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Yuan D, He H, Song W, Ma D, Xie M, Wang Y, Wei J, He Q, Bao Y, Zhao Y. Allosteric genetically encoded biosensor for spatiotemporal monitoring of endogenous RNA dynamics in living cells. Proc Natl Acad Sci U S A 2025; 122:e2409309122. [PMID: 39933002 PMCID: PMC11848333 DOI: 10.1073/pnas.2409309122] [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: 05/10/2024] [Accepted: 01/14/2025] [Indexed: 02/13/2025] Open
Abstract
Functions of RNAs are associated with their abundance and unique subcellular localizations. RNA imaging methods for spatiotemporal monitoring of RNA dynamics would facilitate the discovery of unknown functions of RNA, yet improving RNA imaging is challenging because of limitations in methods for directly monitoring native RNA, especially the dynamics of RNA transport and concentration fluctuation. Herein, a label-free and conformation switching-based genetically encoded sensor, termed the Dual-locked RNAtracker (Ducker), that realizes spatiotemporal monitoring of endogenous RNA dynamics in living cells is developed. In this Ducker system, a distinctive strategy is developed by employing one RNA target to initiate an allosteric event that triggers the two locked fluorogenic RNA aptamer (M18 Pepper) to restore the active structure and transmit adequate fluorescence signals. The intracellular circular Ducker (circDucker) realizes high-contrast and unbiased imaging of native mRNA abundance and monitors the fluctuations in RNA concentration. Importantly, it also enables spatiotemporal dynamic tracking of RNA translocation by directly visualizing the process of the mitochondrial lncCyt b undergoing bidirectional nucleocytoplasmic transport, indicating the bidirectional regulatory events in mitochondria and nucleus. Therefore, this highly accessible sensor affords a universal and robust platform for spatiotemporal monitoring of RNA abundance and translocation in complicated dynamic reaction networks in live systems, including mRNA, lncRNA, and microRNA, expanding the current toolbox of RNA research and shedding light on the unknown functions of RNA.
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Affiliation(s)
- Deyu Yuan
- National Engineering Laboratory for Druggable Gene and Protein Screening, College of Life Science, Northeast Normal University, Changchun130024, People’s Republic of China
- Department Center for Functional Genomics and Bioinformatics, College of Life Science, Institution Sichuan University, Chengdu, Sichuan610064, People’s Republic of China
| | - Huan He
- National Engineering Laboratory for Druggable Gene and Protein Screening, College of Life Science, Northeast Normal University, Changchun130024, People’s Republic of China
- Department Center for Functional Genomics and Bioinformatics, College of Life Science, Institution Sichuan University, Chengdu, Sichuan610064, People’s Republic of China
| | - William Song
- lncTAC Biology, Chengdu, Sichuan610200, People’s Republic of China
| | - Duhan Ma
- National Engineering Laboratory for Druggable Gene and Protein Screening, College of Life Science, Northeast Normal University, Changchun130024, People’s Republic of China
- Department Center for Functional Genomics and Bioinformatics, College of Life Science, Institution Sichuan University, Chengdu, Sichuan610064, People’s Republic of China
| | - Mingfeng Xie
- National Engineering Laboratory for Druggable Gene and Protein Screening, College of Life Science, Northeast Normal University, Changchun130024, People’s Republic of China
| | - Yuchun Wang
- National Engineering Laboratory for Druggable Gene and Protein Screening, College of Life Science, Northeast Normal University, Changchun130024, People’s Republic of China
| | - Jinliang Wei
- National Engineering Laboratory for Druggable Gene and Protein Screening, College of Life Science, Northeast Normal University, Changchun130024, People’s Republic of China
| | - Qianyu He
- National Engineering Laboratory for Druggable Gene and Protein Screening, College of Life Science, Northeast Normal University, Changchun130024, People’s Republic of China
| | - Yongli Bao
- National Engineering Laboratory for Druggable Gene and Protein Screening, College of Life Science, Northeast Normal University, Changchun130024, People’s Republic of China
| | - Yongyun Zhao
- National Engineering Laboratory for Druggable Gene and Protein Screening, College of Life Science, Northeast Normal University, Changchun130024, People’s Republic of China
- Department Center for Functional Genomics and Bioinformatics, College of Life Science, Institution Sichuan University, Chengdu, Sichuan610064, People’s Republic of China
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Long L, Zhang H, Zhou Z, Duan L, Fan D, Wang R, Xu S, Qiao D, Zhu W. Pyrrole-containing hybrids as potential anticancer agents: An insight into current developments and structure-activity relationships. Eur J Med Chem 2024; 273:116470. [PMID: 38762915 DOI: 10.1016/j.ejmech.2024.116470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/21/2024]
Abstract
Cancer poses a significant threat to human health. Therefore, it is urgent to develop potent anti-cancer drugs with excellent inhibitory activity and no toxic side effects. Pyrrole and its derivatives are privileged heterocyclic compounds with significant diverse pharmacological effects. These compounds can target various aspects of cancer cells and have been applied in clinical settings or are undergoing clinical trials. As a result, pyrrole has emerged as a promising drug scaffold and has been further probed to get novel entities for the treatment of cancer. This article reviews recent research progress on anti-cancer drugs containing pyrrole. It focuses on the mechanism of action, biological activity, and structure-activity relationships of pyrrole derivatives, aiming to assist in designing and synthesizing innovative pyrrole-based anti-cancer compounds.
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Affiliation(s)
- Li Long
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China
| | - Han Zhang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China
| | - ZhiHui Zhou
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China
| | - Lei Duan
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China
| | - Dang Fan
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China
| | - Ran Wang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China
| | - Shan Xu
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China.
| | - Dan Qiao
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China.
| | - Wufu Zhu
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China.
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Yuan J, Liu Z, Dong Y, Gao F, Xia X, Wang P, Luo Y, Zhang Z, Yan D, Zhang W. Pioneering 4,11-Dioxo-4,11-dihydro-1 H-anthra[2,3- d]imidazol-3-ium Compounds as Promising Survivin Inhibitors by Targeting ILF3/NF110 for Cancer Therapy. J Med Chem 2023; 66:16843-16868. [PMID: 38079530 DOI: 10.1021/acs.jmedchem.3c01551] [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: 12/29/2023]
Abstract
Survivin is a novel attractive target for cancer therapy; however, it is considered undruggable because it lacks enzymatic activities. Herein, we describe our efforts toward the discovery of a novel series of 4,11-dioxo-4,11-dihydro-1H-anthra[2,3-d]imidazol-3-ium derivatives as survivin inhibitors by targeting ILF3/NF110. Intensive structural modifications led us to identify a lead compound AQIM-I, which remarkably inhibited nonsmall cell lung cancer cells A549 with an IC50 value of 9 nM and solid tumor cell proliferation with more than 700-fold selectivity against human normal cells. Further biological studies revealed that compound AQIM-I significantly inhibited survivin expression and colony formation and induced ROS production, apoptosis, cell cycle arrest, DNA damage, and autophagy. Furthermore, the promoter-luciferase reporter assay showed that AQIM-I attenuated the survivin promoter activity enhanced by the overexpression of ILF3/NF110 in a concentration-dependent manner, and specific binding (KD = 163 nM) of AQIM-I to ILF3/NF110 was detected by surface plasmon resonance.
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Affiliation(s)
- Jing Yuan
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Zhanxiong Liu
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Yachun Dong
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Feng Gao
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Xuelin Xia
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Penghui Wang
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Yanli Luo
- Department of Pathology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, P. R. China
| | - Zhenfeng Zhang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Deyue Yan
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Wanbin Zhang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
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Li QM, Lin GS, Duan WG, Cui YC, Li FY, Lei FH, Li DP. Design, synthesis, and antiproliferative evaluation of novel longifolene-derived tetraline pyrimidine derivatives with fluorescence properties. NEW J CHEM 2022. [DOI: 10.1039/d2nj01054b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the search for novel compounds with both survivin inhibitory activity and fluorescence properties, 18 novel longifolene-derived tetralin pyrimidine compounds were designed using survivin as the target and synthesized from the sustainable natural resource longifolene.
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Affiliation(s)
- Qing-Min Li
- School of Chemistry and Chemical Engineering, Guangxi University, No. 100, Daxue Dong Road, Nanning, Guangxi, 530004, People's Republic of China
| | - Gui-Shan Lin
- School of Chemistry and Chemical Engineering, Guangxi University, No. 100, Daxue Dong Road, Nanning, Guangxi, 530004, People's Republic of China
| | - Wen-Gui Duan
- School of Chemistry and Chemical Engineering, Guangxi University, No. 100, Daxue Dong Road, Nanning, Guangxi, 530004, People's Republic of China
| | - Yu-Cheng Cui
- School of Chemistry and Chemical Engineering, Guangxi University, No. 100, Daxue Dong Road, Nanning, Guangxi, 530004, People's Republic of China
| | - Fang-Yao Li
- College of Pharmacy, Guilin Medical University, Guilin, Guangxi, 530004, People's Republic of China
| | - Fu-Hou Lei
- Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi University for Nationalities, Nanning, Guangxi, 530004, People's Republic of China
| | - Dian-Peng Li
- Guangxi Key Laboratory of Functional Phytochemicals Research and Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
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Sharma P, LaRosa C, Antwi J, Govindarajan R, Werbovetz KA. Imidazoles as Potential Anticancer Agents: An Update on Recent Studies. Molecules 2021; 26:molecules26144213. [PMID: 34299488 PMCID: PMC8307698 DOI: 10.3390/molecules26144213] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/30/2021] [Accepted: 07/05/2021] [Indexed: 12/14/2022] Open
Abstract
Nitrogen-containing heterocyclic rings are common structural components of marketed drugs. Among these heterocycles, imidazole/fused imidazole rings are present in a wide range of bioactive compounds. The unique properties of such structures, including high polarity and the ability to participate in hydrogen bonding and coordination chemistry, allow them to interact with a wide range of biomolecules, and imidazole-/fused imidazole-containing compounds are reported to have a broad spectrum of biological activities. This review summarizes recent reports of imidazole/fused imidazole derivatives as anticancer agents appearing in the peer-reviewed literature from 2018 through 2020. Such molecules have been shown to modulate various targets, including microtubules, tyrosine and serine-threonine kinases, histone deacetylases, p53-Murine Double Minute 2 (MDM2) protein, poly (ADP-ribose) polymerase (PARP), G-quadraplexes, and other targets. Imidazole-containing compounds that display anticancer activity by unknown/undefined mechanisms are also described, as well as key features of structure-activity relationships. This review is intended to provide an overview of recent advances in imidazole-based anticancer drug discovery and development, as well as inspire the design and synthesis of new anticancer molecules.
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Affiliation(s)
- Pankaj Sharma
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (P.S.); (C.L.)
| | - Chris LaRosa
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (P.S.); (C.L.)
| | - Janet Antwi
- Division of Mathematics, Computer & Natural Sciences Division, Ohio Dominican University, Columbus, OH 43219, USA;
| | - Rajgopal Govindarajan
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
| | - Karl A. Werbovetz
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (P.S.); (C.L.)
- Correspondence:
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Yuan J, Liu Z, Zhang Z, Yan D, Zhang W. Synthesis and biological evaluation of naphthoquinone phenacylimidazolium derivatives. Bioorg Med Chem Lett 2021; 41:127977. [PMID: 33766771 DOI: 10.1016/j.bmcl.2021.127977] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/14/2021] [Indexed: 01/19/2023]
Abstract
In order to expand structural diversity and improve antitumor efficiency, forty new naphthoquinone phenacylimidazolium derivatives were designed, synthesized and evaluated. Good synthetic yields were obtained under mild conditions using easily available starting materials. Cytotoxicity of these compounds was evaluated in vitro against a panel of human tumor cell lines: human breast carcinoma cell lines (MCF-7), human cervical carcinoma cell lines (HeLa), and human lung carcinoma cell lines (A549). Among them, the optimal compound 7m showed splendid antiproliferative activity with low to 50 nM IC50 values against MCF-7 and excellent selectivity of 256-fold compared with the normal cell lines L929. Compound 7m induced apoptosis in a dose-dependent manner. Further mechanism experiments showed that compound 7m dramatically inhibited the expression of survivin and activated the pro-apoptotic protein caspase-3. Our results indicated that the structural modification on the 1,3-substituents of naphthoquinone imidazoliums without 2-substituent is also promising to obtain new antitumor compounds.
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Affiliation(s)
- Jing Yuan
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontier Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Zhanxiong Liu
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontier Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Zhenfeng Zhang
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China.
| | - Deyue Yan
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontier Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Wanbin Zhang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontier Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China; School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
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Ahenkorah S, Coertzen D, Tong JX, Fridianto K, Wittlin S, Birkholtz LM, Tan KSW, Lam Y, Go ML, Haynes RK. Antimalarial N 1, N 3-Dialkyldioxonaphthoimidazoliums: Synthesis, Biological Activity, and Structure-activity Relationships. ACS Med Chem Lett 2020; 11:49-55. [PMID: 31938463 DOI: 10.1021/acsmedchemlett.9b00457] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/11/2019] [Indexed: 12/19/2022] Open
Abstract
Here we report the nanomolar potencies of N 1,N 3-dialkyldioxonaphthoimidazoliums against asexual forms of sensitive and resistant Plasmodium falciparum. Activity was dependent on the presence of the fused quinone-imidazolium entity and lipophilicity imparted by the N1/N3 alkyl residues on the scaffold. Gametocytocidal activity was also detected, with most members active at IC50 < 1 μM. A representative analog with good solubility, limited PAMPA permeability, and microsomal stability demonstrated oral efficacy on a humanized mouse model of P. falciparum.
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Affiliation(s)
| | - Dina Coertzen
- Institute for Sustainable Malaria Control, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, 0028 Pretoria, South Africa
| | | | | | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland
- University of Basel, 4003 Basel, Switzerland
| | - Lyn-Marie Birkholtz
- Institute for Sustainable Malaria Control, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, 0028 Pretoria, South Africa
| | | | | | | | - Richard K. Haynes
- Centre of Excellence for Pharmaceutical Sciences, North-West University, 2531 Potchefstroom, South Africa
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Sabour R, Harras MF, Mehany AB. Design, synthesis, cytotoxicity screening and molecular docking of new 3-cyanopyridines as survivin inhibitors and apoptosis inducers. Bioorg Chem 2020; 94:103358. [DOI: 10.1016/j.bioorg.2019.103358] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 09/23/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022]
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Choudhari D, Salunke-Gawali S, Chakravarty D, Shaikh SR, Lande DN, Gejji SP, Rao PK, Satpute S, Puranik VG, Gonnade R. Synthesis and biological activity of imidazole based 1,4-naphthoquinones. NEW J CHEM 2020. [DOI: 10.1039/c9nj04339j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Design and development of drugs in multi-drug resistant (MDR) infections have been of growing interest. The syntheses, structural studies, antibacterial and antifungal activities of imidazole-based 1,4-naphthoquinones are studied in this investigation.
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Affiliation(s)
- Dinkar Choudhari
- Department of Chemistry
- Savitribai Phule Pune University
- Pune 411007
- India
| | | | | | - Samir R. Shaikh
- Centre for Material Characterization
- National Chemical Laboratory
- Pune 411008
- India
| | - Dipali N. Lande
- Department of Chemistry
- Savitribai Phule Pune University
- Pune 411007
- India
| | - Shridhar P. Gejji
- Department of Chemistry
- Savitribai Phule Pune University
- Pune 411007
- India
| | - Pradeep Kumar Rao
- Department of Chemistry
- Savitribai Phule Pune University
- Pune 411007
- India
| | - Surekha Satpute
- Department of Microbiology
- Savitribai Phule Pune University
- Pune 411007
- India
| | - Vedavati G. Puranik
- Centre for Material Characterization
- National Chemical Laboratory
- Pune 411008
- India
| | - Rajesh Gonnade
- Centre for Material Characterization
- National Chemical Laboratory
- Pune 411008
- India
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