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Voriconazole Eye Drops: Enhanced Solubility and Stability through Ternary Voriconazole/Sulfobutyl Ether β-Cyclodextrin/Polyvinyl Alcohol Complexes. Int J Mol Sci 2023; 24:ijms24032343. [PMID: 36768671 PMCID: PMC9917179 DOI: 10.3390/ijms24032343] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
Voriconazole (VCZ) is a broad-spectrum antifungal agent used to treat ocular fungal keratitis. However, VCZ has low aqueous solubility and chemical instability in aqueous solutions. This study aimed to develop VCZ eye drop formulations using cyclodextrin (CD) and water-soluble polymers, forming CD complex aggregates to improve the aqueous solubility and chemical stability of VCZ. The VCZ solubility was greatly enhanced using sulfobutyl ether β-cyclodextrin (SBEβCD). The addition of polyvinyl alcohol (PVA) showed a synergistic effect on VCZ/SBEβCD solubilization and a stabilization effect on the VCZ/SBEβCD complex. The formation of binary VCZ/SBEβCD and ternary VCZ/SBEβCD/PVA complexes was confirmed by spectroscopic techniques and in silico studies. The 0.5% w/v VCZ eye drop formulations were developed consisting of 6% w/v SBEβCD and different types and concentrations of PVA. The VCZ/SBEβCD systems containing high-molecular-weight PVA prepared under freeze-thaw conditions (PVA-H hydrogel) provided high mucoadhesion, sustained release, good ex vivo permeability through the porcine cornea and no sign of irritation. Additionally, PVA-H hydrogel was effective against the filamentous fungi tested. The stability study revealed that our VCZ eye drops provide a shelf-life of more than 2.5 years at room temperature, while a shelf-life of only 3.5 months was observed for the extemporaneous Vfend® eye drops.
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Early Life Stage Folic Acid Deficiency Delays the Neurobehavioral Development and Cognitive Function of Rat Offspring by Hindering De Novo Telomere Synthesis. Int J Mol Sci 2022; 23:ijms23136948. [PMID: 35805953 PMCID: PMC9266327 DOI: 10.3390/ijms23136948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 06/19/2022] [Accepted: 06/20/2022] [Indexed: 11/20/2022] Open
Abstract
Early life stage folate status may influence neurodevelopment in offspring. The developmental origin of health and disease highlights the importance of the period of the first 1000 days (from conception to 2 years) of life. This study aimed to evaluate the effect of early life stage folic acid deficiency on de novo telomere synthesis, neurobehavioral development, and the cognitive function of offspring rats. The rats were divided into three diet treatment groups: folate-deficient, folate-normal, and folate-supplemented. They were fed the corresponding diet from 5 weeks of age to the end of the lactation period. After weaning, the offspring rats were still fed with the corresponding diet for up to 100 days. Neurobehavioral tests, folic acid and homocysteine (Hcy) levels, relative telomere length in brain tissue, and uracil incorporation in telomere in offspring were measured at different time points. The results showed that folic acid deficiency decreased the level of folic acid, increased the level of Hcy of brain tissue in offspring, increased the wrong incorporation of uracil into telomeres, and hindered de novo telomere synthesis. However, folic acid supplementation increased the level of folic acid, reduced the level of Hcy of brain tissue in offspring, reduced the wrong incorporation of uracil into telomeres, and protected de novo telomere synthesis of offspring, which was beneficial to the development of early sensory-motor function, spatial learning, and memory in adolescence and adulthood. In conclusion, early life stage folic acid deficiency had long-term inhibiting effects on neurodevelopment and cognitive function in offspring.
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3
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Mahalapbutr P, Charoenwongpaiboon T, Phongern C, Kongtaworn N, Hannongbua S, Rungrotmongkol T. Molecular encapsulation of a key odor-active 2-acetyl-1-pyrroline in aromatic rice with β-cyclodextrin derivatives. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Solubility enhancement of poorly water soluble domperidone by complexation with the large ring cyclodextrin. Int J Pharm 2021; 606:120909. [PMID: 34298103 DOI: 10.1016/j.ijpharm.2021.120909] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/10/2021] [Accepted: 07/18/2021] [Indexed: 12/25/2022]
Abstract
The water solubility of domperidone (DMP) could be improved by complexation with large ring cyclodextrins (LR-CDs). LR-CDs contain a relatively hydrophobic cavity that is capable of entrapping the molecules to form inclusion complexes. The complex formation capability of mixture LR-CDs having a degree of polymerization (DP) of 22-48, with DMP was investigated. The phase solubility profile of mixture LR-CD/DMP was classified as AN-type, resulting in increased DMP solubility in water by 3-fold. Various physicochemical techniques confirmed the mixture LR-CD/DMP complex formation. Single LR-CD with DP of 26, 27, 28, 29, 30, 33 and 34 (CD26 ~ CD34) were isolated from LR-CD mixtures using ODS column for HPLC separation. The CD33/DMP complex has demonstrated the most significant improvement compared to other single LR-CD complexes with a 2.7-fold increase in DMP solubility. The molecular dynamic result revealed that DMP formed stable complexes with CD33 by positioned fully encapsulated inside the cavity and covered by 13-14 subunits of CD33.
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Glimelius B, Stintzing S, Marshall J, Yoshino T, de Gramont A. Metastatic colorectal cancer: Advances in the folate-fluoropyrimidine chemotherapy backbone. Cancer Treat Rev 2021; 98:102218. [PMID: 34015686 DOI: 10.1016/j.ctrv.2021.102218] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 12/22/2022]
Abstract
Notwithstanding recent treatment advances in metastatic colorectal cancer (mCRC), chemotherapy with a combination of a fluoropyrimidine and a folate agent, often 5-fluorouracil (5-FU) and leucovorin, remains the backbone of treatment regimens for the majority of patients with mCRC. This is despite a recent focus on molecular-targeted treatments and patient stratification according to mutational status or expression levels of specific genes. Intracellular folate concentration was discovered to be pivotal in the cytotoxic efficacy of 5-FU, paving the way to the current standard combination therapy approach. Subsequent discovery that systemic chemotherapy agents, such as irinotecan and oxaliplatin, can further increase the efficacy of 5-FU-based treatments led to the development of several combination chemotherapy regimens, including FOLFOX, FOLFIRI and FOLFOXIRI. Subsequent efforts to optimise 5-FU-based treatments have focused on 5-FU analogues, initially capecitabine and the combination drug tegafur/gimeracil/oteracil (S-1) and then TAS-102, which has recently been evaluated in phase 3 clinical trials for refractory colorectal cancer. Further approaches taken to improve the efficacy of 5-FU chemotherapy regimens have focused on optimising the route and dosing schedules and regulating folate metabolism. Pharmacokinetic variability caused by the requirement for metabolic conversion of leucovorin has been central to recent research, and the development of agents such as arfolitixorin which bypass the need for metabolic conversion remains promising for future therapeutic candidates. In this review, we summarise the evidence leading to the current treatment regimens employing 5-FU and leucovorin, focusing on recent approaches taken to optimise and refine treatments to improve clinical outcomes in patients with mCRC.
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Affiliation(s)
- Bengt Glimelius
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
| | - Sebastian Stintzing
- Department of Hematology, Oncology, and Tumor Immunology (CCM) Charité, University Medicine Berlin, Berlin, Germany
| | - John Marshall
- Georgetown University Medical Center, Washington, DC, USA
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Effect of Water Microsolvation on the Excited-State Proton Transfer of 3-Hydroxyflavone Enclosed in γ-Cyclodextrin. Molecules 2021; 26:molecules26040843. [PMID: 33562757 PMCID: PMC7914428 DOI: 10.3390/molecules26040843] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 12/19/2022] Open
Abstract
The effect of microsolvation on excited-state proton transfer (ESPT) reaction of 3-hydroxyflavone (3HF) and its inclusion complex with γ-cyclodextrin (γ-CD) was studied using computational approaches. From molecular dynamics simulations, two possible inclusion complexes formed by the chromone ring (C-ring, Form I) and the phenyl ring (P-ring, Form II) of 3HF insertion to γ-CD were observed. Form II is likely more stable because of lower fluctuation of 3HF inside the hydrophobic cavity and lower water accessibility to the encapsulated 3HF. Next, the conformation analysis of these models in the ground (S0) and the first excited (S1) states was carried out by density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations, respectively, to reveal the photophysical properties of 3HF influenced by the γ-CD. The results show that the intermolecular hydrogen bonding (interHB) between 3HF and γ-CD, and intramolecular hydrogen bonding (intraHB) within 3HF are strengthened in the S1 state confirmed by the shorter interHB and intraHB distances and the red-shift of O–H vibrational modes involving in the ESPT process. The simulated absorption and emission spectra are in good agreement with the experimental data. Significantly, in the S1 state, the keto form of 3HF is stabilized by γ-CD, explaining the increased quantum yield of keto emission of 3HF when complexing with γ-CD in the experiment. In the other word, ESPT of 3HF is more favorable in the γ-CD hydrophobic cavity than in aqueous solution.
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Verma K, Mahalapbutr P, Auepattanapong A, Khaikate O, Kuhakarn C, Takahashi K, Rungrotmongkol T. Molecular dynamics simulations of sulfone derivatives in complex with DNA topoisomerase IIα ATPase domain. J Biomol Struct Dyn 2020; 40:1692-1701. [PMID: 33089727 DOI: 10.1080/07391102.2020.1831961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Human topoisomerase II alpha (TopoIIα) is a crucial enzyme involved in maintaining genomic integrity during the process of DNA replication and mitotic division. It is a vital therapeutic target for designing novel anticancer agents in targeted cancer therapy. Sulfones, members of organosulfur compounds, have been reported to possess various biological activities such as antimicrobial, anti-inflammatory, anti-HIV, anticancer, and antimalarial properties. In the present study, a series of sulfones was selected to evaluate their inhibitory activity against TopoIIα using computational approaches. Molecular docking results revealed that several sulfone analogs bind efficiently to the ATPase domain of TopoIIα. Among them, sulfones 18a, 60a, *4 b, *8 b, *3c, and 8c exhibit higher binding affinity than the known TopoII inhibitor, salvicine. Molecular dynamics simulations and free energy calculations based on MM/PB(GB)SA method demonstrated that sulfone *8 b strongly interacts with amino acid residues in the ATP-binding pocket (E87, N91, D94, I125, I141, F142, S149, G161, and A167), driven mainly by an electrostatic attraction and a strong H-bond formation at G161 residue. Altogether, the obtained results predicted that sulfones could have a high potential to be a lead molecule for targeting TopoIIα.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kanika Verma
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Panupong Mahalapbutr
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Atima Auepattanapong
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Onnicha Khaikate
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Chutima Kuhakarn
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kaito Takahashi
- Institute of Atomic and Sciences, Academia Sinica, Taipei, Taiwan
| | - Thanyada Rungrotmongkol
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
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8
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Gaurav K, Adhikary T, Satpati P. dUMP/F-dUMP Binding to Thymidylate Synthase: Human Versus Mycobacterium tuberculosis. ACS OMEGA 2020; 5:17182-17192. [PMID: 32715203 PMCID: PMC7376888 DOI: 10.1021/acsomega.0c01224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/18/2020] [Indexed: 06/11/2023]
Abstract
Thymidylate synthase is an enzyme that catalyzes deoxythymidine monophosphate (dTMP) synthesis from substrate deoxyuridine monophosphate (dUMP). Thymidylate synthase of Mycobacterium tuberculosis (MtbThyX) is structurally distinct from its human analogue human thymidylate synthase (hThyA), thus drawing attention as an attractive drug target for combating tuberculosis. Fluorodeoxyuridylate (F-dUMP) is a successful inhibitor of both MtbThyX and hThyA, thus limited by poor selectivity. Understanding the dynamics and energetics associated with substrate/inhibitor binding to thymidylate synthase in atomic details remains a fundamental unsolved problem, which is necessary for a new selective inhibitor design. Structural studies of MtbThyX and hThyA bound substrate/inhibitor complexes not only revealed the extensive specific interaction network between protein and ligands but also opened up the possibility of directly computing the energetics of the substrate versus inhibitor recognition. Using experimentally determined structures as a template, we report extensive computer simulations (∼4.5 μs) that allow us to quantitatively estimate ligand selectivity (dUMP vs F-dUMP) by MtbThyX and hThyA. We show that MtbThyX prefers deprotonated dUMP (enolate form) as the substrate, whereas hThyA binds to the keto form of dUMP. Computed energetics clearly show that MtbThyX is less selective between dUMP and F-dUMP, favoring the latter, relative to hThyA. The simulations reveal the role of tyrosine at position 135 (Y135) of hThyA in amplifying the selectivity. The protonation state of the pyrimidine base of the ligand (i.e., keto or enolate) seems to have no role in MtbThyX ligand selectivity. A molecular gate (consists of Y108, K165, H203, and a water molecule) restricts water accessibility and offers a desolvated dry ligand-binding pocket for MtbThyX. The ligand-binding pocket of hThyA is relatively wet and exposed to bulk water.
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9
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Boonma T, Nutho B, Rungrotmongkol T, Nunthaboot N. Understanding of the drug resistance mechanism of hepatitis C virus NS3/4A to paritaprevir due to D168N/Y mutations: A molecular dynamics simulation perspective. Comput Biol Chem 2019; 83:107154. [PMID: 31751885 DOI: 10.1016/j.compbiolchem.2019.107154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/26/2019] [Accepted: 10/21/2019] [Indexed: 02/08/2023]
Abstract
Hepatitis C virus (HCV) NS3/4A protease is an attractive target for the development of antiviral therapy. However, the evolution of antiviral drug resistance is a major problem for treatment of HCV infected patients. Understanding of drug-resistance mechanisms at molecular level is therefore very important for the guidance of further design of antiviral drugs with high efficiency and specificity. Paritaprevir is a potent inhibitor against HCV NS3/4A protease genotype 1a. Unfortunately, this compound is highly susceptible to the substitution at D168 in the protease. In this work, molecular dynamics simulations of paritaprevir complexed with wild-type (WT) and two mutated strains (D168 N and D168Y) were carried out. Due to such mutations, the inhibitor-protein hydrogen bonding between them was weakened and the salt-bridge network among residues R123, R155 and D168 responsible for inhibitor binding was disrupted. Moreover, the per-residue free energy decomposition suggested that the main contributions from key residues such as Q80, V132, K136, G137 and R155 were lost in the D168 N/Y mutations. These lead to a lower binding affinity of paritaprevir for D168 N/Y variants of the HCV NS3/4A protease, consistent with the experimental data. This detailed information could be useful for further design of high potency anti-HCV NS3/4A inhibitors.
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Affiliation(s)
- Thitiya Boonma
- Supramolecular Chemistry Research Unit and Department of Chemistry, Faculty of Science, Mahasarakham University, Maha Sarakham, 44150, Thailand; Center of Excellence for Innovation in Chemistry (PERCH‒CIC), Faculty of Science, Mahasarakham University, Maha Sarakham, 44150, Thailand
| | - Bodee Nutho
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand; Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nadtanet Nunthaboot
- Supramolecular Chemistry Research Unit and Department of Chemistry, Faculty of Science, Mahasarakham University, Maha Sarakham, 44150, Thailand; Center of Excellence for Innovation in Chemistry (PERCH‒CIC), Faculty of Science, Mahasarakham University, Maha Sarakham, 44150, Thailand.
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10
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Mahalapbutr P, Darai N, Panman W, Opasmahakul A, Kungwan N, Hannongbua S, Rungrotmongkol T. Atomistic mechanisms underlying the activation of the G protein-coupled sweet receptor heterodimer by sugar alcohol recognition. Sci Rep 2019; 9:10205. [PMID: 31308429 PMCID: PMC6629994 DOI: 10.1038/s41598-019-46668-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/03/2019] [Indexed: 12/03/2022] Open
Abstract
The human T1R2-T1R3 sweet taste receptor (STR) plays an important role in recognizing various low-molecular-weight sweet-tasting sugars and proteins, resulting in the release of intracellular heterotrimeric G protein that in turn leads to the sweet taste perception. Xylitol and sorbitol, which are naturally occurring sugar alcohols (polyols) found in many fruits and vegetables, exhibit the potential caries-reducing effect and are widely used for diabetic patients as low-calorie sweeteners. In the present study, computational tools were applied to investigate the structural details of binary complexes formed between these two polyols and the T1R2-T1R3 heterodimeric STR. Principal component analysis revealed that the Venus flytrap domain (VFD) of T1R2 monomer was adapted by the induced-fit mechanism to accommodate the focused polyols, in which α-helical residues 233-268 moved significantly closer to stabilize ligands. This finding likely suggested that these structural transformations might be the important mechanisms underlying polyols-STR recognitions. The calculated free energies also supported the VFD of T1R2 monomer as the preferential binding site for such polyols, rather than T1R3 region, in accord with the lower number of accessible water molecules in the T1R2 pocket. The E302 amino acid residue in T1R2 was found to be the important recognition residue for polyols binding through a strongly formed hydrogen bond. Additionally, the binding affinity of xylitol toward the T1R2 monomer was significantly higher than that of sorbitol, making it a sweeter tasting molecule.
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Affiliation(s)
- Panupong Mahalapbutr
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nitchakan Darai
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Wanwisa Panman
- Multidisciplinary Program of Petrochemistry and Polymer Science, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Aunchan Opasmahakul
- Computational Chemistry Center of Excellent, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nawee Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
- Center of Excellence in Materials Science and Technology, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Supot Hannongbua
- Computational Chemistry Center of Excellent, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
- Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
- Molecular Sensory Science Center, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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Nutho B, Mulholland AJ, Rungrotmongkol T. The reaction mechanism of Zika virus NS2B/NS3 serine protease inhibition by dipeptidyl aldehyde: a QM/MM study. Phys Chem Chem Phys 2019; 21:14945-14956. [PMID: 31236554 DOI: 10.1039/c9cp02377a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Zika virus (ZIKV) infection has become a global public health problem, associated with microcephaly in newborns and Guillain-Barré syndrome in adults. Currently, there are no commercially available anti-ZIKV drugs. The viral protease NS2B/NS3, which is involved in viral replication and maturation, is a potential drug target. Peptidomimetic aldehyde inhibitors bind covalently to the catalytic S135 of the NS3 protease. Here, we apply hybrid quantum mechanics/molecular mechanics (QM/MM) free-energy simulations at the PDDG-PM3/ff14SB level to investigate the inhibition mechanism of the ZIKV protease by a dipeptidyl aldehyde inhibitor (acyl-KR-aldehyde). The results show that proton transfer from the catalytic S135 to H51 occurs in concert with nucleophilic addition on the aldehyde warhead by S135. The anionic covalent complex between the dipeptidyl aldehyde and the ZIKV protease is analogous to the tetrahedral intermediate for substrate hydrolysis. Spontaneous protonation by H51 forms the hemiacetal. In addition, we use correlated ab initio QM/MM potential energy path calculations at levels up to LCCSD(T)/(aug)-cc-pVTZ to obtain accurate potential energy profiles of the reaction, which also support a concerted mechanism. These results provide detailed insight into the mechanism of ZIKV protease inhibition by a peptidyl aldehyde inhibitor, which will guide in the design of inhibitors.
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Affiliation(s)
- Bodee Nutho
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
| | - Thanyada Rungrotmongkol
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand. and Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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12
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Ubonprasert S, Jaroensuk J, Pornthanakasem W, Kamonsutthipaijit N, Wongpituk P, Mee-Udorn P, Rungrotmongkol T, Ketchart O, Chitnumsub P, Leartsakulpanich U, Chaiyen P, Maenpuen S. A flap motif in human serine hydroxymethyltransferase is important for structural stabilization, ligand binding, and control of product release. J Biol Chem 2019; 294:10490-10502. [PMID: 31118236 DOI: 10.1074/jbc.ra119.007454] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 05/21/2019] [Indexed: 12/13/2022] Open
Abstract
Human cytosolic serine hydroxymethyltransferase (hcSHMT) is a promising target for anticancer chemotherapy and contains a flexible "flap motif" whose function is yet unknown. Here, using size-exclusion chromatography, analytical ultracentrifugation, small-angle X-ray scattering (SAXS), molecular dynamics (MD) simulations, and ligand-binding and enzyme-kinetic analyses, we studied the functional roles of the flap motif by comparing WT hcSHMT with a flap-deleted variant (hcSHMT/Δflap). We found that deletion of the flap results in a mixture of apo-dimers and holo-tetramers, whereas the WT was mostly in the tetrameric form. MD simulations indicated that the flap stabilizes structural compactness and thereby enhances oligomerization. The hcSHMT/Δflap variant exhibited different catalytic properties in (6S)-tetrahydrofolate (THF)-dependent reactions compared with the WT but had similar activity in THF-independent aldol cleavage of β-hydroxyamino acid. hcSHMT/Δflap was less sensitive to THF inhibition than the WT (Ki of 0.65 and 0.27 mm THF at pH 7.5, respectively), and the THF dissociation constant of the WT was also 3-fold lower than that of hcSHMT/Δflap, indicating that the flap is important for THF binding. hcSHMT/Δflap did not display the burst kinetics observed in the WT. These results indicate that, upon removal of the flap, product release is no longer the rate-limiting step, implying that the flap is important for controlling product release. The findings reported here improve our understanding of the functional roles of the flap motif in hcSHMT and provide fundamental insight into how a flexible loop can be involved in controlling the enzymatic reactions of hcSHMT and other enzymes.
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Affiliation(s)
- Sakunrat Ubonprasert
- From the Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Juthamas Jaroensuk
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Wichai Pornthanakasem
- Biomolecular Analysis and Application Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), and
| | | | - Peerapong Wongpituk
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, and
| | - Pitchayathida Mee-Udorn
- Bioinformatics and Computational Biology Program, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand, and
| | - Thanyada Rungrotmongkol
- Bioinformatics and Computational Biology Program, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand, and.,Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, and
| | - Onuma Ketchart
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathumthani 12120, Thailand
| | - Penchit Chitnumsub
- Biomolecular Analysis and Application Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), and
| | - Ubolsree Leartsakulpanich
- Biomolecular Analysis and Application Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), and
| | - Pimchai Chaiyen
- From the Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.,School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi 20131, Thailand
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Karim HAA, Rungrotmongkol T, Zain SM, Rahman NA, Tayapiwattana C, Lee V. Designed antiviral ankyrin – A computational approach to combat HIV-1 via intracellular pathway by targeting the viral capsid of HIV-1. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.12.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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14
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A theoretical study on the molecular encapsulation of luteolin and pinocembrin with various derivatized beta-cyclodextrins. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.12.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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15
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Kongkaew S, Rungrotmongkol T, Punwong C, Noguchi H, Takeuchi F, Kungwan N, Wolschann P, Hannongbua S. Interactions of HLA-DR and Topoisomerase I Epitope Modulated Genetic Risk for Systemic Sclerosis. Sci Rep 2019; 9:745. [PMID: 30679605 PMCID: PMC6345791 DOI: 10.1038/s41598-018-37038-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 11/29/2018] [Indexed: 12/11/2022] Open
Abstract
The association of systemic sclerosis with anti-Topoisomerase 1 antibody (ATASSc) with specific alleles of human leukocyte antigen (HLA)-DR has been observed among various ethnics. The anti-Topoisomerase 1 antibody is a common autoantibody in SSc with diffuse cutaneous scleroderma, which is one of the clinical subtypes of SSc. On the other hand, an immunodominant peptide of topoisomerase 1 (Top1) self-protein (residues 349-368) was reported to have strong association with ATASSc. In this study, molecular dynamics simulation was performed on the complexes of Top1 peptide with various HLA-DR subtypes divided into ATASSc-associated alleles (HLA-DRB1*08:02, HLA-DRB1*11:01 and HLA-DRB1*11:04), suspected allele (HLA-DRB5*01:02), and non-associated allele (HLA-DRB1*01:01). The unique interaction for each system was compared to the others in terms of dynamical behaviors, binding free energies and solvation effects. Our results showed that three HLA-DR/Top1 complexes of ATASSc association mostly exhibited high protein stability and increased binding efficiency without solvent interruption, in contrast to non-association. The suspected case (HLA-DRB5*01:02) binds Top1 as strongly as the ATASSc association case, which implied a highly possible risk for ATASSc development. This finding might support ATASSc development mechanism leading to a guideline for the treatment and avoidance of pathogens like Top1 self-peptide risk for ATASSc.
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Affiliation(s)
- Sirilak Kongkaew
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.,The Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thanyada Rungrotmongkol
- Biocatalyst and Environmental Biotechnology Research unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand. .,Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Chutintorn Punwong
- Department of Physics, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Hiroshi Noguchi
- School of Pharmacy, Nihon Pharmaceutical University, Saitama, 361-0806, Japan.,School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan
| | - Fujio Takeuchi
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan.,Faculty of Health and Nutrition, Tokyo Seiei University, Tokyo, 124-8530, Japan
| | - Nawee Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Excellence in Materials Science and Technology, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Peter Wolschann
- The Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.,Department of Pharmaceutical Chemistry, University of Vienna, Vienna, 1090, Austria.,Institute of Theoretical Chemistry, University of Vienna, Vienna, 1090, Austria
| | - Supot Hannongbua
- The Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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16
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Binding pattern and susceptibility of epigallocatechin gallate against envelope protein homodimer of Zika virus: A molecular dynamics study. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.10.111] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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17
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Sangpheak K, Mueller M, Darai N, Wolschann P, Suwattanasophon C, Ruga R, Chavasiri W, Seetaha S, Choowongkomon K, Kungwan N, Rungnim C, Rungrotmongkol T. Computational screening of chalcones acting against topoisomerase IIα and their cytotoxicity towards cancer cell lines. J Enzyme Inhib Med Chem 2018; 34:134-143. [PMID: 30394113 PMCID: PMC6225485 DOI: 10.1080/14756366.2018.1507029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Targeted cancer therapy has become one of the high potential cancer treatments. Human topoisomerase II (hTopoII), which catalyzes the cleavage and rejoining of double-stranded DNA, is an important molecular target for the development of novel cancer therapeutics. In order to diversify the pharmacological activity of chalcones and to extend the scaffold of topoisomerase inhibitors, a series of chalcones was screened against hTopoIIα by computational techniques, and subsequently tested for their in vitro cytotoxicity. From the experimental IC50 values, chalcone 3d showed a high cytotoxicity with IC50 values of 10.8, 3.2 and 21.1 µM against the HT-1376, HeLa and MCF-7 cancer-derived cell lines, respectively, and also exhibited an inhibitory activity against hTopoIIα-ATPase that was better than the known inhibitor, salvicine. The observed ligand-protein interactions from a molecular dynamics study affirmed that 3d strongly interacts with the ATP-binding pocket residues. Altogether, the newly synthesised chalcone 3d has a high potential to serve as a lead compound for topoisomerase inhibitors.
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Affiliation(s)
- Kanyani Sangpheak
- a Faculty of Science, Program in Biotechnology , Chulalongkorn University , Bangkok , Thailand
| | - Monika Mueller
- b Department of Pharmaceutical Technology and Biopharmaceutics , University of Vienna , Vienna , Austria
| | - Nitchakan Darai
- a Faculty of Science, Program in Biotechnology , Chulalongkorn University , Bangkok , Thailand
| | - Peter Wolschann
- b Department of Pharmaceutical Technology and Biopharmaceutics , University of Vienna , Vienna , Austria.,c Institute of Theoretical Chemistry , University of Vienna , Vienna , Austria
| | - Chonticha Suwattanasophon
- b Department of Pharmaceutical Technology and Biopharmaceutics , University of Vienna , Vienna , Austria
| | - Ritbey Ruga
- d Faculty of Science, Center of Excellence in Natural Products Chemistry, Department of Chemistry , Chulalongkorn University , Bangkok , Thailand
| | - Warinthon Chavasiri
- d Faculty of Science, Center of Excellence in Natural Products Chemistry, Department of Chemistry , Chulalongkorn University , Bangkok , Thailand
| | - Supaporn Seetaha
- e Faculty of Science, Department of Biochemistry , Kasetsart University , Bangkok , Thailand
| | - Kiattawee Choowongkomon
- e Faculty of Science, Department of Biochemistry , Kasetsart University , Bangkok , Thailand
| | - Nawee Kungwan
- f Faculty of Science, Department of Chemistry , Chiang Mai University , Chiang Mai , Thailand.,g Center of Excellence in Materials Science and Technology , Chiang Mai University , Chiang Mai , Thailand
| | - Chompoonut Rungnim
- h Nanoscale Simulation Laboratory, National Nanotechnology Center , National Science and Technology Development Agency , Pathum Thani , Thailand
| | - Thanyada Rungrotmongkol
- i Faculty of Science, Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry , Chulalongkorn University , Bangkok , Thailand.,j Faculty of Science, Ph.D. Program in Bioinformatics and Computational Biology , Chulalongkorn University , Bangkok , Thailand
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18
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Panman W, Nutho B, Chamni S, Dokmaisrijan S, Kungwan N, Rungrotmongkol T. Computational screening of fatty acid synthase inhibitors against thioesterase domain. J Biomol Struct Dyn 2018; 36:4114-4125. [PMID: 29161996 DOI: 10.1080/07391102.2017.1408496] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/10/2017] [Indexed: 12/17/2022]
Abstract
Thioesterase (TE) domain of fatty acid synthase (FAS) is an attractive therapeutic target for design and development of anticancer drugs. In this present work, we search for the potential FAS inhibitors of TE domain from the ZINC database based on similarity search using three natural compounds as templates, including flavonoids, terpenoids, and phenylpropanoids. Molecular docking was used to predict the interaction energy of each screened ligand compared to the reference compound, which is methyl γ-linolenylfluorophosphonate (MGLFP). Based on this computational technique, rosmarinic acid and its eight analogs were observed as a new series of potential FAS inhibitors, which showed a stronger binding affinity than MGLFP. Afterward, nine docked complexes were studied by molecular dynamics simulations for investigating protein-ligand interactions and binding free energies using MM-PB(GB)SA, MM-3DRISM-KH, and QM/MM-GBSA methods. The binding free energy calculation indicated that the ZINC85948835 (R34) displayed the strongest binding efficiency against the TE domain of FAS. There are eight residues (S2308, I2250, E2251, Y2347, Y2351, F2370, L2427, and E2431) mainly contributed for the R34 binding. Moreover, R34 could directly form hydrogen bonds with S2308, which is one of the catalytic triad of TE domain. Therefore, our finding suggested that R34 could be a potential candidate as a novel FAS-TE inhibitor for further drug design.
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Affiliation(s)
- Wanwisa Panman
- a Multidisciplinary Program of Petrochemistry and Polymer Science, Faculty of Science , Chulalongkorn University , Bangkok 10330 , Thailand
| | - Bodee Nutho
- b Program in Biotechnology, Faculty of Science , Chulalongkorn University , Bangkok 10330 , Thailand
| | - Supakarn Chamni
- c Faculty of Pharmaceutical Sciences, Department of Pharmacognosy and Pharmaceutical Botany , Chulalongkorn University , Bangkok 10330 , Thailand
| | - Supaporn Dokmaisrijan
- d Division of Chemistry, School of Science , Walailak University , Nakon Si Thammarat 80161 , Thailand
| | - Nawee Kungwan
- e Faculty of Science, Department of Chemistry , Chiang Mai University , 239 Huay Kaew Road, Muang District, Chiang Mai 50200 , Thailand
- f Research Center on Chemistry for Development of Health Promoting Products from Northern Resources , Chiang Mai University , Chiang Mai , 50200 , Thailand
| | - Thanyada Rungrotmongkol
- g Faculty of Science, Structural and Computational Biology Research Group, Department of Biochemistry , Chulalongkorn University , Bangkok 10330 , Thailand
- h Faculty of Science, Program in Bioinformatics and Computational Biology , Chulalongkorn University , Bangkok 10330 , Thailand
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19
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Abstract
Fluorinated nucleosides constitute a large class of chemotherapeutics approved for clinical use. The pharmacokinetic and pharmacodynamic properties of a drug can be affected, as a consequence of modulation of electronic, lipophilic and steric parameters, by the introduction of fluorine into the structure of drug-like molecule. Herein, we focus on fluorinated-nucleoside analogs, their therapeutic use and applications based on the patent literature from 2014 to 2018. We briefly discuss the clinical properties of anticancer and antiviral fluorine-containing nucleos(t)ides US FDA-approved or in development, and highlight their resistance mechanisms and limitations in the clinic. We emphasize patent inventions related to improved synthetic methods toward selected nucleos(t)ide analogs including the phosphoramidate sofosbuvir and 18F-labeled nucleosides FLT and FMAU, used as a 18F-PET tracers.
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20
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Hanpaibool C, Chakcharoensap T, Arifin, Hijikata Y, Irle S, Wolschann P, Kungwan N, Pongsawasdi P, Ounjai P, Rungrotmongkol T. Theoretical analysis of orientations and tautomerization of genistein in β-cyclodextrin. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.05.109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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21
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The inclusion complexation of daidzein with β-cyclodextrin and 2,6-dimethyl-β-cyclodextrin: a theoretical and experimental study. MONATSHEFTE FUR CHEMIE 2018. [DOI: 10.1007/s00706-018-2209-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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22
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Maiuthed A, Bhummaphan N, Luanpitpong S, Mutirangura A, Aporntewan C, Meeprasert A, Rungrotmongkol T, Rojanasakul Y, Chanvorachote P. Nitric oxide promotes cancer cell dedifferentiation by disrupting an Oct4:caveolin-1 complex: A new regulatory mechanism for cancer stem cell formation. J Biol Chem 2018; 293:13534-13552. [PMID: 29986880 DOI: 10.1074/jbc.ra117.000287] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 06/19/2018] [Indexed: 01/11/2023] Open
Abstract
Cancer stem cells (CSCs) are unique populations of cells that can self-renew and generate different cancer cell lineages. Although CSCs are believed to be a promising target for novel therapies, the specific mechanisms by which these putative therapeutics could intervene are less clear. Nitric oxide (NO) is a biological mediator frequently up-regulated in tumors and has been linked to cancer aggressiveness. Here, we search for targets of NO that could explain its activity. We find that it directly affects the stability and function of octamer-binding transcription factor 4 (Oct4), known to drive the stemness of lung cancer cells. We demonstrated that NO promotes the CSC-regulatory activity of Oct4 through a mechanism that involves complex formation between Oct4 and the scaffolding protein caveolin-1 (Cav-1). In the absence of NO, Oct4 forms a molecular complex with Cav-1, which promotes the ubiquitin-mediated proteasomal degradation of Oct4. NO promotes Akt-dependent phosphorylation of Cav-1 at tyrosine 14, disrupting the Cav-1:Oct4 complex. Site-directed mutagenesis and computational modeling studies revealed that the hydroxyl moiety at tyrosine 14 of Cav-1 is crucial for its interaction with Oct4. Both removal of the hydroxyl via mutation to phenylalanine and phosphorylation lead to an increase in binding free energy (ΔGbind) between Oct4 and Cav-1, destabilizing the complex. Together, these results unveiled a novel mechanism of CSC regulation through NO-mediated stabilization of Oct4, a key stem cell transcription factor, and point to new opportunities to design CSC-related therapeutics.
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Affiliation(s)
- Arnatchai Maiuthed
- From the Department of Pharmacology and Physiology.,Cell-based Drug and Health Products Development Research Unit, Faculty of Pharmaceutical Sciences
| | - Narumol Bhummaphan
- Cell-based Drug and Health Products Development Research Unit, Faculty of Pharmaceutical Sciences.,the Inter-Department Program of Biomedical Sciences, Faculty of Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sudjit Luanpitpong
- the Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700 Thailand, and
| | - Apiwat Mutirangura
- the Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, and
| | | | - Arthitaya Meeprasert
- Structural and Computational Biology Research Group, and Department of Biochemistry, Faculty of Science
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Group, and Department of Biochemistry, Faculty of Science.,Ph.D. Program in Bioinformatics and Computational Biology
| | - Yon Rojanasakul
- WVU Cancer Institute, West Virginia University, Morgantown, West Virginia 26506
| | - Pithi Chanvorachote
- From the Department of Pharmacology and Physiology, .,Cell-based Drug and Health Products Development Research Unit, Faculty of Pharmaceutical Sciences
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23
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Lin FY, MacKerell AD. Polarizable Empirical Force Field for Halogen-Containing Compounds Based on the Classical Drude Oscillator. J Chem Theory Comput 2018; 14:1083-1098. [PMID: 29357257 PMCID: PMC5811359 DOI: 10.1021/acs.jctc.7b01086] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The quality of the force field is crucial to ensure the accuracy of simulations used in molecular modeling, including computer-aided drug design (CADD). To perform more accurate modeling and simulations of halogenated molecules, in this study the polarizable force field based on the classical Drude oscillator model was extended to both aliphatic and aromatic systems using halogenated ethane and benzene model compounds for the halogens F, Cl, Br, and I. The force field parameters were optimized targeting quantum mechanical dipole moments, water interactions, and molecular polarizabilities as well as experimental observables, including enthalpies of vaporization, molecular volumes, hydration free energies, and dielectric constants. The developed halogenated polarizable force field is capable of reproducing QM relative energies and geometries of both halogen bonds and halogen-hydrogen bond donor interactions at an unprecedented level due to the inclusion of a virtual particle and anisotropic atomic polarizability on the halogen and, notably, the inclusion of Lennard-Jones parameters on the halogen Drude particle. The model was validated on the basis of its ability to accurately reproduce pure solvent properties for halogenated naphthalenes and alkanes, including species analogous to those used as refrigerants. Accordingly, it is anticipated that the model will be applicable for the study of halogenated derivatives in CADD as well as in other chemical and biophysical studies.
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Affiliation(s)
- Fang-Yu Lin
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Alexander D. MacKerell
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
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24
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Srivarangkul P, Yuttithamnon W, Suroengrit A, Pankaew S, Hengphasatporn K, Rungrotmongkol T, Phuwapraisirisan P, Ruxrungtham K, Boonyasuppayakorn S. A novel flavanone derivative inhibits dengue virus fusion and infectivity. Antiviral Res 2018; 151:27-38. [PMID: 29360474 DOI: 10.1016/j.antiviral.2018.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 10/10/2017] [Accepted: 01/17/2018] [Indexed: 01/24/2023]
Abstract
Dengue infection is a global burden affecting millions of world population. Previous studies indicated that flavanones were potential dengue virus inhibitors. We discovered that a novel flavanone derivative, 5-hydroxy-7-methoxy-6-methylflavanone (FN5Y), inhibited DENV2 pH-dependent fusion in cell-based system with strong binding efficiency to DENV envelope protein at K (P83, L107, K128, L198), K' (T48, E49, A50, L198, Q200, L277), X' (Y138, V354, I357), and Y' (V97, R99, N103, K246) by molecular dynamic simulation. FN5Y inhibited DENV2 infectivity with EC50s (and selectivity index) of 15.99 ± 5.38 (>6.25), and 12.31 ± 1.64 (2.23) μM in LLC/MK2 and Vero cell lines, respectively, and inhibited DENV4 at 11.70 ± 6.04 (>8.55) μM. CC50s in LLC/MK2, HEK-293, and HepG2 cell lines at 72 h were higher than 100 μM. Time-of-addition study revealed that the maximal efficacy was achieved at early after infection corresponded with pH-dependent fusion. Inactivating the viral particle, interfering with cellular receptors, inhibiting viral protease, or the virus replication complex were not major targets of this compound. FN5Y could become a potent anti-flaviviral drug and can be structurally modified for higher potency using simulation to DENV envelope as a molecular target.
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Affiliation(s)
- Pimsiri Srivarangkul
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Wanchalerm Yuttithamnon
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Aphinya Suroengrit
- Graduate Program, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Saran Pankaew
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Kowit Hengphasatporn
- Bioinformatics and Computational Biology Program, Graduated School, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thanyada Rungrotmongkol
- Bioinformatics and Computational Biology Program, Graduated School, Chulalongkorn University, Bangkok, 10330, Thailand; Structural and Computational Biology Research Group, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | | | - Kiat Ruxrungtham
- Chula Vaccine Research Center (Chula VRC), Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Siwaporn Boonyasuppayakorn
- Chula Vaccine Research Center (Chula VRC), Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand; Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
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25
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Yan Y, Qing Y, Pink JJ, Gerson SL. Loss of Uracil DNA Glycosylase Selectively Resensitizes p53-Mutant and -Deficient Cells to 5-FdU. Mol Cancer Res 2018; 16:212-221. [PMID: 29117941 DOI: 10.1158/1541-7786.mcr-17-0215] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 08/02/2017] [Accepted: 10/26/2017] [Indexed: 11/16/2022]
Abstract
Thymidylate synthase (TS) inhibitors including fluoropyrimidines [e.g., 5-Fluorouracil (5-FU) and 5-Fluorodeoxyuridine (5-FdU, floxuridine)] and antifolates (e.g., pemetrexed) are widely used against solid tumors. Previously, we reported that shRNA-mediated knockdown (KD) of uracil DNA glycosylase (UDG) sensitized cancer cells to 5-FdU. Because p53 has also been shown as a critical determinant of the sensitivity to TS inhibitors, we further interrogated 5-FdU cytotoxicity after UDG depletion with regard to p53 status. By analyzing a panel of human cancer cells with known p53 status, it was determined that p53-mutated or -deficient cells are highly resistant to 5-FdU. UDG depletion resensitizes 5-FdU in p53-mutant and -deficient cells, whereas p53 wild-type (WT) cells are not affected under similar conditions. Utilizing paired HCT116 p53 WT and p53 knockout (KO) cells, it was shown that loss of p53 improves cell survival after 5-FdU, and UDG depletion only significantly sensitizes p53 KO cells. This sensitization can also be recapitulated by UDG depletion in cells with p53 KD by shRNAs. In addition, sensitization is also observed with pemetrexed in p53 KO cells, but not with 5-FU, most likely due to RNA incorporation. Importantly, in p53 WT cells, the apoptosis pathway induced by 5-FdU is activated independent of UDG status. However, in p53 KO cells, apoptosis is compromised in UDG-expressing cells, but dramatically elevated in UDG-depleted cells. Collectively, these results provide evidence that loss of UDG catalyzes significant cell death signals only in cancer cells mutant or deficient in p53.Implications: This study reveals that UDG depletion restores sensitivity to TS inhibitors and has chemotherapeutic potential in the context of mutant or deficient p53. Mol Cancer Res; 16(2); 212-21. ©2017 AACR.
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Affiliation(s)
- Yan Yan
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio
| | - Yulan Qing
- Case Comprehensive Cancer Center, Division of General Medical Sciences-Oncology, Case Western Reserve University, Cleveland, Ohio
| | - John J Pink
- Case Comprehensive Cancer Center, Division of General Medical Sciences-Oncology, Case Western Reserve University, Cleveland, Ohio
| | - Stanton L Gerson
- Case Comprehensive Cancer Center, Division of General Medical Sciences-Oncology, Case Western Reserve University, Cleveland, Ohio.
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26
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Mahalapbutr P, Chusuth P, Kungwan N, Chavasiri W, Wolschann P, Rungrotmongkol T. Molecular recognition of naphthoquinone-containing compounds against human DNA topoisomerase IIα ATPase domain: A molecular modeling study. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.10.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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Mahalapbutr P, Nutho B, Wolschann P, Chavasiri W, Kungwan N, Rungrotmongkol T. Molecular insights into inclusion complexes of mansonone E and H enantiomers with various β-cyclodextrins. J Mol Graph Model 2017; 79:72-80. [PMID: 29154164 DOI: 10.1016/j.jmgm.2017.11.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 10/18/2022]
Abstract
The structural dynamics and stability of inclusion complexes of mansonone E (ME) and H (MH) including their stereoisomers with various βCDs (methylated- and hydroxypropylated-βCDs) were investigated by classical molecular dynamics (MD) simulations and binding free energy calculations. The simulation results revealed that mansonones are able to form inclusion complexes with βCDs. The guest molecules are not completely inserted into the host cavity, their preferably positions are nearby the secondary rim with the oxane ring dipping into the hydrophobic inner cavity. The encapsulation process leads to a higher rigidity of the βCDs enhancing the intramolecular hydrogen bond formation ability and decreasing the chance of glucopyranose rotation. According to the MM-PBSA binding free energy calculation, all considered inclusion complexes are stable and the binding energies are mainly caused by van der Waals interactions. Moreover, the free energy calculations showed significant differences in the complexation energies for the stereoisomers, which could enable the separation of the isomers by analytical techniques for further pharmaceutical applications.
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Affiliation(s)
- Panupong Mahalapbutr
- Structural and Computational Biology Research Group, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Bodee Nutho
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Peter Wolschann
- Structural and Computational Biology Research Group, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand; Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna, 1090, Austria; Institute of Theoretical Chemistry, University of Vienna, Vienna, 1090, Austria
| | - Warinthorn Chavasiri
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nawee Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand; Research Center on Chemistry for Development of Health Promoting Products from Northern Resources, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Group, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand; Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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28
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Sun DR, Zheng QC, Zhang HX. Molecular dynamics investigation of stereoselective inhibition mechanism of HIF-2α/ARNT heterodimer. J Mol Recognit 2017; 31. [PMID: 28990233 DOI: 10.1002/jmr.2675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/27/2017] [Accepted: 09/05/2017] [Indexed: 12/19/2022]
Abstract
Hypoxia-inducible factors (HIFs) are heterodimeric transcription factors related with the onset and progression of solid tumors. Studies demonstrated a class of tetrazole containing chiral inhibitors could stereoselectively disrupt the HIF-2 dimerization and reduce the target gene expression. However, the dynamical features and structural motifs of the HIF-2 heterodimer caused by the binding of enantiomers have not been rationalized at the atomistic level. In this work, molecular dynamics (MD) simulations combined with adaptive steered MD (ASMD) simulations were used to investigate stereoselective interrupting mechanism of HIF-2. Our results decipher that the binding of ligand A (S, R)-24 begets the significant conformation changes of β-sheets and interrupts the HIF-2α/ARNT heterodimerization, which may be attributed to the disruption of the hydrogen bond and salt bridge interactions formed by the 4 foremost residues (Asp240, Arg247, Glu362, and Arg366) and the destruction of hydrophobic interactions on the binding interface. By contrast, the binding of ligand B (R, S)-24 does not disrupt protein dimerization and causes the motion of Fα helix in HIF-2α PAS-B domain to further change the major tunnel for ligand ingress and engress. The present work provides important molecular-level insight into the effect of the binding enantiomers on HIF-2 heterodimerization and bridges the gap between theory and the experimental results, which may conduce to develop highly potent antagonists for intervening the HIF-2-driven tumors.
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Affiliation(s)
- Dong-Ru Sun
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, China
| | - Qing-Chuan Zheng
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, China.,Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, China
| | - Hong-Xing Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, China
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Fluorinated nucleosides as an important class of anticancer and antiviral agents. Future Med Chem 2017; 9:1809-1833. [DOI: 10.4155/fmc-2017-0095] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Fluorine-containing nucleoside analogs (NAs) represent a significant class of the US FDA-approved chemotherapeutics widely used in the clinic. The incorporation of fluorine into drug-like agents modulates lipophilic, electronic and steric parameters, thus influencing pharmacodynamic and pharmacokinetic properties of drugs. Fluorine can block oxidative metabolism of drugs and the formation of undesired metabolites by changing H-bonding interactions. In this review, we focus our attention on chemical fluorination reagents and methods used in the NAs field, including positron emission tomography radiochemistry. We briefly discuss both the cellular biology and clinical properties of FDA-approved and fluorine-containing nucleoside/nucleotide analogs in development as well as common resistance mechanisms associated with their use. Finally, we emphasize pronucleotide strategies used to improve therapeutic outcome of NAs in the clinic.
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Wongpituk P, Nutho B, Panman W, Kungwan N, Wolschann P, Rungrotmongkol T, Nunthaboot N. Structural dynamics and binding free energy of neral-cyclodextrins inclusion complexes: molecular dynamics simulation. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1356458] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Peerapong Wongpituk
- Faculty of Science, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Mahasarakham University, Mahasarakham, Thailand
| | - Bodee Nutho
- Faculty of Science, Program in Biotechnology, Chulalongkorn University, Bangkok, Thailand
| | - Wanwisa Panman
- Faculty of Science, Multidisciplinary Program of Petrochemistry and Polymer Science, Chulalongkorn University, Bangkok, Thailand
| | - Nawee Kungwan
- Faculty of Science, Department of Chemistry, Chiang Mai University, Chiang Mai, Thailand
| | - Peter Wolschann
- Faculty of Science, Structural and Computational Biology Research Group, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna, Austria
- Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Thanyada Rungrotmongkol
- Faculty of Science, Structural and Computational Biology Research Group, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
- Faculty of Science, Ph.D. Program in Bioinformatics and Computational Biology, Chulalongkorn University, Bangkok, Thailand
- Faculty of Science, Molecular Sensory Science Center, Chulalongkorn University, Bangkok, Thailand
| | - Nadtanet Nunthaboot
- Faculty of Science, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Mahasarakham University, Mahasarakham, Thailand
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31
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Meeprasert A, Hannongbua S, Kungwan N, Rungrotmongkol T. Effect of D168V mutation in NS3/4A HCV protease on susceptibilities of faldaprevir and danoprevir. MOLECULAR BIOSYSTEMS 2017; 12:3666-3673. [PMID: 27731877 DOI: 10.1039/c6mb00610h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Hepatitis C virus (HCV) is a serious cause of liver inflammation, cirrhosis and the development of hepatocellular carcinoma. Its NS3/4A serine protease functions to cleave a specific peptide bond, which is an important step in HCV replication. Thus the NS3/4A protease has become one of the main drug-targets in the design and development of anti-HCV agents. Unfortunately, high mutation rates in HCV have been reported due to the lack of RNA proofreading activity resulting in drug resistance. Herein, all-atom molecular dynamics simulations were employed to understand and illustrate the effects of the NS3/4A D168V mutation on faldaprevir (FDV) and danoprevir (DNV) binding efficiency. The D168V mutation was shown to interrupt the hydrogen bonding network of Q80R155D168R123 embedded in the extended S2 and partial S4 subsites of the NS3 protein and as a result the R123 side chain was displaced and moved out from the binding pocket. By means of MM/PBSA and MM/GBSA binding free energy calculations, the FDV and DNV binding affinities were shown to be significantly reduced by ∼10-15 kcal mol-1 and ∼4-9 kcal mol-1 relative to the wild-type complexes, respectively, which somewhat agrees with the experimental resistance folds.
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Affiliation(s)
- Arthitaya Meeprasert
- Structural and Computational Biology Research Group, Department of Biochemistry, Faculty of Science Chulalongkorn University, 254, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Supot Hannongbua
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Nawee Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Group, Department of Biochemistry, Faculty of Science Chulalongkorn University, 254, Phayathai Road, Pathumwan, Bangkok 10330, Thailand and PhD Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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Di Paolo A, Orlandi P, Di Desidero T, Danesi R, Bocci G. Simultaneous, But Not Consecutive, Combination With Folinate Salts Potentiates 5-Fluorouracil Antitumor Activity In Vitro and In Vivo. Oncol Res 2017; 25:1129-1140. [PMID: 28109077 PMCID: PMC7841196 DOI: 10.3727/096504017x14841698396900] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The combination of folinate salts to 5-fluoruracil (5-FU)-based schedules is an established clinical routine in the landscape of colorectal cancer treatment. The aim of this study was to investigate the pharmacological differences between the sequential administration of folinate salts (1 h before, as in clinical routine) followed by 5-FU and the simultaneous administration of both drugs. Proliferation and apoptotic assays were performed on human colon cancer cells exposed to 5-FU, calcium (CaLV), or disodium (NaLV) levofolinate or their simultaneous and sequential combination for 24 and 72 h. TYMS and SLC19A1 gene expression was performed with real-time PCR. In vivo experiments were performed in xenografted nude mice, which were treated with 5-FU escalating doses and CaLV or NaLV alone or in simultaneous and sequential combination. The simultaneous combination of folinate salts and 5-FU was synergistic (NaLV) or additive (CaLV) in a 24-h treatment in both cell lines. In contrast, the sequential combination of both folinate salts and 5-FU was antagonistic at 24 and 72 h. The simultaneous combination of 5-FU and NaLV or CaLV inhibited TYMS gene expression at 24 h, whereas the sequential combination reduced SLC19A1 gene expression. In vivo experiments confirmed the enhanced antitumor activity of the 5-FU + NaLV simultaneous combination with a good toxicity profile, whereas the sequential combination with CaLV failed to potentiate 5-FU activity. In conclusion, only the simultaneous, but not the consecutive, in vitro and in vivo combination of 5-FU and both folinate salt formulations potentiated the antiproliferative effects of the drugs.
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33
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Nutho B, Nunthaboot N, Wolschann P, Kungwan N, Rungrotmongkol T. Metadynamics supports molecular dynamics simulation-based binding affinities of eucalyptol and beta-cyclodextrin inclusion complexes. RSC Adv 2017. [DOI: 10.1039/c7ra09387j] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The development of various molecular dynamics methods enables the detailed investigation of association processes, like host–guest complexes, including their dynamics and, additionally, the release of the guest compound.
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Affiliation(s)
- Bodee Nutho
- Program in Biotechnology
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330
- Thailand
| | - Nadtanet Nunthaboot
- Department of Chemistry
- Center of Excellence for Innovation in Chemistry
- Faculty of Science
- Mahasarakham University
- Mahasarakham 44150
| | - Peter Wolschann
- Structural and Computational Biology Research Group
- Department of Biochemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330
| | - Nawee Kungwan
- Department of Chemistry
- Faculty of Science
- Chiang Mai University
- Chiang Mai 50200
- Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Group
- Department of Biochemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330
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Jetsadawisut W, Nutho B, Meeprasert A, Rungrotmongkol T, Kungwan N, Wolschann P, Hannongbua S. Susceptibility of inhibitors against 3C protease of coxsackievirus A16 and enterovirus A71 causing hand, foot and mouth disease: A molecular dynamics study. Biophys Chem 2016; 219:9-16. [PMID: 27668727 DOI: 10.1016/j.bpc.2016.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/16/2016] [Accepted: 09/17/2016] [Indexed: 10/21/2022]
Abstract
Hand foot and mouth disease (HFMD) epidemic has occurred in many countries. Coxsackievirus A16 (CV-A16) and Enterovirus A71 (EV-A71) are the main causes of HFMD. Up to now, there are no anti-HFMD drugs available. Rupintrivir, a broad-spectrum inhibitor, is a drug candidate for HFMD treatment, while other HFMD inhibitors designed from several studies have a relatively low efficiency. Therefore, in this work we aim to study the binding mechanisms of rupintrivir and a peptidic α,β-unsaturated ethyl ester (SG85) against both CV-A16 and EV-A71 3C proteases (3Cpro) using all-atoms molecular dynamics simulation. The obtained results indicate that SG85 shows a stronger binding affinity than rupintrivir against CV-A16. Both inhibitors exhibit a comparable affinity against EV-A71 3Cpro. The molecular information of the binding of the two inhibitors to the proteases will be elucidated. Thus, it is implied that these two compounds may be used as leads for further anti-HFMD drug design and development.
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Affiliation(s)
- W Jetsadawisut
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - B Nutho
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand
| | - A Meeprasert
- Structural and Computational Biology Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand
| | - T Rungrotmongkol
- Structural and Computational Biology Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand; Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Patumwan, Bangkok 10330, Thailand.
| | - N Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Muang District, Chiang Mai 50200, Thailand
| | - P Wolschann
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Patumwan, Bangkok 10330, Thailand; Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna 1090, Austria; Institute of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
| | - S Hannongbua
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Patumwan, Bangkok 10330, Thailand.
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35
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Tantong S, Pringsulaka O, Weerawanich K, Meeprasert A, Rungrotmongkol T, Sarnthima R, Roytrakul S, Sirikantaramas S. Two novel antimicrobial defensins from rice identified by gene coexpression network analyses. Peptides 2016; 84:7-16. [PMID: 27527801 DOI: 10.1016/j.peptides.2016.07.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 07/22/2016] [Accepted: 07/23/2016] [Indexed: 11/26/2022]
Abstract
Defensins form an antimicrobial peptides (AMP) family, and have been widely studied in various plants because of their considerable inhibitory functions. However, their roles in rice (Oryza sativa L.) have not been characterized, even though rice is one of the most important staple crops that is susceptible to damaging infections. Additionally, a previous study identified 598 rice genes encoding cysteine-rich peptides, suggesting there are several uncharacterized AMPs in rice. We performed in silico gene expression and coexpression network analyses of all genes encoding defensin and defensin-like peptides, and determined that OsDEF7 and OsDEF8 are coexpressed with pathogen-responsive genes. Recombinant OsDEF7 and OsDEF8 could form homodimers. They inhibited the growth of the bacteria Xanthomonas oryzae pv. oryzae, X. oryzae pv. oryzicola, and Erwinia carotovora subsp. atroseptica with minimum inhibitory concentration (MIC) ranging from 0.6 to 63μg/mL. However, these OsDEFs are weakly active against the phytopathogenic fungi Helminthosporium oryzae and Fusarium oxysporum f.sp. cubense. This study describes a useful method for identifying potential plant AMPs with biological activities.
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Affiliation(s)
- Supaluk Tantong
- Biotechnology Program, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Onanong Pringsulaka
- Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand.
| | - Kamonwan Weerawanich
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Arthitaya Meeprasert
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Thanyada Rungrotmongkol
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Rakrudee Sarnthima
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham 44150, Thailand.
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Klong Luang, Pathumthani, 12120, Thailand.
| | - Supaart Sirikantaramas
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Omics Sciences and Bioinformatics Center, Chulalongkorn University, Bangkok 10330, Thailand.
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Sangpheak W, Kicuntod J, Schuster R, Rungrotmongkol T, Wolschann P, Kungwan N, Viernstein H, Mueller M, Pongsawasdi P. Physical properties and biological activities of hesperetin and naringenin in complex with methylated β-cyclodextrin. Beilstein J Org Chem 2015; 11:2763-73. [PMID: 26877798 PMCID: PMC4734351 DOI: 10.3762/bjoc.11.297] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 12/02/2015] [Indexed: 01/26/2023] Open
Abstract
The aim of this work is to improve physical properties and biological activities of the two flavanones hesperetin and naringenin by complexation with β-cyclodextrin (β-CD) and its methylated derivatives (2,6-di-O-methyl-β-cyclodextrin, DM-β-CD and randomly methylated-β-CD, RAMEB). The free energies of inclusion complexes between hesperetin with cyclodextrins (β-CD and DM-β-CD) were theoretically investigated by molecular dynamics simulation. The free energy values obtained suggested a more stable inclusion complex with DM-β-CD. The vdW force is the main guest–host interaction when hesperetin binds with CDs. The phase solubility diagram showed the formation of a soluble complex of AL type, with higher increase in solubility and stability when hesperetin and naringenin were complexed with RAMEB. Solid complexes were prepared by freeze-drying, and the data from differential scanning calorimetry (DSC) confirmed the formation of inclusion complexes. The data obtained by the dissolution method showed that complexation with RAMEB resulted in a better release of both flavanones to aqueous solution. The flavanones-β-CD/DM-β-CD complexes demonstrated a similar or a slight increase in anti-inflammatory activity and cytotoxicity towards three different cancer cell lines. The overall results suggested that solubilities and bioactivities of both flavanones were increased by complexation with methylated β-CDs.
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Affiliation(s)
- Waratchada Sangpheak
- Structural and Computational Biology Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Jintawee Kicuntod
- Structural and Computational Biology Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Roswitha Schuster
- Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna 1090, Austria
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Peter Wolschann
- Structural and Computational Biology Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna 1090, Austria; Institute of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
| | - Nawee Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Helmut Viernstein
- Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna 1090, Austria
| | - Monika Mueller
- Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna 1090, Austria
| | - Piamsook Pongsawasdi
- Starch and Cyclodextrin Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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Kicuntod J, Khuntawee W, Wolschann P, Pongsawasdi P, Chavasiri W, Kungwan N, Rungrotmongkol T. Inclusion complexation of pinostrobin with various cyclodextrin derivatives. J Mol Graph Model 2015; 63:91-8. [PMID: 26709752 DOI: 10.1016/j.jmgm.2015.11.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 11/03/2015] [Accepted: 11/06/2015] [Indexed: 01/07/2023]
Abstract
Pinostrobin (PNS) is one of the important flavonoids and can be abundantly found in the rhizomes of fingerroot (Boesenbergia rotrunda) and galangal (Alpinia galangal and Alpinia officinarum), the herbal basis of Southeast Asian cooking. Similar to other flavonoids, PNS exhibits anti-oxidative, anti-inflammatory and anti-cancer properties. However, this compound has an extremely low water solubility that limits its use in pharmaceutical applications. Beta-cyclodextrin (βCD) and its derivatives, 2,6-dimethyl-βCD (2,6-DMβCD) and the three hydroxypropyl-βCDs (2-HPβCD, 6-HPβCD and 2,6-DHPβCD), have unique properties that enhance the stability and solubility of such low-soluble guest molecules. In the present study, molecular dynamics simulations were applied to investigate the dynamics and stability of PNS inclusion complexes with βCD and its derivatives (2,6-DMβCD, 2,6-DHPβCD, 2-HPβCD and 6-HPβCD). PNS was able to form complexes with βCD and all four of its derivatives by either the chromone (C-PNS) or phenyl (P-PNS) ring dipping toward the cavity. According to the molecular mechanics-generalized Born surface area binding free energy values, the stability of the different PNS/βCD complexes was ranked as 2,6-DHPβCD>2,6-DMβCD>2-HPβCD>6-HPβCD>βCD. These theoretical results were in good agreement with the stability constants that had been determined by the solubility method.
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Affiliation(s)
- Jintawee Kicuntod
- Structural and Computational Biology Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Starch and Cyclodextrin Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wasinee Khuntawee
- Nanoscience and Technology Program, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Peter Wolschann
- Structural and Computational Biology Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna 1090, Austria; Institute of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
| | - Piamsook Pongsawasdi
- Starch and Cyclodextrin Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Warinthorn Chavasiri
- Natural Products Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nawee Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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Odin E, Sondén A, Gustavsson B, Carlsson G, Wettergren Y. Expression of Folate Pathway Genes in Stage III Colorectal Cancer Correlates with Recurrence Status Following Adjuvant Bolus 5-FU-Based Chemotherapy. Mol Med 2015; 21:597-604. [PMID: 26193446 DOI: 10.2119/molmed.2014.00192] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 07/17/2015] [Indexed: 11/06/2022] Open
Abstract
Colorectal cancer is commonly treated with 5-fluorouracil and 5-formyltetrahydrofolate (leucovorin). Metabolic action of leucovorin requires several enzymatic steps that are dependent on expression of corresponding coding genes. To identify folate pathway genes with possible impact on leucovorin metabolism, a retrospective study was performed on 193 patients with stage III colorectal cancer. Relative expression of 22 genes putatively involved in leucovorin transport, polyglutamation and metabolism was determined in tumor and mucosa samples using quantitative real-time polymerase chain reaction. After surgery, patients received adjuvant 5-fluorouracil-based bolus chemotherapy with leucovorin during six months, and were followed for 3 to 5 years. Cox regression analysis showed that high tumoral expression of the genes SLC46A1/PCFT (proton-coupled folate transporter) and SLC19A1/RFC-1 (reduced folate carrier 1) correlated significantly (p < 0.001 and p < 0.01, respectively) with a decreased risk of recurrent disease, measured as disease-free survival (DFS). These two genes are involved in the transport of folates into the cells and each functions optimally at a different pH. We conclude that SLC46A1/PCFT and SLC19A1/RFC-1 are associated with DFS of patients with colorectal cancer and hypothesize that poor response to 5-fluorouracil plus leucovorin therapy in some patients may be linked to low expression of these genes. Such patients might need a more intensified therapeutic approach than those with high gene expression. Future prospective studies will determine if the expression of any of these genes can be used to predict response to leucovorin.
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Affiliation(s)
- Elisabeth Odin
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska University Hospital/Östra, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Arvid Sondén
- Genomics and Bioinformatics Core Facilities, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Bengt Gustavsson
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska University Hospital/Östra, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Göran Carlsson
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska University Hospital/Östra, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Yvonne Wettergren
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska University Hospital/Östra, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
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Nutho B, Khuntawee W, Rungnim C, Pongsawasdi P, Wolschann P, Karpfen A, Kungwan N, Rungrotmongkol T. Binding mode and free energy prediction of fisetin/β-cyclodextrin inclusion complexes. Beilstein J Org Chem 2014; 10:2789-99. [PMID: 25550745 PMCID: PMC4273227 DOI: 10.3762/bjoc.10.296] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 11/06/2014] [Indexed: 12/26/2022] Open
Abstract
In the present study, our aim is to investigate the preferential binding mode and encapsulation of the flavonoid fisetin in the nano-pore of β-cyclodextrin (β-CD) at the molecular level using various theoretical approaches: molecular docking, molecular dynamics (MD) simulations and binding free energy calculations. The molecular docking suggested four possible fisetin orientations in the cavity through its chromone or phenyl ring with two different geometries of fisetin due to the rotatable bond between the two rings. From the multiple MD results, the phenyl ring of fisetin favours its inclusion into the β-CD cavity, whilst less binding or even unbinding preference was observed in the complexes where the larger chromone ring is located in the cavity. All MM- and QM-PBSA/GBSA free energy predictions supported the more stable fisetin/β-CD complex of the bound phenyl ring. Van der Waals interaction is the key force in forming the complexes. In addition, the quantum mechanics calculations with M06-2X/6-31G(d,p) clearly showed that both solvation effect and BSSE correction cannot be neglected for the energy determination of the chosen system.
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Affiliation(s)
- Bodee Nutho
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wasinee Khuntawee
- Nanoscience and Technology Program, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chompoonut Rungnim
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Thanon Phahonyothin Tambon Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand
| | - Piamsook Pongsawasdi
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Peter Wolschann
- Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna 1090, Austria ; Institute of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
| | - Alfred Karpfen
- Institute of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
| | - Nawee Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Thanyada Rungrotmongkol
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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Wettergren Y, Taflin H, Odin E, Kodeda K, Derwinger K. A pharmacokinetic and pharmacodynamic investigation of Modufolin® compared to Isovorin® after single dose intravenous administration to patients with colon cancer: a randomized study. Cancer Chemother Pharmacol 2014; 75:37-47. [PMID: 25342290 PMCID: PMC4281361 DOI: 10.1007/s00280-014-2611-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
Abstract
PURPOSE Leucovorin is commonly used as folate supplement in 5-fluorouracil-based chemotherapy, but needs to be converted to active 5,10-methylenetetrahydrofolate (methyleneTHF) intracellularly. This provides for interindividual differences. MethyleneTHF has recently been developed into the stable, distributable drug, Modufolin®. The aim was to compare the concentration of folate metabolites in tumor, mucosa, and plasma of patients with colon cancer after administration of Modufolin® or Isovorin® (levo-leucovorin). METHODS Thirty-two patients scheduled for colon resection were randomized to receive Modufolin® or Isovorin® at dosage of 60 or 200 mg/m². The study drug was given as one i.v. bolus injection after anesthesia. Plasma was collected for pharmacokinetic (PK) analysis before, during, and after surgery. Tissue biopsies were collected at surgery. Folate metabolites were analyzed by LC-MS/MS. RESULTS MethyleneTHF and THF concentrations were significantly higher in mucosa (p < 0.01, both dosages) and tumors (p < 0.01, 200 mg/m²) after Modufolin® as compared to Isovorin® administration. The results correlated with PK observations. The Modufolin® to Isovorin® C(max) ratio for methyleneTHF was 113 at 200 mg/m² and 52 at 60 mg/m²; the AUC(last) ratios were 17 and 9, respectively. The THF plasma concentrations were also higher after Modufolin® administration (C(max) ratio 23, AUC(last) ratio 13 at 200 mg/m²; C(max) ratio 15, AUC(last) ratio 11 at 60 mg/m²). CONCLUSION Modufolin® administration resulted in significantly higher methyleneTHF levels than Isovorin® and may potentially increase the efficacy of 5-fluorouracil-based chemotherapy. The results encourage further evaluation of Modufolin® as a substitute to Isovorin® including the potential clinical benefits.
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Affiliation(s)
- Yvonne Wettergren
- Department of Surgery, Institute of Clinical Sciences, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden,
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Meeprasert A, Hannongbua S, Rungrotmongkol T. Key binding and susceptibility of NS3/4A serine protease inhibitors against hepatitis C virus. J Chem Inf Model 2014; 54:1208-17. [PMID: 24689657 DOI: 10.1021/ci400605a] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Hepatitis C virus (HCV) causes an infectious disease that manifests itself as liver inflammation, cirrhosis, and can lead to the development of liver cancer. Its NS3/4A serine protease is a potent target for drug design and development since it is responsible for cleavage of the scissile peptide bonds in the polyprotein important for the HCV life cycle. Herein, the ligand-target interactions and the binding free energy of the four current NS3/4A inhibitors (boceprevir, telaprevir, danoprevir, and BI201335) were investigated by all-atom molecular dynamics simulations with three different initial atomic velocities. The per-residue free energy decomposition suggests that the key residues involved in inhibitor binding were residues 41-43, 57, 81, 136-139, 155-159, and 168 in the NS3 domain. The van der Waals interactions yielded the main driving force for inhibitor binding at the protease active site for the cleavage reaction. In addition, the highest number of hydrogen bonds was formed at the reactive P1 site of the four studied inhibitors. Although the hydrogen bond patterns of these inhibitors were different, their P3 site was most likely to be recognized by the A157 backbone. Both molecular mechanic (MM)/Poisson-Boltzmann surface area and MM/generalized Born surface area approaches predicted the relative binding affinities of the four inhibitors in a somewhat similar trend to their experimentally derived biological activities.
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Affiliation(s)
- Arthitaya Meeprasert
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University , 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand
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Sangpheak W, Khuntawee W, Wolschann P, Pongsawasdi P, Rungrotmongkol T. Enhanced stability of a naringenin/2,6-dimethyl β-cyclodextrin inclusion complex: molecular dynamics and free energy calculations based on MM- and QM-PBSA/GBSA. J Mol Graph Model 2014; 50:10-5. [PMID: 24681901 DOI: 10.1016/j.jmgm.2014.03.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 02/27/2014] [Accepted: 03/01/2014] [Indexed: 10/25/2022]
Abstract
The structure, dynamic behavior and binding affinity of the inclusion complexes between naringenin and the two cyclodextrins (CDs), β-CD and its 2,6-dimethyl derivative (DM-β-CD), were theoretically studied by multiple molecular dynamics simulations and free energy calculations. Naringenin most likely prefers to bind with CDs through the phenyl ring. Although a lower hydrogen bond formation of naringenin with the 3-hydroxyl group of DM-β-CD (relative to β-CD) was observed, the higher cavity could encapsulate almost the whole naringenin molecule. In contrast for the naringenin/β-CD complex, the phenyl ring feasibly passed through the primary rim resulting in the chromone ring binding inside instead. MM-PBSA/GBSA and QM-PBSA/GBSA binding free energies strongly suggested a greater stability of the naringenin/DM-β-CD inclusion complex. Van der Waals force played an important role as the key guest-host interaction for the complexation between naringenin and each cyclodextrin.
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Affiliation(s)
- Waratchada Sangpheak
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wasinee Khuntawee
- Nanoscience and Technology Program, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Peter Wolschann
- Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna 1090, Austria; Institute of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
| | - Piamsook Pongsawasdi
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thanyada Rungrotmongkol
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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