Associating 197 Chinese herbal medicine with drug targets and diseases using the similarity ensemble approach.

Chinese herbal medicine (CHM) addresses complex diseases through polypharmacological interactions. However, systematic studies of herbal medicine pharmacology remain challenging due to the complexity of CHM ingredients and their interactions with various targets. In this study, we aim to address this challenge with computational approaches. We investigated the herb-target-disease associations of 197 commonly prescribed CHMs using the similarity ensemble approach and DisGeNET database. We demonstrated that this method can be applied to associate herbs with their putative targets. In the case study of three well-known herbs, Radix Glycyrrhizae, Flos Lonicerae, and Rhizoma Coptidis, approximately 70% of the predicted targets were supported by scientific literature. By linking 406 targets to 2439 annotated diseases, we further analyzed the pharmacological functions of 197 herbs. Finally, we proposed a strategy of target-oriented herbal formula design and illustrated the target profiles for four common chronic diseases, namely, Alzheimer's disease, depressive disorder, hypertensive disease, and non-insulin-dependent diabetes mellitus. This computational approach holds great potential in the target identification of herbs, understanding the molecular mechanisms of CHM, and designing novel herbal formulas.

An allosteric PGAM1 inhibitor effectively suppresses pancreatic ductal adenocarcinoma.

Glycolytic enzyme phosphoglycerate mutase 1 (PGAM1) plays a critical role in cancer metabolism by coordinating glycolysis and biosynthesis. A well-validated PGAM1 inhibitor, however, has not been reported for treating pancreatic ductal adenocarcinoma (PDAC), which is one of the deadliest malignancies worldwide. By uncovering the elevated PGAM1 expressions were statistically related to worse prognosis of PDAC in a cohort of 50 patients, we developed a series of allosteric PGAM1 inhibitors by structure-guided optimization. The compound KH3 significantly suppressed proliferation of various PDAC cells by down-regulating the levels of glycolysis and mitochondrial respiration in correlation with PGAM1 expression. Similar to PGAM1 depletion, KH3 dramatically hampered the canonic pathways highly involved in cancer metabolism and development. Additionally, we observed the shared expression profiles of several signature pathways at 12 h after treatment in multiple PDAC primary cells of which the matched patient-derived xenograft (PDX) models responded similarly to KH3 in the 2 wk treatment. The better responses to KH3 in PDXs were associated with higher expression of PGAM1 and longer/stronger suppressions of cancer metabolic pathways. Taken together, our findings demonstrate a strategy of targeting cancer metabolism by PGAM1 inhibition in PDAC. Also, this work provided "proof of concept" for the potential application of metabolic treatment in clinical practice.

The susceptible HLA class II alleles and their presenting epitope(s) in Goodpasture's disease.

Goodpasture's disease is closely associated with HLA, particularly DRB1*1501. Other susceptible or protective HLA alleles are not clearly elucidated. The presentation models of epitopes by susceptible HLA alleles are also unclear. We genotyped 140 Chinese patients and 599 controls for four-digit HLA II genes, and extracted the encoding sequences from the IMGT/HLA database. T-cell epitopes of α3(IV)NC1 were predicted and the structures of DR molecule-peptide-T-cell receptor were constructed. We confirmed DRB1*1501 (OR = 4·6, P = 5·7 × 10-28 ) to be a risk allele for Goodpasture's disease. Arginine at position 13 (ARG13) (OR = 4·0, P = 1·0 × 10-17 ) and proline at position 11 (PRO11) (OR = 4·0, P = 2·0 × 10-17 ) on DRß1, encoded by DRB1*1501, were associated with disease susceptibility. α134-148 (HGWISLWKGFSFIMF) was predicted as a T-cell epitope presented by DRB1*1501. Isoleucine137 , tryptophan140 , glycine142 , phenylalanine143 and phenylalanine145 , were presented in peptide-binding pockets 1, 4, 6, 7 and 9 of DR2b, respectively. ARG13 in pocket 4 interacts with tryptophan140 and forms a hydrogen bond. In conclusion, we propose a mechanism for DRB1*1501 susceptibility for Goodpasture's disease through encoding ARG13 and PRO11 on MHC-DRß1 chain and presenting T-cell epitope, α134-148 , with five critical residues.

MHC Class II Risk Alleles and Amino Acid Residues in Idiopathic Membranous Nephropathy.

Epitopes of phospholipase A2 receptor (PLA2R), the target antigen in idiopathic membranous nephropathy (iMN), must be presented by the HLA-encoded MHC class II molecules to stimulate autoantibody production. A genome-wide association study identified risk alleles at HLA and PLA2R loci, with the top variant rs2187668 within HLA-DQA1 showing a risk effect greater than that of the top variant rs4664308 within PLA2R1. How the HLA risk alleles affect epitope presentation by MHC class II molecules in iMN is unknown. Here, we genotyped 261 patients with iMN and 599 healthy controls at the HLA-DRB1, HLA-DQA1, HLA-DQB1, and HLA-DPB1 loci with four-digit resolution and extracted the encoded amino acid sequences from the IMGT/HLA database. We predicted T cell epitopes of PLA2R and constructed MHC-DR molecule-PLA2R peptide-T cell receptor structures using Modeler. We identified DRB1*1501 (odds ratio, 4.65; 95% confidence interval [95% CI], 3.39 to 6.41; P<0.001) and DRB1*0301 (odds ratio, 3.96; 95% CI, 2.61 to 6.05; P<0.001) as independent risk alleles for iMN and associated with circulating anti-PLA2R antibodies. Strong gene-gene interaction was noted between rs4664308(AA) and HLA-DRB1*1501/DRB1*0301. Amino acid positions 13 (P<0.001) and 71 (P<0.001) in the MHC-DRß1 chain independently associated with iMN. Structural models showed that arginine13 and alanine71, encoded by DRB1*1501, and lysine71, encoded by DRB1*0301, facilitate interactions with T cell epitopes of PLA2R. In conclusion, we identified two risk alleles of HLA class II genes and three amino acid residues on positions 13 and 71 of the MHC-DRß1 chain that may confer susceptibility to iMN by presenting T cell epitopes on PLA2R.

Structural basis for the autoprocessing of zinc metalloproteases in the thermolysin family.

Thermolysin-like proteases (TLPs), a large group of zinc metalloproteases, are synthesized as inactive precursors. TLPs with a long propeptide (∼200 residues) undergo maturation following autoprocessing through an elusive molecular mechanism. We report the first two crystal structures for the autoprocessed complexes of a typical TLP, MCP-02. In the autoprocessed complex, Ala205 shifts upward by 33 Å from the previously covalently linked residue, His204, indicating that, following autocleavage of the peptide bond between His204 and Ala205, a large conformational change from the zymogen to the autoprocessed complex occurs. The eight N-terminal residues (residues Ala205-Gly212) of the catalytic domain form a new ß-strand, nestling into two other ß-strands. Simultaneously, the apparent T(m) of the autoprocessed complex increases 20 °C compared to that of the zymogen. The stepwise degradation of the propeptide begins with two sequential cuttings at Ser49-Val50 and Gly57-Leu58, which lead to the disassembly of the propeptide and the formation of mature MCP-02. Our findings give new insights into the molecular mechanism of TLP maturation.

[Controlling arachidonic acid metabolic network: from single- to multi-target inhibitors of key enzymes].

Inflammatory diseases are common medical conditions seen in disorders of human immune system. There is a great demand for anti-inflammatory drugs. There are major inflammatory mediators in arachidonic acid metabolic network. Several enzymes in this network have been used as key targets for the development of anti-inflammatory drugs. However, specific single-target inhibitors can not sufficiently control the network balance and may cause side effects at the same time. Most inflammation induced diseases come from the complicated coupling of inflammatory cascades involving multiple targets. In order to treat these complicated diseases, drugs that can intervene multi-targets at the same time attracted much attention. The goal of this review is mainly focused on the key enzymes in arachidonic acid metabolic network, such as phospholipase A2, cyclooxygenase, 5-lipoxygenase and eukotriene A4 hydrolase. Advance in single target and multi-targe inhibitors is summarized.

Protein-surfactant interaction: differences between fluorinated and hydrogenated surfactants.

The interactions of proteins with fluorinated/hydrogenated surfactants were investigated by circular dichroism and turbidity measurement. Pairs of fluorinated and hydrogenated surfactants with similar critical micelle concentrations (cmc), including sodium perfluorooctanoate/sodium decylsulfate and lithium perfluorononanoate/sodium dodecylsulfate were compared in view of their interactions with proteins including BSA, lysozyme, beta-lactoglobulin and ubiquitin. It was found that fluorinated surfactants exhibited stronger interactions with proteins than hydrogenated ones, which, however, depended on the structures of both proteins and surfactant molecules. If the proteins are very stable, or the surfactant-protein interactions are very strong, such differences between the two kinds of surfactants might be indistinguishable.

Interaction between lysozyme and mixtures of cationic-anionic surfactants decyltriethylammonium bromide-sodium decylsulfonate.

The interaction of lysozyme with the mixtures of cationic-anionic surfactants decyltriethylammonium bromide-sodium decylsulfonate (C10NE-C10SO3) was investigated by turbidity, circular dichroism (CD) and lysozyme activity assay. At pH 3.0, the mixtures of C10NE-C10SO3 formed precipitates with lysozyme at a wide range around the equal molar ratio of C10NE to C10SO3. Homogeneous solutions were formed when the mixtures of C10NE-C10SO3 were far from equimolar. CD and lysozyme activity assay showed that lysozyme was in different state in the C10SO3-rich and C10NE-rich mixtures of C10NE-C10SO3. Lysozyme structure changed in C10SO3-rich C10NE-C10SO3 mixtures, while was almost kept in native state in C10NE-rich ones.

Interactions of beta-lactoglobulin with sodium decylsulfonate, decyltriethylammonium bromide, and their mixtures.

The interactions of beta-lactoglobulin (BLG) with anionic surfactant sodium decylsulfonate (C10SO3), cationic surfactant decyltriethylammonium bromide (C10NE), and the mixtures of cationic-anionic surfactants (C10NE-C10SO3) were investigated by circular dichroism (CD) and fluorescence methods. At pH 7.0, C10NE and the C10NE-rich surfactant mixtures of C10NE-C10SO3 could form precipitates with BLG, while C10SO3, equimolar mixtures of C10NE-C10SO3, or C10SO3-rich mixtures of C10NE-C10SO3 form homogeneous solutions with BLG. CD observed that both C10NE and C10SO3 could change the BLG structure. The effects of the mixtures of C10NE-C10SO3 on BLG structure depended on the ratio of C10NE to C10SO3. The C10NE-rich or the C10SO3-rich mixtures of C10NE-C10SO3 could significantly affect BLG structure, while the equimolar mixtures of C10NE-C10SO3 exhibited weaker interaction with BLG. Fluorescence measurements showed that both C10NE and C10SO3 could induce the enhancement of fluorescence of BLG, and C10NE enhanced the BLG fluorescence more than C10SO3 did. The effect of the mixtures of C10NE-C10SO3 on the fluorescence of BLG became stronger with the increase of the molar fraction of C10NE in C10NE-C10SO3 mixtures.

Effect of cationic surfactants on the interaction between sodium perfluorooctanoate and beta-lactoglobulin.

The interaction between the fluorocarbon surfactant, sodium perfluorooctanoate (SPFO), and beta-lactoglobulin (BLG) was studied. In particular, the effects of cationic surfactants, such as alkyltriethylammonium bromide (C(n)NE, n=8, 10, 12), on SPFO-BLG interaction were examined. It was shown that the anionic fluorocarbon surfactant, SPFO, was a strong denaturant of BLG. The ability of SPFO to denature BLG could be weakened by the addition of C(n)NE. The effect of C(n)NE on SPFO-BLG interaction was related to the hydrocarbon chain length of C(n)NE, and also the molar ratio of the added C(n)NE to the SPFO in SPFO-BLG solutions ([C(n)NE]/[SPFO]). Our findings might provide a way to design surfactant systems that are less denaturing to proteins or tailor the ability of surfactant to denature proteins through the appropriate mixing with other surfactants.

3D-QSAR studies on tripeptide aldehyde inhibitors of proteasome using CoMFA and CoMSIA methods.

The ubiquitin-proteasome pathway plays a crucial role in the regulation of many physiological processes and in the development of a number of major human diseases, such as cancer, Alzheimer's, Parkinson's, diabetes, etc. As a new target, the study on the proteasome inhibitors has received much attention recently. Three-dimensional quantitative structure-activity relationship (3D-QSAR) studies using comparative molecule field analysis (CoMFA) and comparative molecule similarity indices analysis (CoMSIA) techniques were applied to analyze the binding affinity of a set of tripeptide aldehyde inhibitors of 20S proteasome. The optimal CoMFA and CoMSIA models obtained for the training set were all statistically significant with cross-validated coefficients (q(2)) of 0.615, 0.591 and conventional coefficients (r(2)) of 0.901, 0.894, respectively. These models were validated by a test set of eight molecules that were not included in the training set. The predicted correlation coefficients (r(2)) of CoMFA and CoMSIA are 0.944 and 0.861, respectively. The CoMFA and CoMSIA field contour maps agree well with the structural characteristics of the binding pocket of beta5 subunit of 20S proteasome, which suggests that the 3D-QSAR models built in this paper can be used to guide the development of novel inhibitors of 20S proteasome.

Indole-5-phenylcarbamate derivatives as human non-pancreatic secretory phospholipase A2 inhibitor.

The synthesis of the human non-pancreatic secretory phospholipase A2 inhibitor (IC(50)=1.81+/-0.59 microM) is reported.

Interaction between bovine serum albumin and equimolarly mixed cationic-anionic surfactants decyltriethylammonium bromide-sodium decyl sulfonate.

The interactions of bovine serum albumin (BSA) with the anionic surfactant sodium decylsulfonate (C10SO3), the cationic surfactant decyltriethylammonium bromide (C10NE) and equimolarly mixed cationic-anionic surfactants C10NE-C10SO3 were investigated by surface tension, viscosity, dynamic light scattering (DLS) and circular dichroism (CD). It was shown that the single ionic surfactant C10SO3 or C10NE has obvious interaction with BSA. The presence of C10SO3 or C10NE modified BSA structure. However, the equimolarly mixed cationic-anionic surfactants C10NE-C10SO3 showed very weak interactions with BSA. The surface tension-log concentration (gamma-logC) plot for the aqueous solutions of C10NE-C10SO3/BSA mixtures coincided with that of C10NE-C10SO3 solutions. Viscometry showed that there is no significant change in the rheological properties for the C10NE-C10SO3/BSA mixed solutions. DLS showed that BSA monomers and mixed aggregates of C10NE-C10SO3 existed in the C10NE-C10SO3/BSA mixed solutions. From CD spectra no obvious modification of BSA structure in the presence of C10NE-C10SO3 mixtures was observed. The weak interactions between BSA and C10NE-C10SO3 might be explained in terms of the very low critical micelle concentration (cmc) of C10NE-C10SO3 mixtures that made the concentration of ionic surfactant monomers much lower than that needed for inducing the modification of BSA structure. In other words, the very strong synergism between oppositely charged cationic and anionic surfactants makes the formation of cationic-anionic surfactant mixed aggregates in the bulk solution a more favorable process than binding to proteins.

Surfactant-induced refolding of lysozyme.

The surfactant-lysozyme interaction was investigated by circular dichroism, fluorescence, UV, dynamic light scattering, surface tension, turbidity measurements and lysozyme activity assay. A new way of refolding of lysozyme was found. It was shown that the lysozyme unfolded by anionic surfactants could be renatured by adding cationic surfactants. That is, lysozyme formed precipitate with anionic surfactants, the precipitates could be dissolved by adding a cationic surfactant solution, and then the lysozyme was refolded to its native state spontaneously. Different couples of anionic surfactants and cationic surfactants including C10SO3/C10NE, C12SO3/C10NE, C10SO3/C12NE, C10SO3/C12NB, C10SO4/C10NE and C12SO4/C10NE (C(n)SO3, C(n)SO4, C(n)NE and C(n)NB represent sodium alkyl sulfonate/sulfate, alkyl triethyl/butyl ammonium bromide respectively) were investigated, all of them gave similar results. The results were explained in terms of the differences between the interaction of anionic-cationic surfactants and that of surfactant-lysozyme. It was thought that the formation of mixed micelles of anionic-cationic surfactants is a more favorable process than that of lysozyme-surfactant complexes, which induces the dissociation of lysozyme-surfactant complexes when cationic surfactants were added.

Synthesis, fungicidal activity, and 3D-QSAR of pyridazinone-substituted 1,3,4-oxadiazoles and 1,3,4-thiadiazoles.

A series of novel 5-[1-aryl-1,4-dihydro-6-methylpyridazin-4-one-3-yl] -2-arylamino-1,3,4-oxadiazoles, fungicidally active, were synthesized based on bioisosterism and tested in vivo against wheat leaf rust, Puccinia recondita. These compounds were shown to be fungicidally active, and their activity was influenced by the nature of the substituents. By using the three-dimensional quantitative structure-activity relationships (3D-QSAR) method of comparative molecular field analysis (CoMFA), we have studied the structure and activity relationship of the compounds containing both pyridazinone-substituted 1,3,4-thiadiazoles and pyridazinone-substituted 1,3,4-oxadiazoles. The 3D-QSAR modes gave good correlation between the variations on percent inhibition and the steric-electrostatic properties. The results are consistent with a common mode of action for the pyridazinone-substituted 1,3,4-thiadiazoles and the pyridazinone-substituted 1,3,4-oxadiazoles, which further confirms that the 1,3,4-oxadiazole ring is a bioisosteric analogue of the 1,3,4-thiadiazole ring. These offer important structural insights into designing highly active compounds prior to their synthesis.