• Genomics & Informatics
• /
• 제18권4호
• /
• pp.43.1-43.13
• /
• 2020

The coronavirus disease 2019 is a contagious disease and had caused havoc throughout the world by creating widespread mortality and morbidity. The unavailability of vaccines and proper antiviral drugs encourages the researchers to identify potential antiviral drugs to be used against the virus. The presence of RNA binding domain in the nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could be a potential drug target, which serves multiple critical functions during the viral life cycle, especially the viral replication. Since vaccine development might take some time, the identification of a drug compound targeting viral replication might offer a solution for treatment. The study analyzed the phylogenetic relationship of N protein sequence divergence with other 49 coronavirus species and also identified the conserved regions according to protein families through conserved domain search. Good structural binding affinities of a few natural and/or synthetic phytocompounds or drugs against N protein were determined using the molecular docking approaches. The analyzed compounds presented the higher numbers of hydrogen bonds of selected chemicals supporting the drug-ability of these compounds. Among them, the established antiviral drug glycyrrhizic acid and the phytochemical theaflavin can be considered as possible drug compounds against target N protein of SARS-CoV-2 as they showed lower binding affinities. The findings of this study might lead to the development of a drug for the SARS-CoV-2 mediated disease and offer solution to treatment of SARS-CoV-2 infection.

• Molecules and Cells
• /
• 제42권6호
• /
• pp.460-469
• /
• 2019

Bacterial ${\alpha}-type$ carbonic anhydrase (${\alpha}-CA$) is a zinc metalloenzyme that catalyzes the reversible and extremely rapid interconversion of carbon dioxide to bicarbonate. In this study, we report the first crystal structure of a hyperthermostable ${\alpha}-CA$ from Persephonella marina EX-H1 (pmCA) in the absence and presence of competitive inhibitor, acetazolamide. The structure reveals a compactly folded pmCA homodimer in which each monomer consists of a 10-stranded ${\beta}-sheet$ in the center. The catalytic zinc ion is coordinated by three highly conserved histidine residues with an exchangeable fourth ligand (a water molecule, a bicarbonate anion, or the sulfonamide group of acetazolamide). Together with an intramolecular disulfide bond, extensive interfacial networks of hydrogen bonds, ionic and hydrophobic interactions stabilize the dimeric structure and are likely responsible for the high thermal stability. We also identified novel binding sites for calcium ions at the crystallographic interface, which serve as molecular glue linking negatively charged and otherwise repulsive surfaces. Furthermore, this large negatively charged patch appears to further increase the thermostability at alkaline pH range via favorable charge-charge interactions between pmCA and solvent molecules. These findings may assist development of novel ${\alpha}-CAs$ with improved thermal and/or alkaline stability for applications such as $CO_2$ capture and sequestration.

• Bulletin of the Korean Chemical Society
• /
• 제14권2호
• /
• pp.200-206
• /
• 1993

Structures of two polymorphs of ${\alpha},{\alpha}$-trehalose octaacetate monohydrate, $C_{28}H_{38}O_{19}\;{\cdot}\;H_2O$, have been studied by X-ray diffraction method. ${\alpha},{\alpha}$-trehalose (${\alpha}$-D-glucopyranosyl ${\alpha}$-D-glucopyranoside) is a nonreducing disaccharide. The polymorph I belongs to the monoclinic $P2_1$, and has unit cell parameters of a=10.725(l), b=15.110(4), c=11.199(5) ${\AA}$, ${\beta}=108.16(2)^{\circ}$ and Z=2. The polymorph II is orthorhombic $P2_12_12_1$, with a=13.684(4), b=15.802(4), c=17.990(9) ${\AA}$ and Z=4. The final R and R$_w$ values for monoclinic polymorph I are 0.043 and 0.048 and for orthorhombic polymorph II are 0.116 and 0.118, respectively. Those R values of polymorph II are high because the large thermal motions of acetyl groups and the poor quality of the crystal. The molecular conformations in the two polymorphs are similar. Both D-glucopyranosyl rings have chair $^4C_1$ conformations and atoms of glycosidic chain ${\alpha}(1{\rightarrow}1)$ linkage are coplanar. The primary acetate groups of the pyranose residues assume both gauche-trans conformations. The molecules of two polymorphs have pseudo-C$_2$ symmetry at glycosidic O(1) atom. The bond lengths and angles are normal compared with those in other acetylated sugar compounds. The molecules in the monoclinic crystal are held by the hydrogen bonds with the water molecules and by van der Waals forces.

• Molecules and Cells
• /
• 제45권8호
• /
• pp.575-587
• /
• 2022

Human ABCB6 is an ATP-binding cassette transporter that regulates heme biosynthesis by translocating various porphyrins from the cytoplasm into the mitochondria. Here we report the cryo-electron microscopy (cryo-EM) structures of human ABCB6 with its substrates, coproporphyrin III (CPIII) and hemin, at 3.5 and 3.7 Å resolution, respectively. Metal-free porphyrin CPIII binds to ABCB6 within the central cavity, where its propionic acids form hydrogen bonds with the highly conserved Y550. The resulting structure has an overall fold similar to the inward-facing apo structure, but the two nucleotide-binding domains (NBDs) are slightly closer to each other. In contrast, when ABCB6 binds a metal-centered porphyrin hemin in complex with two glutathione molecules (1 hemin: 2 glutathione), the two NBDs end up much closer together, aligning them to bind and hydrolyze ATP more efficiently. In our structures, a glycine-rich and highly flexible "bulge" loop on TM helix 7 undergoes significant conformational changes associated with substrate binding. Our findings suggest that ABCB6 utilizes at least two distinct mechanisms to fine-tune substrate specificity and transport efficiency.

• 대한약침학회지
• /
• 제26권3호
• /
• pp.247-256
• /
• 2023

Objectives: Enterococcus faecalis is a gram positive diplococci, highly versatile and a normal commensal of the gut microbiome. Resistance to vancomycin is a serious issue in various health-care setting exhibited by vancomycin resistant Enterococci (VRE) due to the alteration in the peptidoglycan synthesis pathway. This study is thus aimed to detect the VRE from the patients with root caries from the clinical isolates of E. faecalis and to evaluate the in-silico interactions between vanA and the Aegles marmelos bio-compounds. Methods: E. faecalis was phenotypically characterized from 20 root caries samples and the frequency of vanA and vanB genes was detected by polymerase chain reaction (PCR). Further crude methanolic extracts from the dried leaves of A. marmelos was assessed for its antimicrobial activity. This is followed by the selection of five A. marmelos bio-compounds for the computational approach towards the drug ligand interactions. Results: 12 strains (60%) of E. faecalis was identified from the root caries samples and vanA was detected from two strains (16%). Both the stains showed the presence of vanA and none of the strains possessed vanB. Crude extract of A. marmelos showed promising antibacterial activity against the VRE strains. In-silico analysis of the A. marmelos biocompounds revealed Imperatonin as the best compound with high docking energy (-8.11) and hydrogen bonds with < 140 TPSA (Topological polar surface area) and zero violations. Conclusion: The present study records the VRE strains among the root caries with imperatorin from A. marmelos as a promising drug candidate. However the study requires further experimentation and validation.

• Journal of Microbiology and Biotechnology
• /
• 제33권6호
• /
• pp.788-796
• /
• 2023

Canine parvovirus type 2 (CPV-2) has high morbidity and mortality rates in canines. Nonstructural protein 1 (NS1) of CPV-2 has endonuclease activity, initiates viral DNA replication, and is highly conserved. Thus, it is a promising target for antiviral inhibitor development. We overexpressed a 41.9 kDa active recombinant endonuclease in Escherichia coli and designed a nicking assay using carboxyfluorescein and quencher-linked ssDNA as substrates. The optimal temperature and pH of the endonuclease were 37℃ and pH 7, respectively. Curcumin, bisdemethoxycurcumin, demethoxycurcumin, linoleic acid, tannic acid, and α-tocopherol inhibited CPV-2 NS1 endonuclease with IC₅₀ values of 0.29 to 8.03 µM. The extracted turmeric, yerba mate, and sesame cake suppressed CPV-2 NS1 endonuclease with IC₅₀ values of 1.48, 7.09, and 52.67 ㎍/ml, respectively. The binding affinity between curcumin, the strongest inhibitor, and CPV-2 NS1 endonuclease by molecular docking was -6.4 kcal/mol. Curcumin inhibited CPV-2 NS1 endonuclease via numerous hydrophobic interactions and two hydrogen bonds with Lys97 and Pro111 in the allosteric site. These results suggest that adding curcuminoids, linoleic acid, tannic acid, α-tocopherol, extracted turmeric, sesame cake, and yerba to the diet could prevent CPV-2 infection.

• 분석과학
• /
• 제19권4호
• /
• pp.309-315
• /
• 2006

Two piperazine-templated metal sulfate complexes, $(C_4N_2H_{12})[Ni(H_2O)_6](SO_4)_2$, I and ($C_4N_2H_{12}$) $[Co(H_2O)_6](SO_4)_2$, II, have been synthesized by hydro/solvothermal reactions and their crystal structures analyzed by single crystal X-ray diffraction methods. Complex I crystallizes in the monoclinic system, $P2_1/n$ space group, a=12.920(3), b=10.616(2), $c=13.303(2){\AA}$, ${\beta}=114.09(1)^{\circ}$, Z=4, $R_1=0.030$ for 3683 reflections; II: monoclinic $P2_1/n$, a=12.906(3), b=10.711(2), $c=13.303(2){\AA}$, ${\beta}=114.10(2)^{\circ}$, Z=4, $R_1=0.032$ for 4010 reflections. The crystal structures of the piperazine-templated metal(II) sulfates demonstrate zero-dimensional compound constituted by diprotonated piperazine cations, metal(II) cations and sulfate anions. The structures of complex I and II are substantially isostructural to that of the previously reported our piperazine-templated copper(II) sulfate complex $(C_4N_2H_{12})[Cu(H_2O)_6](SO_4)_2$. The central metal(II) atoms are coordinated by six water molecules in the octahedral geometry. The crystal structures are stabilized by three-dimensional networks of the $O_{water}-H{\cdots}O_{sulfate}$ and $N_{pip}-H{\cdots}O_{sulfate}$ hydrogen bonds between the water molecules and sulfate anions and protonated piperazine cations. Based on the results of thermal analysis, the thermal decomposition reactions of the complex I was analyzed to have three distinctive stages whereas the complex II proceed through several stages.

• Korean Chemical Engineering Research
• /
• 제44권5호
• /
• pp.444-452
• /
• 2006

298.15 K 및 1 atm에서 2성분계 {1,2-dichloropropane+2-(2-methoxyethoxy)ethanol} 및 {1,2-dichloropropane+2-(2-ethoxyethoxy)ethanol}에 대한 과잉몰부피와 과잉몰엔탈피를 측정하였다. 과잉몰부피를 측정하기 위한 밀도는 vibrating glass-tube 방식의 densimeter를 이용하였고, 과잉몰엔탈피는 flow mixing 형의 isothermal microcalorimeter를 이용하였다. 측정한 과잉몰부피 및 과잉몰엔탈피는 조성과 상관지어 모두 S자형을 나타내었다. 초기 2-(2-alkoxyethoxy)ethanol 의 강한 자체 회합현상으로 음의 편차를 나타내며, 할로겐화탄화수소 분자의 증가에 따라 2-(2-alkoxyethoxy)ethanol 분자간의 수소결합을 끊기 위한 에너지가 상대적 더 많이 필요함을 보여주고 있다. 실험으로부터 얻어진 $V^E_m$ 및 $H^E_m$ data는 Nelder-Mead의 simplex pattern search method를 이용하여 Redlich-Kister 다항식에 접합(fitting)하였고, Wilson, NRTL 및 UNIQUAC model을 이용하여 $V^E_m$ data와 조성과의 상관관계를 조사하였다.

• 한국수소및신에너지학회논문집
• /
• 제26권2호
• /
• pp.170-178
• /
• 2015

In this study, we carry out a study on how to improve performance of vanadium redox flow battery (VRFB) through promoting reaction rate of rate determining vanadium reaction ($[VO]^{2+}/[VO_2]^+$). In order to do that, three different carbons like Vulcan (XC-72), CMK3 and MSU-F-C are adopted as the catalysts, while their catalytic activity and reaction reversibility are evaluated using half-cell tests. Their topological images are also measured by TEM. For estimation of the VRFB performance, multiple charge-discharge curves of VRFBs including the catalysts are measured by single cell tests. As a result of that, MSU-F-C shows relatively excellent catalytic activity and reaction reversibility as well as large surface area compared to those of Vulcan (XC-72) and CMK3. Also, in terms of the performance of VRFBs including the catalysts, VRFB including MSU-F-C indicates (i) low charging/discharging overpotentials and low internal resistance, (ii) high charge/discharge capacities and (iii) high energy efficiency. These VRFB performance data are well agreed with results on catalytic activity and reaction reversibility. The reason that MSU-F-C induces superior VRFB performances is attributed to (i) its large surface area and (ii) its hydrophilic surface functional groups that mainly consist of hydroxyl bonds that are supposed to play active surface site role for facilitaing $[VO]^{2+}/[VO_2]^+$ redox reaction. Based on the above results, it is found that adoption of MSU-F-C as catalyst for VRFB results in improvement in VRFB performance by promoting the languid $[VO]^{2+}/[VO_2]^+$ redox reaction.

• 한국재료학회지
• /
• 제18권6호
• /
• pp.339-346
• /
• 2008

Single-crystal $ZnIn_2S_4$ layers were grown on a thoroughly etched semi-insulating GaAs (100) substrate at $450^{\circ}C$ with a hot wall epitaxy (HWE) system by evaporating a $ZnIn_2S_4$ source at $610^{\circ}C$. The crystalline structures of the single-crystal thin films were investigated via the photoluminescence (PL) and Double-crystal X-ray rocking curve (DCRC). The temperature dependence of the energy band gap of the $ZnIn_2S_4$ obtained from the absorption spectra was well described by Varshni's relationship, $E_g(T)=2.9514\;eV-(7.24{\times}10^{-4}\;eV/K)T2/(T＋489K)$. After the as-grown $ZnIn_2S_4$ single-crystal thin films was annealed in Zn-, S-, and In-atmospheres, the origin-of-point defects of the $ZnIn_2S_4$ single-crystal thin films were investigated via the photoluminescence (PL) at 10 K. The native defects of $V_{Zn}$, $V_S$, $Zn_{int}$, and $S_{int}$ obtained from the PL measurements were classified as donor or acceptor types. Additionally, it was concluded that a heat treatment in an S-atmosphere converted $ZnIn_2S_4$ single crystal thin films into optical p-type films. Moreover, it was confirmed that In in $ZnIn_2S_4$/GaAs did not form a native defects, as In in $ZnIn_2S_4$ single-crystal thin films existed in the form of stable bonds.