1
|
Riaz MT, Yaqub M, Javed S, Hussain D, Ashiq MN, Shafiq Z. In situ evaluation of the biological active poly functionalized novel amino-1,8-naphthyridine derivatives as DNA-electrochemical biosensor. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2021. [DOI: 10.1080/16583655.2021.1991718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Muhammad Tariq Riaz
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Yaqub
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, Pakistan
| | - Shumaila Javed
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, Pakistan
| | - Dilshad Hussain
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, Pakistan
| | | | - Zahid Shafiq
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, Pakistan
| |
Collapse
|
2
|
Khoshbin Z, Housaindokht MR, Izadyar M, Bozorgmehr MR, Verdian A. Temperature and molecular crowding effects on the sensitivity of T30695 aptamer toward Pb2+ion: a joint molecular dynamics simulation and experimental study. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1751842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Zahra Khoshbin
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Mohammad Izadyar
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Asma Verdian
- Department of Food Safety and Quality Control, Research Institute of Food Science and Technology (RIFST), Mashhad, Iran
| |
Collapse
|
3
|
Yang HB, Wang ZH, Li JM, Wu C. Modular synthesis of α-aryl β-perfluoroalkyl ketones via N-heterocyclic carbene catalysis. Chem Commun (Camb) 2020; 56:3801-3804. [DOI: 10.1039/d0cc00293c] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A new strategy of assembling alkene, aldehyde and perfluoroalkyl reagents under the catalysis of an N-heterocyclic carbene afforded valuable α-aryl β-perfluoroalkyl ketones.
Collapse
Affiliation(s)
- Hai-Bin Yang
- School of Chemical Engineering and Light Industry
- Guangdong University of Technology
- Guangzhou 510006
- P. R. China
| | - Zhi-Hou Wang
- School of Chemical Engineering and Light Industry
- Guangdong University of Technology
- Guangzhou 510006
- P. R. China
| | - Jin-Mei Li
- School of Chemical Engineering and Light Industry
- Guangdong University of Technology
- Guangzhou 510006
- P. R. China
| | - Chuande Wu
- School of Chemical Engineering and Light Industry
- Guangdong University of Technology
- Guangzhou 510006
- P. R. China
- State Key Laboratory of Silicon Materials
| |
Collapse
|
4
|
Khoshbin Z, Housaindokht MR, Izadyar M, Bozorgmehr MR, Verdian A. The investigation of the G-quadruplex aptamer selectivity to Pb 2+ ion: a joint molecular dynamics simulation and density functional theory study. J Biomol Struct Dyn 2019; 38:3659-3675. [PMID: 31496379 DOI: 10.1080/07391102.2019.1664933] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The aptamers with the ability to form a G-quadruplex structure can be stable in the presence of some ions. Hence, study of the interactions between such aptamers and ions can be beneficial to determine the highest selective aptamer toward an ion. In this article, molecular dynamics (MD) simulations and quantum mechanics (QM) calculations have been applied to investigate the selectivity of the T30695 aptamer toward Pb2+ in comparison with some ions. The Free Energy Landscape (FEL) analysis indicates that Pb2+ has remained inside the aptamer during the MD simulation, while the other ions have left it. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding energies prove that the conformational stability of the aptamer is the highest in the presence of Pb2+. According to the compaction parameters, the greatest compressed ion-aptamer complex, and hence, the highest ion-aptamer interaction have been induced in the presence of Pb2+. The contact maps clarify the closer contacts between the nucleotides of the aptamer in the presence of Pb2+. The density functional theory (DFT) results show that Pb2+ forms the most stable complex with the aptamer, which is consistent with the MD results. The QM calculations reveal that the N-H bonds and the O…H distances are the longest and the shortest, respectively, in the presence of Pb2+. The obtained results verify that the strongest hydrogen bonds (HBs), and hence, the most compressed aptamer structure are induced by Pb2+. Besides, atoms in molecules (AIM) and natural bond orbital (NBO) analyses confirm the results.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Zahra Khoshbin
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Mohammad Izadyar
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Asma Verdian
- Department of Food Safety and Quality Control, Research Institute of Food Science and Technology (RIFST), Mashhad, Iran
| |
Collapse
|
5
|
Theoretical design and experimental study of new aptamers with the improved target-affinity: New insights into the Pb2+-specific aptamers as a case study. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111159] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
6
|
Chen B, Wang H, Wu Z, Duan B, Bai P, Zhang K, Li W, Zheng J, Xing J. Conformational stabilization of FOX-DNA complex architecture to sensitize prostate cancer chemotherapy. Amino Acids 2017; 49:1247-1254. [PMID: 28474127 DOI: 10.1007/s00726-017-2426-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 04/17/2017] [Indexed: 11/26/2022]
Abstract
The forkhead box (FOX) transcription factor is a family of tumor suppressors that negatively regulates the tumorigenesis activity of prostate cancer; stabilization of FOX-DNA complex architecture has been recognized as a new and promising strategy for sensitizing cancer chemotherapy. Here, we described a systematic method that combined in silico analysis and in vitro assay to investigate the intermolecular interaction between FOX DNA-binding domain (DBD) and its cognate DNA partner. The structural and energetic information harvested from the molecular investigation were used to guide high-throughput virtual screening against a structurally diverse, nonredundant library of natural product compounds, aiming at discovery of novel small-molecule medicines that can conformationally stabilize and promote FOX-DNA recognition and interaction. The screening identified a number of theoretically promising hits, which were then examined by using fluorescence anisotropy assay to determine their binding potency for FOX DBD domain. The antitumor activity of identified high-affinity compounds was also tested at cellular level. Structural dynamics analysis found that the small-molecule stabilizers can shift the conformational equilibrium of FOX DBD to DNA-bound state, thus promoting the protein domain to bind tightly with its DNA partner.
Collapse
Affiliation(s)
- Bin Chen
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Huiqiang Wang
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Zhun Wu
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Bo Duan
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Peide Bai
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Kaiyan Zhang
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Wei Li
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Jiaxin Zheng
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Jinchun Xing
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China.
| |
Collapse
|
7
|
Yu J, Wang S, Yu J, Liu C, Xu F, Wang S, Yi Y, Yin Y. Structure-based rational design of self-inhibitory peptides to disrupt the intermolecular interaction between the troponin subunits C and I in neuropathic pain. Bioorg Chem 2017; 73:10-15. [PMID: 28525735 DOI: 10.1016/j.bioorg.2017.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 04/08/2017] [Accepted: 05/01/2017] [Indexed: 11/26/2022]
Abstract
The troponin (Tn) is a ternary complex consisting of three subunits TnC, TnI and TnT; molecular disruption of the Tn complex has been recognized as an attractive strategy against neuropathic pain. Here, a self-inhibitory peptide is stripped from the switch region of TnI interaction interface with TnC, which is considered as a lead molecular entity and then used to generate potential peptide disruptors of TnC-TnI interaction based on a rational molecular design protocol. The region is a helical peptide segment capped by N- and C-terminal disorders. Molecular dynamics simulation and binding free energy analysis suggests that the switch peptide can interact with TnC in a structurally and energetically independent manner. Terminal truncation of the peptide results in a number of potent TnC binders with considerably simplified structure and moderately decreased activity relative to the native switch. We also employ fluorescence polarization assays to substantiate the computational findings; it is found that the rationally designed peptides exhibit moderate or high affinity to TnC with dissociation constants KD at micromolar level.
Collapse
Affiliation(s)
- Junmin Yu
- Department of Pain Management, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Shilei Wang
- Department of Anesthesiology, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Junjie Yu
- Chinese Traditional Patent Medicine Dispensary, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Chuansheng Liu
- Department of Pain Management, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Fenghe Xu
- Department of Pain Management, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Shijie Wang
- Department of Pain Management, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Yusheng Yi
- Department of Pain Management, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Yanwei Yin
- Department of Pain Management, The Affiliated Hospital of Qingdao University, Qingdao 266003, China.
| |
Collapse
|