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Ratanabunyong S, Siriwaseree J, Wanaragthai P, Krobthong S, Yingchutrakul Y, Kuaprasert B, Choowongkomon K, Aramwit P. Exploring the apoptotic effects of sericin on HCT116 cells through comprehensive nanostring transcriptomics and proteomics analysis. Sci Rep 2024; 14:2366. [PMID: 38287097 PMCID: PMC10825148 DOI: 10.1038/s41598-024-52789-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 01/23/2024] [Indexed: 01/31/2024] Open
Abstract
Sericin, a silk protein from Bombyx mori (silkworms), has many applications, including cosmetics, anti-inflammation, and anti-cancer. Sericin complexes with nanoparticles have shown promise for breast cancer cell lines. Apoptosis, a programmed cell death mechanism, stops cancer cell growth. This study found that Sericin urea extract significantly affected HCT116 cell viability (IC50 = 42.00 ± 0.002 µg/mL) and caused apoptosis in over 80% of treated cells. S-FTIR analysis showed significant changes in Sericin-treated cells' macromolecule composition, particularly in the lipid and nucleic acid areas, indicating major cellular modifications. A transcriptomics study found upregulation of the apoptotic signaling genes FASLG, TNFSF10, CASP3, CASP7, CASP8, and CASP10. Early apoptotic proteins also showed that BAD, AKT, CASP9, p53, and CASP8 were significantly upregulated. A proteomics study illuminated Sericin-treated cells' altered protein patterns. Our results show that Sericin activated the extrinsic apoptosis pathway via the caspase cascade (CASP8/10 and CASP3/7) and the death receptor pathway, involving TNFSF10 or FASLG, in HCT116 cells. Upregulation of p53 increases CASP8, which activates CASP3 and causes HCT116 cell death. This multi-omics study illuminates the molecular mechanisms of Sericin-induced apoptosis, sheds light on its potential cancer treatment applications, and helps us understand the complex relationship between silk-derived proteins and cellular processes.
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Affiliation(s)
- Siriluk Ratanabunyong
- Department of Pharmacy Practice, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Jeeraprapa Siriwaseree
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Panatda Wanaragthai
- Interdisciplinary Graduate Program in Genetic Engineering, Kasetsart University, Bangkok, 10900, Thailand
| | - Sucheewin Krobthong
- Thailand Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Yodying Yingchutrakul
- National Center for Genetic Engineering and Biotechnology, NSTDA, Pathum Thani, 12120, Thailand
| | - Buabarn Kuaprasert
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
- Interdisciplinary Graduate Program in Genetic Engineering, Kasetsart University, Bangkok, 10900, Thailand.
| | - Pornanong Aramwit
- Department of Pharmacy Practice, Faculty of Pharmaceutical Sciences and Center of Excellence in Bioactive Resources for Innovative Clinical Applications, Chulalongkorn University, Phayathai Road, Phatumwan, Bangkok, 10330, Thailand.
- The Academy of Science, The Royal Society of Thailand, Dusit, Bangkok, 10330, Thailand.
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Wongkhieo S, Tangmesupphaisan W, Siriwaseree J, Aramsirirujiwet Y, Wiriyajitsomboon P, Kaewgrajang T, Pumloifa S, Paemanee A, Kuaprasert B, Choowongkomon K, Chester AH, Swainson NM. In vitro cholesterol lowering activity of Ganoderma australe mycelia based on mass spectrometry, synchrotron Fourier-transform infrared analysis and liver-spheroid bioactivity. Sci Rep 2023; 13:13619. [PMID: 37604902 PMCID: PMC10442327 DOI: 10.1038/s41598-023-40861-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/17/2023] [Indexed: 08/23/2023] Open
Abstract
Mycelia were cultivated from a Thai wild mushroom identified as Ganoderma australe based on polymerase chain reaction (PCR) and morphological analyses. The mycelial extracts were examined for their active ingredients using a liquid chromatography-tandem mass spectrometry (LC‒MS/MS) method. This revealed the presence of lovastatin and tentative compounds including p-coumaric, nicotinamide, gamma-aminobutyric acid, choline, nucleosides, amino acids, and saccharides. The extracts had an inhibitory effect on the activity of HMG-CoA reductase in a concentration-dependent manner. At 2.5 mg/mL, the G. australe extracts did not interfere with the viability of HepG2 spheroids, but their biochemical composition was altered as determined by Fourier-transform infrared (FTIR) spectroscopy. The lipid profile of the spheroids treated with the mycelial extract was distinct from that of the control and the 5 µM lovastatin treatment, corresponding with the production of cholesterol by the spheroids. The mycelia of G. australe increased the percentage of high-density lipoprotein (HDL) production to 71.35 ± 2.74%, compared to the control and lovastatin-treated spheroids (33.26 ± 3.15% and 32.13 ± 3.24%, respectively). This study revealed the superior effect of natural compound mixtures to pure lovastatin, and the potential use of Thailand's wild G. australe as a functional food to prevent or alleviate hypercholesterolemia.
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Affiliation(s)
- Sudthirak Wongkhieo
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | | | - Jeeraprapa Siriwaseree
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Yaovapa Aramsirirujiwet
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | | | - Tharnrat Kaewgrajang
- Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan Rd, Lat Yao, Chatuchak, Bangkok, 10900, Thailand
| | - Saifa Pumloifa
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Atchara Paemanee
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Buabarn Kuaprasert
- Research Facility Department, Synchrotron Light Research Institute (Public Organization), 111 University Avenue, Muang District, Nakhon Ratchasima, 30000, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Adrian H Chester
- Heart Science Centre, Magdi Yacoub Institute, Harefield, UK
- National Heart and Lung Institute (NHLI), Imperial College London, London, UK
| | - Napachanok M Swainson
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
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Paemanee A, Rattanabunyong S, Ketngamkum Y, Siriwaseree J, Pongpamorn P, Romyanon K, Tangphatsornruang S, Kuaprasert B, Choowongkomon K. Mass spectrometry and synchrotron-FTIR microspectroscopy reveal the anti-inflammatory activity of Bua Bok extracts. Phytochem Anal 2022; 33:1086-1098. [PMID: 35790045 DOI: 10.1002/pca.3161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
INTRODUCTION Bua Bok or Centella asiatica (CA) is an Asian vegetable with anti-inflammatory benefits. Asiaticoside, asiatic acid, madecassoside and madecassic have been characterised as major active ingredients with a wide range of pharmacological advantages. In manufacturing processes, high-performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LCMS) are used to routinely determine the active compounds in raw materials. OBJECTIVES This research aims to explore anti-inflammatory properties, characterise metabolites and observe the biochemical changes of the inflammatory induced macrophages after pretreatment with the potential extracted fractions. METHODS Bua Bok leaf extracts were prepared. Macrophages were pretreated with non-toxic fractions to determine the anti-inflammatory action. Tentative metabolites of effective fractions were identified by LC-MS. Synchrotron fourier-transform infrared (S-FTIR) microspectroscopy was utilised to observe the biochemical change of the lipopolysaccharide (LPS)-induced cells after pretreatment with potential fractions. RESULTS Fractions of ethyl acetate, 30% and 100% ethanol highly increased the nitrile scavenging and suppressed the function of phospholipase A2 . Fractions of 70% and 100% ethanol strongly decreased nitric oxide production. The comparison of 39 chemical compounds was presented. The change of proteins was improved after pretreatment of macrophages with fraction 70% ethanol. Fraction of 100% ethanol revealed the lipid accumulation was lower than 70% ethanol and diclofenac. CONCLUSION While the anti-inflammatory actions of 70% and 100% ethanol were similar. S-FTIR expressed they inhibited inflammatory response with the distinct features of biomolecules. The S-FTIR, LC-MS and biological assay confidently provided the efficient strategies to inform the advantage of herbal extract on cellular organisation instead of a single compound.
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Affiliation(s)
- Atchara Paemanee
- National Omics Centre, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | | | - Yanisa Ketngamkum
- National Omics Centre, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | | | - Ponkanok Pongpamorn
- National Omics Centre, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Kanokwan Romyanon
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | | | - Buabarn Kuaprasert
- Research Facility Department, Synchrotron Light Research Institute (Public Organisation), Nakhon Ratchasima, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Centre for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
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Kuaprasert B, Chitnumsub P, Leartsakulpanich U, Suginta W, Leelayoova S, Mungthin M, Sitthichot N, Rattanabunyong S, Kiriwan D, Choowongkomon K. Dual role of azo compounds in inhibiting Plasmodium falciparum adenosine deaminase and hemozoin biocrystallization. Exp Parasitol 2022; 243:108384. [PMID: 36154837 DOI: 10.1016/j.exppara.2022.108384] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 08/09/2022] [Accepted: 09/17/2022] [Indexed: 11/28/2022]
Abstract
Protein-ligand (GOLD) docking of the NCI compounds into the ligand-binding site of Plasmodium falciparum adenosine deaminase (PfADA) identified three most active azo compounds containing 4-[(4-hydroxy-2-oxo-1H-quinolin-3-yl) moiety. These compounds showed IC50 of 3.7-15.4 μM against PfADA, as well as inhibited the growth of P. falciparum strains 3D7 (chloroquine (CQ)-sensitive) and K1 (CQ-resistant) with IC50 of 1.8-3.1 and 1.7-3.6 μM, respectively. The identified compounds have structures similar to the backbone structure (4-N-(7-chloroquinolin-4-yl)) in CQ, and NSC45545 could mimic CQ by inhibiting the bioformation of hemozoin in parasitic food vacuole. The amount of in situ hemozoin in the ring-stage parasite was determined using a combination of synchrotron transmission Fourier transform infrared microspectroscopy and Principal Component Analysis. Stretching of the C-O bond of hemozoin propionate group measured at 1220-1210 cm-1 in untreated intraerythrocytic P. falciparum strains 3D7 and K1 was disappeared following treatment with 1.85 and 1.74 μM NSC45545, similar to those treated with 0.02 and 0.13 μM CQ, respectively. These findings indicate a novel dual function of 4-[(4-hydroxy-2-oxo-1H-quinolin-3-yl) azo compounds in inhibiting both PfADA and in situ hemozoin biocrystallization. These lead compounds hold promise for further development of new antimalarial therapeutics that could delay the onset of parasitic drug resistance.
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Affiliation(s)
- Buabarn Kuaprasert
- Research and Facility Department, Synchrotron Light Research Institute (Public Organization), 111 University Avenue, Muang District, Nakhon Ratchasima, 30000, Thailand.
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Phahon Yothin Road, Klong Luang, Pathumthani, 12120, Thailand
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Phahon Yothin Road, Klong Luang, Pathumthani, 12120, Thailand
| | - Wipa Suginta
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Payupnai, Wangchan, Rayong, 21210, Thailand
| | - Saovanee Leelayoova
- Department of Parasitology, Phramongkutklao College of Medicine, 317 Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Mathirut Mungthin
- Department of Parasitology, Phramongkutklao College of Medicine, 317 Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Naruemon Sitthichot
- Department of Parasitology, Phramongkutklao College of Medicine, 317 Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Siriluk Rattanabunyong
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Ladyaow, Chatuchak, Bangkok, 10900, Thailand
| | - Duangnapa Kiriwan
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Ladyaow, Chatuchak, Bangkok, 10900, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Ladyaow, Chatuchak, Bangkok, 10900, Thailand; Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, 50 Ngam Wong Wan Road, Ladyaow, Chatuchak, Kasetsart University, Bangkok, 10700, Thailand
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5
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Siriwaseree J, Sanachai K, Aiebchun T, Tabtimmai L, Kuaprasert B, Choowongkomon K. Synchrotron Fourier Transform Infrared Microscopy Spectra in Cellular Effects of Janus Kinase Inhibitors on Myelofibrosis Cancer Cells. ACS Omega 2022; 7:22797-22803. [PMID: 35811912 PMCID: PMC9260937 DOI: 10.1021/acsomega.2c02404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Janus kinase (JAK) deregulation of the JAK/signal transducers and activators of transcription pathway leads to myelofibrosis that can be treated by JAK inhibitors including Ruxolitinib and Tofacitinib. Even though both inhibitors are effective against myelofibrosis, each of them has a different mode of action in the cells. Ruxolitinib is an inhibitor for selective JAK1/2, and Tofacitinib is an inhibitor for JAK3. This study evaluated the chemical fingerprints of TF-1 cells after JAK inhibitor treatments by the synchrotron Fourier transform infrared microspectroscopy (S-FTIR) spectrum. Tofacitinib and Ruxolitinib treatments in TF-1 cells were applied with a chemical fingerprint approach in S-FTIR spectroscopy and in vitro cytotoxicity in a cell-based assay. Principal component analysis or PCA was utilized to classify three cell treatments with three biochemical alteration absorbances of lipid vibration by the C-H stretching, protein amide I that appeared from the C=O stretching, and a P=O phosphodiester bond from nucleic acids. The results showed that the inhibition effect of Ruxolitinib on the TF-1 cell lines was two-fold higher than Tofacitinib. PCA distinguishes untreated and drug-treated cells by detecting cellular biochemical alteration. The loading plots identify that proteins and nucleic acids were the different main components in disparate cell treatments. Tofacitinib was distinct from the others in lipid and nucleic acid. The second derivative spectra of the three molecular components had decreased lipid production and accumulation, changes in secondary structures in proteins, and a high level of RNA overexpression in cell treatment. The JAK inhibitors caused different spectroscopic biomarkers of the modifications of secondary protein conformation, stimulated cell lipid accumulation, and phosphorylation from untreated cells. The alteration of cellular biochemical components suggests that FTIR is a potential tool to analyze specific patterns of drug cellular responses at the molecular level.
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Affiliation(s)
- Jeeraprapa Siriwaseree
- Faculty
of Science, Department of Biochemistry, Kasetsart University, Bangkok 10900, Thailand
| | - Kamonpan Sanachai
- Faculty
of Science, Department of Biochemistry, Structural and Computational
Biology Research Unit, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thitinan Aiebchun
- Faculty
of Science, Department of Biochemistry, Kasetsart University, Bangkok 10900, Thailand
| | - Lueacha Tabtimmai
- Faculty
of Applied Science, Department of Biotechnology, King Mongkut’s University of Technology of North Bangkok, Bangkok 10800, Thailand
| | - Buabarn Kuaprasert
- Synchrotron
Light Research Institute (Public Organization), Nakhon Ratchasrima 30000, Thailand
| | - Kiattawee Choowongkomon
- Faculty
of Science, Department of Biochemistry, Kasetsart University, Bangkok 10900, Thailand
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Boonsri B, Choowongkomon K, Kuaprasert B, Thitiphatphuvanon T, Supradit K, Sayinta A, Duangdara J, Rudtanatip T, Wongprasert K. Probing the Anti-Cancer Potency of Sulfated Galactans on Cholangiocarcinoma Cells Using Synchrotron FTIR Microspectroscopy, Molecular Docking, and In Vitro Studies. Mar Drugs 2021; 19:md19050258. [PMID: 33946151 PMCID: PMC8145517 DOI: 10.3390/md19050258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 03/19/2021] [Revised: 04/24/2021] [Accepted: 04/28/2021] [Indexed: 12/13/2022] Open
Abstract
Sulfated galactans (SG) isolated from red alga Gracilaria fisheri have been reported to inhibit the growth of cholangiocarcinoma (CCA) cells, which was similar to the epidermal growth factor receptor (EGFR)-targeted drug, cetuximab. Herein, we studied the anti-cancer potency of SG compared to cetuximab. Biological studies demonstrated SG and cetuximab had similar inhibition mechanisms in CCA cells by down-regulating EGFR/ERK pathway, and the combined treatment induced a greater inhibition effect. The molecular docking study revealed that SG binds to the dimerization domain of EGFR, and this was confirmed by dimerization assay, which showed that SG inhibited ligand-induced EGFR dimer formation. Synchrotron FTIR microspectroscopy was employed to examine alterations in cellular macromolecules after drug treatment. The SR-FTIR-MS elicited similar spectral signatures of SG and cetuximab, pointing towards the bands of RNA/DNA, lipids, and amide I vibrations, which were inconsistent with the changes of signaling proteins in CCA cells after drug treatment. Thus, this study demonstrates the underlined anti-cancer mechanism of SG by interfering with EGFR dimerization. In addition, we reveal that FTIR signature spectra offer a useful tool for screening anti-cancer drugs’ effect.
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Affiliation(s)
- Boonyakorn Boonsri
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (B.B.); (K.S.); (A.S.); (J.D.)
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
| | - Buabarn Kuaprasert
- Research and Facility Division, Synchrotron Light Research Institute (Public Organization), Nakhorn Ratchasima 30000, Thailand;
| | | | - Kittiya Supradit
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (B.B.); (K.S.); (A.S.); (J.D.)
| | - Apinya Sayinta
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (B.B.); (K.S.); (A.S.); (J.D.)
| | - Jinchutha Duangdara
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (B.B.); (K.S.); (A.S.); (J.D.)
| | - Tawut Rudtanatip
- Department of Anatomy, Faculty of Medicine, Khon Kean University, Khon Kean 40002, Thailand;
| | - Kanokpan Wongprasert
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (B.B.); (K.S.); (A.S.); (J.D.)
- Correspondence: ; Tel.: +66-2201-5412
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7
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Tabtimmai L, Srisook P, Kuaprasert B, Thumanu K, Choowongkomon K. FTIR spectra signatures reveal different cellular effects of EGFR inhibitors on nonsmall cell lung cancer cells. J Biophotonics 2020; 13:e201960012. [PMID: 31595681 DOI: 10.1002/jbio.201960012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/25/2019] [Accepted: 10/02/2019] [Indexed: 06/10/2023]
Abstract
ATP-analogue inhibitors, Gefitinib (Iressa) and Erlotinib (Tarceva) had been approved for advanced and metastatic nonsmall cell lung cancer (NSCLC) cells against tyrosine kinase domain of epidermal growth factor receptor (EGFR). Many techniques have been developed to better understand the drug mechanism which is multistep, time-consuming and expensive. Herein, we performed Fourier-transform infrared (FTIR) microscopy for evaluating the biochemical change on NSCLC (A549) cells after treatment. At levels that produced equivalent effects, Gefitinib dramatically induced cell apoptosis via impaired mitochondrial transmembrane potential. Whereas, Erlotinib had a slight effect on A549. Principal component analysis was performed to distinguish the effect of EGFR inhibitors on A549. FTIR spectra regions were divided into three regions: lipids (3000-2800 cm-1 ), proteins (1700-1500 cm-1 ) and carbohydrates and nuclei acids (1200-1000 cm-1 ). Biochemical changes can be evaluated by these spectral regions. This work may be a novel concept for utilizing FTIR spectroscopy for high-throughput discriminative effects of a drug or compound and its derivatives on cells.
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Affiliation(s)
- Lueacha Tabtimmai
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Pimonwan Srisook
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Buabarn Kuaprasert
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasrima, Thailand
| | - Kanjana Thumanu
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasrima, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
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Jaruwat A, Riangrungroj P, Ubonprasert S, Sae-Ueng U, Kuaprasert B, Yuthavong Y, Leartsakulpanich U, Chitnumsub P. Crystal structure of Plasmodium falciparum adenosine deaminase reveals a novel binding pocket for inosine. Arch Biochem Biophys 2019; 667:6-13. [PMID: 31002765 DOI: 10.1016/j.abb.2019.04.002] [Citation(s) in RCA: 4] [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: 01/08/2019] [Revised: 03/14/2019] [Accepted: 04/11/2019] [Indexed: 10/27/2022]
Abstract
Plasmodium falciparum (Pf), a malarial pathogen, can only synthesize purine nucleotides employing a salvage pathway because it lacks de novo biosynthesis. Adenosine deaminase (ADA), one of the three purine salvage enzymes, catalyzes the irreversible hydrolytic deamination of adenosine to inosine, which is further converted to GMP and AMP for DNA/RNA production. In addition to adenosine conversion, Plasmodium ADA also catalyzes the conversion of 5'-methylthioadenosine, derived from polyamine biosynthesis, into 5'-methylthioinosine whereas the human enzyme is not capable of this function. Here we report the crystal structure of a surface engineered PfADA at a resolution of 2.48 Å, together with results on kinetic studies of PfADA wild-type and active site variants. The structure reveals a novel inosine binding pocket linked to a distinctive PfADA substructure (residues 172-179) derived from a non-conserved gating helix loop (172-188) in Plasmodium spp. and other ADA enzymes. Variants of PfADA and human (h) ADA active site amino acids were generated in order to study their role in catalysis, including PfADA- Phe136, -Thr174, -Asp176, and -Leu179, and hADA-Met155, equivalent to PfADA-Asp176. PfADA-Leu179His showed no effect on kinetic parameters. However, kinetic results of PfADA-Asp176Met/Ala mutants and hADA-Met155Asp/Ala showed that the mutation reduced adenosine and 5'-methylthioadenosine substrate affinity in PfADA and kcat in hADA, thereby reducing catalytic efficiency of the enzyme. Phe136Leu mutant showed increased Km (>10-fold) for both substrates whereas Thr174Ile/Ala only affected 5'-methylthioadenosine binding affinity. Together, the structure with the novel inosine binding pocket and the kinetic data provide insights for rational design of inhibitors against PfADA.
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Affiliation(s)
- Aritsara Jaruwat
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand
| | - Pinpunya Riangrungroj
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand
| | - Sakunrat Ubonprasert
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand
| | - Udom Sae-Ueng
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand
| | - Buabarn Kuaprasert
- Synchrotron Light Research Institute (Public Organization), 111 Suranaree University Avenue, Suranaree Sub-district, Muang, Nakhon Ratchasima, 30000, Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand.
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand.
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Uawonggul N, Sukprasert S, Incamnoi P, Patramanon R, Thammasirirak S, Preecharram S, Bunyatratchata W, Kuaprasert B, Daduang J, Daduang S. Bacterial overexpression of recombinant heteroscorpine-1 (rHS-1), a toxin from Heterometrus laoticus scorpion venom: trends for antibacterial application and antivenom production. Biochem Genet 2014; 52:459-73. [PMID: 24980735 DOI: 10.1007/s10528-014-9660-y] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 06/05/2014] [Indexed: 11/26/2022]
Abstract
Heteroscorpine-1 (HS-1) was identified as a member of the scorpine family. HS-1 shows insecticidal activities, exhibiting a low median lethal dose (LD50) in mealworm (Tenebrio molitor L.) and inhibitory activities against Bacillus subtilis, Klebsiella pneumoniae, and Pseudomonas aeruginosa. In this study, a recombinant HS-1 (rHS-1) was produced by overexpression in E. coli. A large yield of product was obtained. The structure of purified rHS-1 was confirmed through mass spectrometry. Both anti-crude venom and anti-rHS-1 antibodies specifically recognized rHS-1, suggesting its structural similarity. Reactivated rHS-1 caused roughening and blebbing of bacterial cell surfaces. It showed higher activity than that of pre-refolded protein. Antisera raised against a partially purified and mis- or unfolded peptide can inhibit relevant bioactivity.
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Affiliation(s)
- Nunthawun Uawonggul
- Department of Biochemistry, Faculty of Science, Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, 40002, Thailand
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Pengthaisong S, Chen CF, Withers SG, Kuaprasert B, Ketudat Cairns JR. Rice BGlu1 glycosynthase and wild type transglycosylation activities distinguished by cyclophellitol inhibition. Carbohydr Res 2012; 352:51-9. [DOI: 10.1016/j.carres.2012.02.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 02/06/2012] [Accepted: 02/10/2012] [Indexed: 11/29/2022]
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Pengthaisong S, Withers SG, Kuaprasert B, Svasti J, Cairns JRK. The role of the oligosaccharide binding cleft of rice BGlu1 in hydrolysis of cellooligosaccharides and in their synthesis by rice BGlu1 glycosynthase. Protein Sci 2012; 21:362-72. [PMID: 22238157 DOI: 10.1002/pro.2021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Revised: 12/26/2011] [Accepted: 12/27/2011] [Indexed: 11/11/2022]
Abstract
Rice BGlu1 β-glucosidase nucleophile mutant E386G is a glycosynthase that can synthesize p-nitrophenyl (pNP)-cellooligosaccharides of up to 11 residues. The X-ray crystal structures of the E386G glycosynthase with and without α-glucosyl fluoride were solved and the α-glucosyl fluoride complex was found to contain an ordered water molecule near the position of the nucleophile of the BGlu1 native structure, which is likely to stabilize the departing fluoride. The structures of E386G glycosynthase in complexes with cellotetraose and cellopentaose confirmed that the side chains of N245, S334, and Y341 interact with glucosyl residues in cellooligosaccharide binding subsites +2, +3, and +4. Mutants in which these residues were replaced in BGlu1 β-glucosidase hydrolyzed cellotetraose and cellopentaose with k(cat) /K(m) values similar to those of the wild type enzyme. However, the Y341A, Y341L, and N245V mutants of the E386G glycosynthase synthesize shorter pNP-cellooligosaccharides than do the E386G glycosynthase and its S334A mutant, suggesting that Y341 and N245 play important roles in the synthesis of long oligosaccharides. X-ray structural studies revealed that cellotetraose binds to the Y341A mutant of the glycosynthase in a very different, alternative mode not seen in complexes with the E386G glycosynthase, possibly explaining the similar hydrolysis, but poorer synthesis of longer oligosaccharides by Y341 mutants.
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Affiliation(s)
- Salila Pengthaisong
- Schools of Biochemistry and Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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Kuaprasert B, Silprasit K, Horata N, Khunrae P, Wongpanya R, Boonyalai N, Vanavichit A, Choowongkomon K. Purification, crystallization and preliminary X-ray analysis of recombinant betaine aldehyde dehydrogenase 2 (OsBADH2), a protein involved in jasmine aroma, from Thai fragrant rice (Oryza sativa L.). Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1221-3. [PMID: 22102032 DOI: 10.1107/s1744309111030971] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2011] [Accepted: 08/01/2011] [Indexed: 11/10/2022]
Abstract
Fragrant rice (Oryza sativa L.) betaine aldehyde dehydrogenase 2 (OsBADH2) is a key enzyme in the synthesis of fragrance aroma compounds. The extremely low activity of OsBADH2 in catalyzing the oxidation of acetaldehyde is believed to be crucial for the accumulation of the volatile compound 2-acetyl-1-pyrroline (2AP) in many scented plants, including fragrant rice. Recombinant fragrant rice OsBADH2 was expressed in Escherichia coli as an N-terminal hexahistidine fusion protein, purified using Ni Sepharose affinity chromatography and crystallized using the microbatch method. Initial crystals were obtained within 24 h using 0.1 M Tris pH 8.5 with 30%(w/v) PEG 4000 and 0.2 M magnesium chloride as the precipitating agent at 291 K. Crystal quality was improved when the enzyme was cocrystallized with NAD(+). Improved crystals were grown in 0.1 M HEPES pH 7.4, 24%(w/v) PEG 4000 and 0.2 M ammonium chloride and diffracted to beyond 2.95 Å resolution after being cooled in a stream of N(2) immediately prior to X-ray diffraction experiments. The crystals belonged to space group C222(1), with unit-cell parameters a = 66.03, b = 183.94, c = 172.28 Å. An initial molecular-replacement solution has been obtained and refinement is in progress.
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Affiliation(s)
- Buabarn Kuaprasert
- Synchrotron Light Research Institute (Public Organization), 111 University Avenue, Muang District, Nakhon Ratchasima 30000, Thailand.
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Sansenya S, Opassiri R, Kuaprasert B, Chen CJ, Ketudat Cairns JR. The crystal structure of rice (Oryza sativa L.) Os4BGlu12, an oligosaccharide and tuberonic acid glucoside-hydrolyzing β-glucosidase with significant thioglucohydrolase activity. Arch Biochem Biophys 2011; 510:62-72. [DOI: 10.1016/j.abb.2011.04.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2011] [Revised: 04/08/2011] [Accepted: 04/10/2011] [Indexed: 11/17/2022]
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Katekaew S, Kuaprasert B, Torikata T, Kakuta Y, Kimura M, Yoneda K, Araki T. Structure of the newly found green turtle egg-white ribonuclease. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:755-9. [PMID: 20606267 DOI: 10.1107/s1744309110016751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Accepted: 05/07/2010] [Indexed: 11/10/2022]
Abstract
Marine green turtle (Chelonia mydas) egg-white ribonuclease (GTRNase) was crystallized from 1.1 M ammonium sulfate pH 5.5 and 30% glycerol using the sitting-drop vapour-diffusion method. The structure of GTRNase has been solved at 1.60 A resolution by the molecular-replacement technique using a model based on the structure of RNase 5 (murine angiogenin) from Mus musculus (46% identity). The crystal belonged to the monoclinic space group C2, with unit-cell parameters a = 86.271, b = 34.174, c = 39.738 A, alpha = 90, beta = 102, gamma = 90 degrees . GTRNase consists of three helices and seven beta-strands and displays the alpha+beta folding topology typical of a member of the RNase A superfamily. Superposition of the C(alpha) coordinates of GTRNase and RNase A superfamily members indicates that the overall structure is highly similar to that of angiogenin or RNase 5 from M. musculus (PDB code 2bwl) and RNase A from Bos taurus (PDB code 2blz), with root-mean-square deviations of 3.9 and 2.0 A, respectively. The catalytic residues are conserved with respect to the RNase A superfamily. The three disulfide bridges observed in the reptilian enzymes are conserved in GTRNase, while one further disulfide bond is required for the structural stability of mammalian RNases. GTRNase is expressed in egg white and the fact that its sequence has the highest similarity to that of snapping turtle pancreatic RNase suggests that the GTRNase secreted from oviduct cells to form egg white is probably the product of the same gene as activated in pancreatic cells.
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Affiliation(s)
- Somporn Katekaew
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen 42000, Thailand
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Nowicki MW, Kuaprasert B, McNae IW, Morgan HP, Harding MM, Michels PAM, Fothergill-Gilmore LA, Walkinshaw MD. Crystal structures of Leishmania mexicana phosphoglycerate mutase suggest a one-metal mechanism and a new enzyme subclass. J Mol Biol 2009; 394:535-43. [PMID: 19781556 DOI: 10.1016/j.jmb.2009.09.041] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Revised: 09/11/2009] [Accepted: 09/16/2009] [Indexed: 01/23/2023]
Abstract
The structures of Leishmania mexicana cofactor-independent phosphoglycerate mutase (Lm iPGAM) crystallised with the substrate 3-phosphoglycerate at high and low cobalt concentrations have been solved at 2.00- and 1.90-A resolutions. Both structures are very similar and the active site contains both 3-phosphoglycerate and 2-phosphoglycerate at equal occupancies (50%). Lm iPGAM co-crystallised with the product 2-phosphoglycerate yields the same structure. Two Co(2+) are coordinated within the active site with different geometries and affinities. The cobalt at the M1 site has a distorted octahedral geometry and is present at 100% occupancy. The M2-site Co(2+) binds with distorted tetrahedral geometry, with only partial occupancy, and coordinates with Ser75, the residue involved in phosphotransfer. When the M2 site is occupied, the side chain of Ser75 adopts a position that is unfavourable for catalysis, indicating that this site may not be occupied under physiological conditions and that catalysis may occur via a one-metal mechanism. The geometry of the M2 site suggests that it is possible for Ser75 to be activated for phosphotransfer by H-bonding to nearby residues rather than by metal coordination. The 16 active-site residues of Lm iPGAM are conserved in the Mn-dependent iPGAM from Bacillus stearothermophilus (33% overall sequence identity). However, Lm iPGAM has an inserted tyrosine (Tyr210) that causes the M2 site to diminish in size, consistent with its reduced metal affinity. Tyr210 is present in trypanosomatid and plant iPGAMs, but not in the enzymes from other organisms, indicating that there are two subclasses of iPGAMs.
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Affiliation(s)
- Matthew W Nowicki
- Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, King's Buildings, Edinburgh, UK
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Seshadri S, Akiyama T, Opassiri R, Kuaprasert B, Cairns JK. Structural and enzymatic characterization of Os3BGlu6, a rice beta-glucosidase hydrolyzing hydrophobic glycosides and (1->3)- and (1->2)-linked disaccharides. Plant Physiol 2009; 151:47-58. [PMID: 19587102 PMCID: PMC2735989 DOI: 10.1104/pp.109.139436] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Accepted: 07/02/2009] [Indexed: 05/18/2023]
Abstract
Glycoside hydrolase family 1 (GH1) beta-glucosidases play roles in many processes in plants, such as chemical defense, alkaloid metabolism, hydrolysis of cell wall-derived oligosaccharides, phytohormone regulation, and lignification. However, the functions of most of the 34 GH1 gene products in rice (Oryza sativa) are unknown. Os3BGlu6, a rice beta-glucosidase representing a previously uncharacterized phylogenetic cluster of GH1, was produced in recombinant Escherichia coli. Os3BGlu6 hydrolyzed p-nitrophenyl (pNP)-beta-d-fucoside (k(cat)/K(m) = 67 mm(-1) s(-1)), pNP-beta-d-glucoside (k(cat)/K(m) = 6.2 mm(-1) s(-1)), and pNP-beta-d-galactoside (k(cat)/K(m) = 1.6 mm(-1)s(-1)) efficiently but had little activity toward other pNP glycosides. It also had high activity toward n-octyl-beta-d-glucoside and beta-(1-->3)- and beta-(1-->2)-linked disaccharides and was able to hydrolyze apigenin beta-glucoside and several other natural glycosides. Crystal structures of Os3BGlu6 and its complexes with a covalent intermediate, 2-deoxy-2-fluoroglucoside, and a nonhydrolyzable substrate analog, n-octyl-beta-d-thioglucopyranoside, were solved at 1.83, 1.81, and 1.80 A resolution, respectively. The position of the covalently trapped 2-F-glucosyl residue in the enzyme was similar to that in a 2-F-glucosyl intermediate complex of Os3BGlu7 (rice BGlu1). The side chain of methionine-251 in the mouth of the active site appeared to block the binding of extended beta-(1-->4)-linked oligosaccharides and interact with the hydrophobic aglycone of n-octyl-beta-d-thioglucopyranoside. This correlates with the preference of Os3BGlu6 for short oligosaccharides and hydrophobic glycosides.
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Affiliation(s)
- Supriya Seshadri
- School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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