• The Plant Pathology Journal
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• v.33 no.6
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• pp.529-542
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• 2017

Control of plant diseases is largely dependent on use of agrochemicals. However, there are widening gaps between our knowledge on plant diseases gained from genetic/mechanistic studies and rapid translation of the knowledge into target-oriented development of effective agrochemicals. Here we propose that the time is ripe for computer-aided drug discovery/design (CADD) in molecular plant pathology. CADD has played a pivotal role in development of medically important molecules over the last three decades. Now, explosive increase in information on genome sequences and three dimensional structures of biological molecules, in combination with advances in computational and informational technologies, opens up exciting possibilities for application of CADD in discovery and development of agrochemicals. In this review, we outline two categories of the drug discovery strategies: structure- and ligand-based CADD, and relevant computational approaches that are being employed in modern drug discovery. In order to help readers to dive into CADD, we explain concepts of homology modelling, molecular docking, virtual screening, and de novo ligand design in structure-based CADD, and pharmacophore modelling, ligand-based virtual screening, quantitative structure activity relationship modelling and de novo ligand design for ligand-based CADD. We also provide the important resources available to carry out CADD. Finally, we present a case study showing how CADD approach can be implemented in reality for identification of potent chemical compounds against the important plant pathogens, Pseudomonas syringae and Colletotrichum gloeosporioides.

• Journal of Integrative Natural Science
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• v.3 no.3
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• pp.162-167
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• 2010

A pseudoreceptor combines structure-based and ligand-based techniques to represent a unifying concept for both receptor mapping and ligand matching. In this molecular modeling approach, there are opportunities to construct the pseudoreceptor models using a set of small molecules. To build a reliable pseudoreceptor model, we need a set of ligand molecules with known affinity (biological activity) to generate 3D bioactive conformation for each of these ligand molecules. Several software packages are available to generate a pseudoreceptor model and this can provide an entry point for structure based drug discovery in cases where receptor structure information is not available. In this review, we presented the concept of pseudoreceptor, as well as discussed about various software packages available to generate a pseudoreceptor model.

• Bulletin of the Korean Chemical Society
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• v.18 no.9
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• pp.976-981
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• 1997

The magnetic susceptibilities of molybdenum ions with 4d1 electronic configuration in the octahedral crystal field were calculated on the basis of ligand field theory. The experimental magnetic susceptibilities for molybdenum ions, which are stabilized at the octahedral site in the perovskite lattice of Ba2ScMoⅤO6 and Sr2YMoⅤO6, were compared with the theoretical ones. We have tried to fit their temperature dependence of magnetic susceptibility with ligand field parameters, spin-orbit coupling constant ζSO, and orbital reduction parameter κ according to intermediate field coupling and strong field theory. Strong field coupling theory could not explain experimental curves without unrealistically large axial ligand field, since it ignores the mixing up between different state via spin-orbit interaction and ligand field. On the other hand, the intermediate field coupling theory could successfully reproduce experimental data in octahedral and trigonal ligand field. The fitting result demonstrates not only the fact that spin-orbit interaction is primarily responsible for the variation of magnetic behavior but also the fact that effective orbital overlap, enhanced by cubic crystal structure, reduces significantly orbital angular momentum as indicated by κ parameter.

• Reproductive and Developmental Biology
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• v.32 no.3
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• pp.141-146
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• 2008

To search a new porcine pheromonal odorant, the models of four type (2D-QSAR, HQSAR, CoMFA & CoMSlA) were derived from quantitative structure-activity relationship (QSAR) between tetrahydrofuran-2-yl family compounds and their observed binding affinity constants (Obs.p$[Od]_{50}$). The optimized CoMFA model (predictability; $r^{2}_{cv.}(q^2)$=0.886 & correlation coefficient: $r^{2}_{ncv.}$=0.984) from ligand based approaches was confirmed as the best model among them. The $N^{1}$-allyl-$N^{2}$-(tetrahydrofuran-2-yl)methyl)oxalamide (P1), 2-(4-trimethylammoniummethylcyclohexyloxy)tetrahydrofurane (P5) and 2-(3-trimethylammoniummethylcyclohexyloxy)tetrahydrofurane (P6) molecules predicted as porcine pheromonal odorant by the CoMFA model were showed relatively high binding affinity constant values (Pred.p$[Od]_{50}=8{\sim}10$) and very lower toxicity values against some sorts of toxicity.

• Food Science and Biotechnology
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• v.17 no.3
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• pp.547-552
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• 2008

The detection of carbamate (carbofuran, carbaryl, benfracarb, thiodicarb, and methomil) and organophosphate (diazinon, cadusafos, ethoprofos, parathion-methyl, and chlorpyrifos) pesticide residues with very low detection limits was carried out using surface plasmon resonance (SPR) based equipment. The capacity to develop a portable SPR biosensor for food safety was also investigated. The applied ligand for the immunoassays was polyclonal goat anti-rabbit immunoglobulin (IgG) peroxidase conjugate. Concentration tests using direct binding assays showed the possibility of quantitative analysis. For ligand fishing to find a proper antibody to respond to each pesticide, acetylcholinesterase (AChE), and glutathione-S-transferase (GST) were tested. The reproducibility and precision of SPR measurements were evaluated. With this approach, the limit of detection for pesticide residues was 1 ng/mL and analysis took less than 11 min. Thus, it was demonstrated that detecting multi-class pesticide residues using SPR and IgG antibodies provides enough sensitivity and speed for use in portable SPR biosensors.

• Molecules and Cells
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• v.27 no.6
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• pp.629-634
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• 2009

G protein-coupled receptors (GPCRs) are part of multi-protein networks called 'receptosomes'. These GPCR interacting proteins (GIPs) in the receptosomes control the targeting, trafficking and signaling of GPCRs. PDZ domain proteins constitute the largest protein family among the GIPs, and the predominant function of the PDZ domain proteins is to assemble signaling pathway components into close proximity by recognition of the last four C-terminal amino acids of GPCRs. We present here a machine learning based approach for the identification of GPCR-binding PDZ domain proteins. In order to characterize the network of interactions between amino acid residues that contribute to the stability of the PDZ domain-ligand complex and to encode the complex into a feature vector, amino acid contact matrices and physicochemical distance matrix were constructed and adopted. This novel machine learning based method displayed high performance for the identification of PDZ domain-ligand interactions and allowed the identification of novel GPCR-PDZ domain protein interactions.

• Bulletin of the Korean Chemical Society
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• v.31 no.6
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• pp.1501-1505
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• 2010

We report design and synthesis of the novel TRPV1 ligands through a rational approach. Simplified analogues of 12(S)-HPETE showing TRPV1 agonistic effect are disclosed. Biological evaluation revealed that substitution of functional groups without any change in conformation converted agonist into antagonist. Our work provided key information with regard to TRPV1 agonist/antagonist switching.

• Journal of Chest Surgery
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• v.56 no.2
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• pp.67-74
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• 2023

Perioperative treatment with conventional cytotoxic chemotherapy for resectable non-small cell lung cancer (NSCLC) has proven clinical benefits in terms of achieving a higher overall survival (OS) rate. With its success in the palliative treatment of NSCLC, immune checkpoint blockade (ICB) has now become an essential component of treatment, even as neoadjuvant or adjuvant therapy in patients with operable NSCLC. Both pre- and post-surgery ICB applications have proven clinical efficacy in preventing disease recurrence. In addition, neoadjuvant ICB combined with cytotoxic chemotherapy has shown a significantly higher rate of pathologic regression of viable tumors compared with cytotoxic chemotherapy alone. To confirm this, an early signal of OS benefit has been shown in a selected population, with programmed death ligand 1 expression ≥50%. Furthermore, applying ICB both pre- and post-surgery enhances its clinical benefits, as is currently under evaluation in ongoing phase III trials. Simultaneously, as the number of available perioperative treatment options increases, the variables to be considered for making treatment decisions become more complex. Thus, the role of a multidisciplinary team-based treatment approach has not been fully emphasized. This review presents up-to-date pivotal data that lead to practical changes in managing resectable NSCLC. From the medical oncologist's perspective, it is time to dance with surgeons to decide on the sequence of systemic treatment, particularly the ICB-based approach, accompanying surgery for operable NSCLC.

• Journal of the Korean Vacuum Society
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• v.16 no.1
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• pp.52-57
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• 2007

The interaction force between biomolecules(DNA-DNA, antigen-antibody, ligand-receptor, protein-protein) defines not only biomolecular function, but also their mechanical properties and hence bio-sensor. Atomic force microscopy(AFM) is nowadays frequently applied to determine interaction forces between biological molecules and biomolecular force measurements, obtained for example using AFM can provide valuable molecular-level information on the interactions between biomolecules. A proper modification of an AFM tip and/or a substrate with biomolecules permits the direct measurement of intermolecular interactions, such as DNA-DNA, protein-protein, and ligand-receptor, etc. and a microcantilever-based sensor appeared as a promising approach for ultra sensitive detection of biomolecular interactions.

• Molecules and Cells
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• v.41 no.11
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• pp.933-942
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• 2018

Traditionally, small-molecule or antibody-based therapies against human diseases have been designed to inhibit the enzymatic activity or compete for the ligand binding sites of pathological target proteins. Despite its demonstrated effectiveness, such as in cancer treatment, this approach is often limited by recurring drug resistance. More importantly, not all molecular targets are enzymes or receptors with druggable 'hot spots' that can be directly occupied by active site-directed inhibitors. Recently, a promising new paradigm has been created, in which small-molecule chemicals harness the naturally occurring protein quality control machinery of the ubiquitin-proteasome system to specifically eradicate disease-causing proteins in cells. Such 'chemically induced protein degradation' may provide unprecedented opportunities for targeting proteins that are inherently undruggable, such as structural scaffolds and other non-enzymatic molecules, for therapeutic purposes. This review focuses on surveying recent progress in developing E3-guided proteolysis-targeting chimeras (PROTACs) and small-molecule chemical modulators of deubiquitinating enzymes upstream of or on the proteasome.