Prospects in computational molecular medicine: a millennial mega-project on peptide folding

During the second half of the 20th century, Molecular Computations have reached to a level that can revolutionize chemistry. The next target will be structural biology, which will be followed soon by Molecular Medicine. The present paper outlines where we are at, in this field, at the end of the 20th century, and in what direction the development may take in the new millennium. In view of the gigantic nature of the problem, it is suggested that a suitably designed cooperative Millennial Mega-project might accelerate our schedule.     

In silico designing breast cancer peptide vaccine for binding to MHC class I and II: A molecular docking study

Antigenic peptides or cancer peptide vaccines can be directly delivered to cancer patients to produce immunologic responses against cancer cells. Specifically, designed peptides can associate with Major Histocompatibility Complex (MHC) class I or II molecules on the cell surface of antigen presenting cells activating anti-tumor effector mechanisms by triggering helper T cell (Th) or cytotoxic T cells (CTL). In general, high binding to MHCs approximately correlates with in vivo immunogenicity. Consequently, a molecular docking technique was run on a library of novel discontinuous peptides predicted by PEPOP from Human epidermal growth factor receptor 2 (HER2 ECD) subdomain III. This technique is expected to improve the prediction accuracy in order to identify the best MHC class I and II binder peptides. Molecular docking analysis through GOLD identified the peptide 1412 as the best MHC binder peptide to both MHC class I and II molecules used in the study. The GOLD results predicted HLA-DR4, HLA-DP2 and TCR as the most often targeted receptors by the peptide 1412. These findings, based on bioinformatics analyses, can be exploited in further experimental analyses in vaccine design and cancer therapy to find possible proper approaches providing beneficial effects.     

Multifunctional nanoprobe for cancer cell targeting and simultaneous fluorescence/magnetic resonance imaging

Multifunctional nanoprobes with distinctive magnetic and fluorescent properties are highly useful in accurate and early cancer diagnosis. In this study, nanoparticles of Fe₃O₄ core with fluorescent SiO₂ shell (MFS) are synthesized by a facile improved Stöber method. These nanoparticles owning a significant core-shell structure exhibit good dispersion, stable fluorescence, low cytotoxicity and excellent biocompatibility. TLS11a aptamer (Apt1), a specific membrane protein for human liver cancer cells which could be internalized into cells, is conjugated to the MFS nanoparticles through the formation of amide bond working as a target-specific moiety. The attached TLS11a aptamers on nanoparticles are very stable and can't be hydrolyzed by DNA hydrolytic enzyme in vivo. Both fluorescence and magnetic resonance imaging show significant uptake of aptamer conjugated nanoprobe by HepG2 cells compared to 4T1, SGC-7901 and MCF-7 cells. In addition, with the increasing concentration of the nanoprobe, T₂-weighted MRI images of the as-treated HepG2 cells are significantly negatively enhanced, indicating that a high magnetic field gradient is generated by MFS-Apt1 which has been specifically captured by HepG2 cells. The relaxivity of nanoprobe is calculated to be 11.5 mg⁻¹s⁻¹. The MR imaging of tumor-bearing nude mouse is also confirmed. The proposed multifunctional nanoprobe with the size of sub-100 nm has the potential to provide real-time imaging in early liver cancer cell diagnosis.     

Design and synthesis of novel chiral molecular tweezers based on deoxycholic acid

A novel type of chiral molecular tweezers has been designed and synthesized by using deoxycholic acid as backbone and ethanoyl and the chiral unsymmetrical urea unit as arms. Their structures were characterized by 1H NMR, IR, MS spectra and elemental analysis. These molecular tweezers showed good binding ability for neutral molecules and chiral molecules.     

A quantitative LC–MS/MS method for determination of a small molecule agonist of EphA2 in mouse plasma and brain tissue

Compound 27 {1, 12‐bis[4‐(4‐amino‐6,7‐dimethoxyquinazolin‐2‐yl)piperazin‐1‐yl]dodecane‐1,12‐dione} is a novel small molecule agonist of EphA2 receptor tyrosine kinase. It showed much improved activity for the activation of EphA2 receptor compared with the parental compound doxazosin. To support further pharmacological and toxicological studies of the compound, a method using liquid chromatography and electrospray ionization tandem mass spectrometry (LC–MS/MS) has been developed for the quantification of this compound. Liquid–liquid extraction was used to extract the compound from mouse plasma and brain tissue homogenate. Reverse‐phase chromatography with gradient elution was performed to separate compound 27 from the endogenous molecules in the matrix, followed by MS detection using positive ion multiple reaction monitoring mode. Multiple reaction monitoring transitions m/z 387.3 → 290.1 and m/z 384.1 → 247.1 were selected for monitoring compound 27 and internal standard prazosin, respectively. The linear calibration range was 2–200 ng/mL with the intra‐ and inter‐day precision and accuracy within the acceptable range. This method was successfully applied to the quantitative analysis of compound 27 in mouse plasma and brain tissue with different drug administration routes.     

基于计算机模拟技术对JAK2抑制剂的定量构效关系、分子设计和分子动力学研究

本文选取了52个对Janus激酶2(JAK2)有抑制作用的小分子化合物,分别使用3D-QSAR中的CoMFA和CoMSIA方法构建了两个可靠的、具有预测能力的模型,并利用分子对接分析数据集化合物与JAK2蛋白的相互作用,表明化合物主要通过氢键和范德华作用与JAK2靶蛋白结合。根据3D-QSAR模型的分析结果,设计了40个化合物,利用构建的模型预测其抑制活性;使用软件预测了化合物的药代动力学(ADME)参数,开展分子对接模拟,最终选择化合物D01和D22与JAK2靶蛋白进行了分子动力学模拟研究,结果显示两个复合物结合构象稳定,与分子对接结果趋势一致。本研究的结果可以为JAK2抑制剂的研发提供一些新的思路,为临床开发此类药物提供理论支撑。     

A novel aptamer-based histochemistry assay for specific diagnosis of clinical breast cancer tissues

Pathological detection using immunohistochemistry (IHC) has become an indispensable process in the diagnosis confirmation of various cancers. However, the production of monoclonal antibodies is always very complex, expensive and time-consuming, and the batch differences are significant due to the corporeity and health statuses of animals may be different. In this work, an aptamer-based histochemistry (aptahistochemistry) assay was developed using a DNA aptamer for specific diagnosis of clinical breast cancer tissue sections. This aptahistochemistry assay can specifically distinguish Luminal A breast cancer molecular subtype from Luminal B (HER2+), HER2-enriched, and triple-negative breast cancer molecular subtypes, as well as para-carcinoma tissue, mastitis tissue and normal breast tissue. The accuracy of this aptahistochemistry assay for the diagnosis of Luminal A breast cancer was as high as 80%, which showed a great potential for clinical pathological diagnosis applications.     

A facile synthesis of α-amino-DOTA as a versatile molecular imaging probe

An amino group has been introduced into one ligand of DOTA that can couple to peptidyl carboxylates by coupling α-brominated glycine to DO3A-^tBu (1,4,7,10-tetraazacyclododecane-1,4,7-tris(acetic acid, tert-butylester)). α-Amino-DOTA was coupled to the carboxylate backbone terminus of a peptide to demonstrate the utility for derivatization.     

Design and synthesis of a novel fluorescent protein probe for easy and rapid electrophoretic gel staining by using a commonly available UV‐based fluorescent imaging system

A new fluorescent molecular probe, methyl 3‐(3,5‐bis((bis(pyridin‐2‐ylmethyl)amino)‐methyl)‐4‐hydroxyphenyl)‐2‐(5‐(dimethylamino)naphthalene‐1‐sulfonamido) propanoate, dizinc(II) chloride salt (Dansyl‐ 1 ‐Zn(II)), which possesses Zn(II) complexes and a dansyl group, was designed and synthesized to enable the detection of proteins in solution and in high‐throughput electrophoresis by using a UV‐based detection system. Dansyl‐ 1 ‐Zn(II) exhibited weak fluorescence in the absence of proteins and strong green fluorescence at approximately 510 nm in the presence of BSA upon irradiation with light at a wavelength of 345 nm. Compared with conventional protocols for in‐gel SDS‐PAGE protein staining (e.g. silver staining, SYPRO Ruby, and Oriole), the operating times of which range from 90 min to overnight, Dansyl‐ 1 ‐Zn(II) allowed 1‐step protein staining (SDS‐PAGE →Staining →Detection) and shortened the operating time (35 min) with high sensitivity (LOD: 1 ng or less) under 312‐nm or 365‐nm light excitation with orange or red emission filters, respectively. Moreover, Dansyl‐ 1 ‐Zn(II) was successfully applied to protein identification by MS via in‐gel tryptic digestion, Western blotting, and Native‐PAGE. Accordingly, Dansyl‐ 1 ‐Zn(II) may facilitate highly sensitive and high‐throughput protein detection, and it may be widely applicable as a convenient tool in various scientific and medical fields.     

Rationalizing some experimental facts on the complexation of 2-methyl naphthalenecarboxylate and hydroxypropyled cyclodextrins by molecular mechanics and molecular dynamics

Molecular mechanics (MM) and Molecular dynamics (MD) calculations were applied to study the complexation of 2-Methyl naphthalenecarboxylate (2MN) and 2-hydroxypropyl -α-, -β-, and γ-cyclodextrins (HPCDs) in the presence of water. Results showed that 1:1 complexes of 2MN with modified cyclodextrins are stable and that the non-bonded van der Waals interactions are mainly responsible for the complexation. Theoretical results are in good agreement with fluoresence results and they permit us to explain the signs and quantitative differences of ΔH ⁰ and ΔS ⁰ on the basis of the different cavity sizes and the movement of the guest inside the HPCD cavity. Results also reveal a more favorable complexation when 2MN approaches on its polar side.     

Evaluation of novel sample identification approach based on chromatographic fingerprint set correlation homogeneity analysis

Instead of usual rationale for chromatographic fingerprint based sample identification which relies upon visual inspection or principal component analysis of raw or aligned chromatograms novel nonparametric statistical measure of fingerprint set homogeneity is proposed. Randomization test is applied for significance analysis of fingerprint set homogeneity while average maximum crosscorrelation is used as a merit function. Chromatogram sets generated by random selection from standard and unknown sample chromatogram collections are compared with respect to merit function values with set of chromatograms that represents standard and/or unknown sample. In that instance fingerprint homogeneity significance is represented by the fraction of random chromatogram sets that have higher merit values than the standard and/or unknown sample sets. A set of peptide maps corresponding to different haemoglobin variants has been selected for evaluation of proposed test. This approach is compared to chromatogram alignment based on correlation optimized warping coupled with principal component or cluster analysis. Proposed method is simple i.e. straightforward sample identification procedure which reliability has been evaluated here. Impact of this approach on peptide mapping validation and system suitability analysis is discussed.     

Discovery of novel indene-based hybrids as breast cancer inhibitors targeting Hsp90: Synthesis,bio-evaluation and molecular docking study

Inhibition of Heat-shock protein 90 (Hsp90) is considered an attractive route in fighting against cancer proliferation. Herein, new indene derivatives targeting Hsp90 were synthesized, and biologically evaluated. The new series of indeno-pyrimidine and indeno-pyridine were synthesized from the reaction of indene-enaminone with various heterocyclic amines and active methylene derivatives. Two breast cancer cell lines were used to examine the new compounds in vitro for their anticancer activity, namely, MCF-7 and MDA-MB231 cancer cells. The new indene derivatives 8a-c, 17a, and 25 displayed significant antitumor effect especially on MCF-7 cell line compared to doxorubicin. Derivative 8a was further subjected to Hsp90 enzyme assay aiming to ensure the inhibitory potential of such compound on Hsp90, it displayed IC₅₀ = 18.79 ± 0.68 nM relative to Alvespimycin as a reference drug. Finally, molecular modeling of the most active compounds in the Hsp90 binding site was done presenting agreement with the in vitro anti-Hsp90 activity.     

In silico design novel (5-imidazol-2-yl-4-phenylpyrimidin-2-yl)[2-(2-pyridylamino)ethyl]amine derivatives as inhibitors for glycogen synthase kinase 3 based on 3D-QSAR,molecular docking and molecular dynamics simulation

Glycogen Synthase Kinase 3 (GSK-3) is a member of cellular kinase with various functions, such as glucose regulation, cellular differentiation, neuronal function and cell apoptosis. It has been proved as an important therapeutic target in type 2 diabetes mellitus and Alzheimer's disease. To better understand their structure–activity relationships and mechanism of action, an integrated computational study, including three dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking, and molecular dynamics (MD), was performed on 79 (5-Imidazol-2-yl-4-phenylpyrimidin-2-yl)[2-(2-pyridylamino)ethyl]amine GSK-3 inhibitors. In this paper, we constructed 3D-QSAR using comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) method. The results showed that the CoMFA model (q ² = 0.743, r² = 0.980) and the CoMSIA model (q² = 0.813, r² = 0.976) had stable and reliable predictive ability. The electrostatic and H-bond donor fields play important roles in the models. The contour maps of the model visually showed the relationship between the activity of compounds and their three-dimensional structure. Molecular docking was used to identify the key amino acid residues at the active site of GSK-3 and explore its binding mode with ligands. Based on 3D-QSAR models, contour maps and the binding feature between GSK-3 and inhibitor, we designed 10 novel compounds with good potential activity and ADME/T profile. Molecular dynamics simulation results validated that Ile62, Val70 and Lys85 located in the active site play a key role for GSK-3 complexed with inhibitors. These results might provide important information for designing GSK-3 inhibitors with high activity.     

Evaluation of a simple and novel fluorescent anion sensor, 4-quinolone, and modification of the emission color by substitutions based on molecular orbital calculations

4-Quinolone (4-QO) was evaluated as a simple and novel fluorescent anion sensor, and the modification of its emission color was carried out. The series of 4-QO derivatives having molecular orbitals with different energy levels was designed by substitutions at the 6 and 7 positions based on the molecular orbital calculations. All derivatives showed drastic fluorescence enhancements in the presence of F⁻ via the intramolecular charge transfer mechanism, and the successful modification of the emission color was achieved. The anion-induced emission colors of these derivatives as well as their binding affinities for F⁻ could be predicted by ab initio quantum chemical calculations, indicating that the present calculations are useful in designing new anion sensors.     

Electrochemical behaviour of a molecular capsule based on methylviologen-resorcinarene and sulfonatomethylene-resorcinarene

A new molecular capsule based on viologen-resorcinarene and sulfonatomethylene-resorcinarene is synthesized and its redox-controlled stability is investigated.     

A novel aptamer functionalized CuInS2 quantum dots probe for daunorubicin sensing and near infrared imaging of prostate cancer cells

In this paper, a novel daunorubicin (DNR)-loaded MUC1 aptamer-near infrared (NIR) CuInS₂ quantum dot (DNR–MUC1–QDs) conjugates were developed, which can be used as a targeted cancer imaging and sensing system. After the NIR CuInS₂ QDs conjugated with the MUC1 aptamer–(CGA)₇, DNR can intercalate into the double-stranded CG sequence of the MUC1–QDs. The incorporation of multiple CG sequences within the stem of the aptamers may further increase the loading efficiency of DNR on these conjugates. DNR–MUC1–QDs can be used to target prostate cancer cells. We evaluated the capacity of MUC1–CuInS₂ QDs for delivering DNR to cancer cells in vitro, and its binding affinity to MUC1-positive and MUC1-negative cells. This novel aptamer functionalized QDs bio-nano-system can not only deliver DNR to the targeted prostate cancer cells, but also can sense DNR by the change of photoluminescence intensity of CuInS₂ QDs, which concurrently images the cancer cells. The quenched fluorescence intensity of MUC1–QDs was proportional to the concentration of DNR in the concentration ranges of 33–88 nmol L⁻¹. The detection limit (LOD) for DNR was 19 nmol L⁻¹. We demonstrate the specificity and sensitivity of this DNR–MUC1–QDs probe as a cancer cell imaging, therapy and sensing system in vitro.     

Correlation of thermodynamic modeling and molecular simulations for liquid-liquid equilibrium of ternary polymer mixtures based on a phenomenological scaling method

In our previous study [S.Y. Oh, Y.C. Bae, J. Phys. Chem. B 114 (2010) 8948-8953], we presented a new method to predict liquid-liquid equilibria in ternary simple liquid mixtures by using a combination of a thermodynamic model and molecular simulations. As a continuation of that effort, we extend our previously developed method to ternary polymer systems. In the simulations, we used the dummy atoms to calculate the pair interaction energy values between the polymer segments and the solvent molecules. Furthermore, a thermodynamic model scaling concept is introduced to consider the chain length dependence of the energy parameters. This method was applied to ternary mixtures incorporating low to high molecular weight polymers. The method presented here well described the experimental observations using one or no adjustable parameters.