• Bulletin of the Korean Chemical Society
• /
• 제18권9호
• /
• pp.976-981
• /
• 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.

• Bulletin of the Korean Chemical Society
• /
• 제32권7호
• /
• pp.2433-2442
• /
• 2011

The three dimensional quantitative structure activity relationship (3D QSAR) models were developed using Comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) and docking studies. The fit of Quinazolinone antifolates inside the active site of modeled bovine dihydrofolate reductase (DHFR) was assessed. Both ligand based (LB) and receptor based (RB) QSAR models were generated, these models showed good internal and external statistical reliability that is evident from the $q^2_{loo}$, $r^2_{ncv}$ and $r^2_{pred}$. The identified key features enabled us to design new Quinazolinone analogues as DHFR inhibitors. This study is a building bridge between docking studies of homology modeled bovine DHFR protein as well as ligand and target based 3D QSAR techniques of CoMFA and CoMSIA approaches.

• 통합자연과학논문집
• /
• 제2권2호
• /
• pp.55-58
• /
• 2009

A ligand-receptor docking program is an indispensible tool in modern pharmaceutical design. An accurate prediction of small molecular docking pose to a receptor is essential in drug design as well as molecular recognition. An effective docking program requires the ability to locate a correct binding pose in a surprisingly complex conformational space. However, there is an inherent difficulty to predict correct binding pose. The odds are more demanding than finding a needle in a haystack. This mainly comes from the flexibility of both ligand and receptor. Because the searching space to consider is so vast, receptor rigidity has been often applied in docking programs. Even nowadays the receptor may not be considered to be fully flexible although there have been some progress in search algorithm. Improving the efficiency of searching algorithm is still in great demand to explore other applications areas with inherently flexible ligand and/or receptor. In addition to classical search algorithms such as molecular dynamics, Monte Carlo, genetic algorithm and simulated annealing, rather recent algorithms such as tabu search, stochastic tunneling, particle swarm optimizations were also found to be effective. A good search algorithm would require a good balance between exploration and exploitation. It would be a good strategy to combine algorithms already developed. This composite algorithms can be more effective than an individual search algorithms.

• Journal of Photoscience
• /
• 제11권1호
• /
• pp.35-40
• /
• 2004

[Ru(2,2'-bipyridine)$_2$(4,4'-dicarboxy-2,2'-bipyridine)]$^{2+}$(RuBDc) is a very photostable probe that possesses favorable photophysical properties including long lifetime, high quantum yield, large Stokes' shift, and highly polarized emission. To evaluate the usefulness of this luminophore (RuBDc) for studying macromolecular dynamics, its intensity and anisotropy decays when conjugated to RNA bacteriophage MS2 were examined using frequency-domain fluorometry with a high-intensity, blue light-emitting diode (LED) as the modulated light source. The intensity decays were best fit by a sum of two exponentials, and the mean intensity decay time was 442.2 ns. The anisotropy decay data showed a single rotational correlation time (2334.9 ns), which is typical for a spherical molecule. The use of RuBDc enabled us to measure the rotational correlation time up to several microseconds. These results indicate that RuBDc can be useful for studying rotational diffusion of biological macromolecules.s.

• 한국정보과학회논문지:시스템및이론
• /
• 제35권6호
• /
• pp.237-247
• /
• 2008

가상 탐색은 대규모의 화학분자 데이타베이스의 화학분자 데이타들을 분자 다킹과 같은 컴퓨팅 기술을 이용하여 한정된 소규모의 화학분자만을 스크리닝하는 과정으로, 대규모 컴퓨팅 파워와 데이터 저장 용량을 요구하는 대표적인 대규모의 과학 어플리케이션이다. AutoDock, FlexX, Glide, DOCK, LigandFit, ViSION 등과 같은 기존의 분자 다킹 소프트웨어나 어플리케이션들은 슈퍼 컴퓨터, 단일 클러스터, 또는 단일 워크스테이션 둥을 이용하여 작업을 수행하도록 개발되었다. 하지만 슈퍼컴퓨터를 이용한 가상 탐색은 너무 많은 비용이 든다는 문제점이 있고, 단일 클러스터나 워크스테이션을 이용한 가상 탐색은 오랜 수행 시간이 요구되는 문제점을 가지고 있다. 이에 본 논문에서는 대규모의 데이타 집약적인 연산을 지원하는 그리드 컴퓨팅 기술을 이용하는 서비스 기반 가상 탐색 시스템을 제안한다. 이를 위해 본 논문에서는 가상 탐색을 위한 3차원 화학 데이타베이스를 구축하였다. 그리고 효율적인 분자 다킹 서비스를 제공하기 위해 자원 브로커와 데이타 브로커를 설계하고 가상 탐색을 위한 다양한 서비스들을 제안하였다. 본 논문에서는 DOCK 5.0과 Globus 3.2를 이용하여 서비스 기반 가상 탐색 시스템을 구현하고 성능 평가를 실시하였다. 본 논문에서 구현한 서비스 기반 가상 탐색 시스템은 신약 개발이나 신소재 개발 과정에서 연구 개발 기간을 단축하고 개발 비용을 절감할 수 있다.

• Bulletin of the Korean Chemical Society
• /
• 제31권1호
• /
• pp.52-58
• /
• 2010

Human histamine H1 receptor (HHR1) is a G protein-coupled receptor and a primary target for antiallergic therapy. Here, the ligand-based three-dimensional pharmacophore models were built from a set of known HHR1 inverse agonists using HypoGen module of CATALYST software. All ten generated pharmacophore models consist of five essential features: hydrogen bond acceptor, ring aromatic, positive ionizable and two hydrophobic functions. Best model had a correlation coefficient of 0.854 for training set compounds and it was validated with an external test set with a high correlation value of 0.925. Using this model Maybridge database containing 60,000 compounds was screened for potential leads. A rigorous screening for drug-like compounds unveiled RH01692 and SPB00834, two novel molecules for HHR1 with good CATALYST fit and estimated activity values. The new lead molecules were docked into the active site of constructed HHR1 homology model based on recently crystallized squid rhodopsin as template. Both the hit compounds were found to have critical interactions with Glu177, Phe432 and other important amino acids. The interpretations of this study may effectively be deployed in designing of novel HHR1 inverse agonists.

• Bulletin of the Korean Chemical Society
• /
• 제30권7호
• /
• pp.1603-1606
• /
• 2009

A new 1D oxalato bridged compound Ni(en)(ox)-2$H_2$O, (ox = oxalate; en = ethylenediamine) has been hydrothermally synthesized and characterized by single crystal X-ray diffraction, IR spectrum, TG analysis, and magnetic measurements. In the structure the Ni atoms are coordinated with four oxygen atoms in two oxalate ions and two nitrogen atoms in one ethylenediamine molecule. The oxalate anion acts as a bis-bidentate ligand bridging Ni atoms in cis-configuration. This completes the infinite zigzag neutral chain, [Ni(en)(ox)]. The interchain space is filled by water molecules that link the chains through a network of hydrogen bonds. Thermal variance of the magnetic susceptibility shows a broad maximum around 50 K characteristic of one-dimensional antiferromagnetic coupling. The theoretical fit of the data for T > 20 K led to the nearest neighbor spin interaction J = -43 K and g = 2.25. The rapid decrease in susceptibility below 20 K indicate this compound to be a likely Haldane gap candidate material with S = 1.

• Asian Pacific Journal of Cancer Prevention
• /
• 제13권11호
• /
• pp.5605-5611
• /
• 2012

Background: In the last two decades, pioneering research on anti-tumour activity of saffron has shed light on the role of crocetin, picrocrocin and safranal, as broad spectrum anti-neoplastic agents. However, the exact mechanisms have yet to be elucidated. Identification and characterization of the targets of bioactive constituents will play an imperative role in demystifying the complex anti-neoplastic machinery. Methods: In the quest of potential target identification, a dual virtual screening approach utilizing two inverse screening systems, one predicated on idTarget and the other on PharmMapper was here employed. A set of target proteins associated with multiple forms of cancer and ranked by Fit Score and Binding energy were obtained from the two independent inverse screening platforms. The validity of the results was checked by meticulously analyzing the post-docking binding pose of the picrocrocin with Hsp90 alpha in AutoDock. Results: The docking pose reveals that electrostatic and hydrogen bonds play the key role in inter-molecular interactions in ligand binding. Picrocrocin binds to the Hsp90 alpha with a definite orientation appropriate for nucleophilic attacks by several electrical residues inside the Hsp90-alpha ATPase catalytic site. Conclusion: This study reveals functional information about the anti-tumor mechanism of saffron bioactive constituents. Also, a tractable set of anti-neoplastic targets for saffron has been generated in this study which can be further authenticated by in vivo and in vitro experiments.

• Genomics & Informatics
• /
• 제21권2호
• /
• pp.17.1-17.12
• /
• 2023

Coronavirus has left severe health impacts on the human population, globally. Still a significant number of cases are reported daily as no specific medications are available for its effective treatment. The presence of the CD147 receptor (human basigin) on the host cell facilitates the severe acute respiratory disease coronavirus 2 (SARS-CoV-2) infection. Therefore, the drugs that efficiently alter the formation of CD147 and spike protein complex could be the right drug candidate to inhibit the replication of SARS-CoV-2. Hence, an e-Pharmacophore model was developed based on the receptor-ligand cavity of CD147 protein which was further mapped against pre-existing drugs of coronavirus disease treatment. A total of seven drugs were found to be suited as pharmacophores out of 11 drugs screened which was further docked with CD147 protein using CDOCKER of Biovia discovery studio. The active site sphere of the prepared protein was 101.44, 87.84, and 97.17 along with the radius being 15.33 and the root-mean-square deviation value obtained was 0.73 Å. The protein minimization energy was calculated to be -30,328.81547 kcal/mol. The docking results showed ritonavir as the best fit as it demonstrated a higher CDOCKER energy (-57.30) with correspond to CDOCKER interaction energy (-53.38). However, authors further suggest in vitro studies to understand the potential activity of the ritonavir.

• Bulletin of the Korean Chemical Society
• /
• 제33권5호
• /
• pp.1581-1585
• /
• 2012

Two pyridinecarboxamide dicyanidecobalt(III) building blocks and two mononuclear seven-coordinated macrocycle manganese(II) compounds have been rationally selected to assemble cyanide-bridged heterobimetallic complexes, resulting in three cyanide-bridged $Co^{III}-Mn^{II}$ complexes. Single X-ray diffraction analysis show that these complexes $\{[Mn(L^1)][Co(bpb)]\}ClO_4{\cdot}CH_3OH{\cdot}0.5H_2O$ ($\mathbf{1}$), $\{[Mn(L^2)][Co(bpb)]\}ClO_4{\cdot}0.5CH_3OH$ ($\mathbf{2}$) and ${[Mn(L^1)][Co(bpb)]\}ClO_4{\cdot}H_2O$ ($\mathbf{3}$) ($L^1$ = 3,6-diazaoctane-1,8-diamine, $L^2$ = 3,6-dioxaoctano-1,8-diamine; $bpb2^{2-}$ = 1,2-bis(pyridine-2-carboxamido)benzenate, $bpmb2^{2-}$ = 1,2-bis(pyridine-2-carboxamido)-4-methyl-benzenate) all present predictable one-dimensional single chain structures. The molecular structures of these one-dimensional complexes consists of alternating units of $[Mn(L)]^{2+}$ ($L=L^1$ or $L^2$) and $[Co(L^{\prime})(CN)2]^-$ ($L^{\prime}=bpb2^{2-}$, or $bpmb2^{2-}$), forming a cyanide-bridged cationic polymeric chain with free $ClO_4{^-}$ as the balance anion. The coordination geometry of manganese(II) ion in the three one-dimensional complexes is a slightly distorted pentagonal-bipyrimidal with two cyanide nitrogen atoms at the trans positions and $N_5$ or $N_3O_2$ coordinating mode at the equatorial plane from ligand $L^1$ or $L^2$. Investigation over magnetic properties of these complexes reveals that the very weak magnetic coupling between neighboring Mn(II) ions connected by the diamagnetic dicyanidecobalt(III) building block. A best-fit to the magnetic susceptibility of complex ${\mathbf}{1}$ leads to the magnetic coupling constants $J=-0.084(3)cm^{-1}$.