• Proceedings of the Plant Resources Society of Korea Conference
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• 2020.12a
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• pp.14-14
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• 2020

In December 2019, the COVID-19 epidemic was discovered in Wuhan, China, and since has disseminated around the world impacting human health for millions. Herein, in-silico drug discovery approaches were utilized to identify potential candidates as Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) main protease (M^pro) inhibitors. We investigated several databases including natural and natural-like products (>100,000 molecules), DrugBank database (10,036 drugs), major metabolites isolated from daily used spices (32 molecules), and current clinical drug candidates for the treatment of COVID-19 (18 drugs). All tested compounds were prepared and screened using molecular docking techniques. Based on the calculated docking scores, the top ones from each project under investigation were selected and subjected to molecular dynamics (MD) simulations followed by molecular mechanics-generalized Born surface area (MM-GBSA) binding energy calculations. Combined long MD simulations and MM-GBSA calculations revealed the potent compounds with prospective binding affinities against M^pro. Structural and energetic analyses over the simulated time demonstrated the high stabilities of the selected compounds. Our results showed that 4-bis([1,3]dioxolo)pyran-5-carboxamide derivatives (natural and natural-like products database), DB02388 and Cobicistat (DB09065) (DrugBank database), salvianolic acid A (spices secondary metabolites) and TMC-310911 (clinical-trial drugs database) exhibited high binding affinities with SARS-CoV-2 M^pro. In conclusion, these compounds are up-and-coming anti-COVID-19 drug candidates that warrant further detailed in vitro and in vivo experimental estimations.

• Bulletin of the Korean Chemical Society
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• v.29 no.4
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• pp.833-841
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• 2008

Principal component-genetic algorithm-multiparameter linear regression (PC-GA-MLR) and principal component-genetic algorithm-artificial neural network (PC-GA-ANN) models were applied for prediction of melting point for 323 drug-like compounds. A large number of theoretical descriptors were calculated for each compound. The first 234 principal components (PC’s) were found to explain more than 99.9% of variances in the original data matrix. From the pool of these PC’s, the genetic algorithm was employed for selection of the best set of extracted PC’s for PC-MLR and PC-ANN models. The models were generated using fifteen PC’s as variables. For evaluation of the predictive power of the models, melting points of 64 compounds in the prediction set were calculated. Root-mean square errors (RMSE) for PC-GA-MLR and PC-GA-ANN models are 48.18 and $12.77{^{\circ}C}$, respectively. Comparison of the results obtained by the models reveals superiority of the PC-GA-ANN relative to the PC-GA-MLR and the recently proposed models (RMSE = $40.7{^{\circ}C}$). The improvements are due to the fact that the melting point of the compounds demonstrates non-linear correlations with the principal components.

• Genomics & Informatics
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• v.14 no.4
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• pp.241-254
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• 2016

Environmental microbes like Bordetella petrii has been established as a causative agent for various infectious diseases in human. Again, development of drug resistance in B. petrii challenged to combat against the infection. Identification of potential drug target and proposing a novel lead compound against the pathogen has a great aid and value. In this study, bioinformatics tools and technology have been applied to suggest a potential drug target by screening the proteome information of B. petrii DSM 12804 (accession No. PRJNA28135) from genome database of National Centre for Biotechnology information. In this regards, the inhibitory effect of nine natural compounds like ajoene (Allium sativum), allicin (A. sativum), cinnamaldehyde (Cinnamomum cassia), curcumin (Curcuma longa), gallotannin (active component of green tea and red wine), isoorientin (Anthopterus wardii), isovitexin (A. wardii), neral (Melissa officinalis), and vitexin (A. wardii) have been acknowledged with anti-bacterial properties and hence tested against identified drug target of B. petrii by implicating computational approach. The in silico studies revealed the hypothesis that lpxD could be a potential drug target and with recommendation of a strong inhibitory effect of selected natural compounds against infection caused due to B. petrii, would be further validated through in vitro experiments.

• CELLMED
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• v.6 no.4
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• pp.22.1-22.19
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• 2016

The biologically active compounds derived from different natural organisms such as animals, plants, and microorganisms like algae, fungi, bacteria and merine organisms. These natural compounds possess diverse biological activities like anthelmintic, antibacterial, antifungal, antimalarial, antiprotozoal, antituberculosis, and antiviral activities. These biological active compounds were acted by variety of molecular targets and thus may potentially contribute to several pharmacological classes. The synthesis of natural products and their analogues provides effect of structural modifications on the parent compounds which may be useful in the discovery of potential new drug molecules with different biological activities. Natural organisms have developed complex chemical defense systems by repelling or killing predators, such as insects, microorganisms, animals etc. These defense systems have the ability to produce large numbers of diverse compounds which can be used as new drugs. Thus, research on natural products for novel therapeutic agents with broad spectrum activities and will continue to provide important new drug molecules.

• Journal of environmental and Sanitary engineering
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• v.22 no.3
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• pp.89-96
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• 2007

To determine 8 anti-impotence drug/drug-like compounds such as sildenafil, vardenafil, tadalafil, homosildenafil, hydroxyhomosildenafil, aminotadalafil, pseudovardenafil and hongdenafil in foods, simultaneously, high performance liquid chromatography(HPLC) and liquid chromatography-mass spectrometry (LC/MS) were used. The HPLC/UV analysis was performed on a column of capcellpak $C_{18}$ with 0.1% sodium-1-hexansulfonate in 0.2M ammonium formate/acetonitrile as a mobile phase. Mass spectra of the compounds by LC/MS were investigated with SCAN mode(Mass range and Fragment voltage) and SIM(Selected Ion Monitoring) mode (Ion target and Fragment voltage). The results follow as; 1. The HPLC/UV analysis was detected from 5 out of 63 samples. The content of sildenafil was in the range of 32.80 ppm ${\sim}$ 60.13 ppm from 4 out of 5 samples. The contents of sildenafil, vardenafil, homosildenafil were in the range 47.14 ppm from 1 out of 5 samples. 2. The conformed result of LC/MS was equal of detected from 5 out of 63 samples in HPLC/UV analysis. An easily available, simultaneous determination of 8 standards in adulterated health related foods was established by using a combination of LC/MS methods.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.4
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• pp.2291-2295
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• 2016

Small molecule tyrosine kinase inhibitors targeting HER 2 receptors have emerged as an important therapeutic approach in inhibition of downstream proliferation and survival signals for the treatment of breast cancers. Recent drug discovery efforts have demonstrated that naturally occurring polyphenolic compounds like delphinidin have potential to inhibit proliferation and promote apoptosis of breast cancer cells by targeting HER2 receptors. While delphinidin may thus reduce tumour size, it is associated with serious side effects like dysphonia. Owing to the narrow therapeutic window of delphinidin, the present study aimed to identify high affinity compounds targeting HER2 with safer pharmacological profiles than delphinidin through virtual screening approaches. Delphinidin served as the query parent for identification of structurally similar compounds by Tanimoto-based similarity searching with a threshold of 95% against the PubChem database. The compounds retrieved were further subjected to Lipinski and Verber's filters to obtain drug like agents, then further filtered by diversity based screens with a cut off of 0.6. The compound with Pubchem ID: 91596862 was identified to have higher affinity than its parent. In addition it also proved to be non-toxic with a better ADMET profile and higher kinase activity. The compound identified in the study can be put to further in vitro drug testing to complement the present study.

• Analytical Science and Technology
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• v.20 no.1
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• pp.78-83
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• 2007

To perform proficiency test for determining anti-impotence drug-like compounds in food, interlaboratory test has been done. Targets were 6 such as sildenafil, tadalafil, vardenafil, homosildenafil, hydroxy-homosildenafil and pseudo-vardenafilI. Total 13 institutes were participated and all is in charging of food analysis. To do double blind test, the reference materials were made as 13 different ginseng drink samples and each sample had random 3 targets. By the official method for anti-impotence drug-like compounds in food code, sample was just diluted in water, extracted in organic solvents, determined by HPLC/UV and then confirmed by LC/MS. The analytical duration was 60 days after receiving sample. Ten out of 13 institutes were satisfied by evaluation of Z-score and RSZ according to the regulation for managing analytical quality assurance.

• Proceedings of the PSK Conference
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• 2003.10a
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• pp.90-90
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• 2003

I describe here a novel and promising approach to drug discovery that involves the identification and assembly of drug-like fragments to afford lead compounds. This approach is attractive for a number of reasons. First, the productive assembly of two weakly bound fragments, even fragments with independent dissociation constants in the low mM range, can potentially afford ligands with sub-micromolar affinities for their targets. (omitted)

• Analytical Science and Technology
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• v.17 no.6
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• pp.520-526
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• 2004

To determine 6 anti-impotence drug-like compounds such as sildenafil, vardenafil, tadalafil, homosildenafil, hydroxyhomosildenafil and hongdenafil in food, simultaneously, high performance liquid chromatography was applied. In the case of solid sample, it was extracted in organic solvents after homogenizing with mortar and pestle. Whereas liquid sample was just diluted in water and then extracted in organic solvents. Maximum lengths of UV for targets have been identified on photodiode array spectra. As results, vardenafil, hongdenafil, hydroxyhomosildenafil, sildenafil, homosildenafil, and tadalafil were eluted in order using $C_{18}$ column in acetonitrile containing phosphoric acid as the mobile phase. The maximum wavelength (${\lambda}_{max}$) was 216 nm for vardenafil, 233 and 282 nm for hongdenafil, 222 and 293 nm for hydroxyhomosildenafil, sildenafil and homosildenafil, and 284 nm for tadalafil. The overall recoveries were ranged from 95% to 109% and the limit of detection was about 0.04 mg/kg at signal/noise>3. Levels of targets in the selected food samples were 1.7 (hongdenafil) ~ 63 (tadalafil) mg/one dose.

• Bulletin of the Korean Chemical Society
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• v.31 no.12
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• pp.3760-3764
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• 2010

We screened 10,000 heterocyclic small molecules and identified a novel hit core skeleton of 3-(8-chloro-6-(trifluoromethyl) imidazo[1,2-a]pyridine-2-yl)phenyl acetate derivatives. It has been selected as a potential glucagon-like peptide 1 receptor (GLP-1R) activator and demonstrated its effects in increasing GLP-1 secretion, and thereby increasing the glucose responsiveness in both in vitro and pharmacology analyses. Further studies are currently underway to optimize the potency and selectivity of 3-(8-chloro-6-(trifluoromethyl)imidazo[1,2-a]pyridine-2-yl)phenyl acetate derivatives (hit compounds 2 and 8), and address their in vivo efficacy and therapeutic potential. These molecules may serve as useful evidence showing that compounds with a 3-(8-chloro-6-(trifluoromethyl)imidazo[1,2-a]pyridine-2-yl)phenyl acetate moiety are selective GLP-1R agonists, and have potential as anti-diabetic treatment agents.