• Bulletin of the Korean Chemical Society
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• v.31 no.10
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• pp.2761-2770
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• 2010

In this study, we have developed QSAR models for a series of 38 piperidine-4-carboxamide CCR5 antagonists using CoMFA, CoMSIA and HQSAR methods. Developed models showed good statistics in terms of $q^2$ and $r^2$ values. Best predictions obtained with standard CoMFA model ($r^2$ = 0.888, $q^2$ = 0.651) and combined CoMSIA model ($r^2$ = 0.892, $q^2$ = 0.665) with electrostatics and H-bond acceptor parameter. The validity of developed models was assessed by test set of 9 compounds, which showed good predictive correlation coefficient for CoMFA (0.804) and CoMSIA (0.844). Bootstrapped analysis showed statistically significant and robust CoMFA (0.968) and CoMSIA (0.936) models. Best HQSAR model was obtained with a $q^2$ of 0.662 and $r^2$ of 0.936 using atom, connection, hydrogen, donor and acceptor as parameters and fragment size (7-10) with optimum number of 6 components. Predictive power of developed HQSAR model was proved by test set and it was found to be 0.728.

• The Korean Journal of Pesticide Science
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• v.7 no.1
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• pp.1-11
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• 2003

Acoording to improvement of HTOS (high throughput organic synthesis) and HTS (high throughput screening) technique, the CoMFA (comparative molecular field analysis), CoMSIA (comparative molecular similarity indeces analysis) and molecular HQSAR (hologram quantitative structure-activity relationship) analysis techniques as methodology of computer assisted molecular design (CAMD) were introduced generally and summarized for some application cases.

• Journal of Integrative Natural Science
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• v.10 no.4
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• pp.202-208
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• 2017

Xanthine Oxidase is an enzyme, which oxidizes hypoxanthine to xanthine, and xanthine to uric acid. It is widely distributed throughout various organs including the liver, gut, lungs, kidney, heart, brain and plasma. It is involved in gout pathogenesis. Hence, in the present study, Hologram based Quantitative Structure Activity Relationship Study was performed on a series of Xanthine Oxidase antagonist named 2-(indol-5-yl) thiazole derivatives. The best HQSAR model was obtained using Atoms, Bonds, Connection, Hydrogen, Chirality and Donor Acceptor as fragment distinction parameter using hologram length 71 and 4 components with fragment size of minimum 2 and maximum 5. Significant cross-validated correlation coefficient ($q^2$= 0.563) and non cross-validated correlation coefficients ($r^2$= 0.967) were obtained. The model was then used to evaluate the six external test compounds and its $r^2{_{pred}}$ was found to be 0.798. Contribution map show that presence of propyl ring in indole thiazole makes big contributions for improving the biological activities of the compounds. We hope that our HQSAR model and analysis will be helpful for future design of xanthine oxidase antagonists.

• The Korean Journal of Pesticide Science
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• v.9 no.3
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• pp.199-204
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• 2005

The herbicidal activities against barnyardgrass (Echinochloa crus-galli) by R-groups on the hexahydroisoindol-1-one ring of new 2-(4-chloro-5-(2-chloroallyloxy)-2-fluorophenyl) -3-thioalkoxy-2,3,4,5,6,7-hexahydroisoindol-1-one derivatives were studied using molecular holographic quantitative structure-activity relationships (HQSAR) methodology. Based on the results, the statistical results of the optimised HQSAR model (I-2) exhibited the best predictability and fitness for the herbicidal activities based on the cross-validated value ($r^2_{cv.}$ or $q^2=0.714$) and non-cross-validated value ($r^2_{ncv.}=0.922$), respectively. From the based graphical analyses of atomic contribution maps, herbicidal activities against barnyardgrass were confirmed depends upon the C4-C6 atoms of hexahydroisoindoline-l-one ring, carbon atom of ortho-position and meta-methyl group of 3-tolylthio substituent (8).

• Journal of Integrative Natural Science
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• v.10 no.2
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• pp.85-94
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• 2017

Fibroblast growth factor receptor (FGFR) belongs to the family of receptor tyrosine kinase. They play important roles in cell proliferation, differentiation, development, migration, survival, wound healing, haematopoiesis and tumorigenesis. FGFRs are reported to cause several types of cancers in humans which make it an important drug target. In the current study, HQSAR analysis was performed on a series of recently reported 1H-Pyrazolo [3,4-b]pyridine derivatives as FGFR antagonists. The model was developed with Atom (A) and bond (B) connection (C), chirality (Ch), hydrogen (H) and donor/acceptor (DA) parameters and with different set of atom counts to improve the model. A reasonable HQSAR model ($q^2=0.701$, SDEP=0.654, NOC=5, $r^2=0.926$, SEE=0.325, BHL=71) was generated which showed good predictive ability. The contribution map depicted the atom contribution in inhibitory effect. A contribution map for the most active compound (compound 24) indicated that hydrogen and nitrogen atoms in the side chains of ring B as well as hydrogen atoms in the side chain of ring C and the nitrogen atom in the ring D contributed positively to the activity in inhibitory effect whereas, the lowest active compound (compound 04) showed negative contribution to inhibitory effect. Thus results of our study can provide insights in the designing potent and selective FGFR kinase inhibitors.

• Journal of Integrative Natural Science
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• v.10 no.2
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• pp.78-84
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• 2017

CXC chemokine receptor 2 (CXCR2) is a prominent chemokine receptor on neutrophils. CXCR2 antagonist may reduce the neutrophil chemotaxis and alter the inflammatory response because the neutrophilic inflammation in the lung diseases is found to be largely regulated through CXCR2 receptor. Hence, in the present study, Hologram based Quantitative Structure Activity Relationship Study was performed on a series of CXCR2 antagonist named pyrimidine-5-carbonitrile-6-alkyl derivatives. The best HQSAR model was obtained using atoms, bonds, and chirality as fragment distinction parameter using hologram length 151 and 6 components with fragment size of minimum 4 and maximum 7. Significant cross-validated correlation coefficient ($q^2=0.774$) and non cross-validated correlation coefficients ($r^2=0.977$) were obtained. The model was then used to evaluate the six external test compounds and its $r^2_{pred}$ was found to be 0.614. Contribution map show that presence of cyclopropyl ring and its bulkier substituent's makes big contributions for improving the biological activities of the compounds. We hope that our HQSAR model and analysis will be helpful for future design of novel and structurally related CXCR2 antagonists.

• Korean Journal of Agricultural Science
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• v.34 no.2
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• pp.171-179
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• 2007

The new insecticidal active molecules from the based on the holographic quantitative structure-activity relationships (HQSAR) between a series of $1-(R_1)-2-(n-octyl)-3-(R_2)$, $3-(R_3)-pseudothiourea$ derivatives and their insecticidal activities against Diamond-back moth (Plutella Xylostella Linnaeus) were designed and discussed quantitatively. The most active molecule from the based graphical analyses of atomic contribution maps with the optimized HQSAR C-1 model ($q^2=0.764$ & $r^2{ncv}=0.942$) was 1-(n-butyl)-2-(t-butyl)-3,3-diisopropylpseudothiourea (P1: $pI_{50}=5.30$, $IC_{50}=1.397ppm$). Therefore, it is suggested that the new designed molecule would increased the activity as much as 23.5 times as compared to X=n-octyl substituent 17($pI_{50}=4.00$, $IC_{50}=32.86ppm$) which was the highest active molecule in training set compounds.

• KSBB Journal
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• v.27 no.2
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• pp.121-126
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• 2012

In order to explore structural features of minoxidil analogs with a view of enhancing lysyl hydroxylase (LH) inhibitory activity, molecular holographic QSAR (HQSAR) and CoMSIA (comparative molecular similarity indices analysis) were performed. The results from the atomic contributions with optimized the HQSAR 6-2 model indicated that, in case of pyrimidine-1-N-oxide substituent, C2 atom of pyrimidine ring and C'3-C'4 bond of 4-piperidinol group showed the highest impact on the inhibitory activity towards LH enzyme. It was also evident from the information of the optimized CoMSIA F5 model that the inhibitory activity mainly depended on the hydrophobic field contribution (36%) and the hydrogen bond (H-bond) field contribution (49.2%) of substrate molecule. Particularly, it is predicted that the functional groups which disfavor H-bond acceptors in large space around the piperidinol group and also the functional groups which favor the H-bond acceptors at C'4 (& C'5) atom in $R_5$ group play a role for increased inhibitory activity. With this in mind, it is likely that a novel candidate having more improved inhibitory activity on hair growth could be designed in the future.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.210-218
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• 2004

Poly(ADP-ribose)polymerase-1 (PARP-1) is a nuclear enzyme involved in various physical functions related to genomic repair, and PARP inhibitors have therapeutic application in a variety of neurological diseases. Docking and the QSAR (quantitative structure-activity relationships) studies for 52 PARP-1 inhibitors were conducted using FlexX algorithm, comparative molecular field analysis (CoMFA), and hologram quantitative structure-activity relationship analysis (HQSAR). The resultant FlexX model showed a reasonable correlation (r$^{2}$ = 0.701) between predicted activity and observed activity. Partial least squares analysis produced statistically significant models with q$^{2}$ values of 0.795 (SDEP=0.690, r$^{2}$=0.940, s=0.367) and 0.796 (SDEP=0.678, r$^{2}$ = 0.919, s=0.427) for CoMFA and HQSAR, respectively. The models for the entire inhibitor set were validated by prediction test and scrambling in both QSAR methods. In this work, combination of docking, CoMFA with 3D descriptors and HQSAR based on molecular fragments provided an improved understanding in the interaction between the inhibitors and the PARP. This can be utilized for virtual screening to design novel PARP-1 inhibitors.

• Journal of Integrative Natural Science
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• v.11 no.2
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• pp.93-100
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• 2018

Caspases, a family of cysteinyl aspartate-specific proteases plays a central role in the regulation and the execution of apoptotic cell death. Caspase-3 has been proven to be an effective target for reducing the amount of cellular and tissue damage because the activation of caspases-3 stimulates a signalling pathway that ultimately leads to the death of the cell. In this study, Hologram based Quantitative Structure Activity Relationship (HQSAR) models was generated on a series of Caspase-3 inhibitors named 3, 4-dihydropyrimidoindolones derivatives. The best HQSAR model was obtained using atoms, bonds, and hydrogen atoms (A/B/H) as fragment distinction parameter using hologram length 61 and 3 components with fragment size of minimum 5 and maximum 8. Significant cross-validated correlation coefficient ($q^2=0.684$) and non cross-validated correlation coefficients ($r^2=0.754$) were obtained. The model was then used to evaluate the eight external test compounds and its $r^2_{pred}$ was found to be 0.559. Contribution map show that presence of pyrrolidine sulfonamide ring and its bulkier substituent's makes big contributions for improving the biological activities of the compounds.