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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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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:molecules28041829. [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] [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
- Correspondence: (G.L.); (Z.W.)
| | - Zhiguo Wang
- Institute of Ageing Research, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China
- Correspondence: (G.L.); (Z.W.)
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Nieuwland C, Zaccaria F, Fonseca Guerra C. Understanding alkali metal cation affinities of multi-layer guanine quadruplex DNA. Phys Chem Chem Phys 2021; 22:21108-21118. [PMID: 32954397 PMCID: PMC8612728 DOI: 10.1039/d0cp03433a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
To gain better understanding of the stabilizing interactions between metal ions and DNA quadruplexes, dispersion-corrected density functional theory (DFT-D) based calculations were performed on double-, triple- and four-layer guanine tetrads interacting with alkali metal cations. All computations were performed in aqueous solution that mimics artificial supramolecular conditions where guanine bases assemble into stacked quartets as well as biological environments in which telomeric quadruplexes are formed. To facilitate the computations on these significant larger systems, optimization of the DFT description was performed first by evaluating the performance of partial reduced basis sets. Analysis of the stabilizing interactions between alkali cations and the DNA bases in double and triple-layer guanine quadruplex DNA reproduced the experimental affinity trend of the order Li+< Rb+ < Na+ < K+. The desolvation and the size of alkali metal cations are thought to be responsible for the order of affinity. Nevertheless, for the alkali metal cation species individually, the magnitude of the bond energy stays equal for binding as first, second or third cation in double, triple and four-layer guanine quadruplexes, respectively. This is the result of an interplay between a decreasingly stabilizing interaction energy and increasingly stabilizing solvation effects, along the consecutive binding events. This diminished interaction energy is the result of destabilizing electrostatic repulsion between the hosted alkali metal cations. This work emphasizes the stabilizing effect of aqueous solvent on large highly charged biomolecules. Stabilizing solvent effects and electrostatic repulsion are responsible for the constant alkali metal cation affinity in multi-layer guanine quadruplexes.![]()
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Affiliation(s)
- C Nieuwland
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1085 NL-1081HV Amsterdam, The Netherlands.
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Villani G. Quantum Mechanical Investigation of the G-Quadruplex Systems of Human Telomere. ACS OMEGA 2018; 3:9934-9944. [PMID: 31459122 PMCID: PMC6644616 DOI: 10.1021/acsomega.8b01678] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 08/09/2018] [Indexed: 05/17/2023]
Abstract
The three G-quadruplexes involved in the human telomere have been studied with an accurate quantum mechanical approach, and the possibility of reducing them to a simpler model has been tested. The similarities and the differences of these three systems are shown and discussed. Each system has been analyzed through different properties and compared to the others. In particular, we have considered: (1) the shape of the cavity and the atomic charges around it; (2) the electric field in and out of the cavity; (3) the stabilization energy due to the stacking of G-tetrads, to the H-bonds and to the ion interactions; and, finally, (4) to study the mechanism of the process of the ion inclusion in the cavity, the curves of potential energy due to the movement of the Na+ and K+ ions toward the cavity. The results suggest that a detailed study is essential in order to obtain the quantitative properties of these complex systems, but also that some qualitative behaviors can be schematized. Our study makes it clear that the entry of an ion in the cavity of these systems is a complex process, where it is possible to find stable structures with the ion out and in the cavity. Moreover, it is possible that more than one diabatic state is involved in this process.
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Affiliation(s)
- Giovanni Villani
- Istituto di Chimica dei Composti OrganoMetallici, ICCOM—CNR
(UOS Pisa), Area della Ricerca di Pisa, Via G. Moruzzi, 1, I-56124 Pisa, Italy
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Effects of the central potassium ions on the G-quadruplex and stabilizer binding. J Mol Graph Model 2017; 72:168-177. [PMID: 28092835 DOI: 10.1016/j.jmgm.2017.01.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 12/20/2016] [Accepted: 01/04/2017] [Indexed: 12/30/2022]
Abstract
Human telomeres undertake the structure of intra-molecular parallel G-quadruplex in the presence of K+ in eukaryotic cell. Stabilization of the telomere G-quadruplex represents a potential strategy to prevent telomere lengthening by telomerase in cancer therapy. Current work demonstrates that the binding of central K+ with the parallel G-quadruplex is a coordinated water directed step-wise process. The K+ above the top G-tetrad is prone to leak into environment and the 5'-adenine quickly flips over the top G-tetrad, leading to the bottom gate of G-tetrads as the only viable pathway of K+ binding. Present molecular dynamics studies on the two most potent stabilizers RHPS4 and BRACO-19 reveal that the central K+ has little influence on the binding conformations of the bound stabilizers. But without the central K+, either RHPS4 or BRACO-19 cannot stabilize the structure of G-quadruplex. The binding strength of stabilizers evaluated by the MM-PBSA method follows the order of BRACO-19> RHPS4, which agrees with the experimental results. The difference in binding affinities between RHPS4 and BRACO-19 is probably related to the ability to form intramolecular hydrogen bonds and favorable van del Waals interactions with G-quadruplex. In the models that have one central K+ located at the upper/lower binding site, the corresponding top/bottom stacked stabilizers show more favorable binding affinities, indicating the apparent promoting effect of central K+ on the stabilizer binding. Our findings provide further insights into the regulatory effect of K+ on the G-quadruplex targeted binding, which is meaningful to the development of G-quadruplex stabilizers.
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He M, Zhou S, Cui M, Jin X, Lai D, Zhang S, Wang Z, Chen Z. Efficient Preparation of (S)-N-Boc-3-Hydroxylpiperidine Through Bioreduction by a Thermostable Aldo-KetoReductase. Appl Biochem Biotechnol 2016; 181:1304-1313. [DOI: 10.1007/s12010-016-2285-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
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Zaccaria F, Paragi G, Fonseca Guerra C. The role of alkali metal cations in the stabilization of guanine quadruplexes: why K+ is the best. Phys Chem Chem Phys 2016; 18:20895-904. [DOI: 10.1039/c6cp01030j] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The desolvation and size of monovalent alkali metal ions are of equal importance for the cation affinity of guanine quadruplexes.
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Affiliation(s)
- F. Zaccaria
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling
- Vrije Universiteit Amsterdam
- 1081 HV Amsterdam
- The Netherlands
| | - G. Paragi
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling
- Vrije Universiteit Amsterdam
- 1081 HV Amsterdam
- The Netherlands
- MTA-SZTE Supramolecular and Nanostructured Materials Research Group
| | - C. Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling
- Vrije Universiteit Amsterdam
- 1081 HV Amsterdam
- The Netherlands
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