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Meng T, Wang Z, Zhang H, Zhao Z, Huang W, Xu L, Liu M, Li J, Yan H. In Silico Investigations on the Synergistic Binding Mechanism of Functional Compounds with Beta-Lactoglobulin. Molecules 2024; 29:956. [PMID: 38474468 DOI: 10.3390/molecules29050956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/03/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Piceatannol (PIC) and epigallocatechin gallate (EGCG) are polyphenolic compounds with applications in the treatment of various diseases such as cancer, but their stability is poor. β-lactoglobulin (β-LG) is a natural carrier that provides a protective effect to small molecule compounds and thus improves their stability. To elucidate the mechanism of action of EGCG, PIC, and palmitate (PLM) in binding to β-LG individually and jointly, this study applied molecular docking and molecular dynamics simulations combined with in-depth analyses including noncovalent interaction (NCI) and binding free energy to investigate the binding characteristics between β-LG and compounds of PIC, EGCG, and PLM. Simulations on the binary complexes of β-LG + PIC, β-LG + EGCG, and β-LG + PLM and ternary complexes of (β-LG + PLM) + PIC, (β-LG + PLM) + EGCG, β-LG + PIC) + EGCG, and (β-LG + EGCG) + PIC were performed for comparison and characterizing the interactions between binding compounds. The results demonstrated that the co-bound PIC and EGCG showed non-beneficial effects on each other. However, the centrally located PLM was revealed to be able to adjust the binding conformation of PIC, which led to the increase in binding affinity with β-LG, thus showing a synergistic effect on the co-bound PIC. The current study of β-LG co-encapsulated PLM and PIC provides a theoretical basis and research suggestions for improving the stability of polyphenols.
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Affiliation(s)
- Tong Meng
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng 252059, China
| | - Zhiguo Wang
- Institute of Ageing Research, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Hao Zhang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng 252059, China
| | - Zhen Zhao
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng 252059, China
| | - Wanlin Huang
- School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Liucheng Xu
- School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Min Liu
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng 252059, China
| | - Jun Li
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng 252059, China
| | - Hui Yan
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng 252059, China
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2
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Cao S, Su Q, Chen YH, Wang ML, Xu Y, Wang LH, Lu YH, Li JF, Liu J, Hong XJ, Wang HY, Liu JP, Wang ZG. Molecular Insights into the Specific Targeting of c-MYC G-Quadruplex by Thiazole Peptides. Int J Mol Sci 2024; 25:623. [PMID: 38203794 PMCID: PMC10778990 DOI: 10.3390/ijms25010623] [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: 12/11/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
Stabilization of a G-quadruplex (G4) in the promotor of the c-MYC proto-oncogene leads to inhibition of gene expression, and it thus represents a potentially attractive new strategy for cancer treatment. However, most G4 stabilizers show little selectivity among the many G4s present in the cellular complement of DNA and RNA. Intriguingly, a crescent-shaped cell-penetrating thiazole peptide, TH3, preferentially stabilizes the c-MYC G4 over other promotor G4s, but the mechanisms leading to this selective binding remain obscure. To investigate these mechanisms at the atomic level, we performed an in silico comparative investigation of the binding of TH3 and its analogue TH1 to the G4s from the promotors of c-MYC, c-KIT1, c-KIT2, and BCL2. Molecular docking and molecular dynamics simulations, combined with in-depth analyses of non-covalent interactions and bulk and per-nucleotide binding free energies, revealed that both TH3 and TH1 can induce the formation of a sandwich-like framework through stacking with both the top and bottom G-tetrads of the c-MYC G4 and the adjacent terminal capping nucleotides. This framework produces enhanced binding affinities for c-MYC G4 relative to other promotor G4s, with TH3 exhibiting an outstanding binding priority. Van der Waals interactions were identified to be the key factor in complex formation in all cases. Collectively, our findings fully agree with available experimental data. Therefore, the identified mechanisms leading to specific binding of TH3 towards c-MYC G4 provide valuable information to guide the development of new selective G4 stabilizers.
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Affiliation(s)
- Sen Cao
- Institute of Ageing Research, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China; (S.C.); (Q.S.); (L.-H.W.); (Y.-H.L.); (J.-F.L.); (J.L.); (X.-J.H.); (H.-Y.W.)
| | - Qian Su
- Institute of Ageing Research, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China; (S.C.); (Q.S.); (L.-H.W.); (Y.-H.L.); (J.-F.L.); (J.L.); (X.-J.H.); (H.-Y.W.)
| | - Yong-Hao Chen
- School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China; (Y.-H.C.); (M.-L.W.); (Y.X.)
| | - Meng-Lu Wang
- School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China; (Y.-H.C.); (M.-L.W.); (Y.X.)
| | - Yi Xu
- School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China; (Y.-H.C.); (M.-L.W.); (Y.X.)
| | - Li-Hui Wang
- Institute of Ageing Research, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China; (S.C.); (Q.S.); (L.-H.W.); (Y.-H.L.); (J.-F.L.); (J.L.); (X.-J.H.); (H.-Y.W.)
| | - Yan-Hua Lu
- Institute of Ageing Research, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China; (S.C.); (Q.S.); (L.-H.W.); (Y.-H.L.); (J.-F.L.); (J.L.); (X.-J.H.); (H.-Y.W.)
| | - Jian-Feng Li
- Institute of Ageing Research, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China; (S.C.); (Q.S.); (L.-H.W.); (Y.-H.L.); (J.-F.L.); (J.L.); (X.-J.H.); (H.-Y.W.)
| | - Jun Liu
- Institute of Ageing Research, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China; (S.C.); (Q.S.); (L.-H.W.); (Y.-H.L.); (J.-F.L.); (J.L.); (X.-J.H.); (H.-Y.W.)
| | - Xiao-Jing Hong
- Institute of Ageing Research, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China; (S.C.); (Q.S.); (L.-H.W.); (Y.-H.L.); (J.-F.L.); (J.L.); (X.-J.H.); (H.-Y.W.)
| | - Hong-Yan Wang
- Institute of Ageing Research, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China; (S.C.); (Q.S.); (L.-H.W.); (Y.-H.L.); (J.-F.L.); (J.L.); (X.-J.H.); (H.-Y.W.)
| | - Jun-Ping Liu
- Institute of Ageing Research, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China; (S.C.); (Q.S.); (L.-H.W.); (Y.-H.L.); (J.-F.L.); (J.L.); (X.-J.H.); (H.-Y.W.)
| | - Zhi-Guo Wang
- Institute of Ageing Research, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China; (S.C.); (Q.S.); (L.-H.W.); (Y.-H.L.); (J.-F.L.); (J.L.); (X.-J.H.); (H.-Y.W.)
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3
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Yan F, Fu Z, Li G, Wang Z. In Silico Investigation of the Molecular Mechanism of PARP1 Inhibition for the Treatment of BRCA-Deficient Cancers. Molecules 2023; 28:1829. [PMID: 36838818 PMCID: PMC9961911 DOI: 10.3390/molecules28041829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/05/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
The protein PARP1, which plays a crucial role in DNA repair processes, is an attractive target for cancer therapy, especially for BRCA-deficient cancers. To overcome the acquired drug resistance of PARP1, PARP1 G-quadruplex (G4) identified in the PARP1-promotor region is gaining increasing attention. Aiming to explore the molecular mechanism of PARP1 inhibition with PARP1 G4 and PARP1 as potential targets, a comparative investigation of the binding characteristics of the newly identified G4 stabilizer MTR-106, which showed modest activity against talazoparib-resistant xenograft models and the FDA-approved PARP1 inhibitor (PARPi) talazoparib, were performed through molecular simulations. Combined analyses revealed that, relative to the groove binding of talazoparib, MTR-106 induced the formation of a sandwich framework through stacking with dT1 and the capping G-pair (dG2 and dG14) of PARP1 G4 to present largely enhanced binding affinity. For the binding with PARP1, although both were located in the catalytic pocket of PARP1, MTR-106 formed more extensive interactions with the surrounding PARP1 residues compared to talazoparib, in line with its increased binding strength. Importantly, vdW interaction was recognized as a decisive factor in the bindings with PARP1 G4 and PARP1. Collectively, these findings demonstrated the ascendancy of MTR-106 over talazoparib at the atomic level and revealed that the dual targeting of PARP1 G4 and PARP1 might be pivotal for PARPi that is capable of overcoming acquired drug resistance, providing valuable information for the design and development of novel drugs.
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Affiliation(s)
- Fengqin Yan
- Department of Radiotherapy, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Zhenfu Fu
- Department of Radiotherapy, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Guo Li
- Department of Biochemistry and Molecular Biology, Hainan Medical University, Haikou 571199, China
- Hainan Province Clinical Medical Center, Hainan Hospital Affiliated to Hainan Medical University, Haikou 571199, China
| | - Zhiguo Wang
- Institute of Ageing Research, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China
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4
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Li ML, Yuan JM, Yuan H, Wu BH, Huang SL, Li QJ, Ou TM, Wang HG, Tan JH, Li D, Chen SB, Huang ZS. Design, Synthesis, and Evaluation of New Sugar-Substituted Imidazole Derivatives as Selective c-MYC Transcription Repressors Targeting the Promoter G-Quadruplex. J Med Chem 2022; 65:12675-12700. [PMID: 36121464 DOI: 10.1021/acs.jmedchem.2c00467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
c-MYC is a key driver of tumorigenesis. Repressing the transcription of c-MYC by stabilizing the G-quadruplex (G4) structure with small molecules is a potential strategy for cancer therapy. Herein, we designed and synthesized 49 new derivatives by introducing carbohydrates to our previously developed c-MYC G4 ligand 1. Among these compounds, 19a coupled with a d-glucose 1,2-orthoester displayed better c-MYC G4 binding, stabilization, and protein binding disruption abilities than 1. Our further evaluation indicated that 19a blocked c-MYC transcription by targeting the promoter G4, leading to c-MYC-dependent cancer cell death in triple-negative breast cancer cell MDA-MB-231. Also, 19a significantly inhibited tumor growth in the MDA-MB-231 mouse xenograft model accompanied by c-MYC downregulation. Notably, the safety of 19a was dramatically improved compared to 1. Our findings indicated that 19a could become a promising anticancer candidate, which suggested that introducing carbohydrates to improve the G4-targeting and antitumor activity is a feasible option.
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Affiliation(s)
- Mao-Lin Li
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Jing-Mei Yuan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Hao Yuan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Bi-Han Wu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Shi-Liang Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Qing-Jiang Li
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Hong-Gen Wang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Ding Li
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
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5
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Wang Y, Li G, Meng T, Qi L, Yan H, Wang Z. Molecular insights into the selective binding mechanism targeting parallel human telomeric G-quadruplex. J Mol Graph Model 2021; 110:108058. [PMID: 34736054 DOI: 10.1016/j.jmgm.2021.108058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 12/15/2022]
Abstract
Stabilizing human telomere DNA G-quadruplex (G4) proves a promising anti-cancer strategy. Though plenty of G4 stabilizing molecules have been reported, little is known about their selective binding mechanism among various G4s. Recently, a designed monohydrazone derivative (compound 15) was reported to display specific preference in binding and stabilizing parallel human telomeric G4. To reveal the selective binding mechanism, a comparative theoretical investigation was performed on two monohydrazone derivatives (compounds 1 and 15) and three telomeric G4s showing parallel, hybrid-I, and hybrid-II conformations. Two probable binding modes, i.e. the end-stacking binding and the groove binding, were predicted by molecular dockings for each monohydrazone in its binding with the telomeric G4s. Further long-timescale molecular dynamics simulations reveal the conversion from the groove binding to the end-stacking binding for both compounds, indicating the preference of the end-stacking binding mode. Structural analysis together with binding free energy calculations show that the van der Waals interaction plays a leading role in ranking the binding affinity. By forming extensive van der Waals interactions, the parallel G4-15 binding complex shows the highest binding affinity, and the corresponding compound 15 exhibits the strongest stabilizing effect to the telomeric G4. These findings agree well with the experimental observations. Through characterizing the selective binding between monohydrazones and telomeric G4s at the atomic level, the current study provides support to the design of novel selective stabilizers targeting telomeric G4s.
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Affiliation(s)
- Yue Wang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong Province, 252059, China
| | - Guo Li
- Department of Biochemistry and Molecular Biology, Hainan Medical College, Haikou, Hainan Province, 571199, China
| | - Tong Meng
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong Province, 252059, China
| | - Lin Qi
- Railway Police College, Zhengzhou, Henan Province, 450053, China
| | - Hui Yan
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong Province, 252059, China.
| | - Zhiguo Wang
- Institute of Ageing Research, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, China.
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Platella C, Napolitano E, Riccardi C, Musumeci D, Montesarchio D. Disentangling the Structure-Activity Relationships of Naphthalene Diimides as Anticancer G-Quadruplex-Targeting Drugs. J Med Chem 2021; 64:3578-3603. [PMID: 33751881 PMCID: PMC8041303 DOI: 10.1021/acs.jmedchem.1c00125] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
In the context of
developing efficient anticancer therapies aimed
at eradicating any sort of tumors, G-quadruplexes represent excellent
targets. Small molecules able to interact with G-quadruplexes can
interfere with cell pathways specific of tumors and common to all
cancers. Naphthalene diimides
(NDIs) are among the most promising, putative anticancer G-quadruplex-targeting
drugs, due to their ability to simultaneously target multiple G-quadruplexes
and their strong, selective in vitro and in vivo anticancer activity.
Here, all the available biophysical, biological, and structural data
concerning NDIs targeting G-quadruplexes were systematically analyzed.
Structure–activity correlations were obtained by analyzing
biophysical data of their interactions with G-quadruplex targets and
control duplex structures, in parallel to biological data concerning
the antiproliferative activity of NDIs on cancer and normal cells.
In addition, NDI binding modes to G-quadruplexes were discussed in
consideration of the structures and properties of NDIs by in-depth
analysis of the available structural models of G-quadruplex/NDI complexes.
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Affiliation(s)
- Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.,Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, I-80134 Naples, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
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7
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Wang Z, Li G, Tian Z, Lou X, Huang Y, Wang L, Li J, Hou T, Liu JP. Insight Derived from Molecular Dynamics Simulation into the Selectivity Mechanism Targeting c-MYC G-Quadruplex. J Phys Chem B 2020; 124:9773-9784. [DOI: 10.1021/acs.jpcb.0c05029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Zhiguo Wang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou 311121, Zhejiang, China
| | - Guo Li
- Department of Biochemistry and Molecular Biology, Hainan Medical College, Haikou 571199, Hainan, China
| | - Zhou Tian
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou 311121, Zhejiang, China
| | - Xiaoqin Lou
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou 311121, Zhejiang, China
| | - Yining Huang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou 311121, Zhejiang, China
| | - Lihui Wang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou 311121, Zhejiang, China
| | - Jianfeng Li
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou 311121, Zhejiang, China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Jun-Ping Liu
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou 311121, Zhejiang, China
- Department of Immunology, Monash University Faculty of Medicine, Melbourne, Victoria 3004, Australia
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
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8
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Sullivan HJ, Chen B, Wu C. Molecular Dynamics Study on the Binding of an Anticancer DNA G-Quadruplex Stabilizer, CX-5461, to Human Telomeric, c-KIT1, and c-Myc G-Quadruplexes and a DNA Duplex. J Chem Inf Model 2020; 60:5203-5224. [PMID: 32820923 DOI: 10.1021/acs.jcim.0c00632] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
DNA G-quadruplex (G4) stabilizer, CX-5461, is in phase I/II clinical trials for advanced cancers with BRCA1/2 deficiencies. A FRET-melting temperature increase assay measured the stabilizing effects of CX-5461 to a DNA duplex (∼10 K), and three G4 forming sequences negatively implicated in the cancers upon its binding: human telomeric (∼30 K), c-KIT1 (∼27 K), and c-Myc (∼25 K). Without experimentally solved structures of these CX-5461-G4 complexes, CX-5461's interactions remain elusive. In this study, we performed a total of 73.5 μs free ligand molecular dynamics binding simulations of CX-5461 to the DNA duplex and three G4s. Three binding modes (top, bottom, and side) were identified for each system and their thermodynamic, kinetic, and structural nature were deciphered. The molecular mechanics/Poisson Boltzmann surface area binding energies of CX-5461 were calculated for the human telomeric (-28.6 kcal/mol), c-KIT1 (-23.9 kcal/mol), c-Myc (-22.0 kcal/mol) G4s, and DNA duplex (-15.0 kcal/mol) systems. These energetic differences coupled with structural differences at the 3' site explained the different melting temperatures between the G4s, while CX-5461's lack of intercalation to the duplex explained the difference between the G4s and duplex. Based on the interaction insight, CX-5461 derivatives were designed and docked, showing higher selectivity to the G4s over the duplex.
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Affiliation(s)
- Holli-Joi Sullivan
- College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028 USA
| | - Brian Chen
- College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028 USA
| | - Chun Wu
- College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028 USA
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9
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Mulholland K, Sullivan HJ, Garner J, Cai J, Chen B, Wu C. Three-Dimensional Structure of RNA Monomeric G-Quadruplex Containing ALS and FTD Related G4C2 Repeat and Its Binding with TMPyP4 Probed by Homology Modeling based on Experimental Constraints and Molecular Dynamics Simulations. ACS Chem Neurosci 2020; 11:57-75. [PMID: 31800202 DOI: 10.1021/acschemneuro.9b00572] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The G-quadruplex-forming hexanucleotide repeat expansion (HRE), d(G4C2)n, within the human C9orf72 gene is the root cause for familial amyotrophic lateral sclerosis-frontotemporal dementia (ALS-FTD). A recent study has shown that TMPyP4 has good potential to work as a RNA G-quadruplex binder in treating ALS and FTD. Although the high-resolution structure of the monomeric DNA antiparallel G-quadruplex form of the monomeric hexanucleotide repeat was recently solved, the RNA parallel G-quadruplex structure and its complex with TMPyP4 are not available yet. In this study, we first constructed the homology model for the parallel monomeric RNA G-quadruplex of r(G4C2)3G4 based on experimental constraints and the parallel monomeric G-quadruplex DNA crystal structure. Although the G-tetra core of the homology model was stable observed in 15 μs molecular dynamics (MD) simulations, we observed that the loops adopt additional conformations besides the initial crystal conformation, where TMPyP4 binding was found to reduce the loop fluctuation of the RNA monomeric G-quadruplex. Next, we probed the elusive binding behavior of TMPyP4 to the RNA monomeric G-quadruplex. Encouragingly, the binding modes observed are similar to the modes observed in two experimental complexes of a parallel DNA G-quadruplex with TMPyP4. We also constructed a Markov state model to provide insights into the binding pathways. Together, the findings from our study may assist future development of G-quadruplex-specific ligands in the treatment of neurodegenerative diseases like ALS and FTD.
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Affiliation(s)
- Kelly Mulholland
- College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Holli-Joi Sullivan
- College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Joseph Garner
- College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Jun Cai
- College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Brian Chen
- College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Chun Wu
- College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
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Zhao LL, Cao T, Zhou QY, Zhang XH, Zhou YL, Yang L, Zhang XX. The Exploration of a New Stable G-Triplex DNA and Its Novel Function in Electrochemical Biosensing. Anal Chem 2019; 91:10731-10737. [DOI: 10.1021/acs.analchem.9b02161] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ling-Li Zhao
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ting Cao
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qian-Yu Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiao-Hui Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Lijiang Yang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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11
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Deng N. Using Molecular Dynamics Free Energy Simulation to Compute Binding Affinities of DNA G-Quadruplex Ligands. Methods Mol Biol 2019; 2035:177-199. [PMID: 31444750 DOI: 10.1007/978-1-4939-9666-7_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We provide a practical guide for using molecular dynamics simulation to compute the binding affinity of small molecules in complex with G-quadruplex DNA. Such calculations have a number of applications, such as rescoring docking results and validating docked poses, to inform the discovery of G-quadruplex binders with high affinity and selectivity. This chapter describes two binding free energy protocols: the double decoupling method (DDM) and the potential of mean force method (PMF). We illustrate the application of the two methods using a recent case study of the binding of quindoline with the c-MYC G-quadruplex DNA. For this system, the two methods yield absolute binding free energies within ~2 kcal/mol of the experimental value. We discuss the advantages and disadvantages of these binding free energy methods.
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Affiliation(s)
- Nanjie Deng
- Department of Chemistry and Physical Sciences, Pace University, New York, NY, USA.
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12
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Feng Y, Teng X, Gu J, Yu B, Luo Y, Ye L. Novel anti-cancer agents: design, synthesis, biological activity, molecular docking, and MD simulations of 2, 3, 4, 5-tetrahydro-1H-pyrido-[4,3-b]indole derivatives. Med Chem Res 2018. [DOI: 10.1007/s00044-018-2271-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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13
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Poudel L, Steinmetz NF, French RH, Parsegian VA, Podgornik R, Ching WY. Implication of the solvent effect, metal ions and topology in the electronic structure and hydrogen bonding of human telomeric G-quadruplex DNA. Phys Chem Chem Phys 2018; 18:21573-85. [PMID: 27425864 DOI: 10.1039/c6cp04357g] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We present a first-principles density functional study elucidating the effects of solvent, metal ions and topology on the electronic structure and hydrogen bonding of 12 well-designed three dimensional G-quadruplex (G4-DNA) models in different environments. Our study shows that the parallel strand structures are more stable in dry environments and aqueous solutions containing K(+) ions within the tetrad of guanine but conversely, that the anti-parallel structure is more stable in solutions containing the Na(+) ions within the tetrad of guanine. The presence of metal ions within the tetrad of the guanine channel always enhances the stability of the G4-DNA models. The parallel strand structures have larger HOMO-LUMO gaps than antiparallel structures, which are in the range of 0.98 eV to 3.11 eV. Partial charge calculations show that sugar and alkali ions are positively charged whereas nucleobases, PO4 groups and water molecules are all negatively charged. Partial charges on each functional group with different signs and magnitudes contribute differently to the electrostatic interactions involving G4-DNA and favor the parallel structure. A comparative study between specific pairs of different G4-DNA models shows that the Hoogsteen OH and NH hydrogen bonds in the guanine tetrad are significantly influenced by the presence of metal ions and water molecules, collectively affecting the structure and the stability of G4-DNA.
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Affiliation(s)
- Lokendra Poudel
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA.
| | - Nicole F Steinmetz
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Radiology, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Materials Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Roger H French
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Materials Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - V Adrian Parsegian
- Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Rudolf Podgornik
- Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003, USA and Department of Theoretical Physics, J. Stefan Institute, SI-1000 Ljubljana, Slovenia and Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA.
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14
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Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations. Proc Natl Acad Sci U S A 2017; 114:E2136-E2145. [PMID: 28232513 PMCID: PMC5358390 DOI: 10.1073/pnas.1612627114] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A thorough characterization of the binding interaction between a drug and its molecular target is fundamental to successfully lead drug design. We demonstrate that this characterization is also possible using the recently developed method of funnel-metadynamics (FM), here applied to investigate the binding of berberine to DNA G-quadruplex. We computed a quantitatively well-characterized free-energy landscape that allows identifying two low-energy ligand binding modes and the presence of higher energy prebinding states. We validated the accuracy of our calculations by steady-state fluorescence experiments. The good agreement between the theoretical and experimental binding free-energy value demonstrates that FM is a most reliable method to study ligand/DNA interaction. G-quadruplexes (G4s) are higher-order DNA structures typically present at promoter regions of genes and telomeres. Here, the G4 formation decreases the replicative DNA at each cell cycle, finally leading to apoptosis. The ability to control this mitotic clock, particularly in cancer cells, is fascinating and passes through a rational understanding of the ligand/G4 interaction. We demonstrate that an accurate description of the ligand/G4 binding mechanism is possible using an innovative free-energy method called funnel-metadynamics (FM), which we have recently developed to investigate ligand/protein interaction. Using FM simulations, we have elucidated the binding mechanism of the anticancer alkaloid berberine to the human telomeric G4 (d[AG3(T2AG3)3]), computing also the binding free-energy landscape. Two ligand binding modes have been identified as the lowest energy states. Furthermore, we have found prebinding sites, which are preparatory to reach the final binding mode. In our simulations, the ions and the water molecules have been explicitly represented and the energetic contribution of the solvent during ligand binding evaluated. Our theoretical results provide an accurate estimate of the absolute ligand/DNA binding free energy (ΔGb0 = −10.3 ± 0.5 kcal/mol) that we validated through steady-state fluorescence binding assays. The good agreement between the theoretical and experimental value demonstrates that FM is a most powerful method to investigate ligand/DNA interaction and can be a useful tool for the rational design also of G4 ligands.
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15
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Arba M, Kartasasmita RE, Tjahjono DH. Molecular docking and dynamics simulations on the interaction of cationic porphyrin-anthraquinone hybrids with DNA G-quadruplexes. J Biomol Struct Dyn 2015; 34:427-38. [PMID: 25808513 DOI: 10.1080/07391102.2015.1033015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A series of cationic porphyrin-anthraquinone hybrids bearing either pyridine, imidazole, or pyrazole rings at the meso-positions have been investigated for their interaction with DNA G-quadruplexes by employing molecular docking and molecular dynamics simulations. Three types of DNA G-quadruplexes were utilized, which comprise parallel, antiparallel, and mixed hybrid topologies. The porphyrin hybrids have a preference to bind with parallel and mixed hybrid structures compared to the antiparallel structure. This preference arises from the end stacking of porphyrin moiety following G-stem and loop binding of anthraquinone tail, which is not found in the antiparallel due to the presence of diagonal and lateral loops that crowd the G-quartet. The binding to the antiparallel, instead, occurred with poorer affinity through both the loop and wide groove. All sites of porphyrin binding were confirmed by 6 ns molecular dynamics simulation, as well as by the negative value of the total binding free energies that were calculated using the MMPBSA method. Free energy analysis shows that the favorable contribution came from the electrostatic term, which supposedly originated from the interaction of either cationic pyridinium, pyrazole, or imidazole groups and the anionic phosphate backbone, and also from the van der Waals energy, which primarily contributed through end stacking interaction.
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Affiliation(s)
- Muhammad Arba
- a School of Pharmacy , Bandung Institute of Technology , Jalan Ganesha 10, Bandung 40132 , Indonesia.,b Department of Chemistry , Halu Oleo University , Jl. HEA Mokodompit, Kendari 93232 , Indonesia
| | - Rahmana E Kartasasmita
- a School of Pharmacy , Bandung Institute of Technology , Jalan Ganesha 10, Bandung 40132 , Indonesia
| | - Daryono H Tjahjono
- a School of Pharmacy , Bandung Institute of Technology , Jalan Ganesha 10, Bandung 40132 , Indonesia
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16
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Luo D, Mu Y. All-atomic simulations on human telomeric G-quadruplex DNA binding with thioflavin T. J Phys Chem B 2015; 119:4955-67. [PMID: 25806428 DOI: 10.1021/acs.jpcb.5b01107] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Ligand-stabilized human telomeric G-quadruplex DNA is believed to be an anticancer agent, as it can impede the continuous elongation of telomeres by telomerase in cancer cells. In this study, five well-established human telomeric G-quadruplex DNA models were probed on their binding behaviors with thioflavin T (ThT) via both conventional molecular dynamics (MD) and well-tempered metadynamics (WT-MetaD) simulations. Novel dynamics and characteristic binding patterns were disclosed by the MD simulations. It was observed that the K(+) promoted parallel and hybridized human telomeric G-quadruplex conformations pose higher binding affinities to ThT than the Na(+) and K(+) promoted basket conformations. It is the end, sandwich, and base stacking driven by π-π interactions that are identified as the major binding mechanisms. As the most energy favorable binding mode, the sandwich stacking observed in (3 + 1) hybridized form 1 G-quadruplex conformation is triggered by reversible conformational change of the G-quadruplex. To further examine the free energy landscapes, WT-MetaD simulations were utilized on G-quadruplex-ThT systems. It is found that all of the major binding modes predicted by the MD simulations are confirmed by the WT-MetaD simulations. The results in this work not only accord with existing experimental findings, but also reinforce our understanding on the dynamics of G-quadruplexes and aid future drug developments for G-quadruplex stabilization ligands.
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Affiliation(s)
- Di Luo
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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17
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Verdian Doghaei A, Housaindokht M, Bozorgmehr M. Molecular crowding effects on conformation and stability of G-quadruplex DNA structure: Insights from molecular dynamics simulation. J Theor Biol 2015; 364:103-12. [DOI: 10.1016/j.jtbi.2014.09.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 07/14/2014] [Accepted: 09/10/2014] [Indexed: 11/25/2022]
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18
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Gkionis K, Kruse H, Platts JA, Mládek A, Koča J, Šponer J. Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations. J Chem Theory Comput 2014; 10:1326-40. [DOI: 10.1021/ct4009969] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Konstantinos Gkionis
- CEITEC
- Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Holger Kruse
- CEITEC
- Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - James A. Platts
- School
of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Arnošt Mládek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
| | - Jaroslav Koča
- CEITEC
- Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiří Šponer
- CEITEC
- Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
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