Vannajan Sanghiran Lee

Vannajan Sanghiran Lee
University of Malaya | UM · Department of Chemistry

Ph.d

About

194
Publications
29,115
Reads
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2,192
Citations
Introduction
Computer-aided molecular modeling and computational chemistry using Molecular Dynamics (MD), Monte Carlo Simulations (MC) and Quantum Mechanics (QM) in diverse research and development fields such as biomolecular / material design.
Additional affiliations
August 2011 - present
University of Malaya
Position
  • Professor (Associate)
August 2001 - February 2011
Chiang Mai University
Position
  • Lecturer
August 1997 - June 2001
University of Missouri - Kansas City
Position
  • Teaching/Research Assistance, Video Based Supplementary Instructor at Center of Academic Development

Publications

Publications (194)
Article
Computational and experimental approaches were adopted to utilize a chromophore diglycolic functionalized fluorescein derivative as a Ca2+ receptor. Fluorescein diglycolic acid (Fl-DGA, 1) was synthesized and used in multivariate determination of Ca2+ and K+. Full-structure computation shows that the complexes of 1 and Ca2+ have comparable energies...
Article
An electrochemical sensing platform for the simultaneous detection of methotrexate (MTX) and Ciprofloxacin (CIF) has been presented using nanocellulose and 3dimensional polypyrrole (NC-3DPPY) hybridized silver-gold bimetallic alloy nanoparticle (Ag-Au). The NC-3DPPY composites and Ag-Au bimetallic alloys were prepared by acid hydrolysis and chemica...
Article
Full-text available
The Musashi (MSI) family of RNA-binding proteins, comprising the two homologs Musashi-1 (MSI1) and Musashi-2 (MSI2), typically regulates translation and is involved in cell proliferation and tumorigenesis. MSI proteins contain two ribonucleoprotein-like RNA-binding domains, RBD1 and RBD2, that bind single-stranded RNA motifs with a central UAG trin...
Article
Full-text available
There is an increasing demand in developing new, effective, and affordable anti-cancer against colon and rectal. In this study, our aim is to identify the potential anthraquinone compounds from the root bark of Morinda citrifolia to be tested in vitro against colorectal cancer cell lines. Eight potential anthraquinone compounds were successfully is...
Article
Full-text available
CNS disorders are indications with a very high unmet medical needs, relatively smaller number of available drugs, and a subpar satisfaction level among patients and caregiver. Discovery of CNS drugs is extremely expensive affair with its own unique challenges leading to extremely high attrition rates and low efficiency. With explosion of data in in...
Article
Single-atom catalysts have recently emerged as a promising approach for catalyzing the electrochemical CO2 reduction reaction (CRR). Transition metal (TM) atom doping to 2-dimensional layer material has been studied for CRR, but compared to studies on TM doped single vacancy (TM-SV) sites, those on double vacancies (TM-DV) sites are minor. In this...
Article
Full-text available
SARS-CoV-2 causes the current global pandemic coronavirus disease 2019. Widely-available effective drugs could be a critical factor in halting the pandemic. The main protease (3CL pro ) plays a vital role in viral replication; therefore, it is of great interest to find inhibitors for this enzyme. We applied the combination of virtual screening base...
Article
Full-text available
Anti-interferon gamma autoantibodies (anti-IFN-γ autoAbs) neutralize the IFN-γ-mediated functions, contributing to immunodeficiency. A particular autoAb in patient serum had been previously demonstrated to recognize the same determinant on IFN-γ as the neutralizing anti-IFN-γ monoclonal antibody clone B27 (B27 mAb). This study explored the epitope...
Article
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Cholangiocarcinoma (CCA) is a lethal cancer with rapid progression and poor survival. Novel and more effective therapies than those currently available are, therefore, urgently needed. Our research group previously reported the combination of gemcitabine and cytotoxic T lymphocytes to be more effective than single-agent treatment for the eliminatio...
Article
In the present work, a highly selective and metal-free electrochemical sensor was fabricated from the fusion of nanocellulose and polypyrrole (NNC-PPY), incorporated with single-walled carbon nanotubes (SWCNTs) via drop-casting method for the simultaneous determination of paracetamol (PCM) and ciprofloxacin (CPR). The screen printed electrode (SPE)...
Article
The new sensor, R34 was prepared from the reaction of rhodamine B hydrazide and 3,4-dihydroxybenzaldehyde, and it was characterised by spectroscopic techniques and single crystal X-ray diffraction. Sensor R34 can detect Al³⁺/Cu²⁺ through colorimetric and fluorometric methods in MeCN solution, which displayed a notable colour change from colourless...
Article
Full-text available
Phosphodiesterase10A (PDE10A) is a potential therapeutic target for the treatment of several neurodegenerative disorders.
Article
Global public health has been a critical problem by the sudden increase of the COVID-19 outbreak. The papain-like protease (PLpro) of SARS-CoV-2 is a key promising target for antiviral drug development since it plays a pivotal role in viral replication and innate immunity. Here, we employed the all-atom molecular dynamics (MD) simulations and bindi...
Article
Full-text available
Owing to their ability to maintain a thermodynamically stable fold at extremely high temperatures, thermophilic proteins (TTPs) play a critical role in basic research and a variety of applications in the food industry. As a result, the development of computation models for rapidly and accurately identifying novel TTPs from a large number of unchara...
Conference Paper
Background: The inhibition of Phosphodiesterase 1B (PDE1B) has been proposed as a novel way to improve the cognitive function in many neurodegenerative and neuropsychiatric diseases, while; the inhibition of PDE10A has been proposed to alleviate the symptoms in Huntington’s disease and Schizophrenia. Therefore, the present study aims to identify a...
Article
Full-text available
A series of C4-substituted tertiary nitrogen-bearing 2′-hydroxychalcones were designed and synthesised based on a previous mixed type acetylcholinesterase inhibitor. Majority of the 2′-hydroxychalcone analogues displayed a better inhibition against acetylcholinesterase (AChE) than butyrylcholinesterase (BuChE). Among them, compound 4c was identifie...
Article
Copper complexes have the potential to overcome the limitations of platinum anticancer drugs and to provide a solution to difficult to cure metastatic breast cancer. The anticancer properties of a set of ternary copper(II) complex salts, viz. [Cu(phen)(L-ala)(H2O)]NO3 1, rac-[Cu(phen)(ala)(H2O)]NO3 2, rac-[Cu(phen)(4MeOCA)(H2O)]NO3 3 (1,10-phenanth...
Article
The number of people infected with dengue, as reported by WHO, reaches 390 million yearly, and the global incidence of dengue has grown tremendously. Specific drugs for treating dengue are under development while several antibodies bound to domain III (DIII) envelope (E) protein of dengue virus (DENV) were found to prevent the viral entry process....
Preprint
Assembly and budding in the late-stage of human immunodeficiency virus type 1 (HIV-1) production relies on the polymerization of Gag protein at the inner leaflet of the plasma membrane. We previously generated an ankyrin repeat protein (Ank1D4) that specifically interacts with the CAp24 protein. This study aimed to improve the binding activity of A...
Article
Full-text available
Protein-protein interaction plays an essential role in almost all cellular processes and biological functions. Coupling molecular dynamics (MD) simulations and nanoparticle tracking analysis (NTA) assay offered a simple, rapid, and direct approach in monitoring the protein-protein binding process and predicting the binding affinity. Our case study...
Article
Full-text available
The aim of this review is to highlight and provide an update on the current development of pesticide remediation methods, focusing on the utilization of different cyclodextrin (CD) molecules. Because of less environmental impact and non-toxic nature, CDs are beneficial for pesticide remediation, reducing environmental risk and health hazards. They...
Article
Schizophrenia is a neuropsychiatric disorder characterised by positive symptoms, negative symptoms, and cognitive impairment. Dopamine system dysfunction is strongly implicated in the aetiology of schizophrenia, where the hyperactivity in striatal dopamine and hypoactivity in cortical dopamine is considered the key feature of this serious mental di...
Article
The silver nanoparticles (AgNPs) complexed with curcumin (CUR) extracted from turmeric (TMR) were synthesized and applied for a simple and rapid colorimetric technique for Pb²⁺ detection. The results reveal that our low-cost and rapid AgNPs-CUR sensor is highly selective for Pb²⁺ ions with the detection limit of 13.6 µM (2.8 mg L⁻¹) and can be appl...
Article
Full-text available
Meso-scale simulations have been widely used to probe aggregation caused by structural formation in macromolecular systems. However, the limitations of the long-length scale, resulting from its simulation box, cause difficulties in terms of morphological identification and insufficient classification. In this study, structural knowledge derived fro...
Article
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Extracellular signal-regulated kinases 1 and 2 (ERK1/2) play key roles in promoting cell survival and proliferation through the phosphorylation of various substrates. Remarkable antitumour activity is found in many inhibitors that act upstream of the ERK pathway. However, drug-resistant tumour cells invariably emerge after their use due to the reac...
Preprint
Full-text available
There is an increasing demand in developing new, effective, and affordable anti-cancer against colon and rectal. In this study, our aim is to identify the potential anthraquinone compounds from the root bark of Morinda citrifolia to be tested in vitro against colorectal cancer cell lines. Eight potential anthraquinone compounds were successfully is...
Article
Naturally occurring proteins are emerging as novel therapeutics in the protein-based biopharmaceutical industry for the treatment of diabetes and obesity. However, proteins are not suitable for oral delivery due to short half-life, reduced physical and chemical stability and low permeability across the membrane. Chemical modification has been ident...
Article
A series of Schiff base metal complexes with the formulations [Ni(L1)PPh3]Cl (1), [Ni(L2)PPh3]Cl (2), [Ni(L3)PPh3] (3), and [Ni(L4)PPh3] (4) (where L1 = 2,3,4-trihydroxybenzaldehyde-4-methyl-3-thiosemicarbazone, L2 = 2,3,4-trihydroxybenzaldehyde-4-ethyl-3-thiosemicarbazone, L3 = 2,3,4-trihydroxybenzaldehyde-4-phenyl-3-thiosemicarbazone, and L4 = 2,...
Article
A new chemosensor 1 was synthesized by reacting rhodamine B hydrazide and 2,3,4-trihydroxybenzaldehyde, which was then characterized by spectroscopic techniques and single crystal X-ray crystallography. Sensor 1 has the ability to sense Co2+/Cu2+ ions by “naked-eye” with an apparent colour change from colourless to pink in different solvent system,...
Article
This study attempts to bring about a facile approach to selectively adsorb 2,4-dinitrophenol (2,4-DNP) from an aqueous system using sporopollenin supported ionic liquid (SpIL) biosorbent, namely sporopollenin supported methylimidazolium (Sp-MIM). Sporopollenin acts as the host with the accessible chamber, while methylimidazolium acts as the active...
Article
Full-text available
Dengue virus (DENV) infection causes mild to severe illness in humans that can lead to fatality in severe cases. Currently, no specific drug is available for the treatment of DENV infection. Thus, the development of an anti-DENV drug is urgently required. Cordycepin (3′-deoxyadenosine), which is a major bioactive compound in Cordyceps (ascomycete)...
Article
Conformational search for the most stable geometry connection of 16 sets of polydopamine (PDA) tetramer subunits has been systematically investigated using density functional theory (DFT) calculations. Our results indicated that the more planar subunits are, the more stable they are. This finding is in good agreement with recent experimental observ...
Article
A rhodamine-based colorimetric sensor, RBOV has been synthesized and modified for selective detection of Cu²⁺, Ni²⁺ and Co²⁺ ions simultaneously in aqueous medium. The difference in colour change upon binding with these three cations makes it an interesting multianalyte sensor. Furthermore, the detection limits of RBOV for Cu²⁺, Ni²⁺ and Co²⁺ are d...
Article
Full-text available
A total of 20 of isolates of lactic acid bacteria (LAB) were selected and screened for antagonistic activity against clinical strains of 30 clinical isolates of extremely drug-resistant (XDR) Acinetobacter baumannii using the well diffusion assay method. Results showed that 50% of the highly LAB strains possessed inhibitory activity against (up to...
Article
The present study investigates deep eutectic solvents (DESs) as potential media for enzymatic hydrolysis. A series of ternary ammonium and phosphonium-based DESs were prepared at different molar ratios by mixing with aqueous glycerol (85%). The physicochemical properties including surface tension, conductivity, density, and viscosity were measured...
Article
Full-text available
As anticancer peptides (ACPs) have attracted great interest for cancer treatment, several approaches based on machine learning have been proposed for ACP identification. Although existing methods have afforded high prediction accuracies, however such models are using a large number of descriptors together with complex ensemble approaches that conse...
Article
The emergence outbreak caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hasreceived significant attention on the global risks. Due to itscrucial role in viral replication, the main protease3CLprois an important target for drug discovery and development to combat COVID-19. In this work, the struc-tural and dynamic behav...
Article
Cationic (Malachite Green) and anionic dyes (Indigo carmine) removal by cross-linked chitosan (CSglu) beads has been investigated using experimental and computational approaches. The experimental investigations of the adsorption isotherm, kinetics, and thermodynamics information correlated well with computational studies in term of structures and b...
Article
Molecular level insight into the interactions between donors and acceptors are crucial for understanding how such interactions can modify the optical properties of organic optoelectronic materials. In this paper, tris(4‐(tert‐butyl)phenyl)amine (pTPA) was synthesized as a donor in order to compare with unmodified triphenylamine (TPA) in donor‐accep...
Article
Full-text available
Inhibition of phosphodiesterase 4 (PDE4) is a promising therapeutic approach for the treatment of inflammatory pulmonary disorders, i.e. asthma and chronic obstructive pulmonary disease. However, the treatment with non-selective PDE4 inhibitors is associated with side effects such as nausea and vomiting. Among the subtypes of PDE4 inhibited by thes...
Article
Full-text available
Retinal pigment epithelial (RPE) cells are an essential part of the human eye because they not only mediate and control the transfer of fluids and solutes but also protect the retina against photooxidative damage and renew photoreceptor cells through phagocytosis. However, their function necessitates cumulative exposure to the sun resulting in UV d...
Article
The work was aimed at using Geant4-DNA software to simulate ultra-low-energy particle irradiation of DNA to understand relevant effects and fundamentals on DNA strand breaks. Light particle species of electron, hydrogen, proton, helium (He), He⁺ and He²⁺ with energy ranged in 10 – 1000 eV and fluence varied from 5 × 10³ to 1 × 10⁵ particles/cm² irr...
Article
Human sweet taste receptor (hSTR) recognizes a wide array of sweeteners, resulting in sweet taste perception. Maltitol and lactitol have been extensively used in place of sucrose due to their capability of preventing dental caries. Herein, several molecular modeling approaches were applied to investigate the structural and energetic properties of t...
Article
Full-text available
Glucosidases and β-mannosidases hydrolyze substrates that differ only in the epimer of the nonreducing terminal sugar moiety, but most such enzymes show a strong preference for one activity or the other. Rice Os3BGlu7 and Os7BGlu26 β-glycosidases show a less strong preference, but Os3BGlu7 and Os7BGlu26 prefer glucosides and mannosides, respectivel...
Article
Toxic metabolites that could promote the formation of tumors are generated with high levels of β-glucuronidase activities. Hence, the inhibition of the β-glucuronidase enzyme is effective in the prevention of colonic carcinogenesis, and other diseases. This study aims to investigate the β-glucuronidase inhibitory effect of compounds that were isola...
Article
MCR (mobile colistin resistance) enzymes catalyse phosphoethanolamine (PEA) addition to bacterial lipid A, threatening the “last-resort” antibiotic colistin. Molecular dynamics and density functional theory simulations indicate that monozinc MCR supports...
Article
Full-text available
Poly(3,4-ethylenedioxythiophene)polystyrene sulfonate (PEDOT:PSS) is often used as a hole injection and extractor for various organic electronic devices. This study investigated whether it is possible to n-dope PEDOT:PSS with barium acetylacetonate (Ba(acac)2) to change its work function so that to be more suitable for electron injection and extrac...
Article
Full-text available
Since the emergence of 2019 novel coronavirus (also known as SARS-CoV-2) to date, effective treatment for the patients was reported to be some anti-viral for flu and HIV-1 or anti-malaria drugs. To understand the finer details of the molecular interactions and complexation between these proteinase inhibitors and the COVID-19, virus sequence analysi...
Article
Full-text available
Alzheimer’s disease (AD) is considered one of the greatest global public burdens. Pathophysiology of AD is proposed to be associated with reduced levels of the neurotransmitter acetylcholine (ACh). Cholinesterase enzymes, namely acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) cleave ACh via hydrolysis. Cholinesterase inhibitors (ChEIs)...
Article
Given the fact that lithium aluminum hydride (LiAlH4) can exist in distinct crystalline structures under different conditions, in this study, we aim to theoretically investigate the structural properties and the pressure-induced phase transformations of its 13 closely related crystal structures by means of the density functional theory (DFT). The p...
Article
Full-text available
Enterovirus A71 (EV-A71) causes hand, foot and mouth disease epidemics with neurological complications and fatalities. However, the neuropathogenesis of EV-A71 remains poorly understood. In mice, adaptation and virulence determinants have been mapped to mutations at VP2-149, VP1-145 and VP1-244. We investigate how these amino acids alter heparin-bi...
Article
Full-text available
In this study, we have demonstrated an automated workflow by using KNIME Analytical Platform for modelling and predicting potential HIV-1 protease (HIVP) inhibitors. The workflow has been simplified in three easy steps i.e., 1) retrievethe database of inhibitors for the target disease from ChEMBL website and well-known drug from DrugBank database,...
Article
Dipropylheterocoerdianthrone (DPHCD) was found to be a potential photo-reactive dispersant of single-walled carbon nanotubes (SWNTs). DPHCD was able to well disperse SWNTs in chloroform. DPHCD is easily photo-oxidized by the irradiation of visible light to form the endoperoxide with a bent structure under oxygen or air atmosphere. Then, SWNTs were...
Article
Full-text available
Spontaneous spatial organization behavior and the aggregate morphology of polystyrene-block-polyisoprene (PS-b-PI) copolymer were investigated. Molecular dynamic (MD) and mesoscopic simulations using the dynamic of mean field density functional theory (DDF) were adopted to investigate the morphology changes exhibited by this block copolymer (BCP)....
Article
Organic semiconductors generally display significant conformational flexibility which results in significant energetic disorder. In this research, ultraviolet photoelectron spectra are compared with the Gaussian density of states obtained from the density functional theory on assembly of molecules optimized using molecular dynamic simulations. It w...
Article
Sixteen novel coumarin‐based compounds are reported as potent acetylcholinesterase (AChE) inhibitors. The most active compound in this series, 5a (IC50 0.04 ± 0.01 µM), noncompetitively inhibited AChE with a higher potency than tacrine and galantamine. Compounds 5d, 5j, and 5 m showed a moderate antilipid peroxidation activity. The compounds showed...
Preprint
Full-text available
Enterovirus A71 (EV-A71) causes hand, foot and mouth disease epidemics with neurological complications and fatalities. However, the neuropathogenesis of EV-A71 remains poorly understood. In mice, adaptation and virulence determinants have been mapped to mutations at VP1-145, VP1-244 and VP2-149. We hypothesized that heparin-binding phenotype shapes...
Article
Full-text available
In this study, we investigate the binding interactions of two synthetic antiviral peptides (DET2 and DET4) on type II dengue virus (DENV2) envelope protein domain III. These two antiviral peptides are designed based on the domain III of the DENV2 envelope protein, which has shown significant inhibition activity in previous studies and can be potent...
Article
To date, there is still no approved anti-dengue agent to treat dengue infection in the market. Although the only licensed dengue vaccine, Dengvaxia is available, its protective efficacy against serotypes 1 and 2 of dengue virus was reported to be lower than serotypes 3 and 4. Moreover, according to WHO, the risk of being hospitalized and having sev...
Article
Scaffold known as designed ankyrin repeat proteins (DARPins) have been utilized by scientists extensively in protein binding, as they acquire remarkable binding properties. Trimodular ankyrin repeat protein (Ank1D4) is a potential macromolecular and antiviral intracellular inhibitor that aims the N-terminal domain capsid protein (NTDCA) of viral Hu...