Publications by authors named "Kiattawee Choowongkomon"

92 Publications

Development of loop-mediated isothermal amplification (LAMP) assay using SYBR safe and gold-nanoparticle probe for detection of Leishmania in HIV patients.

Sci Rep 2021 Jun 9;11(1):12152. Epub 2021 Jun 9.

Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.

Asymptomatic leishmaniasis cases have continuously increased, especially among patients with HIV who are at risk to develop further symptoms of cutaneous and visceral leishmaniasis. Thus, early diagnosis using a simple, sensitive and reliable diagnostic assay is important because populations at risk mostly reside in rural communities where laboratory equipment is limited. In this study, the highly sensitive and selective determination of Leishmania infection in asymptomatic HIV patients was achieved using dual indicators (SYBR safe and gold-nanoparticle probe; AuNP-probe) in one-step LAMP method based on basic instruments. The assay can be simply evaluated under the naked eye due to clear interpretation of fluorescent emission of LAMP-SYBR safe dye-complex and colorimetric precipitate of specific AuNP-probes. The sensitivities and specificities of fluorescent SYBR safe dye and AuNP-probe indicators were equal, which were as high as 94.1 and 97.1%, respectively. Additionally, detection limits were 10 parasites/mL (0.0147 ng/µL), ten times more sensitivity than other related studies. To empower leishmaniasis surveillance, this inexpensive one-step SYBR safe and AuNP-LAMP assay is reliably fast and simple for field diagnostics to point-of-care settings, which can be set up in all levels of health care facilities including resource limited areas, especially in low to middle income countries.
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http://dx.doi.org/10.1038/s41598-021-91540-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8190085PMC
June 2021

Discovery of novel JAK2 and EGFR inhibitors from a series of thiazole-based chalcone derivatives.

RSC Med Chem 2021 Mar 26;12(3):430-438. Epub 2021 Feb 26.

Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University Bangkok 10330 Thailand +662 2185418 +662 2185426.

The Janus kinase (JAK) and epidermal growth factor receptor (EGFR) have been considered as potential targets for cancer therapy due to their role in regulating proliferation and survival of cancer cells. In the present study, the aromatic alkyl-amino analogs of thiazole-based chalcone were selected to experimentally and theoretically investigate their inhibitory activity against JAK2 and EGFR proteins as well as their anti-cancer effects on human cancer cell lines expressing JAK2 (TF1 and HEL) and EGFR (A549 and A431). cytotoxicity screening results demonstrated that the HEL erythroleukemia cell line was susceptible to compounds and , whereas the A431 lung cancer cell line was vulnerable to compound . However, TF1 and A549 cells were not sensitive to our thiazole derivatives. From kinase inhibition assay results, compound was found to be a dual inhibitor against JAK2 and EGFR, whereas compounds and selectively inhibited the JAK2 protein. According to the molecular docking analysis, compounds , and formed hydrogen bonds with the hinge region residues Lys857, Leu932 and Glu930 and hydrophobically came into contact with Leu983 at the catalytic site of JAK2, while compound formed a hydrogen bond with Met769 at the hinge region, Lys721 near a glycine loop, and Asp831 at the activation loop of EGFR. Altogether, these potent thiazole derivatives, following Lipinski's rule of five, could likely be developed as a promising JAK2/EGFR targeted drug(s) for cancer therapy.
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http://dx.doi.org/10.1039/d0md00436gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8130606PMC
March 2021

In silico structural elucidation of the rabies RNA-dependent RNA polymerase (RdRp) toward the identification of potential rabies virus inhibitors.

J Mol Model 2021 May 24;27(6):183. Epub 2021 May 24.

Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand.

The rabies virus (RABV) is a non-segmented, negative single-stranded RNA virus which causes acute infection of the central nervous system in humans. Once symptoms appear, the result is nearly always death, and to date, post-exposure prophylaxis (PEP) is the only treatment applicable only immediately after an exposure. Previous studies have identified viral RNA-dependent RNA polymerase (RdRp) as a potential drug target due to its significant role in viral replication and transcription. Herein we generated an energy-minimized homology model of RABIES-RdRp and used it for virtual screening against 2045 NCI Diversity Set III library. The best five ligand-RdRp complexes were picked for further energy minimization via molecular dynamics (MDs) where the complex with ligand Z01690699 shows a minimum score characterized with stable hydrogen bonds and hydrophobic interactions with the catalytic site residues. Our study identified an important ligand for development of remedial approach for treatment of rabies infection.
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http://dx.doi.org/10.1007/s00894-021-04798-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8143072PMC
May 2021

Anti-HIV-1 reverse transcriptase property of some edible mushrooms in Asia.

Saudi J Biol Sci 2021 May 16;28(5):2807-2815. Epub 2021 Feb 16.

Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.

Human immunodeficiency virus (HIV) causes acquired immunodeficiency syndrome (AIDS), which is a serious health threat worldwide. One of its core enzymes, reverse transcriptase (RT), is a target for HIV inhibition. A number of bioactive compounds have been successfully used for HIV treatment. However, HIV rapidly mutates, and long-term treatment can cause drug-resistant strains. Therefore, new inhibitors are required to overcome this problem. In this study, the aqueous, ethanolic and hexane crude extracts of 19 edible and medicinal mushrooms, which are widely grown and available commercially in Thailand, were screened against HIV-1 RT. The results showed that the water extracts of and , the ethanol extracts of and and the hexane extract of exhibited strong anti-HIV-1 RT activity with IC values of 1.92 ± 0.15, 4.39 ± 0.79, 6.17 ± 0.76 and 7.75 ± 246 µg/ml, respectively. These mushrooms have the potential for HIV treatment, and further study on identification of the bioactive compounds against HIV-1 RT should be performed.
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http://dx.doi.org/10.1016/j.sjbs.2021.02.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8116966PMC
May 2021

Probing the Anti-Cancer Potency of Sulfated Galactans on Cholangiocarcinoma Cells Using Synchrotron FTIR Microspectroscopy, Molecular Docking, and In Vitro Studies.

Mar Drugs 2021 Apr 30;19(5). Epub 2021 Apr 30.

Department of Anatomy, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.

Sulfated galactans (SG) isolated from red alga have been reported to inhibit the growth of cholangiocarcinoma (CCA) cells, which was similar to the epidermal growth factor receptor (EGFR)-targeted drug, cetuximab. Herein, we studied the anti-cancer potency of SG compared to cetuximab. Biological studies demonstrated SG and cetuximab had similar inhibition mechanisms in CCA cells by down-regulating EGFR/ERK pathway, and the combined treatment induced a greater inhibition effect. The molecular docking study revealed that SG binds to the dimerization domain of EGFR, and this was confirmed by dimerization assay, which showed that SG inhibited ligand-induced EGFR dimer formation. Synchrotron FTIR microspectroscopy was employed to examine alterations in cellular macromolecules after drug treatment. The SR-FTIR-MS elicited similar spectral signatures of SG and cetuximab, pointing towards the bands of RNA/DNA, lipids, and amide I vibrations, which were inconsistent with the changes of signaling proteins in CCA cells after drug treatment. Thus, this study demonstrates the underlined anti-cancer mechanism of SG by interfering with EGFR dimerization. In addition, we reveal that FTIR signature spectra offer a useful tool for screening anti-cancer drugs' effect.
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http://dx.doi.org/10.3390/md19050258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8145517PMC
April 2021

Identification of Vinyl Sulfone Derivatives as EGFR Tyrosine Kinase Inhibitor: In Vitro and In Silico Studies.

Molecules 2021 Apr 12;26(8). Epub 2021 Apr 12.

Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.

Epidermal growth factor receptor (EGFR), overexpressed in many types of cancer, has been proved as a high potential target for targeted cancer therapy due to its role in regulating proliferation and survival of cancer cells. In the present study, a series of designed vinyl sulfone derivatives was screened against EGFR tyrosine kinase (EGFR-TK) using in silico and in vitro studies. The molecular docking results suggested that, among 78 vinyl sulfones, there were eight compounds that could interact well with the EGFR-TK at the ATP-binding site. Afterwards, these screened compounds were tested for the inhibitory activity towards EGFR-TK using ADP-Glo™ kinase assay, and we found that only VF16 compound exhibited promising inhibitory activity against EGFR-TK with the IC value of 7.85 ± 0.88 nM. In addition, VF16 showed a high cytotoxicity with IC values of 33.52 ± 2.57, 54.63 ± 0.09, and 30.38 ± 1.37 µM against the A431, A549, and H1975 cancer cell lines, respectively. From 500-ns MD simulation, the structural stability of VF16 in complex with EGFR-TK was quite stable, suggesting that this compound could be a novel small molecule inhibitor targeting EGFR-TK.
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http://dx.doi.org/10.3390/molecules26082211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8069501PMC
April 2021

The Effect of the EGFR - Targeting Compound 3-[(4-Phenylpyrimidin-2-yl) Amino] Benzene-1-Sulfonamide (13f) against Cholangiocarcinoma Cell Lines.

Asian Pac J Cancer Prev 2021 Feb 1;22(2):381-390. Epub 2021 Feb 1.

Department of Biochemistry, Kasetsart University, Bangkok, 10900, Thailand.

Objective: Cholangiocarcinoma (CCA) is a noxious malignancy of epithelium of the bile duct with a low response rate to chemotherapy. The epidermal growth factor receptor (EGFR) signaling pathway is implicated in the development of cancerous cells, especially CCA. In this study, we report detailed biological profiling of 13f identified from our earlier hit expansion studies. The aim of this work was to expand our understanding of 13f via more detailed investigations of its mechanism of action against KKU-100, KKU-452 and KKU-M156 CCA cells, as well as in comparison to the EGFR inhibitor Gefitinib and non-specific chemotherapeutic agents such as Cisplatin.

Methods: Inhibiting EGFR-Kinase, cytotoxicity, clonogenic assay, wound healing and apoptosis were performed. Levels of total expression of EGFR and EGFR phosphorylation proteins were detected.

Results: 13f was confirmed as an inhibitor of EGFR with an IC50 value against the tyrosine kinase of EGFR of 22 nM and IC50 values for 48 h incubation period were 1.3 ± 1.9, 1.5 ± 0.4 and 1.7 ± 1.1 µM of KKU-100, KKU-452 and KKU-M156, respectively through dose- and time-dependent induction of early apoptosis of CCA cells. The compound also suppressed the clonogenic ability of KKU-100 and KKU-M156 cells stronger than Gefitinib, while potently inhibiting EGF-stimulated CCA cell migratory activity in KKU-452 cells. It was observed that under normal conditions EGFR was activated in CCA cells. EGF-stimulated basal expression of EGFR in KKU-452 cells was suppressed following 13f treatment, which was significantly greater than that of the marketed EGFR inhibitor Gefitinib.

Conclusion: In summary, our study showed that 13f has potent anti-cancer activities including antiproliferation, clonogenic ability and migration through the modulation of EGFR signaling pathway in CCA for the first time. The compound represents an interesting starting point as a potential chemotherapeutic agent in ongoing efforts to improve response rate in CCA patients.
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http://dx.doi.org/10.31557/APJCP.2021.22.2.381DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8190356PMC
February 2021

Aptasensor for paraquat detection by gold nanoparticle colorimetric method.

J Environ Sci Health B 2021 21;56(4):370-377. Epub 2021 Feb 21.

Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand.

This study aimed to develop an aptasensor for paraquat detection by gold nanoparticles. The specific aptamer for paraquat was selected by using the SELEX process via capillary electrophoresis. Sixty-three aptamer candidates were amplified by asymmetric PCR and screened for paraquat binding using gold nanoparticles (AuNPs). Aggregation of AuNPs was specifically induced by desorption of paraquat binding aptamers from the surface of AuNPs as a result of aptamer-target interaction leading to the color change from red to purple. Aptamer 77F with the following sequence: 5'-AGGCTTACACCTGAAAAGCGGCTTAATTTACACTACTGTAT-3' was selected as a highly specific aptamer for paraquat. The detection limit of paraquat was 0.267 µg/mL by colorimetry and 1.573 µg/mL by the quartz crystal microbalance (QCM) technique. This aptamer showed specificity for paraquat by colorimetry. Dimethyl phophite, diethyl phophite and O,O diethyl thiophosphate potassium salt did not react by colorimetry but, exhibited a weak nonspecific reaction by QCM. This is first time that an aptasensor was used for detection of paraquat based on QCM. However, the aptasensor based on the colorimetric method simply uses a generation of a signal that can be detected by the naked eye. This technique is rapid, low cost easy to use and suitable for on-site detection of herbicide residue.
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http://dx.doi.org/10.1080/03601234.2021.1888615DOI Listing
June 2021

Liposomal Thiostrepton Formulation and Its Effect on Breast Cancer Growth Inhibition.

J Pharm Sci 2021 06 28;110(6):2508-2516. Epub 2021 Jan 28.

National Nanotechnology Centre (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand. Electronic address:

Forkhead box M1 (FOXM1) is known to play a role in breast cancer progression. FOXM1 inhibition becomes one of the strategies in developing the novel cancer therapy. Recently, thiostrepton has been recognized as a potent FOXM1 inhibitor. To improve its potential, we aimed to develop a nanodelivery system for thiostrepton. Here, liposome-encapsulated thiostrepton (TSLP) was developed. Physiochemical properties were characterized by TEM and dynamic light scattering technique. The biological activities were also evaluated, by cellular internalization, MTT assay, spheroid formation assay and RT-PCR. The result showed that the range sizes of TSLP were 152 ± 2 nm, polydispersity index (PdI) of 0.23 ± 0.02 and zeta potential of -20.2 ± 0.1 mV. As expected, TSLP showed a higher potential in reducing FOXM1 levels in MCF-7 cells than free thiostrepton. Additionally, TSLP significantly improved the efficiently and specificity of thiostrepton in reducing cell viability of MCF-7, but not of the fibroblast (HDFn) cells. Interestingly, TSLP had an ability to induce MCF-7 cell death in both 2D monolayer and 3D spheroid culture. In conclusions, TSLP could possibly be one of the potential developments using nano-delivery system to improve abilities and specificity of thiostrepton in breast cancer cell inhibition and death inducing, with decreasing non-specific toxicity.
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http://dx.doi.org/10.1016/j.xphs.2021.01.018DOI Listing
June 2021

Angiotensin-I converting enzyme inhibitory peptide derived from the shiitake mushroom ().

J Food Sci Technol 2021 Jan 15;58(1):85-97. Epub 2020 May 15.

Research Unit in Bioconversion/Bioseparation for Value-Added Chemical Production, Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, 254 Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330 Thailand.

Abstract: Angiotensin-I converting enzyme (ACE) inhibitors are widely used to control hypertension. In this study, protein hydrolysates from shiitake mushroom were hydrolyzed to prepare ACE-inhibitory peptides. Optimum process conditions for the hydrolysis of shiitake mushrooms using Alcalase were optimized using response surface methodology. Monitoring was conducted to check the degree of hydrolysis (DH) and ACE inhibitory activity. In the results, the optimum condition with the highest DH value of 28.88% was 50.2 °C, 3-h hydrolysis time, and 1.16 enzyme/substrate ratios. The highest ACE inhibitory activity (IC of 0.33 μg/mL) was under 47 °C, 3 h 28 min hydrolysis time, and 0.59 enzyme/substrate ratios. The highest activity was fractionated into 5 ranges of molecular weight, and the fraction below 0.65 kDa showed the highest activity with IC of 0.23 μg/mL. This fraction underwent purification using RP-HPLC, meanwhile the peak which offered a retention time of about 37 min showed high ACE inhibitory activity. Mass spectrometry identified the amino acid sequence of this peak as Lys-Ile-Gly-Ser-Arg-Ser-Arg-Phe-Asp-Val-Thr (KIGSRSRFDVT), with a molecular weight of 1265.43 Da. The synthesized variant of this peptide produced an ACE inhibitory activity (IC) of 37.14 μM. The peptide KIGSRSRFDVT was shown to serve as a non-competitive inhibitor according to the Lineweaver-Burk plot findings. A molecular docking study was performed, which showed that the peptide binding occurred at an ACE non-active site. The findings suggest that peptides derived from shiitake mushrooms could serve either as useful components in pharmaceutical products, or in functional foods for the purpose of treating hypertension.

Graphic Abstract:
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http://dx.doi.org/10.1007/s13197-020-04517-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7813967PMC
January 2021

Studies of Anti-EGFR Tyrosine Kinase Activity of Thai nutraceutical Plants.

Iran J Pharm Res 2020 ;19(2):199-206

Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Rd, Chatuchak, Bangkok 10900, Thailand.

Functional foods have emerged as a new approach to improve human health in term of nutraceutical to prevent people from illness rather than cure patients through medical treatment. In Asian society, particularly in Thailand, the utilizations of functional ingredients have been integrated in every parts of ordinary life. In this study, the tyrosine kinase activity of epidermal growth factor receptor (EGFR) inhibiting properties of 23 Thai's herbs-ethanol extracts have been examined. The crude extracts of only four species that inhibit the activity of EGFR-tyrosine kinase, (neem, Sa-dao), (L.) Merr. (Rajadad), L. (Roselle, Krachiap daeng), and Roxb. (Red sugar cane). Moreover, only ethanol extractions from and were also showed antitumor effect to non-small cell lung cancer, A549 cells.
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http://dx.doi.org/10.22037/ijpr.2017.2022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7667552PMC
January 2020

A Synthetic Bioactive Peptide Derived from the Asian Medicinal Plant Binds to Dengue Virus and Inhibits Cell Entry.

Viruses 2020 11 6;12(11). Epub 2020 Nov 6.

Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.

Dengue virus (DENV) infection has become a critically important globally prevalent infectious disease, especially in tropical and subtropical countries. Since neither currently exists, there is an urgent need for an effective vaccine to prevent, and a specific drug to treat DENV infection. Therapeutic peptides represent an attractive alternative for development into anti-DENV drugs due to their safety and their diverse biological and chemical properties. We recently reported novel bioactive peptides extracted from the Asian medicinal plant that efficiently inhibited all four DENV serotypes. In this study, we investigated the anti-DENV activity of a synthetic bioactive peptide derived from this plant. The most effective peptide (designated Pep-RTYM) inhibited DENV infection with a half-maximal inhibition concentration value of 7.9 μM. Time-of-addition study demonstrated that Pep-RTYM interacted with DENV particles and inhibited cellular entry. Pep-RTYM at 50 μM significantly reduced DENV production in Vero-kidney epithelial cells about 1000-fold, but it could decrease the virus production in Huh7 hepatocyte cells approximately 40-fold. Binding of Pep-RTYM to DENV particles may prevent virus interaction with cellular receptor and subsequent virus entry. This finding suggests a potential role of Pep-RTYM in the development of a novel anti-DENV drug.
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http://dx.doi.org/10.3390/v12111267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7694746PMC
November 2020

Anti-feline immunodeficiency virus reverse transcriptase properties of some medicinal and edible mushrooms.

Vet World 2020 Sep 5;13(9):1798-1806. Epub 2020 Sep 5.

Program in Applied Biology, Maejo University Phrae Campus, Phrae 54140, Thailand.

Background And Aim: Feline immunodeficiency virus (FIV) causes AIDS-like symptoms in domestic and wild cats. Treatment of infected cats has been performed using human anti-HIV drugs, which showed some limitations. This study aimed to determine the anti-FIV potential of some mushrooms.

Materials And Methods: A total of 17 medicinal and edible mushrooms were screened to find their inhibitory effect against FIV reverse transcriptase (FIV-RT). Three solvents, water, ethanol, and hexane, were used to prepare crude mushroom extracts. Fluorescence spectroscopy was used to perform relative inhibition and 50% inhibitory concentrations (IC) studies.

Results: The ethanol extract from dried fruiting bodies of showed the strongest inhibition with an IC value of 0.80±0.16 μg/mL. The hexane extract from dried mycelium of and ethanol and water extracts from fresh fruit bodies of also exhibited strong activities with the IC values of 1.22±0.20, 4.33±0.39, and 6.24±1.42 μg/mL, respectively. The ethanol extract from fresh fruiting bodies of , hexane extracts from dried mycelium of , ethanol extracts of , hexane extracts of fresh fruiting bodies of , and fresh fruiting bodies of showed moderate anti-FIV-RT activities with IC values of 29.73±12.39, 49.97±11.86, 65.37±14.14, 77.59±8.31, and 81.41±17.10 μg/mL, respectively. These mushroom extracts show anti-FIV potential.

Conclusion: The extracts from , , , and showed potential anti-FIV activity.
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http://dx.doi.org/10.14202/vetworld.2020.1798-1806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7566271PMC
September 2020

Characterization of New DNA Aptamers for Anti-HIV-1 Reverse Transcriptase.

Chembiochem 2021 Mar 30;22(5):915-923. Epub 2020 Nov 30.

Department of Chemistry, Faculty of Science, Kasetsart University, 10900, Chatuchak, Bangkok, Thailand.

HIV-1 RT is a necessary enzyme for retroviral replication, which is the main target for antiviral therapy against AIDS. Effective anti-HIV-1 RT drugs are divided into two groups; nucleoside inhibitors (NRTI) and non-nucleoside inhibitors (NNRTI), which inhibit DNA polymerase. In this study, new DNA aptamers were isolated as anti-HIV-1 RT inhibitors. The selected DNA aptamer (WT62) presented with high affinity and inhibition against wild-type (WT) HIV-1 RT and gave a KD value of 75.10±0.29 nM and an IC value of 84.81±8.54 nM. Moreover, WT62 decreased the DNA polymerase function of K103 N/Y181 C double mutant (KY) HIV-1 RT by around 80 %. Furthermore, the ITC results showed that this aptamer has small binding enthalpies with both WT and KY HIV-1 RTs through which the complex might form a hydrophobic interaction or noncovalent bonding. The NMR result also suggested that the WT62 aptamer could bind with both WT and KY mutant HIV-1 RTs at the connection domain.
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http://dx.doi.org/10.1002/cbic.202000633DOI Listing
March 2021

Development of a biosensor from aptamers for detection of the porcine reproductive and respiratory syndrome virus.

J Vet Sci 2020 Sep;21(5):e79

Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.

Background: Recently, the pork industry of Thailand faced an epidemic of highly virulent strains of porcine reproductive and respiratory syndrome virus (PRRSV), which spread throughout Southeast Asia, including the Lao People's Democratic Republic and Cambodia. Hence, the rapid and on-site screening of infected pigs on a farm is essential.

Objectives: To develop the new aptamer as a biosensor for detection PRRSV which are rapid and on-site screening of infected pig.

Methods: New aptamers against PRSSV were identified using the combined techniques of capillary electrophoresis, colorimetric assay by gold nanoparticles, and quartz crystal microbalance (QCM).

Results: Thirty-six candidate aptamers of the PRRSV were identified from the systematic evolution of ligands by exponential enrichment (SELEX) by capillary electrophoresis. Only 8 out of 36 aptamers could bind to the PRSSV, as shown in a colorimetric assay. Of the 8 aptamers tested, only the 1F aptamer could bind specifically to the PRSSV when presented with the classical swine fever virus and a pseudo rabies virus. The QCM was used to confirm the specificity and sensitivity of the 1F aptamer with a detection limit of 1.87 × 10 particles.

Conclusions: SELEX screening of the aptamer equipped with capillary electrophoresis potentially revealed promising candidates for detecting the PRRSV. The 1F aptamer exhibited the highest specificity and selectivity against the PRRSV. These findings suggest that 1F is a promising aptamer for further developing a novel PRRSV rapid detection kit.
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http://dx.doi.org/10.4142/jvs.2020.21.e79DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7533388PMC
September 2020

ACE inhibitory peptides derived from de-fatted lemon basil seeds: optimization, purification, identification, structure-activity relationship and molecular docking analysis.

Food Funct 2020 Sep;11(9):8161-8178

Research Unit in Bioconversion/Bioseparation for Value-Added Chemical Production, Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand.

The oil processing industry generates significant quantities of lemon basil seed residue which is not currently used to any significant extent. However, this by-product has important potential as a source of bioactive peptides which may play a role as ingredients in functional foods. This study therefore sought to optimize the preparation techniques used to obtain the necessary protein hydrolysate from de-fatted lemon basil seeds (DLBS), and subsequently to examine the ACE inhibitory capabilities of the resulting hydrolysate. Response Surface Methodology (RSM) was used for the hydrolysis of DLBS by Alcalase®, with observation of the resulting ACE inhibitory activity and degree of hydrolysis (DH). The optimum conditions were 55 °C and 103 minutes with a ratio of enzyme to substrate of 7.0% w/v. The hydrolysate was fractionated by ultrafiltration and purified through RP-HPLC. The results reveal that the F2 sub-fraction demonstrated the highest ACE inhibitory activity. The amino acid sequence of this peak was identified by mass spectrometry as LGRNLPPI and GPAGPAGL with a molecular weight of 879.06 and 639.347 Dalton, respectively. These peptides were classified as non-toxic and bitter peptides. For the synthesized version of these peptides, the ACE inhibitory activity values, measured by IC50, were 0.124 ± 0.02 mM and 0.013 ± 0.001 mM, respectively. Analysis of the Lineweaver-Burk plot confirmed that these peptides served as non-competitive ones. The study of molecular docking showed that the ACE inhibitory behavior of both purified peptides was mainly due to the interactions of the hydrogen bonds between the peptides and ACE. It is therefore suggested that DLBS may be a useful raw material allowing the production of antihypertensive peptides which can offer therapeutic and commercial benefits as an ingredient in functional foods.
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http://dx.doi.org/10.1039/d0fo01240hDOI Listing
September 2020

Novel peptides with HIV-1 reverse transcriptase inhibitory activity derived from the fruits of Quercus infectoria.

Chem Biol Drug Des 2021 Jan 24;97(1):157-166. Epub 2020 Aug 24.

Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand.

The HIV-1 reverse transcriptase (HIV-1 RT), which is responsible for transcription of viral RNA genomes into DNA genomes, has become an important target for the treatment of patients with HIV infection. Hydrolyzed peptides from plants are considered a new source of potential drugs. In order to develop new effective inhibitors, peptides extracted from 111 Asian medicinal plants were screened against the HIV-1 RT. The crude hydrolyzed peptides from the fruit peel of Quercus infectoria were selected for purification and peptide sequence determination by HPLC and LC-MS. Two peptides of interest were synthesized, and an IC test was performed to determine their ability to inhibit the HIV-1 RT. The IC values of the peptides AIHIILI and LIAVSTNIIFIVV were determined to be 274 ± 5.10 nm and 236.4 ± 7.07 nm, respectively. This indicated that these peptides could be further developed as potential HIV-1 RT inhibitors.
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http://dx.doi.org/10.1111/cbdd.13770DOI Listing
January 2021

Sensing the classical swine fever virus with molecularly imprinted polymer on quartz crystal microbalance.

Heliyon 2020 Jun 6;6(6):e04137. Epub 2020 Jun 6.

Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand.

Classical swine fever (CSF) is a highly contagious and fatal viral disease in pigs caused by the virus of the same name (classical swine fever virus - CSFV). Economical reasons dictate the need for rapid early detection of this pathogen. Herein we report on a sensor for CSFV detection based on a quartz crystal microbalance (QCM) making use of molecularly imprinted polymer (MIP) as the receptor. It relies on a copolymer comprising acrylamide (AAM), methacrylic acid (MAA), methyl methacrylate (MMA), and n-vinylpyrrolidone (VP). SEM images of CSFV MIP reveal cavities on the polymer surface with an average diameter of d = 59 nm, which correlates well with the dimensions of CSFV particles. QCM sensor measurements yield concentration-dependent CSFV sensor responses resulting in LOD = 1.7 μg/mL, LOQ = 5.1 μg/mL and R = 0.9963. Furthermore, CSFV-MIP sensors selectively bind CSFV with selectivity factors of 2 over porcine respiratory and reproductive virus (PRRSV) and 62 over pseudorabies virus (PRV), respectively. Finally, sensor responses turned out fully reversible.
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http://dx.doi.org/10.1016/j.heliyon.2020.e04137DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7284075PMC
June 2020

Molecular dynamics, MM/PBSA and in vitro validation of a novel quinazoline-based EGFR tyrosine kinase inhibitor identified using structure-based in silico screening.

J Mol Graph Model 2020 09 19;99:107639. Epub 2020 May 19.

Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, 10210, Thailand. Electronic address:

EGFR-TK has been a target strongly associated with the development of NSCLCs. A structure-based virtual screening campaign was launched against EGFR-TK by virtual screening a 3D library of 167 commercially available small molecules downloaded from ChemBridge Corporation. The virtual screen identified 12 virtual hit molecules, which were biologically evaluated against an EGFR-TK inhibitor-sensitive NSCLC cell line, A549. A quinazoline-based molecule 1, was most active and displayed ∼58% cytotoxicity at 20 μM single dose. The mode of cell death suggests molecule 1 induced apoptosis, which is characteristic of EGFR-TK pathway inhibition. A 50 ns MD simulation was conducted on three different systems: free EGFR-TK, molecule 1 complexed to EGFR-TK, and the positive control, lapatinib, complexed to EGFR-TK. The MD simulations showed increase in stabilisation of the EGFR-TK structure for the complexed systems, i.e., lower RMSDs and RMSFs for complexed EGFR-TK structures compared to the free EGFR-TK system. The binding affinities were estimated using MM/PBSA in the last 10 ns of the MD simulation that revealed comparable binding free energies between molecule 1 and lapatinib, ΔG = -25.0 and -23.9 kcal/mol, respectively. Per residue binding free energy decomposition studies revealed non-polar interactions contributed mostly to the binding free energies. Residues Leu718, Arg841 and Phe856 were predicted to contribute most to the binding free energies for molecule 1.
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http://dx.doi.org/10.1016/j.jmgm.2020.107639DOI Listing
September 2020

Evaluation of tyrosinase inhibitory activity and mechanism of Leucrocin I and its modified peptides.

J Biosci Bioeng 2020 Sep 7;130(3):239-246. Epub 2020 May 7.

Department of Biochemistry, Faculty of Science, Khon Kaen University, 123 Mittraphap Road, Muang District, Khon Kaen 40002, Thailand; Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Faculty of Science, Khon Kaen University, 123 Mittraphap Road, Muang District, Khon Kaen 40002, Thailand. Electronic address:

This research first reports the tyrosinase inhibition and mechanism of Leucrocin I and its modified peptides (TILI-1 and TILI-2). Docking simulation showed that these peptides were predicted to bind and interact to active site of tyrosinase and exhibited the possibility to promote tyrosinase inhibition. Therefore, these peptides were synthesized, and their inhibitory activity was investigated. The results showed that the highest tyrosinase inhibition was achieved by TILI-2 followed by TILI-1 and Leucrocin I. A Lineweaver-Burk plot indicated that Leucrocin I exhibited mixed type characteristics, while its modified peptides exhibited competitive inhibition. Based on the greatest tyrosinase inhibition, TILI-2 was selected for further study. TILI-2 showed irreversible inhibition with two-step inactivation. Additionally, Leucrocin I and its modified peptides showed no toxicity toward B16F1 and HaCaT cells and decreased melanin and tyrosinase content in B16F1 cells. These results suggest that these peptides are promising peptides for the treatment of hyperpigmentation.
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http://dx.doi.org/10.1016/j.jbiosc.2020.04.002DOI Listing
September 2020

Potential tripeptides against the tyrosine kinase domain of human epidermal growth factor receptor (HER) 2 through computational and kinase assay approaches.

J Mol Graph Model 2020 06 4;97:107564. Epub 2020 Feb 4.

Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, 10900, Thailand; Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand. Electronic address:

An abnormal activation of human epidermal growth factor receptor (HER) 2 has been found to associate with several types of human cancer, and thus the protein is a prominent target for cancer therapy. Although several small chemical molecules targeting the tyrosine kinase (TK) of HER family have been identified, the development of a new class of inhibitors, i.e., small peptides inhibiting the function of tyrosine kinase is still promising. Here, we screened 8000 tripeptides for candidate potential inhibitors against HER2-TK using molecular docking. Our in vitro kinase assays showed that the candidate tripeptides had more than 50% relative inhibition to HER2-TK. Even though these tripeptides had much lower inhibitory activity than that of the drug Lapatinib, the tripeptides WWW exhibited high inhibitory activity with the IC of ≈283 μM, while FYW showed lower activity with the IC of ≈1723 μM. The relative binding free energies calculated by MM/PBSA method were comparable to the inhibition experiment in that Lapatinib binding was ≈-139 kJ/mol whereas the binding of WWW and FYW was ≈-112 kJ/mol and ≈-81 kJ/mol, respectively. Energy calculation also indicated that the HER2-TK/inhibitor interactions were dominated by van der Waals over electrostatic contributions. In addition, molecular interaction analyses revealed that several interacting residues with more negative binding free energy could mostly contribute the hydrophobic interaction. Therefore, we suggested preferable interactions for further development of potential tripeptides as a new anticancer peptide targeting HER2-TK.
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http://dx.doi.org/10.1016/j.jmgm.2020.107564DOI Listing
June 2020

Insights into the Binding Recognition and Susceptibility of Tofacitinib toward Janus Kinases.

ACS Omega 2020 Jan 2;5(1):369-377. Epub 2020 Jan 2.

Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science and Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.

Janus kinases (JAKs) are enzymes involved in signaling pathways that affect hematopoiesis and immune cell functions. JAK1, JAK2, and JAK3 play different roles in numerous diseases of the immune system and have also been considered as potential targets for cancer therapy. In the present study, the susceptibility of the oral JAK inhibitor tofacitinib against these three JAKs was elucidated using the 500-ns molecular dynamics (MD) simulations and free energy calculations based on MM-PB(GB)SA, QM/MM-GBSA (PM3 and SCC-DFTB), and SIE methods. The obtained results revealed that tofacitinib could interact with all JAKs at the ATP-binding site via electrostatic attraction, hydrogen bond formation, and in particular van der Waals interaction. The conserved glutamate and leucine residues (E957 and L959 of JAK1, E930 and L932 of JAK2, and E903 and L905 of JAK3) located in the hinge region stabilized tofacitinib binding through strongly formed hydrogen bonds. Complexation with the incoming tofacitinib led to a closed conformation of the ATP-binding site and a decreased protein fluctuation at the glycine loop of the JAK protein. The binding affinities of tofacitinib/JAKs were ranked in the order of JAK3 > JAK2 ∼ JAK1, which are in line with the reported experimental data.
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http://dx.doi.org/10.1021/acsomega.9b02800DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6964278PMC
January 2020

Chamuangone from Garcinia cowa leaves inhibits cell proliferation and migration and induces cell apoptosis in human cervical cancer in vitro.

J Pharm Pharmacol 2020 Mar 25;72(3):470-480. Epub 2019 Dec 25.

Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand.

Objectives: To examine the effects of chamuangone on human cancer cell proliferation, migration and apoptosis.

Methods: An MTT assay was used to study the effect of chamuangone on human cervical carcinoma cell growth. An in-vitro scratch migration assay was used to investigate the activity of cell motility after chamuangone treatment. Chamuangone-induced cell apoptosis in HeLa cells was determined using the apoptotic assay kit. The inhibitory activities of chamuangone were examined by ADP-Glo™ kinase assay. The GOLD docking algorithm was used to demonstrate the mechanism against tyrosine kinase of EGFR.

Key Findings: Chamuangone showed a strong inhibitory cell proliferation of HeLa cells with IC values of 3.59 µm and effectively inhibited HeLa cell migration. In addition, chamuangone exhibited the apoptotic cell death induction in a time and dose-dependent manner. Finally, chamuangone also was tested for EGFR-TK inhibition activity. The IC value of chamuangone was 2.85 nm, whereas the IC value of gefitinib was 15.10 nm.

Conclusions: The above results confirm the inhibitory effects of chamuangone on HeLa cell proliferation and cell migration. In addition, chamuangone also induces cell apoptosis in HeLa cells. These findings indicate that chamuangone is a compound that is a potential chemotherapeutic agent.
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http://dx.doi.org/10.1111/jphp.13216DOI Listing
March 2020

Discovery of New and Potent InhA Inhibitors as Antituberculosis Agents: Structure-Based Virtual Screening Validated by Biological Assays and X-ray Crystallography.

J Chem Inf Model 2020 01 27;60(1):226-234. Epub 2019 Dec 27.

School of Cellular and Molecular Medicine , University of Bristol , Biomedical Sciences Building, University Walk , BS8 1TD Bristol , United Kingdom.

The enoyl-acyl carrier protein reductase InhA of is an attractive, validated target for antituberculosis drug development. Moreover, direct inhibitors of InhA remain effective against InhA variants with mutations associated with isoniazid resistance, offering the potential for activity against MDR isolates. Here, structure-based virtual screening supported by biological assays was applied to identify novel InhA inhibitors as potential antituberculosis agents. High-speed Glide SP docking was initially performed against two conformations of InhA differing in the orientation of the active site Tyr158. The resulting hits were filtered for drug-likeness based on Lipinski's rule and avoidance of PAINS-like properties and finally subjected to Glide XP docking to improve accuracy. Sixteen compounds were identified and selected for in vitro biological assays, of which two (compounds and ) showed MIC of 12.5 and 25 μg/mL against H37Rv, respectively. Inhibition assays against purified recombinant InhA determined IC values for these compounds of 0.38 and 0.22 μM, respectively. A crystal structure of the most potent compound, compound , bound to InhA revealed the inhibitor to occupy a hydrophobic pocket implicated in binding the aliphatic portions of InhA substrates but distant from the NADH cofactor, i.e., in a site distinct from those occupied by the great majority of known InhA inhibitors. This compound provides an attractive starting template for ligand optimization aimed at discovery of new and effective compounds against that act by targeting InhA.
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http://dx.doi.org/10.1021/acs.jcim.9b00918DOI Listing
January 2020

Molecular docking study of lamellarin analogues and identification of potential inhibitors of HIV-1 integrase strand transfer complex by virtual screening.

Heliyon 2019 Nov 14;5(11):e02811. Epub 2019 Nov 14.

Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, 10210, Thailand.

Molecular docking has been applied to elucidate the binding of lamellarin analogues with HIV-1 integrase strand transfer complex (PDB ID: 5U1C). The results suggest hydrogen bond interaction with residue Glu92 is key, and stabilisation by π-π stacking interactions with DNA base is chiefly influential to strand transfer activity. Other residues involved in hydrogen bonding are Cys65, His67, Asp64, Asp116 and chelation with Mg ion was seen for certain analogues. Furthermore, hydrophobic interactions can be accounted for several amino acids including Asp64, Cys65, Asp116, His67, Glu92, Tyr143, Phe121, Gly118, Pro142 and Val72, as well as the DNA base. The molecular docking results are in line with the reported literatures of other inhibitors and strand transfer activity observed previously by Faulkner. We further employed molecular docking simulation to virtually screen and identified 4 novel potential inhibitors of HIV-1 integrase strand transfer complex from a Chembridge diversity collection of 25,132 small molecule compounds; Chembridge ID compound codes: , , and . The candidates clearly formed hydrogen bonding interactions with important residues: His67 and Glu92. In addition, hydrophobic interactions were seen with residues similar to interactions with lamellarin analogues. The calculated drug-like scores are suggestive of these compounds to have clinical potential and ADMET predictions implied of their acceptable pharmacokinetic and toxicity profiles.
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http://dx.doi.org/10.1016/j.heliyon.2019.e02811DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6861579PMC
November 2019

FTIR spectra signatures reveal different cellular effects of EGFR inhibitors on nonsmall cell lung cancer cells.

J Biophotonics 2020 03 8;13(3):e201960012. Epub 2020 Jan 8.

Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand.

ATP-analogue inhibitors, Gefitinib (Iressa) and Erlotinib (Tarceva) had been approved for advanced and metastatic nonsmall cell lung cancer (NSCLC) cells against tyrosine kinase domain of epidermal growth factor receptor (EGFR). Many techniques have been developed to better understand the drug mechanism which is multistep, time-consuming and expensive. Herein, we performed Fourier-transform infrared (FTIR) microscopy for evaluating the biochemical change on NSCLC (A549) cells after treatment. At levels that produced equivalent effects, Gefitinib dramatically induced cell apoptosis via impaired mitochondrial transmembrane potential. Whereas, Erlotinib had a slight effect on A549. Principal component analysis was performed to distinguish the effect of EGFR inhibitors on A549. FTIR spectra regions were divided into three regions: lipids (3000-2800 cm ), proteins (1700-1500 cm ) and carbohydrates and nuclei acids (1200-1000 cm ). Biochemical changes can be evaluated by these spectral regions. This work may be a novel concept for utilizing FTIR spectroscopy for high-throughput discriminative effects of a drug or compound and its derivatives on cells.
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http://dx.doi.org/10.1002/jbio.201960012DOI Listing
March 2020

Novel GH-20 β-N-acetylglucosaminidase inhibitors: Virtual screening, molecular docking, binding affinity, and anti-tumor activity.

Int J Biol Macromol 2020 Jan 5;142:503-512. Epub 2019 Oct 5.

Biochemistry-Electrochemistry Research Unit, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Payupnai, Wangchan, Rayong 21210, Thailand. Electronic address:

β-N-acetylglucosaminidases (GlcNAcases) play a crucial role in the metabolism of glycan-conjugated proteins/lipids in humans. Elevated levels of serum GlcNAcases have been associated with certain types of cancer, and GlcNAcases therefore serve as drug targets. Here, we employed virtual screening to identify two novel GlcNAcase inhibitors from the National Cancer Institute (NCI) Drug Library using a bacterial GH-20 GlcNAcase (VhGlcNAcase) as a search model. NSC73735 was shown to be most potent with IC of 12.7 ± 1.2 μM, agreeing with K of 0.94 ± 0.2 μM obtained by ITC. Molecular docking refinement indicated that Trp582 the key residue that interacted with all the inhibitor molecules. Docking NSC7373 into the active site of human O-GlcNAcase (hOGA) yielded reasonably good fit with the estimated K of 44.7 µM, indicating its possibility to be a true binding partner. NSC73735 was shown to significantly suppress both cell growth and GlcNAcase activity of five cancer cell lines (U937, THP-1, MCF-7, HepG2 and PC-3) that express endogenous GlcNAcases. The cell cytotoxicity assay indicated the inherent effects of the lead compound on GlcNAcase expression with cancer cell proliferation, and therefore this novel GlcNAcase inhibitor may serve as a virtuous candidate for further development of highly potent anti-tumor agents.
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http://dx.doi.org/10.1016/j.ijbiomac.2019.09.122DOI Listing
January 2020

Expression, purification, and characterization of the native intracellular domain of human epidermal growth factor receptors 1 and 2 in Escherichia coli.

Appl Microbiol Biotechnol 2019 Oct 10;103(20):8427-8438. Epub 2019 Sep 10.

Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, 10900, Thailand.

Human epidermal growth factor receptors (EGFR) are an important target in drug discovery in terms of both protein-small-molecule interactions and protein-protein interactions. In this work, the isolation of a stable soluble protein of the tyrosine kinase domain of EGFR in Escherichia coli expression has been accomplished. This successful study presents the expression and purification conditions to obtain a stable soluble protein of the active tyrosine kinase domain of EGFR (EGFR-TK) and ErbB2 (ErbB2-TK) in a bacterial system, albeit in relatively low yields. The recombinant gene was inserted into a pColdI vector and recombinant protein was expressed at low temperature. Purification of EGFR-TK and ErbB2-TK took place under the same conditions by purified supernatant using a diethylaminoethyl sepharose column followed by anion exchange and size-exclusion chromatography columns. The final yields of purified EGFR-TK and ErbB2-TK were 8.4 and 9.5 mg per liter of culture, respectively. Determination of EGFR-TK and ErbB2-TK was performed via enzyme activity with commercial drugs. The IC values of erlotinib and afatinib against EGFR-TK were 13.09 nM and 2.36 nM respectively, while the IC values of lapatinib and afatinib against ErbB2-TK were 24.69 nM and 1.36 nM, respectively. These results confirmed that soluble proteins of the active intracellular domain of the HERs family were successfully expressed and purified in a bacterial system. The new protein expression and purification protocol will greatly facilitate the enzymatic inhibition and structural studies of this protein for drug discovery.
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http://dx.doi.org/10.1007/s00253-019-10116-6DOI Listing
October 2019

FeptideDB: A web application for new bioactive peptides from food protein.

Heliyon 2019 Jul 20;5(7):e02076. Epub 2019 Jul 20.

Functional Food Unit, Department of Nutrition and Health, Institute of Food Research and Product Development, Kasetsart University, Thailand.

Background: Bioactive peptides derived from food are important sources for alternative medicine and possess therapeutic activity. Several biochemical methods have been achieved to isolate bioactive peptides from food, which are tedious and time consuming. methods are an alternative process to reduce cost and time with respect to bioactive peptide production. In this paper, FeptideDB was used to collect bioactive peptide (BP) data from both published research articles and available bioactive peptide databases. FeptideDB was developed to assist in forecasting bioactive peptides from food by combining peptide cleavage tools and database matching. Furthermore, this application was able to predict the potential of cleaved peptides from to identify new ACE (angiotensin converting enzyme) inhibitors using an automatic molecular docking approach.

Results: The FeptideDB web application contains tools for generating all possible peptides cleaved from input protein by various available enzymes. This database was also used for analysis and visualization to assist in bioactive peptide discovery. One module of FeptideDB has the ability to create 3-dimensional peptide structures to further predict inhibitors for the target protein, ACE (angiotensin converting enzyme).

Conclusions: FeptideDB is freely available to researchers who are interested in exploring bioactive peptides. The FeptideDB interface is easy to use, allowing users to rapidly retrieve data based on desired search criteria. FeptideDB is freely available at http://www4g.biotec.or.th/FeptideDB/. Ultimately, FeptideDB is a computational aid for assessing peptide bioactivities.
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http://dx.doi.org/10.1016/j.heliyon.2019.e02076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6656964PMC
July 2019

Cell-penetrable nanobodies (transbodies) that inhibit the tyrosine kinase activity of EGFR leading to the impediment of human lung adenocarcinoma cell motility and survival.

J Cell Biochem 2019 10 6;120(10):18077-18087. Epub 2019 Jun 6.

Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand.

Most patients suffering from non-small cell lung cancer (NSCLC) have epidermal growth factor receptor (EGFR) overexpression. Currently, EGFR tyrosine kinase inhibitors (TKIs) that act as the ATP-analogs and monoclonal antibodies (MAbs) to EGFR-ectodomain that block intracellular signaling are used for the treatment of advanced NSCLC. Unfortunately, adverse effects due to the TKI off-target and drug resistance occur in a significant number of the treated patients while some NSCLC genotypes do not respond to the therapeutic MAbs. Thus, a more effective remedy for the treatment of EGFR-overexpressed cancers is deemed necessary. In this study, VH/V H displayed-phage clones that are bound to recombinant EGFR-TK were fished-out from a humanized-camel VH/V H phage display library. VH/V H of three phage-infected Escherichia coli clones (VH18, V H35, and VH36) were linked molecularly to nonaarginine (R9) for making them cell penetrable. R9-VH18, R9-V H35, and R9-VH36 were cytotoxic to human adenocarcinomic alveolar basal epithelial cells (A549) at the fifty percent inhibitory concentration (IC ) 0.181 ± 0.132, 0.00961 ± 0.00516, and 0.00996 ± 0.00752 μM, respectively, which were approximately 1000-fold more effective than small molecular TKIs. R9-VH18 and R9-VH36 also delayed cancer cell migration in a scratch-wound assay. Computerized homology modeling and intermolecular docking revealed that VH18 and V H35 used CDR3 to interact with EGFR-TK residues close to the catalytic site, which might sterically hinder the ATP-binding of the TK; VH36 used CDR2 to bind at the asymmetric dimerization surface, which might disrupt EGFR dimerization leading to inhibition of intracellular signaling. The humanized-cell penetrable nanobodies have a high potential for developing further towards a clinical application.
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http://dx.doi.org/10.1002/jcb.29111DOI Listing
October 2019