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Anantharajan J, Baburajendran N, Lin G, Loh YY, Xu W, Ahmad NHB, Liu S, Jansson AE, Kuan JWL, Ng EY, Yeo YK, Hung AW, Joy J, Hill J, Ford HL, Zhao R, Keller TH, Kang C. Structure-activity relationship studies of allosteric inhibitors of EYA2 tyrosine phosphatase. Protein Sci 2022; 31:422-431. [PMID: 34761455 PMCID: PMC8819961 DOI: 10.1002/pro.4234] [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: 08/23/2021] [Revised: 10/31/2021] [Accepted: 11/02/2021] [Indexed: 02/03/2023]
Abstract
Human eyes absent (EYA) proteins possess Tyr phosphatase activity, which is critical for numerous cancer and metastasis promoting activities, making it an attractive target for cancer therapy. In this work, we demonstrate that the inhibitor-bound form of EYA2 does not favour binding to Mg2+ , which is indispensable for the Tyr phosphatase activity. We further describe characterization and optimization of this class of allosteric inhibitors. A series of analogues were synthesized to improve potency of the inhibitors and to elucidate structure-activity relationships. Two co-crystal structures confirm the binding modes of this class of inhibitors. Our medicinal chemical, structural, biochemical, and biophysical studies provide insight into the molecular interactions of EYA2 with these allosteric inhibitors. The compounds derived from this study are useful for exploring the function of the Tyr phosphatase activity of EYA2 in normal and cancerous cells and serve as reference compounds for screening or developing allosteric phosphatase inhibitors. Finally, the co-crystal structures reported in this study will aid in structure-based drug discovery against EYA2.
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Affiliation(s)
- Jothi Anantharajan
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Nithya Baburajendran
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Grace Lin
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Yong Yao Loh
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Weijun Xu
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Nur Huda Binte Ahmad
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Shuang Liu
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
- Chemical Biology and Therapeutics ScienceBroad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Anna E. Jansson
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - John Wee Liang Kuan
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Elizabeth Yihui Ng
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Yee Khoon Yeo
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Alvin W. Hung
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Joma Joy
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Jeffrey Hill
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - Heide L. Ford
- Department of Obstetrics and GynecologyUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Rui Zhao
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Thomas H. Keller
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
| | - CongBao Kang
- Experimental Drug Development CentreAgency for Science, Technology and Research (A*STAR)Singapore
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2
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Li Y, Ng EY, Loh YR, Gea CY, Huang Q, Li Q, Kang C. Secondary structures, dynamics, and DNA binding of the homeodomain of human SIX1. J Pept Sci 2021; 28:e3376. [PMID: 34713534 DOI: 10.1002/psc.3376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/03/2021] [Accepted: 10/04/2021] [Indexed: 11/09/2022]
Abstract
Human sine oculis homeobox homolog (SIX) 1 contains a homeodomain (HD), which is important for binding to DNA. In this study, we carried out structural studies on the HD of human SIX1 using nuclear magnetic resonance (NMR) spectroscopy. Its secondary structures and dynamics in solution were explored. HD is well-structured in solution, and our study shows that it contains three α-helices. Dynamics study indicates that the N- and C-terminal residues of HD are flexible in solution. HD of human SIX1 exhibits molecular interactions with a short double-strand DNA sequence evidenced by the 1 H-15 N-heteronuclear single quantum correlation (HSQC) and 19 F-NMR experiments. Our current study provides structural information for HD of human SIX1. Further studies indicate that this construct can be utilized to study SIX1 and DNA interactions.
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Affiliation(s)
- Yan Li
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Elizabeth YiHui Ng
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Ying Ru Loh
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Chong Yu Gea
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Qiwei Huang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore
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3
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Azam MA, Thathan J, Jupudi S. Pharmacophore modeling, atom based 3D-QSAR, molecular docking and molecular dynamics studies on Escherichia coli ParE inhibitors. Comput Biol Chem 2019; 84:107197. [PMID: 31901788 DOI: 10.1016/j.compbiolchem.2019.107197] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/20/2019] [Accepted: 12/22/2019] [Indexed: 10/25/2022]
Abstract
ATP dependent ParE enzyme is as an attractive target for the development of antibacterial agents. Atom based 3D-QSAR model AADHR.187 was developed based on the thirty eight Escherichia coli ParE inhibitors. The generated model showed statistically significant coefficient of determinations for the training (R2 = 0.985) and test (R2 = 0.86) sets. The cross-validated correlation coefficient (q2) was 0.976. The utility of the generated model was validated by the enrichment study. The model was also validated with structurally diverse external test set of ten compounds. Contour plot analysis of the generated model unveiled the chemical features necessary for the E. coli ParE enzyme inhibition. Extra-precision docking result revealed that hydrogen bonding and ionic interactions play a major role in ParE protein-ligand binding. Binding free energy was computed for the data set inhibitors to validate the binding affinity. A 30-ns molecular dynamics simulation showed high stability and effective binding of inhibitor 34 within the active site of ParE enzyme. Using the best fitted model AADHR.187, pharmacophore-based high-throughput virtual screening was performed to identify virtual hits. Based on the above studies three new molecules are proposed as E. coli ParE inhibitors with high binding affinity and favourable ADME properties.
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Affiliation(s)
- Mohammed Afzal Azam
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Ooty, 643001, Tamil Nadu, India(1).
| | - Janarthanan Thathan
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Ooty, 643001, Tamil Nadu, India(1)
| | - Srikanth Jupudi
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Ooty, 643001, Tamil Nadu, India(1)
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Kang C. 19F-NMR in Target-based Drug Discovery. Curr Med Chem 2019; 26:4964-4983. [PMID: 31187703 DOI: 10.2174/0929867326666190610160534] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 08/14/2018] [Accepted: 03/13/2019] [Indexed: 02/06/2023]
Abstract
Solution NMR spectroscopy plays important roles in understanding protein structures, dynamics and protein-protein/ligand interactions. In a target-based drug discovery project, NMR can serve an important function in hit identification and lead optimization. Fluorine is a valuable probe for evaluating protein conformational changes and protein-ligand interactions. Accumulated studies demonstrate that 19F-NMR can play important roles in fragment- based drug discovery (FBDD) and probing protein-ligand interactions. This review summarizes the application of 19F-NMR in understanding protein-ligand interactions and drug discovery. Several examples are included to show the roles of 19F-NMR in confirming identified hits/leads in the drug discovery process. In addition to identifying hits from fluorinecontaining compound libraries, 19F-NMR will play an important role in drug discovery by providing a fast and robust way in novel hit identification. This technique can be used for ranking compounds with different binding affinities and is particularly useful for screening competitive compounds when a reference ligand is available.
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Affiliation(s)
- CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
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5
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Li Y, Kang C. Solution NMR Spectroscopy in Target-Based Drug Discovery. Molecules 2017; 22:E1399. [PMID: 28832542 PMCID: PMC6151424 DOI: 10.3390/molecules22091399] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/18/2017] [Accepted: 08/18/2017] [Indexed: 12/14/2022] Open
Abstract
Solution NMR spectroscopy is a powerful tool to study protein structures and dynamics under physiological conditions. This technique is particularly useful in target-based drug discovery projects as it provides protein-ligand binding information in solution. Accumulated studies have shown that NMR will play more and more important roles in multiple steps of the drug discovery process. In a fragment-based drug discovery process, ligand-observed and protein-observed NMR spectroscopy can be applied to screen fragments with low binding affinities. The screened fragments can be further optimized into drug-like molecules. In combination with other biophysical techniques, NMR will guide structure-based drug discovery. In this review, we describe the possible roles of NMR spectroscopy in drug discovery. We also illustrate the challenges encountered in the drug discovery process. We include several examples demonstrating the roles of NMR in target-based drug discoveries such as hit identification, ranking ligand binding affinities, and mapping the ligand binding site. We also speculate the possible roles of NMR in target engagement based on recent processes in in-cell NMR spectroscopy.
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Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore.
| | - Congbao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore.
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6
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Li Y, Wong YL, Ng FM, Liu B, Wong YX, Poh ZY, Liu S, Then SW, Lee MY, Ng HQ, Huang Q, Hung AW, Cherian J, Hill J, Keller TH, Kang C. Escherichia coli Topoisomerase IV E Subunit and an Inhibitor Binding Mode Revealed by NMR Spectroscopy. J Biol Chem 2016; 291:17743-53. [PMID: 27365392 PMCID: PMC5016168 DOI: 10.1074/jbc.m116.737429] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/29/2016] [Indexed: 11/06/2022] Open
Abstract
Bacterial topoisomerases are attractive antibacterial drug targets because of their importance in bacterial growth and low homology with other human topoisomerases. Structure-based drug design has been a proven approach of efficiently developing new antibiotics against these targets. Past studies have focused on developing lead compounds against the ATP binding pockets of both DNA gyrase and topoisomerase IV. A detailed understanding of the interactions between ligand and target in a solution state will provide valuable information for further developing drugs against topoisomerase IV targets. Here we describe a detailed characterization of a known potent inhibitor containing a 9H-pyrimido[4,5-b]indole scaffold against the N-terminal domain of the topoisomerase IV E subunit from Escherichia coli (eParE). Using a series of biophysical and biochemical experiments, it has been demonstrated that this inhibitor forms a tight complex with eParE. NMR studies revealed the exact protein residues responsible for inhibitor binding. Through comparative studies of two inhibitors of markedly varied potencies, it is hypothesized that gaining molecular interactions with residues in the α4 and residues close to the loop of β1-α2 and residues in the loop of β3-β4 might improve the inhibitor potency.
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Affiliation(s)
- Yan Li
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Ying Lei Wong
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Fui Mee Ng
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Boping Liu
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Yun Xuan Wong
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Zhi Ying Poh
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Shuang Liu
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Siew Wen Then
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Michelle Yueqi Lee
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Hui Qi Ng
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Qiwei Huang
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Alvin W Hung
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Joseph Cherian
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Jeffrey Hill
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Thomas H Keller
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - CongBao Kang
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
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