Papers by Napat Songtawee
Current Research in Pharmacology and Drug Discovery
Context: Six maturity onset diabetes of the young (MODY) genes have been discovered to date but a... more Context: Six maturity onset diabetes of the young (MODY) genes have been discovered to date but account for a small proportion of MODY among Asians, suggesting the existence of other MODY genes in this racial group. Objective: The aim of this study was to investigate whether or not genetic variants in PAX4, a crucial transcription factor in -cell development, contribute to MODY in Thais. Design and Methods: We screened PAX4 coding sequences in 46 MODY probands without mutation in known MODY genes and in 74 nondiabetic controls using PCR-single-stranded conformational polymorphism analysis followed by direct sequencing. Genotyping of variants identified was done by PCR-restriction fragment length polymorphism analysis. Results: Eight sequence differences were identified. Two novel variations (R164W and IVS7–1GA) were found in two different pro
Biochimie, 2018
Plasmodium proteases play both regulatory and effector roles in essential biological processes in... more Plasmodium proteases play both regulatory and effector roles in essential biological processes in this important pathogen and have long been investigated as drug targets. Plasmepsin V from P. falciparum (PfPMV) is an essential protease that processes proteins for export into the host erythrocyte and is a focus of ongoing drug development efforts. In the present study, recombinant protein production, inhibition assays, binding studies as well as molecular docking and molecular dynamics simulation studies were used to investigate the mode of binding of a PEXEL-based peptidomimetic and naphthoquinone compounds to PfPMV. Consistent with our previous study, refolded PfPMVs were produced with functional characteristics similar to the soluble counterpart. Naphthoquinone compounds inhibited PfPMV activity by 50% at 50 mM but did not affect pepsin activity. The IC 50 values of compounds 31 and 37 against PfPMV were 22.25 and 68.94 mM, respectively. Molecular dynamics simulations revealed that PEXEL peptide interacted with PfPMV active site residues via electrostatic interactions while naphthoquinone binding preferred van der Waal interactions. P 1 0-Ser of the PfEMP2 substrate formed an additional H-bond with Asp365 promoting the catalytic efficiency. Additionally, the effect of metal ions on the secondary structure of PfPMV was examined. Our results confirmed that Hg 2þ ions reversibly induced the changes in secondary structure of the protein whereas Fe 3þ ions induced irreversibly. No change was observed in the presence of Ca 2þ ions. Overall, the results here suggested that naphthoquinone derivatives may represent another source of antimalarial inhibitors targeting aspartic proteases but further chemical modifications are required.
Chemical Biology & Drug Design
Journal of Molecular Graphics and Modelling
RSC Advances
Neuronal cells exposed to H2O2 may undergo increase ROS, reduction in cell viability and cell dea... more Neuronal cells exposed to H2O2 may undergo increase ROS, reduction in cell viability and cell death. Butein, isoliquiritigenin, and scopoletin ameliorated H2O2-induced neurotoxicity by reducing ROS, balancing antioxidants and activating SIRT1-FoxO3a-ADAM10 pathway.
Drug Design, Development and Therapy, 2015
Drug Design, Development and Therapy Dovepress submit your manuscript | www.dovepress.com Dovepre... more Drug Design, Development and Therapy Dovepress submit your manuscript | www.dovepress.com Dovepress 4515 O r i g i n a l r e s e a r c h open access to scientific and medical research Open access Full Text article http://dx.
European Journal of Medicinal Chemistry, 2015
Keywords: 17beta-hydroxysteroid dehydrogenase type 1 17beta-HSD1 Breast cancer QSAR Molecular doc... more Keywords: 17beta-hydroxysteroid dehydrogenase type 1 17beta-HSD1 Breast cancer QSAR Molecular docking Data mining a b s t r a c t It is generally known that proliferation of human breast cancer cells is stimulated by excess estrogen namely 17b-estradiol. Therefore, reduction of 17b-estradiol production by inhibiting 17b-hydroxysteroid dehydrogenase type 1 (17b-HSD1) is an interesting route for breast cancer treatment particularly during adjuvant therapy. This study investigated the structureeactivity relationship of 17b-HSD1 inhibitors as to gain insights and understanding on the origins of 17b-HSD1 inhibitory activities. To meet this goal, multiple linear regression model was constructed and correspondingly the results revealed good predictivity (N ¼ 31, R 2 ¼ 0.9438, Q 2 ¼ 0.8530). The model suggested that low molecular weight and energy were preferred as 17b-HSD1 inhibitors. Additionally, high molecular flexibility and high number of hydrogen bond donors were also shown to be important that is in correspondence to previously reported pharmacophore model of 17b-HSD1 inhibitors. Furthermore, molecular docking of inhibitors to 17b-HSD1 followed by anchor analysis suggested that three different pockets comprising of hydrogen bonding sites 1 and 2 as well as van der Waals contacts contributed to protein-ligand interactions. Postdocking analysis of potent compound 9 with 17b-HSD1 suggested that the binding modality was similar to the binding of substrate (i.e. estradiol) and its analog (i.e. equilin). Such information is useful in guiding the further design of novel and robust 17b-HSD1 inhibitors.
Curcumin is a major constituent of the turmeric plant Curcuma longa, a member of the Zingiberacea... more Curcumin is a major constituent of the turmeric plant Curcuma longa, a member of the Zingiberaceae family, which is cultivated in India, most parts of Southeast Asia, Asia and other parts of the world. Curcumin has been shown to afford a wide range of pharmacological activities encompassing antioxidative, anti-inflammatory, antibacterial, antifungal, antiviral, antiproliferative, proapoptotic and anti-atherosclerotic effects as well as medicinal benefits against neurodegenerative diseases, arthritis, allergy, inflammatory bowel disease, nephrotoxicity, AIDS, psoriasis, diabetes, multiple sclerosis, cardiovascular disease and lung fibrosis. Moreover, curcumin could suppress inflammatory cytokines as well as suppress various target proteins in cancer cell lines. Owing to its multi-faceted health benefits, curcumin has been used as health supplements as well as natural remedy while several clinical trials are under way to investigate its potential therapeutic usage. This chapter discus...
Drug Design, Development and Therapy, 2015
Drug Design, Development and Therapy Dovepress submit your manuscript | www.dovepress.com Dovepre... more Drug Design, Development and Therapy Dovepress submit your manuscript | www.dovepress.com Dovepress 2033 O r i g i n a l r e s e a r c h open access to scientific and medical research Open access Full Text article http://dx.
BMC Bioinformatics, 2015
Background: Epidermal growth factor receptor (EGFR) signalling plays a major role in biological p... more Background: Epidermal growth factor receptor (EGFR) signalling plays a major role in biological processes, including cell proliferation, differentiation and survival. Since the over-expression of EGFR causes human cancers, EGFR is an attractive drug target. A tumor suppressor endogenous protein, MIG-6, is known to suppress EGFR over-expression by binding to the C-lobe of EGFR kinase. Thus, this C-lobe of the EGFR kinase is a potential new target for EGFR kinase activity inhibition. In this study, molecular dynamics (MD) simulations and binding free energy calculations were used to investigate the protein-peptide interactions between EGFR kinase and a 27-residue peptide derived from MIG-6_s1 segment (residues 336-362).
Journal of Molecular Graphics and Modelling, 2015
Abnormal activation of EGFR is associated with human cancer, and thus it is a key target for inhi... more Abnormal activation of EGFR is associated with human cancer, and thus it is a key target for inhibition in cancer therapy. There is evidence suggesting that the activation mechanism of EGFR is based upon the formation of the asymmetric dimer of the kinase domains. Here, we performed MD simulations on the asymmetric dimer for both active and inactive conformations of EGFR kinase domain to investigate flexibility and intrinsic motions of the proteins. Simulations of the active conformation showed that the formation of the asymmetric dimer changes the dynamics of EGFR kinase domain by suppressing fluctuation of the protein and altering the direction of motion of the protein. In contrast, the asymmetric dimerization of the inactive conformation does not alter the overall fluctuation of the kinase domain and does not initiate destabilizing of the inactive structure. We also investigated the intermolecular interactions in the EGFR asymmetric dimers and found that in the active conformation the interactions are dominated by loop-loop contacts rather than those from the helix-helix interactions. In contrast, helix-helix interaction seemed to be more significant for the inactive kinase structure. This work helps us to better understand the conformational flexibility and dynamics of the EGFR kinase domain, as well as provides information that may be useful to develop newer classes of inhibitors that can block allosteric sites rather than the more traditional catalytic site.
Journal of Computational Chemistry, 2014
Green fluorescent protein (GFP) has immense utility in biomedical imaging owing to its autofluore... more Green fluorescent protein (GFP) has immense utility in biomedical imaging owing to its autofluorescent nature. In efforts to broaden the spectral diversity of GFP, there have been several reports of engineered mutants via rational design and random mutagenesis. Understanding the origins of spectral properties of GFP could be achieved by means of investigating its structure-activity relationship. The first quantitative structure-property relationship study for modeling the spectral properties, particularly the excitation and emission maximas, of GFP was previously proposed by us some years ago in which quantum chemical descriptors were used for model development. However, such simplified model does not consider possible effects that neighboring amino acids have on the conjugated p-system of GFP chromophore. This study describes the development of a unified proteochemometric model in which the GFP chromophore and amino acids in its vicinity are both considered in the same model. The predictive performance of the model was verified by internal and external validation as well as Y-scrambling. Our strategy provides a general solution for elucidating the contribution that specific ligand and protein descriptors have on the investigated spectral property, which may be useful in engineering novel GFP variants with desired characteristics.
Journal of Molecular Modeling, 2014
Human immunodeficiency virus-1 reverse transcriptase (HIV-1 RT) is considered to be one of the ke... more Human immunodeficiency virus-1 reverse transcriptase (HIV-1 RT) is considered to be one of the key targets for antiviral drug therapy. The emergence of the aptamers as potential inhibitors against HIV-1 reverse transcriptase has attracted the attention of the scientific community because these macromolecules can effectively inhibit HIV-1 RT with between micromolar to picomolar concentrations. However, it is not clear how aptamers interact with HIV-1 RT. We have undertaken a molecular dynamics (MD) study in order to gain a keen insight into the conformational dynamics of HIV-1 RT on the formation of a complex with an aptamer or DNA substrate. We have therefore employed three separate models: apo HIV-1 RT, HIV-1 RT with a bound RNA aptamer, and HIV-1 RT with a bound DNA substrate. The results show that HIV-1 RT complex with an aptamer was more stable than that with DNA substrate. It was found that the aptamer interacted with HIV-1 RT in a fingers-and-thumb-closed conformation, at the bound at the nucleic acid substrate binding site. We identified key residues within the HIV-1 RT-aptamer complex in order to help design, develop, and test a new aptamer based on therapies in the future.
Journal of Molecular Modeling, 2014
Yellow head virus (YHV) is one of the causative agents of shrimp viral disease. The prevention of... more Yellow head virus (YHV) is one of the causative agents of shrimp viral disease. The prevention of YHV infection in shrimp has been developed by various methods, but it is still insufficient to protect the mass mortality in shrimp. New approaches for the antiviral drug development for viral infection have been focused on the inhibition of several potent viral enzymes, and thus the YHV protease is one of the interesting targets for developing antiviral drugs according to the pivotal roles of the enzyme in an early stage of viral propagation. In this study, a theoretical modeling of the YHV protease was constructed based on the folds of several known crystal structures of other viral proteases, and was subsequently used as a target for virtual screening-molecular docking against approximately 1364 NCI structurally diversity compounds. A complex between the protease and the hit compounds was investigated for intermolecular interactions by molecular dynamics simulations. Five best predicted compounds (NSC122819, NSC345647, NSC319990, NSC50650, and NSC5069) were tested against bacterial expressed YHV. The NSC122819 showed the best inhibitory characteristic among the candidates, while others showed more than 50 % of inhibition in the assay condition. These compounds could potentially be inhibitors for curing YHV infection.
Journal of Molecular Modeling, 2013
The structural diversity observed across protein kinases, resulting in subtly different active si... more The structural diversity observed across protein kinases, resulting in subtly different active site cavities, is highly desirable in the pursuit of selective inhibitors, yet it can also be a hindrance from a structure-based design perspective. An important challenge in structure-based design is to better understand the dynamic nature of protein kinases and the underlying reasons for specific conformational preferences in the presence of different inhibitors. To investigate this issue, we performed molecular dynamics simulation on both the active and inactive wild type epidermal growth factor receptor (EGFR) protein with both type-I and type-II inhibitors. Our goal is to better understand the origin of the two distinct EGFR protein conformations, their dynamic differences, and their relative preference for Type-I inhibitors such as gefitinib and Type-II inhibitors such as lapatinib. We discuss the implications of protein dynamics from a structure-based design perspective.
Journal of Clinical Endocrinology & Metabolism, 2007
Six maturity onset diabetes of the young (MODY) genes have been discovered to date but account fo... more Six maturity onset diabetes of the young (MODY) genes have been discovered to date but account for a small proportion of MODY among Asians, suggesting the existence of other MODY genes in this racial group. The aim of this study was to investigate whether or not genetic variants in PAX4, a crucial transcription factor in beta-cell development, contribute to MODY in Thais. We screened PAX4 coding sequences in 46 MODY probands without mutation in known MODY genes and in 74 nondiabetic controls using PCR-single-stranded conformational polymorphism analysis followed by direct sequencing. Genotyping of variants identified was done by PCR-restriction fragment length polymorphism analysis. Eight sequence differences were identified. Two novel variations (R164W and IVS7-1G>A) were found in two different probands. Neither was found in the 74 nondiabetic controls and additional 270 healthy subjects of Thai origin. R164W segregated with diabetes in the family of the proband and in vitro studies showed that it impairs the repressor activity of PAX4 on the insulin and glucagon promoters. The remaining six variants were previously described and observed in both groups. One of them, R192H, was three times more frequent in MODY probands than in 342 nondiabetic controls (minor allele frequency = 0.196 vs. 0.064; P < 0.00001). The same variant was associated with a younger age at diagnosis among 254 Thai subjects with adult-onset type 2 diabetes (44.6 +/- 15 vs. 49.7 +/- 11 yr; P = 0.048). We have identified two possible pathogenic mutations of PAX4, R164W, and IVS7-1G>A. For one of these, we have shown evidence of segregation with diabetes and a functional impact on PAX4 activity. Single-nucleotide polymorphism R192H might influence the age at onset of diabetes.
Journal of Proteome Research, 2007
Clinical diagnostics and biomarker discovery are the major focuses of current clinical proteomics... more Clinical diagnostics and biomarker discovery are the major focuses of current clinical proteomics. In the present study, we applied microfluidic technology on a chip for proteome profiling of human urine from 31 normal healthy individuals (15 males and 16 females), 6 patients with diabetic nephropathy (DN), and 4 patients with IgA nephropathy (IgAN). Using only 4 microL of untreated urine, automated separation of proteins/peptides was achieved, and 1-7 (3.8 +/- 0.3) spectra/bands of urinary proteins/peptides were observed in the normal urine, whereas 8-16 (11.3 +/- 1.2) and 9-14 (10.8 +/- 1.2) spectra were observed in urine samples of DN and IgAN, respectively. Coefficient of variations of amplitudes of lower marker (1.2 kDa), system spectra (6-8 kDa), and upper marker (260.0 kDa) were 22.84, 24.92, and 32.65%, respectively. ANOVA with Tukey post-hoc multiple comparisons revealed 9 spectra of which amplitudes significantly differed between normal and DN urine (DN/normal amplitude ratios ranged from 2.9 to 3102.7). Moreover, the results also showed that 3 spectra (with molecular masses of 12-15, 27-28, and 34-35 kDa) were significantly different between DN and IgAN urine (DN/IgAN amplitude ratios ranged from 3.9 to 7.4). In addition to the spectral amplitudes, frequencies of some spectra could differentiate the normal from the diseased urine but could not distinguish between DN and IgAN. There was no significant difference, regarding the spectral amplitude or frequency, observed between males and females. These data indicate that the microfluidic chip technology is applicable for urinary proteome profiling with potential uses in clinical diagnostics and biomarker discovery.
Journal of Proteome Research, 2007
We have previously shown that the alternative sigma factor σ E (RpoE), encoded by rpoE, is involv... more We have previously shown that the alternative sigma factor σ E (RpoE), encoded by rpoE, is involved in stress tolerance and survival of Burkholderia pseudomallei. However, its molecular and pathogenic mechanisms remain unclear. In the present study, we applied gel-based, differential proteomics to compare the cellular proteome of an rpoE operon knockout mutant (RpoE Mut) to that of wild-type (K96243 WT) B. pseudomallei. Quantitative intensity analysis (n ) 5 gels from 5 individual culture flasks in each group) revealed significantly differential expression of 52 proteins, which were subsequently identified by Q-TOF MS/MS. These included oxidative, osmotic, and other stress response proteins; chaperones; transcriptional/translational regulators; metabolic enzymes; proteins involved in cell wall synthesis, fatty synthesis, glycogen synthesis, and storage; exported proteins; secreted proteins; adhesion molecule; protease/peptidase; protease inhibitor; signaling proteins; and other miscellaneous proteins. The down-regulation of several stress response proteins, chaperones, transcriptional/ translational regulators, and proteins involved in cell wall synthesis in RpoE Mut provided some new insights into the mechanisms of the rpoE operon for the stress tolerance and survival of B. pseudomallei. In addition, the proteomic data and in vivo study indicated that the rpoE operon is also involved in the virulence of B. pseudomallei. Our findings underscore the usefulness of proteomics for unraveling pathogenic mechanisms of diseases at the molecular level.
Analytical and Bioanalytical Chemistry, 2006
There is a need for a simple method that can directly quantify hydrophobic proteins. UV-visible s... more There is a need for a simple method that can directly quantify hydrophobic proteins. UV-visible spectrophotometry was applied in the present study for this purpose. Absorbance at λ=280 nm (A 280) was detected for both Escherichia coli membrane proteins and bovine serum albumin, whereas absorbance at λ=620 nm (A 620) was only detected for E. coli membrane proteins. The A 620 values of the brain samples were greater than those of heart samples when equal concentrations were used, regardless of the type of solubilizing agent employed. Because hydrophobic proteins tend to form colloidal microparticles in solution, we also applied UV-visible spectrophotometry to evaluate the efficacies of different extraction protocols for solubilizing hydrophobic proteins. For brain protein extraction, the highest A 620 was observed in samples recovered using Tris, whereas the lowest was from samples recovered using SDS. Solubilizing brain tissue with 0.25% SDS (above the CMC) gave a lower A 620 than extraction with 0.025% SDS (below the CMC). Addition of 0.25% SDS to samples recovered with Triton caused A 620 to drop. A 620 could also be used to distinguish between the hydrophobic fractions (pellets) of brain and urine proteins and their hydrophilic fractions (supernatants) prefractionated using high-speed centrifugation. Additionally, an A 620/A 280 ratio exceeding 0.12 appears to denote highly hydrophobic samples. Our data suggest that direct UV-visible spectrophotometry can be used as a simple method to quantify and evaluate the solubilities of hydrophobic proteins.
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Papers by Napat Songtawee