1
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Rajan S, Yoon HS. Covalent ligands of nuclear receptors. Eur J Med Chem 2023; 261:115869. [PMID: 37857142 DOI: 10.1016/j.ejmech.2023.115869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023]
Abstract
Nuclear receptors (NRs) are ligand-induced transcriptional factors implicated in several physiological pathways. Naïve ligands bind to their cognate receptors and modulate gene expression as agonists or antagonists. It has been observed that some ligands bind via covalent bonding with the NR Ligand Binding Domain (LBD) residues. While many such instances have been known since the 1980s, a consolidated account of these ligands and their interactions with NR-LBD is yet to be documented. To negate this, we have culled out the human NR-LBDs that form a covalent attachment with ligands. According to the study, 16 of the 48 human NRs have been targeted by covalent ligands. It was found that conserved cysteines prone to covalent attachment are predominantly located in NR-LBD helices 3 and 11. These conserved cysteines are also observed in many of the remaining NRs, which can be probed for their reactivity. Thus, the structural insights into NR-LBD interactions with covalent ligands presented here would aid drug discovery efforts targeting NRs.
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Affiliation(s)
- Sreekanth Rajan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Ho Sup Yoon
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore; College of Pharmacy, CHA University, 120 Haeryong-ro, Pocheon-si, Gyeonggi-do, 11160, Republic of Korea; CHA Advanced Research Institute, 335 Pangyo-ro, Bundang-gu, Seongnam-si, 13488, Republic of Korea.
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2
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Rajan S, Yoon HS. Structural insights into Plasmodium PPIases. Front Cell Infect Microbiol 2022; 12:931635. [PMID: 36118020 PMCID: PMC9478106 DOI: 10.3389/fcimb.2022.931635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
Malaria is one of the most prevalent infectious diseases posing a serious challenge over the years, mainly owing to the emergence of drug-resistant strains, sparking a need to explore and identify novel protein targets. It is a well-known practice to adopt a chemo-genomics approach towards identifying targets for known drugs, which can unravel a novel mechanism of action to aid in better drug targeting proficiency. Immunosuppressive drugs cyclosporin A, FK506 and rapamycin, were demonstrated to inhibit the growth of the malarial parasite, Plasmodium falciparum. Peptidyl prolyl cis/trans isomerases (PPIases), comprising cylcophilins and FK506-binding proteins (FKBPs), the specific target of these drugs, were identified in the Plasmodium parasite and proposed as an antimalarial drug target. We previously attempted to decipher the structure of these proteins and target them with non-immunosuppressive drugs, predominantly on FKBP35. This review summarizes the structural insights on Plasmodium PPIases, their inhibitor complexes and perspectives on drug discovery.
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Affiliation(s)
- Sreekanth Rajan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ho Sup Yoon
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- College of Pharmacy, CHA University, Pocheon-si, South Korea
- CHA Advanced Research Institute, Seongnam-si, South Korea
- *Correspondence: Ho Sup Yoon,
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3
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Bhattacharjya S, Yang D, Yoon HS. Special Issue "Selected Papers from the 8th Asia-Pacific NMR (APNMR) Symposium: Recent Advances in NMR Spectroscopy". Int J Mol Sci 2020; 21:ijms21124419. [PMID: 32580280 PMCID: PMC7352290 DOI: 10.3390/ijms21124419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 11/29/2022] Open
Affiliation(s)
- Surajit Bhattacharjya
- School of Biological Sciences, 60 Nanyang Drive, Nanyang Technological University, Singapore 637551, Singapore
- Correspondence: (S.B.); (D.Y.); (H.S.Y.); Tel.: +65-6316-7997 (S.B.); +65-6516-1014 (D.Y.); +65-6316-2846 (H.S.Y.)
| | - Daiwen Yang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
- Correspondence: (S.B.); (D.Y.); (H.S.Y.); Tel.: +65-6316-7997 (S.B.); +65-6516-1014 (D.Y.); +65-6316-2846 (H.S.Y.)
| | - Ho Sup Yoon
- School of Biological Sciences, 60 Nanyang Drive, Nanyang Technological University, Singapore 637551, Singapore
- Correspondence: (S.B.); (D.Y.); (H.S.Y.); Tel.: +65-6316-7997 (S.B.); +65-6516-1014 (D.Y.); +65-6316-2846 (H.S.Y.)
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Rajan S, Jang Y, Kim CH, Kim W, Toh HT, Jeon J, Song B, Serra A, Lescar J, Yoo JY, Beldar S, Ye H, Kang C, Liu XW, Feitosa M, Kim Y, Hwang D, Goh G, Lim KL, Park HM, Lee CH, Oh SF, Petsko GA, Yoon HS, Kim KS. PGE1 and PGA1 bind to Nurr1 and activate its transcriptional function. Nat Chem Biol 2020; 16:876-886. [PMID: 32451509 DOI: 10.1038/s41589-020-0553-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 04/22/2020] [Indexed: 12/11/2022]
Abstract
The orphan nuclear receptor Nurr1 is critical for the development, maintenance and protection of midbrain dopaminergic (mDA) neurons. Here we show that prostaglandin E1 (PGE1) and its dehydrated metabolite, PGA1, directly interact with the ligand-binding domain (LBD) of Nurr1 and stimulate its transcriptional function. We also report the crystallographic structure of Nurr1-LBD bound to PGA1 at 2.05 Å resolution. PGA1 couples covalently to Nurr1-LBD by forming a Michael adduct with Cys566, and induces notable conformational changes, including a 21° shift of the activation function-2 helix (H12) away from the protein core. Furthermore, PGE1/PGA1 exhibit neuroprotective effects in a Nurr1-dependent manner, prominently enhance expression of Nurr1 target genes in mDA neurons and improve motor deficits in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-lesioned mouse models of Parkinson's disease. Based on these results, we propose that PGE1/PGA1 represent native ligands of Nurr1 and can exert neuroprotective effects on mDA neurons, via activation of Nurr1's transcriptional function.
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Affiliation(s)
- Sreekanth Rajan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yongwoo Jang
- Molecular Neurobiology Laboratory, Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA.,Department of Biomedical Engineering, Hanyang University, Seoul, Korea
| | - Chun-Hyung Kim
- Molecular Neurobiology Laboratory, Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA.,Paean Biotechnology, Daejeon, Korea
| | - Woori Kim
- Molecular Neurobiology Laboratory, Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Hui Ting Toh
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Nanyang Institute of Technology in Health and Medicine, Interdisciplinary Graduate School, Nanyang Technological University, Singapore, Singapore
| | - Jeha Jeon
- Molecular Neurobiology Laboratory, Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Bin Song
- Molecular Neurobiology Laboratory, Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Aida Serra
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Jun Yeob Yoo
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Serap Beldar
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Hong Ye
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Congbao Kang
- Experimental Drug Development Centre, Agency for Science, Technology and Research, Nanos, Singapore, Singapore
| | - Xue-Wei Liu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Melissa Feitosa
- Molecular Neurobiology Laboratory, Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Yeahan Kim
- Molecular Neurobiology Laboratory, Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Dabin Hwang
- Molecular Neurobiology Laboratory, Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Geraldine Goh
- National Neuroscience Institute, Singapore, Singapore
| | - Kah-Leong Lim
- National Neuroscience Institute, Singapore, Singapore.,Lee Kong Chian School of Medicine, Singapore, Singapore
| | - Hye Min Park
- Department of Bioscience and Biotechnology, Konkuk University, Gwangjin-gu, Seoul, Republic of Korea
| | - Choong Hwan Lee
- Department of Bioscience and Biotechnology, Konkuk University, Gwangjin-gu, Seoul, Republic of Korea
| | - Sungwhan F Oh
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gregory A Petsko
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ho Sup Yoon
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore. .,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore.
| | - Kwang-Soo Kim
- Molecular Neurobiology Laboratory, Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA. .,Program in Neuroscience and Harvard Stem Cell Institute, McLean Hospital, Harvard Medical School, Belmont, MA, USA.
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Lee SH, Lee SB, Heo JH, Yoon HS, Byun JW, Choi GS, Shin J. Sebaceous glands participate in the inflammation of rosacea. J Eur Acad Dermatol Venereol 2020; 34:e144-e146. [PMID: 31709649 DOI: 10.1111/jdv.16055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- S H Lee
- Department of Dermatology, Inha University School of Medicine, Incheon, Korea
| | - S B Lee
- Department of Dermatology, Inha University School of Medicine, Incheon, Korea
| | - J H Heo
- Department of Dermatology, Inha University School of Medicine, Incheon, Korea
| | - H S Yoon
- Department of Dermatology, Inha University School of Medicine, Incheon, Korea
| | - J W Byun
- Department of Dermatology, Inha University School of Medicine, Incheon, Korea
| | - G S Choi
- Department of Dermatology, Inha University School of Medicine, Incheon, Korea
| | - J Shin
- Department of Dermatology, Inha University School of Medicine, Incheon, Korea
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Park TY, Jang Y, Kim W, Shin J, Toh HT, Kim CH, Yoon HS, Leblanc P, Kim KS. Chloroquine modulates inflammatory autoimmune responses through Nurr1 in autoimmune diseases. Sci Rep 2019; 9:15559. [PMID: 31664129 PMCID: PMC6820774 DOI: 10.1038/s41598-019-52085-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/12/2019] [Indexed: 12/19/2022] Open
Abstract
For over a half-century the anti-malarial drug chloroquine (CQ) has been used as a therapeutic agent, alone or in combination, to treat autoimmune diseases. However, neither the underlying mechanism(s) of action nor their molecular target(s) are well defined. The orphan nuclear receptor Nurr1 (also known as NR4A2) is an essential transcription factor affecting the development and maintenance of midbrain dopaminergic neurons. In this study, using in vitro T cell differentiation models, we demonstrate that CQ activates TREG cell differentiation and induces Foxp3 gene expression in a Nurr1-dependent manner. Remarkably, CQ appears to induce Nurr1 function by two distinct mechanisms: firstly, by direct binding to Nurr1’s ligand-binding domain and promoting its transcriptional activity and secondly by upregulation of Nurr1 expression through the CREB signaling pathway. In contrast, CQ suppressed gene expression and differentiation of pathogenic TH17 cells. Importantly, using a valid animal model of inflammatory bowel disease (IBD), we demonstrated that CQ promotes Foxp3 expression and differentiation of TREG cells in a Nurr1-dependent manner, leading to significant improvement of IBD-related symptoms. Taken together, these data suggest that CQ ameliorates autoimmune diseases via regulating Nurr1 function/expression and that Nurr1 is a promising target for developing effective therapeutics of human inflammatory autoimmune diseases.
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Affiliation(s)
- Tae-Yoon Park
- Molecular Neurobiology Laboratory, Department of Psychiatry and McLean Hospital, Harvard Medical School, 115 Mill Street, Belmont, Massachusetts, 02478, USA
| | - Yongwoo Jang
- Molecular Neurobiology Laboratory, Department of Psychiatry and McLean Hospital, Harvard Medical School, 115 Mill Street, Belmont, Massachusetts, 02478, USA
| | - Woori Kim
- Molecular Neurobiology Laboratory, Department of Psychiatry and McLean Hospital, Harvard Medical School, 115 Mill Street, Belmont, Massachusetts, 02478, USA
| | - Joon Shin
- School of Biological Sciences, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Hui Ting Toh
- School of Biological Sciences, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Chun-Hyung Kim
- Molecular Neurobiology Laboratory, Department of Psychiatry and McLean Hospital, Harvard Medical School, 115 Mill Street, Belmont, Massachusetts, 02478, USA
| | - Ho Sup Yoon
- School of Biological Sciences, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Pierre Leblanc
- Molecular Neurobiology Laboratory, Department of Psychiatry and McLean Hospital, Harvard Medical School, 115 Mill Street, Belmont, Massachusetts, 02478, USA.
| | - Kwang-Soo Kim
- Molecular Neurobiology Laboratory, Department of Psychiatry and McLean Hospital, Harvard Medical School, 115 Mill Street, Belmont, Massachusetts, 02478, USA. .,Program in Neuroscience and Harvard Stem Cell Institute, McLean Hospital, Harvard Medical School, Belmont, MA, 02478, USA.
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7
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Ngow YS, Rajan S, Ye H, Yoon HS. Crystal structure of human vaccinia-related kinase 1 in complex with AMP-PNP, a non-hydrolyzable ATP analog. Protein Sci 2018; 28:524-532. [PMID: 30461091 DOI: 10.1002/pro.3552] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/12/2018] [Accepted: 11/13/2018] [Indexed: 01/16/2023]
Abstract
Vaccinia-related kinase 1 (VRK1), a serine/threonine mitotic kinase, is widely over-expressed in dividing cells and regarded as a cancer drug target primarily due to its function as an early response gene in cell proliferation. However, the mechanism of VRK1 phosphorylation and substrate activation is not well understood. More importantly even the molecular basis of VRK1 interaction with its cofactor, adenosine triphosphate (ATP), is unavailable to-date. As designing specific inhibitors remains to be the major challenge in kinase research, such a molecular understanding will enable us to design ATP-competitive specific inhibitors of VRK1. Here we report the molecular characterization of VRK1 in complex with AMP-PNP, a non-hydrolyzable ATP-analog, using NMR titration followed by the co-crystal structure determined upto 2.07 Å resolution. We also carried out the structural comparison of the AMP-PNP bound-form with its apo and inhibitor-bound counterparts, which has enabled us to present our rationale toward designing VRK1-specific inhibitors.
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Affiliation(s)
- Yeen Shian Ngow
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Sreekanth Rajan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Hong Ye
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Ho Sup Yoon
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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Lee JS, Park HS, Yoon HS, Cho S. Claudin-1 expression decreases with increasing pathological grade in actinic keratosis and may be a marker of high-risk actinic keratosis. Clin Exp Dermatol 2018; 44:483-490. [PMID: 30315595 DOI: 10.1111/ced.13810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2018] [Indexed: 11/29/2022]
Abstract
BACKGROUND Actinic keratosis (AK) is a common sun-induced skin disorder that can progress to invasive squamous cell carcinoma. However, there is still no reliable method to predict high-risk AK. AIM To identify markers that reflect the biological behaviour of AK and to understand the pathogenesis of AK. METHODS In total, 52 patients with AK and 17 site-matched healthy controls (HCs) were enrolled. We evaluated solar elastosis and immunohistochemical features using antibodies to p53, vitamin D receptor (VDR), claudin-1 and Langerin (CD207). Comparisons between AK and HC skin were performed and analyses carried out according to the pathological grade of AK. RESULTS We found that in both patients and HCs, solar elastosis increased and Langerhans cell (LC) density decreased with ageing. Solar elastosis and p53 expression were higher and VDR expression was lower in patients than in HCs; however, there was no statistical difference between them in relation to the pathological grade of AK. Claudin-1 expression gradually decreased from HC skin to severe AK, and particularly decreased in areas with epidermal atypia. LC density in severe AK was significantly lower than in HC skin and mild AK, while there was no difference in LC density between HC skin, mild AK and moderate AK. CONCLUSIONS Claudin-1 could be a useful marker of the pathological severity of AK. In addition, p53 increases and VDR decreases in AK, not in a gradual manner but in the early steps of carcinogenesis. LC density is relatively maintained in AK until it reaches severe dysplasia.
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Affiliation(s)
- J S Lee
- Department of Dermatology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea.,Institute of Human-Environmental Interface Biology, Medical Research Center, Seoul National University, Seoul, Korea.,Deparment of Biomedical Science
| | - H S Park
- Department of Dermatology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea.,Institute of Human-Environmental Interface Biology, Medical Research Center, Seoul National University, Seoul, Korea.,Deparment of Biomedical Science
| | - H S Yoon
- Department of Dermatology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea.,Institute of Human-Environmental Interface Biology, Medical Research Center, Seoul National University, Seoul, Korea.,Deparment of Biomedical Science
| | - S Cho
- Department of Dermatology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea.,Institute of Human-Environmental Interface Biology, Medical Research Center, Seoul National University, Seoul, Korea.,Deparment of Biomedical Science.,Department of Dermatology, Seoul National University College of Medicine, Seoul, Korea
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Yin F, Anderson T, Panwar N, Zhang K, Tjin SC, Ng BK, Yoon HS, Qu J, Yong KT. Functionalized MoS 2 Nanosheets as Multi-Gene Delivery Vehicles for In Vivo Pancreatic Cancer Therapy. Nanotheranostics 2018; 2:371-386. [PMID: 30324083 PMCID: PMC6170332 DOI: 10.7150/ntno.27308] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/01/2018] [Indexed: 12/13/2022] Open
Abstract
Transition metal dichalcogenides (TMDCs) are categorized as novel two-dimensional (2D) nanomaterials with unique physical and chemical properties, bearing varied applications in medical and materials sciences. However, only a few works report the application of TMDCs for gene therapy in cancer treatment. Here, we engineer a multi-gene delivery system based on functionalized monolayer MoS2, which can co-deliver HDAC1 and KRAS small interfering RNAs (siRNAs) to Panc-1 cancer cells for combinational cancer therapy. The synergistic effect of gene silencing therapy and NIR phototherapy is demonstrated by inhibition of both genes, in vitro cell growth rate, and in vivo tumor volume growth rate, exemplifying pre-eminent anticancer efficacy. This anti-tumor effect is a result of the photothermal effect of MoS2 induced by NIR excitation and inactivation of HDAC1 and KRAS genes, which consequently bring about apoptosis, inhibit migration, and induce cell cycle arrest in the treated Panc-1 cells. Moreover, good biocompatibility and reduced cytotoxicity of MoS2-based nanocarriers enable their metabolism within in vitro and in vivo mouse models over a prolonged duration without any evident ill-effects. In summary, we demonstrate the promising potential of low-toxicity, functionalized MoS2 nanocarriers as a biocompatible gene delivery system for in vivo pancreatic adenocarcinoma therapy.
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Affiliation(s)
- Feng Yin
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Tommy Anderson
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Nishtha Panwar
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Kang Zhang
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Swee Chuan Tjin
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Beng Koon Ng
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Ho Sup Yoon
- Division of Structural Biology & Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Ken-Tye Yong
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
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10
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Kumari G, Wong KH, Serra A, Shin J, Yoon HS, Sze SK, Tam JP. Molecular diversity and function of jasmintides from Jasminum sambac. BMC Plant Biol 2018; 18:144. [PMID: 29996766 PMCID: PMC6042386 DOI: 10.1186/s12870-018-1361-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/02/2018] [Indexed: 06/01/2023]
Abstract
BACKGROUND Jasmintides jS1 and jS2 from Jasminum sambac were previously identified as a novel family of cysteine-rich peptides (CRPs) with an unusual disulfide connectivity. However, very little else is known about jasmintides, particularly their molecular diversity and functions. Here, we report the discovery and characterization of a novel suite of jasmintides from J. sambac using transcriptomic, peptidomic, structural and functional tools. RESULTS Transcriptomic analysis of leaves, flowers and roots revealed 14 unique jasmintide precursors, all of which possess a three-domain architecture comprising a signal peptide, a pro-domain and a mature jasmintide domain. Peptidomic analysis, using fractionated mixtures of jasmintides and chemical derivatization of cysteine to pseudolysine, trypsin digestion and MS/MS sequencing, revealed an additional 86 jasmintides, some of which were post-translationally modified. NMR analysis showed that jasmintide jS3 has three anti-parallel β-strands with a three-disulfide connectivity of CysI-CysV, CysII-CysIV and CysIII-CysVI, which is similar to jasmintide jS1. Jasmintide jS3 was able to withstand thermal, acidic and enzymatic degradation and, importantly, exhibited antifeedant activity against mealworm Tenebrio molitor. CONCLUSION Together, this study expands the existing library of jasmintides and furthers our understanding of the molecular diversity and cystine framework of CRPs as scaffolds and tools for engineering peptides targeting pests.
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Affiliation(s)
- Geeta Kumari
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Ka Ho Wong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Aida Serra
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Joon Shin
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Ho Sup Yoon
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - James P. Tam
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
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11
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Pomplun S, Sippel C, Hähle A, Tay D, Shima K, Klages A, Ünal CM, Rieß B, Toh HT, Hansen G, Yoon HS, Bracher A, Preiser P, Rupp J, Steinert M, Hausch F. Chemogenomic Profiling of Human and Microbial FK506-Binding Proteins. J Med Chem 2018; 61:3660-3673. [PMID: 29578710 DOI: 10.1021/acs.jmedchem.8b00137] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
FK506-binding proteins (FKBPs) are evolutionarily conserved proteins that display peptidyl-prolyl isomerase activities and act as coreceptors for immunosuppressants. Microbial macrophage-infectivity-potentiator (Mip)-type FKBPs can enhance infectivity. However, developing druglike ligands for FKBPs or Mips has proven difficult, and many FKBPs and Mips still lack biologically useful ligands. To explore the scope and potential of C5-substituted [4.3.1]-aza-bicyclic sulfonamides as a broadly applicable class of FKBP inhibitors, we developed a new synthesis method for the bicyclic core scaffold and used it to prepare an FKBP- and Mip-focused library. This allowed us to perform a systematic structure-activity-relationship analysis across key human FKBPs and microbial Mips, yielding highly improved inhibitors for all the FKBPs studied. A cocrystal structure confirmed the molecular-binding mode of the core structure and explained the affinity gained as a result of the preferred substituents. The best FKBP and Mip ligands showed promising antimalarial, antileginonellal, and antichlamydial properties in cellular models of infectivity, suggesting that substituted [4.3.1]-aza-bicyclic sulfonamides could be a novel class of anti-infectives.
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Affiliation(s)
- Sebastian Pomplun
- Department of Translational Research in Psychiatry , Max Planck Institute of Psychiatry , 80804 Munich , Germany
| | - Claudia Sippel
- Department of Translational Research in Psychiatry , Max Planck Institute of Psychiatry , 80804 Munich , Germany
| | - Andreas Hähle
- Department of Translational Research in Psychiatry , Max Planck Institute of Psychiatry , 80804 Munich , Germany.,Technical University Darmstadt , Alarich-Weiss-Straße 4 , 64287 Darmstadt , Germany
| | - Donald Tay
- School of Biological Sciences , Nanyang Technological University , 639798 Singapore
| | - Kensuke Shima
- Department of Infectious Diseases and Microbiology , University of Lübeck , 23562 Lübeck , Germany
| | - Alina Klages
- Technische Universität Braunschweig , 38106 Braunschweig , Germany
| | - Can Murat Ünal
- Technische Universität Braunschweig , 38106 Braunschweig , Germany
| | - Benedikt Rieß
- Department of Translational Research in Psychiatry , Max Planck Institute of Psychiatry , 80804 Munich , Germany
| | - Hui Ting Toh
- School of Biological Sciences , Nanyang Technological University , 639798 Singapore
| | | | - Ho Sup Yoon
- School of Biological Sciences , Nanyang Technological University , 639798 Singapore
| | - Andreas Bracher
- Max Planck Institute of Biochemistry , 82152 Martinsried , Germany
| | - Peter Preiser
- School of Biological Sciences , Nanyang Technological University , 639798 Singapore
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology , University of Lübeck , 23562 Lübeck , Germany
| | - Michael Steinert
- Department of Infectious Diseases and Microbiology , University of Lübeck , 23562 Lübeck , Germany.,Helmholtz Centre for Infection Research , 38124 Braunschweig , Germany
| | - Felix Hausch
- Department of Translational Research in Psychiatry , Max Planck Institute of Psychiatry , 80804 Munich , Germany.,Technical University Darmstadt , Alarich-Weiss-Straße 4 , 64287 Darmstadt , Germany
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12
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Beldar S, Manimekalai MSS, Cho NJ, Baek K, Grüber G, Yoon HS. Self-association and conformational variation of NS5A domain 1 of hepatitis C virus. J Gen Virol 2018; 99:194-208. [PMID: 29300159 DOI: 10.1099/jgv.0.001000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Direct-acting antivirals (DAAs) targeting the non-structural 5A (NS5A) protein of the hepatitis C virus (HCV) are crucial drugs that have shown exceptional clinical success in patients. However, their mode of action (MoA) remains unclear, and drug-resistant HCV strains are rapidly emerging. It is critical to characterize the behaviour of the NS5A protein in solution, which can facilitate the development of new classes of inhibitors or improve the efficacy of the currently available DAAs. Using biophysical methods, including dynamic light scattering, size exclusion chromatography and chemical cross-linking experiments, we showed that the NS5A domain 1 from genotypes 1b and 1a of the HCV intrinsically self-associated and existed as a heterogeneous mixture in solution. Interestingly, the NS5A domain 1 from genotypes 1b and 1a exhibited different dynamic equilibria of monomers to higher-order structures. Using small-angle X-ray scattering, we studied the structural dynamics of the various states of the NS5A domain 1 in solution. We also tested the effect of daclatasvir (DCV), the most prominent DAA, on self-association of the wild and DCV-resistant mutant (Y93H) NS5A domain 1 proteins, and demonstrated that DCV induced the formation of large and irreversible protein aggregates that eventually precipitated out. This study highlights the conformational variability of the NS5A domain 1 of HCV, which may be an intrinsic structural behaviour of the HCV NS5A domain 1 in solution.
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Affiliation(s)
- Serap Beldar
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | | | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Kwanghee Baek
- Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Ho Sup Yoon
- Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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13
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Farrokhi H, Boonruangkan J, Chun BJ, Rohith TM, Mishra A, Toh HT, Yoon HS, Kim YJ. Speckle reduction in quantitative phase imaging by generating spatially incoherent laser field at electroactive optical diffusers. Opt Express 2017; 25:10791-10800. [PMID: 28788768 DOI: 10.1364/oe.25.010791] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We studied quantitative phase imaging (QPI) using coherent laser illumination coupled with static and moving optical diffusers. The spatial coherence of a continuous-wave laser was controlled by tuning the particle size and the diffusion angle of optical diffusers for speckle-reduced 3D phase imaging of transparent objects. We used a common-path QPI configuration to investigate the coherent phase mapping of polystyrene micro-beads and breast cancer cells (MCF-7) under different degrees of coherent speckles. The proposed speckle reduction method could provide an avenue for enhancing lateral resolution and suppressing coherent artifacts of the phase images from QPI.
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14
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Wu X, Tan YJ, Toh HT, Nguyen LH, Kho SH, Chew SY, Yoon HS, Liu XW. Stimuli-responsive multifunctional glyconanoparticle platforms for targeted drug delivery and cancer cell imaging. Chem Sci 2017; 8:3980-3988. [PMID: 28553540 PMCID: PMC5433505 DOI: 10.1039/c6sc05251g] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/17/2017] [Indexed: 12/12/2022] Open
Abstract
Targeted bioimaging or chemotherapeutic drug delivery to achieve the desired therapeutic effects while minimizing side effects has attracted considerable research attention and remains a clinical challenge. Presented herein is a multi-component delivery system based on carbohydrate-functionalized gold nanoparticles conjugated with a fluorophore or prodrug. The system leverages active targeting based on carbohydrate-lectin interactions and release of the payload by biological thiols. Cell-type specific delivery of the activatable fluorophore was examined by confocal imaging on HepG2 cells, and displays distinct selectivity towards HepG2 cells over HeLa and NIH3T3 cells. The system was further developed into a drug delivery vehicle with camptothecin (CPT) as a model drug. It was demonstrated that the complex exhibits similar cytotoxicity to that of free CPT towards HepG2 cells, and is significantly less cytotoxic to normal HDF and NIH3T3 cells, indicating excellent specificity. The delivery vehicle itself exhibits excellent biocompatibility and offers an attractive strategy for cell-type specific delivery depending on the carbohydrates conjugated in the system.
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Affiliation(s)
- Xumeng Wu
- Division of Chemistry and Biological Chemistry , School of Physical & Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371 , Singapore .
| | - Yu Jia Tan
- Division of Chemistry and Biological Chemistry , School of Physical & Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371 , Singapore .
| | - Hui Ting Toh
- Division of Structural Biology & Biochemistry , School of Biological Sciences , Nanyang Technological University , Singapore 639798 , Singapore
| | - Lan Huong Nguyen
- School of Chemical & Biomedical Engineering , Nanyang Technological University , Singapore 637459 , Singapore
| | - Shu Hui Kho
- Division of Chemistry and Biological Chemistry , School of Physical & Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371 , Singapore .
| | - Sing Yian Chew
- School of Chemical & Biomedical Engineering , Nanyang Technological University , Singapore 637459 , Singapore
- Lee Kong Chian School of Medicine , Nanyang Technological University , Singapore 308232 , Singapore
| | - Ho Sup Yoon
- Division of Structural Biology & Biochemistry , School of Biological Sciences , Nanyang Technological University , Singapore 639798 , Singapore
- Department of Genetic Engineering , College of Life Sciences , Kyung Hee University , Yongin-si , Gyeonggi-do 446-701 , Republic of Korea
| | - Xue-Wei Liu
- Division of Chemistry and Biological Chemistry , School of Physical & Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371 , Singapore .
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15
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Choi Y, Yun JH, Yoo J, Lee I, Kim H, Son HN, Kim IS, Yoon HS, Zimmermann P, Couchman JR, Cho HS, Oh ES, Lee W. New structural insight of C-terminal region of Syntenin-1, enhancing the molecular dimerization and inhibitory function related on Syndecan-4 signaling. Sci Rep 2016; 6:36818. [PMID: 27830760 PMCID: PMC5103296 DOI: 10.1038/srep36818] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 10/17/2016] [Indexed: 12/15/2022] Open
Abstract
The PDZ domain-containing scaffold protein, syntenin-1, binds to the transmembrane proteoglycan, syndecan-4, but the molecular mechanism/function of this interaction are unknown. Crystal structure analysis of syntenin-1/syndecan-4 cytoplasmic domains revealed that syntenin-1 forms a symmetrical pair of dimers anchored by a syndecan-4 dimer. The syndecan-4 cytoplasmic domain is a compact intertwined dimer with a symmetrical clamp shape and two antiparallel strands forming a cavity within the dimeric twist. The PDZ2 domain of syntenin-1 forms a direct antiparallel interaction with the syndecan-4 cytoplasmic domain, inhibiting the functions of syndecan-4 such as focal adhesion formation. Moreover, C-terminal region of syntenin-1 reveals an essential role for enhancing the molecular homodimerization. Mutation of key syntenin-1 residues involved in the syndecan-4 interaction or homodimer formation abolishes the inhibitory function of syntenin-1, as does deletion of the homodimerization-related syntenin-1 C-terminal domain. Syntenin-1, but not dimer-formation-incompetent mutants, rescued the syndecan-4-mediated inhibition of migration and pulmonary metastasis by B16F10 cells. Therefore, we conclude that syntenin-1 negatively regulates syndecan-4 function via oligomerization and/or syndecan-4 interaction, impacting cytoskeletal organization and cell migration.
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Affiliation(s)
- Youngsil Choi
- Department of Life Sciences, Division of Life and Pharmaceutical Sciences and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 120-750, Korea
| | - Ji-Hye Yun
- Department of Biochemistry, College of Life Science &Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Jiho Yoo
- Department of Biology, College of Life Science &Biotechnology, Yonsei University, Seoul 136-791, Republic of Korea
| | - Inhwan Lee
- Department of Biochemistry, College of Life Science &Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Heeyoun Kim
- Department of Biochemistry, College of Life Science &Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Hye-Nam Son
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea
| | - In-San Kim
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea
| | - Ho Sup Yoon
- Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, Singapore.,Department of Genetic Engineering, College of Life Sciences, Kyung Hee University,Yongin-si Gyeonggi-do, 446-701, Republic of Korea
| | - Pascale Zimmermann
- Laboratory for Glycobiology, University of Leuven &Flanders Interuniversity Institute for Biotechnology, Leuven, Belgium
| | - John R Couchman
- Department of Biomedical Sciences, University of Copenhagen, Biocenter, 2200 Copenhagen, Denmark
| | - Hyun-Soo Cho
- Department of Biology, College of Life Science &Biotechnology, Yonsei University, Seoul 136-791, Republic of Korea
| | - Eok-Soo Oh
- Department of Life Sciences, Division of Life and Pharmaceutical Sciences and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 120-750, Korea
| | - Weontae Lee
- Department of Biochemistry, College of Life Science &Biotechnology, Yonsei University, Seoul 120-749, Korea
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16
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Yang C, Panwar N, Wang Y, Zhang B, Liu M, Toh H, Yoon HS, Tjin SC, Chong PHJ, Law WC, Chen CK, Yong KT. Biodegradable charged polyester-based vectors (BCPVs) as an efficient non-viral transfection nanoagent for gene knockdown of the BCR-ABL hybrid oncogene in a human chronic myeloid leukemia cell line. Nanoscale 2016; 8:9405-9416. [PMID: 27092903 DOI: 10.1039/c6nr00996d] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
First-line therapy of chronic myelogenous leukemia (CML) has always involved the use of BCR-ABL tyrosine-kinase inhibitors which is associated with an abnormal chromosome called Philadelphia chromosome. Although the overall survival rate has been improved by the current therapeutic regime, the presence of resistance has resulted in limited efficacy. In this study, an RNA interference (RNAi)-based therapeutic regime is proposed with the aim to knockdown the BCR-ABL hybrid oncogene using small interfering RNA (siRNA). The siRNA transfection rates have usually been limited due to the declining contact probability among polyplexes and the non-adherent nature of leukemic cells. Our work aims at addressing this limitation by using a biodegradable charged polyester-based vector (BCPV) as a nanocarrier for the delivery of BCR-ABL-specific siRNA to the suspension culture of a K562 CML cell line. BCR-ABL siRNAs were encapsulated in the BCPVs by electrostatic force. Cell internalization was facilitated by the BCPV and assessed by confocal microscopy and flow cytometry. The regulation of the BCR-ABL level in K562 cells as a result of RNAi was analyzed by real-time polymerase chain reaction (RT-PCR). We observed that BCPV was able to form stable nanoplexes with siRNA molecules, even in the presence of fetal bovine serum (FBS), and successfully assisted in vitro siRNA transfection in the non-adherent K562 cells. As a consequence of downregulation of BCR-ABL, BCPV-siRNA nanoplexes inhibited cell proliferation and promoted cell apoptosis. All results were compared with a commercial transfection reagent, Lipofectamine2000™, which served as a positive control. More importantly, this class of non-viral vector exhibits biodegradable features and negligible cytotoxicity, thus providing a versatile platform to deliver siRNA to non-adherent leukemia cells with high transfection efficiency by effectively overcoming extra- and intra-cellular barriers. Due to the excellent in vitro transfection results from BCPV-siRNA, a newly developed biodegradable transfection agent, BCPV, is being probed for transfection performance in an animal model.
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Affiliation(s)
- Chengbin Yang
- School of Electrical and Electronic Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore.
| | - Nishtha Panwar
- School of Electrical and Electronic Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore.
| | - Yucheng Wang
- School of Electrical and Electronic Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore.
| | - Butian Zhang
- School of Electrical and Electronic Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore.
| | - Maixian Liu
- Department of Chemistry, University of Buffalo, The State University of New York, Buffalo, New York 14260, USA
| | - Huiting Toh
- Division of Structural Biology & Biochemistry, School of Biological Sciences, Nanyang Technological University, 639798, Singapore
| | - Ho Sup Yoon
- Division of Structural Biology & Biochemistry, School of Biological Sciences, Nanyang Technological University, 639798, Singapore and Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Yongin-si Gyeonggi-do, 446701, Republic of Korea
| | - Swee Chuan Tjin
- School of Electrical and Electronic Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore.
| | - Peter Han Joo Chong
- School of Electrical and Electronic Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore.
| | - Wing-Cheung Law
- Department of Industrial and Systems Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, P. R. China
| | - Chih-Kuang Chen
- The Polymeric Biomaterials Lab, Department of Fiber and Composite Materials, Feng Chia University, Taichung, Taiwan 40724, Republic of China.
| | - Ken-Tye Yong
- School of Electrical and Electronic Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore.
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17
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Prakash A, Rajan S, Yoon HS. Crystal structure of the FK506 binding domain of human FKBP25 in complex with FK506. Protein Sci 2016; 25:905-10. [PMID: 26749369 DOI: 10.1002/pro.2875] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/28/2015] [Accepted: 12/30/2015] [Indexed: 01/25/2023]
Abstract
Human FKBP25 (hFKBP25) is a nuclear immunophilin and interacts with several nuclear proteins, hence involving in many nuclear events. Similar to other FKBPs, FK506 binding domain (FKBD) of hFKBP25 also binds to immunosuppressive drugs such as rapamycin and FK506, albeit with a lower affinity for the latter. The molecular basis underlying this difference in affinity could not be addressed due to the lack of the crystal structure of hFKBD25 in complex with FK506. Here, we report the crystal structure of hFKBD25 in complex with FK506 determined at 1.8 Å resolution and its comparison with the hFKBD25-rapamycin complex, bringing out the microheterogeneity in the mode of interaction of these drugs, which could possibly explain the lower affinity for FK506.
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Affiliation(s)
- Ajit Prakash
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Sreekanth Rajan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Ho Sup Yoon
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.,Department of Genetic Engineering, College of Life Sciences, Kyung Hee University Yongin-si, Gyeonggi-do, 446-701, Republic of Korea
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18
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Prakash A, Shin J, Rajan S, Yoon HS. Structural basis of nucleic acid recognition by FK506-binding protein 25 (FKBP25), a nuclear immunophilin. Nucleic Acids Res 2016; 44:2909-25. [PMID: 26762975 PMCID: PMC4824100 DOI: 10.1093/nar/gkw001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 12/30/2015] [Indexed: 12/13/2022] Open
Abstract
The nuclear immunophilin FKBP25 interacts with chromatin-related proteins and transcription factors and is suggested to interact with nucleic acids. Currently the structural basis of nucleic acid binding by FKBP25 is unknown. Here we determined the nuclear magnetic resonance (NMR) solution structure of full-length human FKBP25 and studied its interaction with DNA. The FKBP25 structure revealed that the N-terminal helix-loop-helix (HLH) domain and C-terminal FK506-binding domain (FKBD) interact with each other and that both of the domains are involved in DNA binding. The HLH domain forms major-groove interactions and the basic FKBD loop cooperates to form interactions with an adjacent minor-groove of DNA. The FKBP25–DNA complex model, supported by NMR and mutational studies, provides structural and mechanistic insights into the nuclear immunophilin-mediated nucleic acid recognition.
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Affiliation(s)
- Ajit Prakash
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Joon Shin
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Sreekanth Rajan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Ho Sup Yoon
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore Department of Genetic Engineering, College of Life Sciences, Kyung Hee University Yongin-si, Gyeonggi-do 446-701, Republic of Korea
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19
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Kang HJ, Ko CD, Yoon HS, Kim MB, Ahn SH. The Reliability of Histoculture Drug Response Assay (HDRA) in Chemosensitivity Tests for Breast Cancer. Cancer Res Treat 2015; 33:392-7. [PMID: 26680813 DOI: 10.4143/crt.2001.33.5.392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
PURPOSE Cancers are highly individual in their response to chemotherapy, however attempts to predict tumor response to drugs using in vitro cell culture have largely failed. A new technology, the histoculture drug response assay (HDRA), appears to have solved many previous problems. The purpose of this study is to evaluate the reliability of HDRA in a chemosensitivity test for breast cancer. MATERIALS AND METHODS Tumor specimens from breast cancer patients were evaluated by HDRA using different chemotherapeutic agents. Each specimen was tested using a blind method in order to determine the reproducibility of HDRA results for the same tissue and with a triplicated assay in order to determine reproducibility by different examiners. The evaluative power of this assay and the chemosensitivity of drugs for each specimen was determined. RESULTS Specimens of 92.9% (65/70) were successfully cultured and evaluated for chemosensitivity. The reproducibility of HDRA for the same tissue was 75% (100% agreement) and 100% (over 70% agreement), respectively. And the reproducibility by different examiners was 78.9% (100% agreement) and 94.7% (over 70% agreement), respectively. Each specimen demonstrated a response to at least one agent. CONCLUSION The evaluative power and reproducibility of HDRA were high, therefore it might serve as a reliable clinical method for chemosensitivity testing. However, there is a need for clinical trial in which patients are initially randomized for treatment either by HDRA direction or by clinician's choice.
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20
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Harikishore A, Sup Yoon H. Immunophilins: Structures, Mechanisms and Ligands. Curr Mol Pharmacol 2015; 9:37-47. [DOI: 10.2174/1874467208666150519113427] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 01/22/2015] [Accepted: 05/17/2015] [Indexed: 11/22/2022]
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21
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Wu D, Tang X, Yoon HS, Wang K, Olivier A, Li X. MOCVD Growth of High-Quality and Density-Tunable GaAs Nanowires on ITO Catalyzed by Au Nanoparticles Deposited by Centrifugation. Nanoscale Res Lett 2015; 10:410. [PMID: 26487507 PMCID: PMC4615929 DOI: 10.1186/s11671-015-1121-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 10/11/2015] [Indexed: 06/05/2023]
Abstract
High-quality and density-tunable GaAs nanowires (NWs) are directly grown on indium tin oxide (ITO) using Au nanoparticles (NPs) as catalysts by metal organic chemical vapor deposition (MOCVD). Au catalysts were deposited on ITO glass substrate using a centrifugal method. Compared with the droplet-only method, high-area density Au NPs were uniformly distributed on ITO. Tunable area density was realized through variation of the centrifugation time, and the highest area densities were obtained as high as 490 and 120 NP/μm(2) for 10- and 20-nm diameters of Au NPs, respectively. Based on the vapor-liquid-solid growth mechanism, the growth rates of GaAs NWs at 430 °C were 18.2 and 21.5 nm/s for the highest area density obtained of 10- and 20-nm Au NP-catalyzed NWs. The growth rate of the GaAs NWs was reduced with the increase of the NW density due to the competition of precursor materials. High crystal quality of the NWs was also obtained with no observable planar defects. 10-nm Au NP-induced NWs exhibit wurtzite structure whereas zinc-blende is observed for 20-nm NW samples. Controllable density and high crystal quality of the GaAs NWs on ITO demonstrate their potential application in hybrid a solar cell.
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Affiliation(s)
- Dan Wu
- OPTIMUS, Photonics Centre of Excellence, School of Electrical and Electronic Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Xiaohong Tang
- OPTIMUS, Photonics Centre of Excellence, School of Electrical and Electronic Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.
| | - Ho Sup Yoon
- Division of Structural Biology & Biochemistry, School of Biological Sciences, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Kai Wang
- Department of Electrical & Electronic Engineering, South University of Science and Technology of China, 1088 Xueyuan Avenue, Shenzhen, 518055, China.
| | - Aurelien Olivier
- CINTRA UMI 3288, School of Electrical and Electronic Engineering, Nanyang Technological University, Research Techno Plaza, 50 Nanyang Drive, Border X Block, Level 6, Singapore, 637553, Singapore
| | - Xianqiang Li
- OPTIMUS, Photonics Centre of Excellence, School of Electrical and Electronic Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
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22
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Kumari G, Serra A, Shin J, Nguyen PQT, Sze SK, Yoon HS, Tam JP. Cysteine-Rich Peptide Family with Unusual Disulfide Connectivity from Jasminum sambac. J Nat Prod 2015; 78:2791-9. [PMID: 26555361 DOI: 10.1021/acs.jnatprod.5b00762] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Cysteine-rich peptides (CRPs) are natural products with privileged peptidyl structures that represent a potentially rich source of bioactive compounds. Here, the discovery and characterization of a novel plant CRP family, jasmintides from Jasminum sambac of the Oleaceae family, are described. Two 27-amino acid jasmintides (jS1 and jS2) were identified at the gene and protein levels. Disulfide bond mapping of jS1 by mass spectrometry and its confirmation by NMR spectroscopy revealed disulfide bond connectivity of C-1-C-5, C-2-C-4, and C-3-C-6, a cystine motif that has not been reported in plant CRPs. Structural determination showed that jS1 displays a well-defined structure framed by three short antiparallel β-sheets. Genomic analysis showed that jasmintides share a three-domain precursor arrangement with a C-terminal mature domain preceded by a long pro-domain of 46 residues and an intron cleavage site between the signal sequence and pro-domain. The compact cysteine-rich structure together with an N-terminal pyroglutamic acid residue confers jasmintides high resistance to heat and enzymatic degradation, including exopeptidase treatment. Collectively, these results reveal a new plant CRP structure with an unusual cystine connectivity, which could be useful as a scaffold for designing peptide drugs.
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Affiliation(s)
- Geeta Kumari
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551, Singapore
| | - Aida Serra
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551, Singapore
| | - Joon Shin
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551, Singapore
| | - Phuong Q T Nguyen
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551, Singapore
| | - Ho Sup Yoon
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551, Singapore
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23
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Kim SH, Ryu HG, Lee J, Shin J, Harikishore A, Jung HY, Seul Kim Y, Lyu HN, Oh E, Baek NI, Choi KY, Sup Yoon H, Kim KT. Corrigendum: Ursolic acid exerts anti-cancer activity by suppressing vaccinia-related kinase 1-mediated damage repair in lung cancer cells. Sci Rep 2015; 5:15864. [PMID: 26513475 PMCID: PMC4625475 DOI: 10.1038/srep15864] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Kini SG, Nguyen PQT, Weissbach S, Mallagaray A, Shin J, Yoon HS, Tam JP. Studies on the Chitin Binding Property of Novel Cysteine-Rich Peptides from Alternanthera sessilis. Biochemistry 2015; 54:6639-49. [DOI: 10.1021/acs.biochem.5b00872] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Shruthi G. Kini
- School
of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Phuong Q. T. Nguyen
- School
of Biological Sciences, Nanyang Technological University, Singapore 637551
| | | | | | - Joon Shin
- School
of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Ho Sup Yoon
- School
of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - James P. Tam
- School
of Biological Sciences, Nanyang Technological University, Singapore 637551
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25
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Kim SH, Ryu HG, Lee J, Shin J, Harikishore A, Jung HY, Kim YS, Lyu HN, Oh E, Baek NI, Choi KY, Yoon HS, Kim KT. Ursolic acid exerts anti-cancer activity by suppressing vaccinia-related kinase 1-mediated damage repair in lung cancer cells. Sci Rep 2015; 5:14570. [PMID: 26412148 PMCID: PMC4585938 DOI: 10.1038/srep14570] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 09/04/2015] [Indexed: 01/26/2023] Open
Abstract
Many mitotic kinases have been targeted for the development of anti-cancer drugs, and inhibitors of these kinases have been expected to perform well for cancer therapy. Efforts focused on selecting good targets and finding specific drugs to target are especially needed, largely due to the increased frequency of anti-cancer drugs used in the treatment of lung cancer. Vaccinia-related kinase 1 (VRK1) is a master regulator in lung adenocarcinoma and is considered a key molecule in the adaptive pathway, which mainly controls cell survival. We found that ursolic acid (UA) inhibits the catalytic activity of VRK1 via direct binding to the catalytic domain of VRK1. UA weakens surveillance mechanisms by blocking 53BP1 foci formation induced by VRK1 in lung cancer cells, and possesses synergistic anti-cancer effects with DNA damaging drugs. Taken together, UA can be a good anti-cancer agent for targeted therapy or combination therapy with DNA damaging drugs for lung cancer patients.
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Affiliation(s)
- Seong-Hoon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Hye Guk Ryu
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Juhyun Lee
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Joon Shin
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | | | - Hoe-Youn Jung
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Ye Seul Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Ha-Na Lyu
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Eunji Oh
- The Graduate School of Biotechnology and Plant Metabolism Research Center, Kyung-Hee University, Suwon 449-701, Republic of Korea
| | - Nam-In Baek
- The Graduate School of Biotechnology and Plant Metabolism Research Center, Kyung-Hee University, Suwon 449-701, Republic of Korea
| | - Kwan-Yong Choi
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Ho Sup Yoon
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
- Department of Genetic Engineering, College of Life Sciences, Kyung-Hee University, Suwon 449-701, Republic of Korea
| | - Kyong-Tai Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
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26
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Panwar N, Yang C, Yin F, Yoon HS, Chuan TS, Yong KT. RNAi-based therapeutic nanostrategy: IL-8 gene silencing in pancreatic cancer cells using gold nanorods delivery vehicles. Nanotechnology 2015; 26:365101. [PMID: 26291710 DOI: 10.1088/0957-4484/26/36/365101] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
RNA interference (RNAi)-based gene silencing possesses great ability for therapeutic intervention in pancreatic cancer. Among various oncogene mutations, Interleukin-8 (IL-8) gene mutations are found to be overexpressed in many pancreatic cell lines. In this work, we demonstrate IL-8 gene silencing by employing an RNAi-based gene therapy approach and this is achieved by using gold nanorods (AuNRs) for efficient delivery of IL-8 small interfering RNA (siRNA) to the pancreatic cell lines of MiaPaCa-2 and Panc-1. Upon comparing to Panc-1 cells, we found that the dominant expression of the IL-8 gene in MiaPaCa-2 cells resulted in an aggressive behavior towards the processes of cell invasion and metastasis. We have hence investigated the suitability of using AuNRs as novel non-viral nanocarriers for the efficient uptake and delivery of IL-8 siRNA in realizing gene knockdown of both MiaPaCa-2 and Panc-1 cells. Flow cytometry and fluorescence imaging techniques have been applied to confirm transfection and release of IL-8 siRNA. The ratio of AuNRs and siRNA has been optimized and transfection efficiencies as high as 88.40 ± 2.14% have been achieved. Upon successful delivery of IL-8 siRNA into cancer cells, the effects of IL-8 gene knockdown are quantified in terms of gene expression, cell invasion, cell migration and cell apoptosis assays. Statistical comparative studies for both MiaPaCa-2 and Panc-1 cells are presented in this work. IL-8 gene silencing has been demonstrated with knockdown efficiencies of 81.02 ± 10.14% and 75.73 ± 6.41% in MiaPaCa-2 and Panc-1 cells, respectively. Our results are then compared with a commercial transfection reagent, Oligofectamine, serving as positive control. The gene knockdown results illustrate the potential role of AuNRs as non-viral gene delivery vehicles for RNAi-based targeted cancer therapy applications.
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Affiliation(s)
- Nishtha Panwar
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
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27
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Rajan S, Choi M, Nguyen QT, Ye H, Liu W, Toh HT, Kang C, Kamariah N, Li C, Huang H, White C, Baek K, Grüber G, Yoon HS. Structural transition in Bcl-xL and its potential association with mitochondrial calcium ion transport. Sci Rep 2015; 5:10609. [PMID: 26023881 PMCID: PMC4448555 DOI: 10.1038/srep10609] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 04/21/2015] [Indexed: 11/17/2022] Open
Abstract
Bcl-2 family proteins are key regulators for cellular homeostasis in response to apoptotic stimuli. Bcl-xL, an antiapoptotic Bcl-2 family member, undergoes conformational transitions, which leads to two conformational states: the cytoplasmic and membrane-bound. Here we present the crystal and small-angle X-ray scattering (SAXS) structures of Bcl-xL treated with the mild detergent n-Octyl β-D-Maltoside (OM). The detergent-treated Bcl-xL forms a dimer through three-dimensional domain swapping (3DDS) by swapping helices α6-α8 between two monomers. Unlike Bax, a proapoptotic member of the Bcl-2 family, Bcl-xL is not converted to 3DDS homodimer upon binding BH3 peptides and ABT-737, a BH3 mimetic drug. We also designed Bcl-xL mutants which cannot dimerize and show that these mutants reduced mitochondrial calcium uptake in MEF cells. This illustrates the structural plasticity in Bcl-xL providing hints toward the probable molecular mechanism for Bcl-xL to play a regulatory role in mitochondrial calcium ion transport.
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Affiliation(s)
- Sreekanth Rajan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Minjoo Choi
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Quoc Toan Nguyen
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Hong Ye
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Wei Liu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Hui Ting Toh
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore 138669
| | - Neelagandan Kamariah
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Singapore 138671
| | - Chi Li
- Molecular Targets Program, James Graham Brown Center and Department of Medicine, Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202, USA
| | - Huiya Huang
- Department of Physiology and Biophysics, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064, USA
| | - Carl White
- Department of Physiology and Biophysics, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064, USA
| | - Kwanghee Baek
- Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Singapore 138671
| | - Ho Sup Yoon
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea
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28
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Rajan S, Choi M, Baek K, Yoon HS. Bh3 induced conformational changes in Bcl-Xl revealed by crystal structure and comparative analysis. Proteins 2015; 83:1262-72. [PMID: 25907960 DOI: 10.1002/prot.24816] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 04/09/2015] [Accepted: 04/17/2015] [Indexed: 01/08/2023]
Abstract
Apoptosis or programmed cell death is a regulatory process in cells in response to stimuli perturbing physiological conditions. The Bcl-2 family of proteins plays an important role in regulating homeostasis during apoptosis. In the process, the molecular interactions among the three members of this family, the pro-apoptotic, anti-apoptotic and BH3-only proteins at the mitochondrial outer membrane define the fate of a cell. Here, we report the crystal structures of the human anti-apoptotic protein Bcl-XL in complex with BH3-only BID(BH3) and BIM(BH3) peptides determined at 2.0 Å and 1.5 Å resolution, respectively. The BH3 peptides bind to the canonical hydrophobic pocket in Bcl-XL and adopt an alpha helical conformation in the bound form. Despite a similar structural fold, a comparison with other BH3 complexes revealed structural differences due to their sequence variations. In the Bcl-XL-BID(BH3) complex we observed a large pocket, in comparison with other BH3 complexes, lined by residues from helices α1, α2, α3, and α5 located adjacent to the canonical hydrophobic pocket. These results suggest that there are differences in the mode of interactions by the BH3 peptides that may translate into functional differences in apoptotic regulation.
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Affiliation(s)
- Sreekanth Rajan
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Minjoo Choi
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Kwanghee Baek
- Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Yongin-Si, Gyeonggi-Do, 446-701, Republic of Korea
| | - Ho Sup Yoon
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.,Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Yongin-Si, Gyeonggi-Do, 446-701, Republic of Korea
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29
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Yin F, Yang C, Wang Q, Zeng S, Hu R, Lin G, Tian J, Hu S, Lan RF, Yoon HS, Lu F, Wang K, Yong KT. A Light-Driven Therapy of Pancreatic Adenocarcinoma Using Gold Nanorods-Based Nanocarriers for Co-Delivery of Doxorubicin and siRNA. Theranostics 2015; 5:818-33. [PMID: 26000055 PMCID: PMC4440440 DOI: 10.7150/thno.11335] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 03/14/2015] [Indexed: 01/05/2023] Open
Abstract
In this work, we report the engineering of polyelectrolyte polymers coated Gold nanorods (AuNRs)-based nanocarriers that are capable of co-delivering small interfering RNA (siRNA) and an anticancer drug doxorubicin (DOX) to Panc-1 cancer cells for combination of both chemo- and siRNA-mediated mutant K-Ras gene silencing therapy. Superior anticancer efficacy was observed through synergistic combination of promoted siRNA and DOX release upon irradiating the nanoplex formulation with 665 nm light. Our antitumor study shows that the synergistic effect of AuNRs nanoplex formulation with 665 nm light treatment is able to inhibit the in vivo tumor volume growth rate by 90%. The antitumor effect is contributed from the inactivation of K-Ras gene and thereby causing a profound synthesis (S) phase arrest in treated Panc-1 cells. Our study shows that the percentage of Panc-1 cells treated by nanoplex formulation with S phase is determined to be 35% and it is 17% much higher than that of Panc-1 cells without any treatments. The developed nanotherapy formulation here, that combines chemotherapy, RNA silencing and NIR window light-mediated therapy, will be seen to be the next natural step to be taken in the clinical research for improving the therapeutic outcomes of the pancreatic adenocarcinoma treatment.
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Affiliation(s)
- Feng Yin
- 1. School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Chengbin Yang
- 1. School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Qianqian Wang
- 3. Laboratory of Chemical Genetics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Shuwen Zeng
- 1. School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
- 6. CINTRA CNRS/NTU/THALES, UMI 3288, Research Techno Plaza, 50 Nanyang Drive, Border X Block, Singapore, 637553
| | - Rui Hu
- 1. School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Guimiao Lin
- 5. The key lab of Biomedical Engineering and Research Institute of Uropoiesis and Reproduction, School of Medical Sciences, Shenzhen University, Shenzhen, 518060, China
| | - Jinglin Tian
- 5. The key lab of Biomedical Engineering and Research Institute of Uropoiesis and Reproduction, School of Medical Sciences, Shenzhen University, Shenzhen, 518060, China
| | - Siyi Hu
- 7. School of Science, Changchun University of Science and Technology, Changchun, 130022, China
| | - Rong Feng Lan
- 8. Institute of Research and Continuing Education, Hong Kong Baptist University (Shenzhen), Shenzhen 518057, China
| | - Ho Sup Yoon
- 2. Division of Structural Biology & Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore
- 9. Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Yongin-si Gyeonggi-do, 446-701, Republic of Korea
| | - Fei Lu
- 3. Laboratory of Chemical Genetics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Kuan Wang
- 4. Nanomedicine Program and Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Ken-Tye Yong
- 1. School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
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30
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Harikishore A, Li E, Lee JJ, Cho NJ, Yoon HS. Combination of pharmacophore hypothesis and molecular docking to identify novel inhibitors of HCV NS5B polymerase. Mol Divers 2015; 19:529-39. [PMID: 25862642 DOI: 10.1007/s11030-015-9591-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Accepted: 03/25/2015] [Indexed: 01/03/2023]
Abstract
Hepatitis C virus (HCV) infection or HCV-related liver diseases are now shown to cause more than 350,000 deaths every year. Adaptability of HCV genome to vary its composition and the existence of multiple strains makes it more difficult to combat the emergence of drug-resistant HCV infections. Among the HCV polyprotein which has both the structural and non-structural regions, the non-structural protein NS5B RNA-dependent RNA polymerase (RdRP) mainly mediates the catalytic role of RNA replication in conjunction with its viral protein machinery as well as host chaperone proteins. Lack of such RNA-dependent RNA polymerase enzyme in host had made it an attractive and hotly pursued target for drug discovery efforts. Recent drug discovery efforts targeting HCV RdRP have seen success with FDA approval for sofosbuvir as a direct-acting antiviral against HCV infection. However, variations in drug-binding sites induce drug resistance, and therefore targeting allosteric sites could delay the emergence of drug resistance. In this study, we focussed on allosteric thumb site II of the non-structural protein NS5B RNA-dependent RNA polymerase and developed a five-feature pharmacophore hypothesis/model which estimated the experimental activity with a strong correlation of 0.971 & 0.944 for training and test sets, respectively. Further, the Güner-Henry score of 0.6 suggests that the model was able to discern the active and inactive compounds and enrich the true positives during a database search. In this study, database search and molecular docking results supported by experimental HCV viral replication inhibition assays suggested ligands with best fitness to the pharmacophore model dock to the key residues involved in thumbs site II, which inhibited the HCV 1b viral replication in sub-micro-molar range.
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Affiliation(s)
- Amaravadhi Harikishore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore,
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31
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Prakash A, Shin J, Yoon HS. (1)H, (13)C and (15)N resonance assignments of human FK506 binding protein 25. Biomol NMR Assign 2015; 9:43-46. [PMID: 24414276 DOI: 10.1007/s12104-014-9541-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 01/04/2014] [Indexed: 06/03/2023]
Abstract
Human FKBP25, a nuclear protein, is a member of FK506 binding protein family (FKBP) and binds to immunosuppressive drugs such as FK506 and rapamycin. Human FKBP25 interacts with several nuclear proteins and regulates nuclear events. To understand the molecular basis of such interactions, we have performed NMR studies. Here, we report (1)H, (15)N and (13)C resonance assignments of the full-length human FKBP25 protein.
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Affiliation(s)
- Ajit Prakash
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637665, Singapore
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32
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Wang Y, Yang C, Hu R, Toh HT, Liu X, Lin G, Yin F, Yoon HS, Yong KT. Assembling Mn:ZnSe quantum dots-siRNA nanoplexes for gene silencing in tumor cells. Biomater Sci 2015. [DOI: 10.1039/c4bm00306c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In this work, we demonstrate the use of manganese doped zinc selenide QDs (Mn:ZnSe d-dots) for gene delivery in vitro.
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Affiliation(s)
- Yucheng Wang
- School of Electrical and Electronic Engineering
- Nanyang Technological University
- Singapore 639798
- Singapore
| | - Chengbin Yang
- School of Electrical and Electronic Engineering
- Nanyang Technological University
- Singapore 639798
- Singapore
| | - Rui Hu
- School of Electrical and Electronic Engineering
- Nanyang Technological University
- Singapore 639798
- Singapore
| | - Hui Ting Toh
- Division of Structural Biology & Biochemistry
- School of Biological Sciences
- Nanyang Technological University
- Singapore 639798
- Singapore
| | - Xin Liu
- Department of Chemical and Biological Engineering
- University at Buffalo (SUNY)
- Buffalo
- USA
| | - Guimiao Lin
- The Engineering Lab of Synthetic Biology and the Key Lab of Biomedical Engineering
- School of Medicine
- Shenzhen University
- Shenzhen
- China
| | - Feng Yin
- School of Electrical and Electronic Engineering
- Nanyang Technological University
- Singapore 639798
- Singapore
| | - Ho Sup Yoon
- Division of Structural Biology & Biochemistry
- School of Biological Sciences
- Nanyang Technological University
- Singapore 639798
- Singapore
| | - Ken-Tye Yong
- School of Electrical and Electronic Engineering
- Nanyang Technological University
- Singapore 639798
- Singapore
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33
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Yang C, Hu R, Anderson T, Wang Y, Lin G, Law WC, Lin WJ, Nguyen QT, Toh HT, Yoon HS, Chen CK, Yong KT. Biodegradable nanoparticle-mediated K-ras down regulation for pancreatic cancer gene therapy. J Mater Chem B 2015; 3:2163-2172. [DOI: 10.1039/c4tb01623h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Biodegradable nanoparticle-mediated K-ras siRNA delivery has shown inhibition of cell proliferation, migration and invasion in pancreatic cancer cells.
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34
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Abstract
Dermatofibromas are slow-growing solitary nodules, composed mostly of a dermal proliferation of spindle cells and epithelioid cells. Some dermatofibromas present with multinucleated giant cells, such as Touton, foreign body, and osteoclast-like cells. We report a case of dermatofibroma containing both Touton giant cells and floret-type cells. A 12-year-old boy presented with a 6-mm, firm, nontender, dusky-red to greyish dermal nodule on his left popliteal fossa. As suggested clinically by the central opening, perforation of the epidermis with partial extrusion of the dermal components, including macrophages and vertically oriented collagen bundles, via transepidermal elimination, were detected. In the upper dermis, collagen trapping and mostly epithelioid cells with many giant cells were seen, while the lower part contained mainly spindle cells in a storiform pattern. Multinucleated giant cells scattered in the upper dermis were mainly floret-type multinucleated giant cells with star-shaped cytoplasmic projections, associated with some Touton giant cells. To our knowledge, this is the first report of a perforating dermatofibroma with floret-type multinucleated giant cells.
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Affiliation(s)
- E J Kim
- Department of Dermatology, Seoul National University Boramae Hospital, Seoul, Korea
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35
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Kim EJ, Park HS, Yoon HS, Kim KH, Cho S. Demographic and clinical differences between unilateral and bilateral forms of naevoid telangiectasia: a retrospective study with review of the literature. Br J Dermatol 2014; 172:1651-1653. [PMID: 25495722 DOI: 10.1111/bjd.13615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- E J Kim
- Department of Dermatology, Seoul National University Boramae Hospital, 20 Boramae Road 5-gil, Dongjak-gu, Seoul, 156-707, Korea
| | - H S Park
- Department of Dermatology, Seoul National University Boramae Hospital, 20 Boramae Road 5-gil, Dongjak-gu, Seoul, 156-707, Korea
| | - H S Yoon
- Department of Dermatology, Seoul National University Boramae Hospital, 20 Boramae Road 5-gil, Dongjak-gu, Seoul, 156-707, Korea
| | - K H Kim
- Department of Dermatology, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu 2, Seoul, 110-744, Korea
| | - S Cho
- Department of Dermatology, Seoul National University Boramae Hospital, 20 Boramae Road 5-gil, Dongjak-gu, Seoul, 156-707, Korea
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36
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Choi BH, Chattopadhaya S, Thanh LN, Feng L, Nguyen QT, Lim CB, Harikishore A, Nanga RPR, Bharatham N, Zhao Y, Liu X, Yoon HS. Suprafenacine, an indazole-hydrazide agent, targets cancer cells through microtubule destabilization. PLoS One 2014; 9:e110955. [PMID: 25354194 PMCID: PMC4212991 DOI: 10.1371/journal.pone.0110955] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 09/26/2014] [Indexed: 12/11/2022] Open
Abstract
Microtubules are a highly validated target in cancer therapy. However, the clinical development of tubulin binding agents (TBA) has been hampered by toxicity and chemoresistance issues and has necessitated the search for new TBAs. Here, we report the identification of a novel cell permeable, tubulin-destabilizing molecule - 4,5,6,7-tetrahydro-1H-indazole-3-carboxylic acid [1p-tolyl-meth-(E)-ylidene]-hydrazide (termed as Suprafenacine, SRF). SRF, identified by in silico screening of annotated chemical libraries, was shown to bind microtubules at the colchicine-binding site and inhibit polymerization. This led to G2/M cell cycle arrest and cell death via a mitochondria-mediated apoptotic pathway. Cell death was preceded by loss of mitochondrial membrane potential, JNK - mediated phosphorylation of Bcl-2 and Bad, and activation of caspase-3. Intriguingly, SRF was found to selectively inhibit cancer cell proliferation and was effective against drug-resistant cancer cells by virtue of its ability to bypass the multidrug resistance transporter P-glycoprotein. Taken together, our results suggest that SRF has potential as a chemotherapeutic agent for cancer treatment and provides an alternate scaffold for the development of improved anti-cancer agents.
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Affiliation(s)
- Bo-Hwa Choi
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Souvik Chattopadhaya
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Le Nguyen Thanh
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lin Feng
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Quoc Toan Nguyen
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chuan Bian Lim
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Amaravadhi Harikishore
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ravi Prakash Reddy Nanga
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nagakumar Bharatham
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yan Zhao
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Xuewei Liu
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ho Sup Yoon
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
- * E-mail:
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Kwon HS, Cho SJ, Ha TJ, Harikishore A, Yoon HS, Park KH, Kim IS, Jang DS. Lipoxygenase Inhibitory Effects of Dibenzylbutane Lignans from the Seeds of Myristica fragrans (Nutmeg). B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.10.3095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Kim YS, Kim SH, Shin J, Harikishore A, Lim JK, Jung Y, Lyu HN, Baek NI, Choi KY, Yoon HS, Kim KT. Luteolin suppresses cancer cell proliferation by targeting vaccinia-related kinase 1. PLoS One 2014; 9:e109655. [PMID: 25310002 PMCID: PMC4195671 DOI: 10.1371/journal.pone.0109655] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 09/02/2014] [Indexed: 12/02/2022] Open
Abstract
Uncontrolled proliferation, a major feature of cancer cells, is often triggered by the malfunction of cell cycle regulators such as protein kinases. Recently, cell cycle-related protein kinases have become attractive targets for anti-cancer therapy, because they play fundamental roles in cellular proliferation. However, the protein kinase-targeted drugs that have been developed so far do not show impressive clinical results and also display severe side effects; therefore, there is undoubtedly a need to investigate new drugs targeting other protein kinases that are critical in cell cycle progression. Vaccinia-related kinase 1 (VRK1) is a mitotic kinase that functions in cell cycle regulation by phosphorylating cell cycle-related substrates such as barrier-to-autointegration factor (BAF), histone H3, and the cAMP response element (CRE)-binding protein (CREB). In our study, we identified luteolin as the inhibitor of VRK1 by screening a small-molecule natural compound library. Here, we evaluated the efficacy of luteolin as a VRK1-targeted inhibitor for developing an effective anti-cancer strategy. We confirmed that luteolin significantly reduces VRK1-mediated phosphorylation of the cell cycle-related substrates BAF and histone H3, and directly interacts with the catalytic domain of VRK1. In addition, luteolin regulates cell cycle progression by modulating VRK1 activity, leading to the suppression of cancer cell proliferation and the induction of apoptosis. Therefore, our study suggests that luteolin-induced VRK1 inhibition may contribute to establish a novel cell cycle-targeted strategy for anti-cancer therapy.
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Affiliation(s)
- Ye Seul Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Seong-Hoon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Joon Shin
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | | | - Jong-Kwan Lim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Youngseob Jung
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Ha-Na Lyu
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Nam-In Baek
- The Graduate School of Biotechnology and Plant Metabolism Research Center, Kyung-Hee University, Suwon, Republic of Korea
| | - Kwan Yong Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Ho Sup Yoon
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kyong-Tai Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
- * E-mail:
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39
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Anderson T, Hu R, Yang C, Yoon HS, Yong KT. Pancreatic cancer gene therapy using an siRNA-functionalized single walled carbon nanotubes (SWNTs) nanoplex. Biomater Sci 2014; 2:1244-1253. [DOI: 10.1039/c4bm00019f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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40
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Rajan S, Baek K, Yoon HS. C-H…O hydrogen bonds in FK506-binding protein-ligand interactions. J Mol Recognit 2014; 26:550-5. [PMID: 24089362 DOI: 10.1002/jmr.2299] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 07/16/2013] [Accepted: 07/17/2013] [Indexed: 11/11/2022]
Abstract
Hydrogen bonds are important interaction forces observed in protein structures. They can be classified as stronger or weaker depending on their energy, thereby reflecting on the type of donor. The contribution of weak hydrogen bonds is deemed as an important factor toward structure stability along with the stronger bonds. One such bond, the C-H…O type hydrogen bond, is shown to make a contribution in maintaining three dimensional structures of proteins. Apart from their presence within protein structures, the role of these bonds in protein-ligand interactions is also noteworthy. In this study, we present a statistical analysis on the presence of C-H…O hydrogen bonds observed between FKBPs and their cognate ligands. The FK506-binding proteins (FKBPs) carry peptidyl cis-trans isomerase activity apart from the immunosuppressive property by binding to the immunosuppressive drugs FK506 or rapamycin. Because the active site of FKBPs is lined up by many hydrophobic residues, we speculated that the prevalence of C-H…O hydrogen bonds will be considerable. In a total of 25 structures analyzed, a higher frequency of C-H…O hydrogen bonds is observed in comparison with the stronger hydrogen bonds. These C-H…O hydrogen bonds are dominated by a highly conserved donor, the C(α/β) of Val55 and an acceptor, the backbone oxygen of Glu54. Both these residues are positioned in the β4-α1 loop, whereas the other residues Tyr26, Phe36 and Phe99 with higher frequencies are lined up at the opposite face of the active site. These preferences could be implicated in FKBP pharmacophore models toward enhancing the ligand affinity. This study could be a prelude to studying other proteins with hydrophobic pockets to gain better insights into ligand recognition.
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Affiliation(s)
- Sreekanth Rajan
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
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41
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Kim YM, Li Q, Ng HQ, Yoon HS, Kang C. ¹H, ¹³C and ¹⁵N chemical shift assignments for the N-terminal PAS domain of the KCNH channel from zebrafish. Biomol NMR Assign 2014; 8:165-168. [PMID: 23595857 DOI: 10.1007/s12104-013-9475-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 04/09/2013] [Indexed: 06/02/2023]
Abstract
The KCNH channels are voltage-gated potassium channels that play important roles in heart and nerve cells. The N-terminal region of the KCNH channel contains a Per-Arnt-Sim (PAS) domain which is important for the channel gating through interaction with other regions of the channel. To study the solution structure of the N-terminal PAS domain of the KCNH channel from Zebrafish (zNTD), we over-expressed and purified zNTD. We report the resonance assignments for zNTD. The data will allow us to perform structural studies for this domain, which will provide insight into its structural basis for the molecular interaction with other regions of the KCNH channel.
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Affiliation(s)
- Young Mee Kim
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
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Shin J, Chakraborty G, Yoon HS. Backbone ¹H, ¹³C and ¹⁵N resonance assignments of human vaccinia-related kinase 1 (VRK1). Biomol NMR Assign 2014; 8:29-31. [PMID: 23212441 DOI: 10.1007/s12104-012-9446-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 11/24/2012] [Indexed: 06/01/2023]
Abstract
Vaccinia-related kinase 1 (VRK1) is one of the mitotic kinases which play key roles in cell cycle control and chromatin modifications. To understand the biological role of the kinase and gain insights into its catalytic mechanism, we performed NMR assignments of catalytically active form of VRK1 with 361 amino acids residues. Here, we present the backbone NMR resonance assignments of the kinase.
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Affiliation(s)
- Joon Shin
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
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43
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Li Q, Ng HQ, Yoon HS, Kang C. Solution structure of the cyclic-nucleotide binding homology domain of a KCNH channel. J Struct Biol 2014; 186:68-74. [PMID: 24632450 DOI: 10.1016/j.jsb.2014.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 03/03/2014] [Accepted: 03/10/2014] [Indexed: 12/28/2022]
Abstract
The carboxy-terminal region of the KCNH family of potassium channels contains a cyclic-nucleotide binding homology domain (CNBHD) that is important for channel gating and trafficking. The solution structure of the CNBHD of the KCNH potassium of zebrafish was determined using solution NMR spectroscopy. This domain exists as a monomer under solution conditions and adopts a similar fold to that determined by X-ray crystallography. The CNBHD does not bind cAMP because residue Y740 blocks the entry of cyclic-nucleotide to the binding pocket. Relaxation results show that the CNBHD is rigid except that some residues in the loop between β6 and β7 are flexible. Our results will be useful to understand the gating mechanism of KCNH family members through the CNBHD.
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Affiliation(s)
- Qingxin Li
- Institute of Chemical & Engineering Sciences, Agency for Science, Technology and Research (A∗STAR), Singapore 627833, Singapore
| | - Hui Qi Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A∗STAR), Singapore 138669, Singapore
| | - Ho Sup Yoon
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637511, Singapore
| | - Congbao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A∗STAR), Singapore 138669, Singapore.
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44
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Lee DH, Ha JH, Kim Y, Jang M, Park SJ, Yoon HS, Kim EH, Bae KH, Park BC, Park SG, Yi GS, Chi SW. A conserved mechanism for binding of p53 DNA-binding domain and anti-apoptotic Bcl-2 family proteins. Mol Cells 2014; 37:264-9. [PMID: 24646834 PMCID: PMC3969048 DOI: 10.14348/molcells.2014.0001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 01/14/2014] [Indexed: 01/12/2023] Open
Abstract
The molecular interaction between tumor suppressor p53 and the anti-apoptotic Bcl-2 family proteins plays an essential role in the transcription-independent apoptotic pathway of p53. In this study, we investigated the binding of p53 DNA-binding domain (p53DBD) with the anti-apoptotic Bcl-2 family proteins, Bcl-w, Mcl-1, and Bcl-2, using GST pull-down assay and NMR spectroscopy. The GST pull-down assays and NMR experiments demonstrated the direct binding of the p53DBD with Bcl-w, Mcl-1, and Bcl-2. Further, NMR chemical shift perturbation data showed that Bcl-w and Mcl-1 bind to the positively charged DNA-binding surface of p53DBD. Noticeably, the refined structural models of the complexes between p53DBD and Bcl-w, Mcl-1, and Bcl-2 showed that the binding mode of p53DBD is highly conserved among the anti-apoptotic Bcl-2 family proteins. Furthermore, the chemical shift perturbations on Bcl-w, Mcl-1, and Bcl-2 induced by p53DBD binding occurred not only at the p53DBD-binding acidic region but also at the BH3 peptide-binding pocket, which suggests an allosteric conformational change similar to that observed in Bcl-XL. Taken altogether, our results revealed a structural basis for a conserved binding mechanism between p53DBD and the anti-apoptotic Bcl-2 family proteins, which shed light on to the molecular understanding of the transcription-independent apoptosis pathway of p53.
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Affiliation(s)
- Dong-Hwa Lee
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806,
Korea
| | - Ji-Hyang Ha
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806,
Korea
| | - Yul Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute for Science and Technology, Daejeon 305-701,
Korea
| | - Mi Jang
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806,
Korea
| | - Sung Jean Park
- College of Pharmacy, Gachon University, Incheon 406-799,
Korea
| | - Ho Sup Yoon
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore 637511,
Singapore
| | - Eun-Hee Kim
- Division of Magnetic Resonance, Korea Basic Science Institute, Cheongwon 363-883,
Korea
| | - Kwang-Hee Bae
- Research Center for Integrated Cellulomics, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806,
Korea
| | - Byoung Chul Park
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806,
Korea
| | - Sung Goo Park
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806,
Korea
| | - Gwan-Su Yi
- Department of Bio and Brain Engineering, Korea Advanced Institute for Science and Technology, Daejeon 305-701,
Korea
| | - Seung-Wook Chi
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806,
Korea
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45
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Lin G, Yang C, Hu R, Chen CK, Law WC, Anderson T, Zhang B, Nguyen QT, Toh HT, Yoon HS, Cheng C, Yong KT. Interleukin-8 gene silencing on pancreatic cancer cells using biodegradable polymer nanoplexes. Biomater Sci 2014; 2:1007-1015. [DOI: 10.1039/c3bm60325c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Biodegradable polymer nanoplexes were used as siRNA carriers for interleukin-8 gene silencing to attenuate cell proliferation in pancreatic cancer cells.
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Affiliation(s)
- Guimiao Lin
- School of Electrical and Electronic Engineering
- Nanyang Technological University
- Singapore 639798, Singapore
- The Engineering Lab of Synthetic Biology and the Key Lab of Biomedical Engineering
- School of Medicine
| | - Chengbin Yang
- School of Electrical and Electronic Engineering
- Nanyang Technological University
- Singapore 639798, Singapore
| | - Rui Hu
- School of Electrical and Electronic Engineering
- Nanyang Technological University
- Singapore 639798, Singapore
| | - Chih-Kuang Chen
- Department of Chemical and Biological Engineering
- University at Buffalo
- The State University of New York
- Buffalo, USA
| | - Wing-Cheung Law
- Department of Industrial and Systems Engineering
- The Hong Kong Polytechnic University
- Kowloon, P.R. China
| | - Tommy Anderson
- School of Electrical and Electronic Engineering
- Nanyang Technological University
- Singapore 639798, Singapore
| | - Butian Zhang
- School of Electrical and Electronic Engineering
- Nanyang Technological University
- Singapore 639798, Singapore
| | - Quoc Toan Nguyen
- Division of Structural Biology & Biochemistry
- School of Biological Sciences
- Nanyang Technological University
- Singapore 639798, Singapore
| | - Hui Ting Toh
- Division of Structural Biology & Biochemistry
- School of Biological Sciences
- Nanyang Technological University
- Singapore 639798, Singapore
| | - Ho Sup Yoon
- Division of Structural Biology & Biochemistry
- School of Biological Sciences
- Nanyang Technological University
- Singapore 639798, Singapore
| | - Chong Cheng
- Department of Chemical and Biological Engineering
- University at Buffalo
- The State University of New York
- Buffalo, USA
| | - Ken-Tye Yong
- School of Electrical and Electronic Engineering
- Nanyang Technological University
- Singapore 639798, Singapore
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46
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Rajan S, Austin D, Harikishore A, Nguyen QT, Baek K, Yoon HS. Crystal structure of Plasmodium vivax
FK506-binding protein 25 reveals conformational changes responsible for its noncanonical activity. Proteins 2013; 82:1235-44. [DOI: 10.1002/prot.24487] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/30/2013] [Accepted: 11/09/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Sreekanth Rajan
- Division of Structural Biology and Biochemistry; School of Biological Science; Nanyang Technological University, Singapore; 637665 Singapore
| | - David Austin
- Division of Structural Biology and Biochemistry; School of Biological Science; Nanyang Technological University, Singapore; 637665 Singapore
| | - Amaravadhi Harikishore
- Division of Structural Biology and Biochemistry; School of Biological Science; Nanyang Technological University, Singapore; 637665 Singapore
| | - Quoc Toan Nguyen
- Division of Structural Biology and Biochemistry; School of Biological Science; Nanyang Technological University, Singapore; 637665 Singapore
| | - Kwanghee Baek
- Department of Genetic Engineering; College of Life Sciences, Kyung Hee University; Gyeonggi-do 446-701 Republic of Korea
| | - Ho Sup Yoon
- Division of Structural Biology and Biochemistry; School of Biological Science; Nanyang Technological University, Singapore; 637665 Singapore
- Department of Genetic Engineering; College of Life Sciences, Kyung Hee University; Gyeonggi-do 446-701 Republic of Korea
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47
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Harikishore A, Leow ML, Niang M, Rajan S, Pasunooti KK, Preiser PR, Liu X, Yoon HS. Adamantyl derivative as a potent inhibitor of Plasmodium FK506 binding protein 35. ACS Med Chem Lett 2013; 4:1097-101. [PMID: 24900611 DOI: 10.1021/ml400306r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 09/16/2013] [Indexed: 11/29/2022] Open
Abstract
FKBP35, FK506 binding protein family member, in Plasmodium species displays a canonical peptidyl-prolyl isomerase (PPIase) activity and is intricately involved in the protein folding process. Inhibition of PfFKBP35 by FK506 or its analogues were shown to interfere with the in vitro growth of Plasmodium falciparum. In this study, we have synthesized adamantyl derivatives, Supradamal (SRA/4a) and its analogues SRA1/4b and SRA2/4c, which demonstrate submicromolar inhibition of Plasmodium falciparum FK506 binding domain 35 (FKBD35) PPIase activity. SRA and its analogues not only inhibit the in vitro growth of Plasmodium falciparum 3D7 strain but also show stage specific activity by inhibiting the trophozoite stage of the parasite. SRA/4a also inhibits the Plasmodium vivax FKBD35 PPIase activity and our crystal structure of PvFKBD35 in complex with the SRA provides structural insights in achieving selective inhibition against Plasmodium FKBPs.
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Affiliation(s)
- Amaravadhi Harikishore
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, 637665 Singapore
| | - Min Li Leow
- School
of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637731 Singapore
| | - Makhtar Niang
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, 637665 Singapore
| | - Sreekanth Rajan
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, 637665 Singapore
| | - Kalyan Kumar Pasunooti
- School
of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637731 Singapore
| | - Peter Rainer Preiser
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, 637665 Singapore
| | - Xuewei Liu
- School
of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637731 Singapore
| | - Ho Sup Yoon
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, 637665 Singapore
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48
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Kang C, Ye H, Chia J, Choi BH, Dhe-Paganon S, Simon B, Schütz U, Sattler M, Yoon HS. Functional role of the flexible N-terminal extension of FKBP38 in catalysis. Sci Rep 2013; 3:2985. [PMID: 24145868 PMCID: PMC3804861 DOI: 10.1038/srep02985] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 09/30/2013] [Indexed: 11/09/2022] Open
Abstract
FKBP38 regulates apoptosis through unique interactions with multiple regulators including Bcl-2. Interestingly, the peptidylprolyl isomerase activity of FKBP38 is only detectable when it binds to calcium-saturated calmodulin (CaM/Ca2+). This, in turn, permits the formation of a complex with Bcl-2. FKBP38 thereby provides an important link between isomerase activity and apoptotic pathways. Here, we show that the N-terminal extension (residues 1-32) preceding the catalytic domain of FKBP38 has an autoinhibitory activity. The core isomerase activity of FKBP38 is inhibited by transient interactions involving the flexible N-terminal extension that precedes the catalytic domain. Notably, CaM/Ca2+ binds to this N-terminal extension and thereby releases the autoinhibitory contacts between the N-terminal extension and the catalytic domain, thus potentiating the isomerase activity of FKBP38. Our data demonstrate how CaM/Ca2+ modulates the catalytic activity of FKBP38.
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Affiliation(s)
- Congbao Kang
- 1] School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore [2] [3]
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49
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Choi BH, Chakraborty G, Baek K, Yoon HS. Aspirin-induced Bcl-2 translocation and its phosphorylation in the nucleus trigger apoptosis in breast cancer cells. Exp Mol Med 2013; 45:e47. [PMID: 24113271 PMCID: PMC3809363 DOI: 10.1038/emm.2013.91] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 05/14/2013] [Accepted: 06/24/2013] [Indexed: 12/21/2022] Open
Abstract
Here, we report that B-cell lymphoma 2 (Bcl-2) is a novel target molecule of aspirin in breast cancer cells. Aspirin influenced the formation of a complex by Bcl-2 and FKBP38 and induced the nuclear translocation of Bcl-2 and its phosphorylation. These events inhibited cancer cell proliferation and subsequently enhanced MCF-7 breast cancer cell apoptosis. Bcl-2 knockdown using small interfering RNA (siRNA) delayed apoptotic cell death, which correlated with increased proliferation following aspirin exposure. In contrast, Bcl-2 overexpression enhanced the onset of aspirin-induced apoptosis, which was also associated with a significant increase in Bcl-2 phosphorylation in the nucleus. Therefore, this study may provide novel insight into the molecular mechanism of aspirin, particularly its anticancer effects in Bcl-2- and estrogen receptor-positive breast cancer cells.
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Affiliation(s)
- Bo-Hwa Choi
- 1] School of Biological Science, Nanyang Technological University, Singapore, Singapore [2] Pohang Center for Evaluation of Biomaterials, Pohang Technopark, Pohang, South Korea
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50
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He S, Ni D, Ma B, Lee JH, Zhang T, Ghozalli I, Pirooz SD, Zhao Z, Bharatham N, Li B, Oh S, Lee WH, Takahashi Y, Wang HG, Minassian A, Feng P, Deretic V, Pepperkok R, Tagaya M, Yoon HS, Liang C. PtdIns(3)P-bound UVRAG coordinates Golgi-ER retrograde and Atg9 transport by differential interactions with the ER tether and the beclin 1 complex. Nat Cell Biol 2013; 15:1206-1219. [PMID: 24056303 PMCID: PMC3805255 DOI: 10.1038/ncb2848] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 08/21/2013] [Indexed: 12/14/2022]
Abstract
Endoplasmic reticulum (ER)-Golgi membrane transport and autophagy are intersecting trafficking pathways that are tightly regulated and crucial for homeostasis, development and disease. Here, we identify UVRAG, a beclin-1-binding autophagic factor, as a phosphatidylinositol-3-phosphate (PtdIns(3)P)-binding protein that depends on PtdIns(3)P for its ER localization. We further show that UVRAG interacts with RINT-1, and acts as an integral component of the RINT-1-containing ER tethering complex, which couples phosphoinositide metabolism to COPI-vesicle tethering. Displacement or knockdown of UVRAG profoundly disrupted COPI cargo transfer to the ER and Golgi integrity. Intriguingly, autophagy caused the dissociation of UVRAG from the ER tether, which in turn worked in concert with the Bif-1-beclin-1-PI(3)KC3 complex to mobilize Atg9 translocation for autophagosome formation. These findings identify a regulatory mechanism that coordinates Golgi-ER retrograde and autophagy-related vesicular trafficking events through physical and functional interactions between UVRAG, phosphoinositide and their regulatory factors, thereby ensuring spatiotemporal fidelity of membrane trafficking and maintenance of organelle homeostasis.
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Affiliation(s)
- Shanshan He
- Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, CA 90033, USA
| | - Duojiao Ni
- Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, CA 90033, USA
| | - Binyun Ma
- Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, CA 90033, USA
| | - Joo-Hyung Lee
- Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, CA 90033, USA
| | - Tian Zhang
- Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, CA 90033, USA
| | - Irene Ghozalli
- Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, CA 90033, USA
| | - Sara Dolatshahi Pirooz
- Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, CA 90033, USA
| | - Zhen Zhao
- Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, CA 90033, USA
| | - Nagakumar Bharatham
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Baihong Li
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Soohwan Oh
- Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, CA 90033, USA
| | - Wen-Hwa Lee
- Department of Biological Chemistry, University of California, Irvine, Irvine, California 92697
| | - Yoshinori Takahashi
- Department of Pharmacology and Penn State Hershey Cancer Institute; The Pennsylvania State University College of Medicine; Hershey, PA USA
| | - Hong-Gang Wang
- Department of Pharmacology and Penn State Hershey Cancer Institute; The Pennsylvania State University College of Medicine; Hershey, PA USA
| | - Arlet Minassian
- Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, CA 90033, USA
| | - Pinghui Feng
- Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, CA 90033, USA
| | - Vojo Deretic
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131
| | - Rainer Pepperkok
- European Molecular Biology Laboratory, Heidelberg, Cell Biology/Cell Biophysics Unit, Meyerhofstr. 1, D-69117 Heidelberg Germany
| | - Mitsuo Tagaya
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0393, Japan
| | - Ho Sup Yoon
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore 637551
- Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea
| | - Chengyu Liang
- Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, CA 90033, USA
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