifying α-syn imaging agents. A multiscale simulation workflow including molecular docking, molecular dynamics, metadynamics, and QM/MM calculations was implemented. We find that DCVJ can bind to multiple sites of α-syn which are located either at the surface or in the core. Free energy calculations using implicit solvent models reveal that the most favorable binding mode for DCVJ is associated with the core binding site and is further confirmed by metadyamics simulation. Besides, a dynamic binding pathway is discovered, which reveals that DCVJ binds gradually into the core of the fibril passing through several intermediate states. The conformational arrest of the dicyano vinyl group in the fibrillar environment could explain the reason behind the fibril-specific fluorescence of DCVJ. Furthermore, based on hybrid QM/MM calculations, the molecular geometry of the dicyano vinyl group is found to be environment specific which explains why DCVJ serves as a staining agent for such fibrillar-like environments. Our results could be helpful for elucidating the binding mechanism of imaging tracers with the fibrillar form of α-syn and explain their fibrillar-specific optical properties, a knowledge that in turn can be used to guide the design and development of compounds with higher affinity and selectivity for α-syn using structure-based strategies.
Collapse
Affiliation(s)
- Guanglin Kuang
- Department of Theoretical Chemistry and Biology, Royal Institute of Technology (KTH), AlbaNova University Center, S-106 91 Stockholm, Sweden
| | - N. Arul Murugan
- Department of Theoretical Chemistry and Biology, Royal Institute of Technology (KTH), AlbaNova University Center, S-106 91 Stockholm, Sweden
| | - Hans Ågren
- Department of Theoretical Chemistry and Biology, Royal Institute of Technology (KTH), AlbaNova University Center, S-106 91 Stockholm, Sweden
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan, 475004P. R. China
| |
Collapse
|
15
|
Xia Z, Guo X, Zhu Y, Wang Y, Wang J. A julolidine-fused anthracene derivative: synthesis, photophysical properties, and oxidative dimerization. RSC Adv 2018; 8:13588-13591. [PMID: 35542525 PMCID: PMC9079783 DOI: 10.1039/c8ra02205d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 04/03/2018] [Indexed: 11/21/2022] Open
Abstract
We describe the synthesis and characterization of a julolidine-fused anthracene derivative J-A, which exhibits a maximum absorption of 450 nm and a maximum emission of 518 nm. The fluorescent quantum yield was determined to be 0.55 in toluene. J-A dimerizes in solution via oxidative coupling. Structure of the dimer was characterized using single crystal X-ray diffraction. A julolidine fused anthracene derivative with unique photophysical and redox properties was presented.![]()
Collapse
Affiliation(s)
- Zeming Xia
- School of Chemistry
- Sun Yat-Sen University
- Guangzhou 510275
- People's Republic of China
| | - Xiaoyu Guo
- School of Chemistry
- Sun Yat-Sen University
- Guangzhou 510275
- People's Republic of China
| | - Yanpeng Zhu
- School of Chemistry
- Sun Yat-Sen University
- Guangzhou 510275
- People's Republic of China
| | - Yonggen Wang
- School of Chemistry
- Sun Yat-Sen University
- Guangzhou 510275
- People's Republic of China
| | - Jiaobing Wang
- School of Chemistry
- Sun Yat-Sen University
- Guangzhou 510275
- People's Republic of China
| |
Collapse
|
16
|
Kalel R, Mora AK, Patro BS, Palit DK, Nath S. Synergistic enhancement in the drug sequestration power and reduction in the cytotoxicity of surfactants. Phys Chem Chem Phys 2017; 19:25446-25455. [DOI: 10.1039/c7cp05042a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Surfactants in supramolecular assemblies show a significant increase in their drug sequestration power with a remarkably reduced cytotoxicity.
Collapse
Affiliation(s)
- Rahul Kalel
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai-400085
- India
| | - Aruna K. Mora
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai-400085
- India
- Homi Bhabha National Institute
| | - Birija S. Patro
- Homi Bhabha National Institute
- Training School Complex
- Anushaktinagar
- Mumbai 400094
- India
| | - Dipak K. Palit
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai-400085
- India
- Homi Bhabha National Institute
| | - Sukhendu Nath
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai-400085
- India
- Homi Bhabha National Institute
| |
Collapse
|