Ginkgo biloba extract attenuates cisplatin-induced renal interstitial fibrosis by inhibiting the activation of renal fibroblasts through down-regulating the HIF-1α/STAT3/IL-6 pathway in renal tubular epithelial cells.

BACKGROUND: Activation of renal fibroblasts into myofibroblasts plays an important role in promoting renal interstitial fibrosis (RIF). Ginkgo biloba extract (EGb) can alleviate RIF induced by cisplatin (CDDP). PURPOSE: To elucidate the effect of EGb treatment on cisplatin-induced RIF and reveal its potential mechanism. METHODS: The two main active components in EGb were determined by high-performance liquid chromatography (HPLC) analysis. Rats were induced by CDDP and then treated with EGb, 2ME2 (HIF-1α inhibitor) or amifostine. After HK-2 cells and HIF-1α siRNA HK-2 cells were treated with CDDP, EGb or amifostine, the conditioned medium from each group was cultured with NRK-49F cells. The renal function of rats was detected. The renal damage and fibrosis were evaluated by H&E and Masson trichrome staining. The IL-6 content in the cell medium was detected by ELISA. The expression levels of indicators related to renal fibrosis and signaling pathway were examined by western blotting and qRT-PCR. RESULTS: HPLC analysis showed that the contents of quercetin and kaempferol in EGb were 36.0 µg/ml and 45.7 µg/ml, respectively. In vivo, EGb and 2ME2 alleviated renal damage and fibrosis, as well as significantly decreased the levels of α-SMA, HIF-1α, STAT3 and IL-6 in rat tissues induced by CDDP. In vitro, the levels of HIF-1α, STAT3 and IL-6 were significantly increased in HK-2 cells and HIF-1α siRNA HK-2 cells induced by CDDP. Notably, HIF-1α siRNA significantly decreased the levels of HIF-1α, STAT3 and IL-6 in HK-2 cells, as well as the IL-6 level in medium from HK-2 cells. Additionally, the α-SMA level in NRK-49F cells was significantly increased after being cultured with conditioned medium from HK-2 cells or HIF-1α siRNA HK-2 cells exposed to CDDP. Furthermore, exogenous IL-6 increased the α-SMA level in NRK-49F cells. Importantly, the expression levels of the above-mentioned indicators were significantly decreased after the HK-2 cells and HIF-1α siRNA HK-2 cells were treated with EGb. CONCLUSION: This study revealed that EGb improves CDDP-induced RIF, and the mechanism may be related to its inhibition of the renal fibroblast activation by down-regulating the HIF-1α/STAT3/IL-6 pathway in renal tubular epithelial cells.

Physicochemical and Functional Changes in Lotus Root Polysaccharide Associated with Noncovalent Binding of Polyphenols.

To promote the functional applications of lotus root polysaccharides (LRPs), the effects of noncovalent polyphenol binding on their physicochemical properties, as well as antioxidant and immunomodulatory activities, were investigated. Ferulic acid (FA) and chlorogenic acid (CHA) were spontaneously bound to the LRP to prepare the complexes LRP-FA1, LRP-FA2, LRP-FA3, LRP-CHA1, LRP-CHA2 and LRP-CHA3, and their mass ratios of polyphenol to LRP were, respectively, 121.57, 61.18, 34.79, 2359.58, 1276.71 and 545.08 mg/g. Using the physical mixture of the LRP and polyphenols as a control, the noncovalent interaction between them in the complexes was confirmed by ultraviolet and Fourier-transform infrared spectroscopy. The interaction increased their average molecular weights by 1.11~2.27 times compared to the LRP. The polyphenols enhanced the antioxidant capacity and macrophage-stimulating activity of the LRP depending on their binding amount. Particularly, the DPPH radical scavenging activity and FRAP antioxidant ability were positively related to the FA binding amount but negatively related to the CHA binding amount. The NO production of the macrophages stimulated by the LRP was inhibited by the co-incubation with free polyphenols; however, the inhibition was eliminated by the noncovalent binding. The complexes could stimulate the NO production and tumor necrosis factor-α secretion more effectively than the LRP. The noncovalent binding of polyphenols may be an innovative strategy for the structural and functional modification of natural polysaccharides.

Cryo-EM structure of adeno-associated virus 4 at 2.2†Šresolution.

Adeno-associated virus (AAV) is the vector of choice for several approved gene-therapy treatments and is the basis for many ongoing clinical trials. Various strains of AAV exist (referred to as serotypes), each with their own transfection characteristics. Here, a high-resolution cryo-electron microscopy structure (2.2 Å) of AAV serotype 4 (AAV4) is presented. The receptor responsible for transduction of the AAV4 clade of AAV viruses (including AAV11, AAV12 and AAVrh32.33) is unknown. Other AAVs interact with the same cell receptor, adeno-associated virus receptor (AAVR), in one of two different ways. AAV5-like viruses interact exclusively with the polycystic kidney disease-like 1 (PKD1) domain of AAVR, while most other AAVs interact primarily with the PKD2 domain. A comparison of the present AAV4 structure with prior corresponding structures of AAV5, AAV2 and AAV1 in complex with AAVR provides a foundation for understanding why the AAV4-like clade is unable to interact with either PKD1 or PKD2 of AAVR. The conformation of the AAV4 capsid in variable regions I, III, IV and V on the viral surface appears to be sufficiently different from AAV2 to ablate binding with PKD2. Differences between AAV4 and AAV5 in variable region VII appear to be sufficient to exclude binding with PKD1.

Tailoring the pore chemistry in porous aromatic frameworks for selective separation of acetylene from ethylene.

The separation of acetylene from ethylene is a crucial process in the petrochemical industry, because even traces of acetylene impurities can poison the catalysts of ethylene polymerization. Herein, we synthesize a new family of 3D porous aromatic frameworks (PAFs), non-functionalized PAF-28, carbene-functionalized PAF-28 (cPAF-28) and imidazolium-functionalized PAF-28 (iPAF-28), via Sonogashira coupling reactions. These PAFs show high porosity and good thermal stability. Both cPAF-28 and iPAF-28 are proved to be good candidates for C2H2 adsorption, demonstrated by C2H2/C2H4 selectivity of 12.2 and 15.4, and C2H2 capacity of 48 cm3 g-1 and 57 cm3 g-1, which are significantly higher than those of non-functionalized PAF-28 (1.8, 37 cm3 g-1). Furthermore, the cPAF-28 and iPAF-28 display good breakthrough performance and remarkable recyclability for the separation of the C2H2/C2H4 gas mixture. In addition, the C2H2/C2H4 adsorption sites are revealed by DFT calculations. This work sheds a new light on gas molecular recognition by tailoring the pore chemistry of PAFs.

Drug-Induced Liver Injury during Consolidation Therapy in Childhood Acute Lymphoblastic Leukemia as Assessed for Causality Using the Updated RUCAM.

Purpose: The presence of serious toxicities is a major problem in the treatment of childhood acute lymphoblastic leukemia (ALL). The objective of this research is to evaluate drug-induced liver injury (DILI) during consolidation therapy in childhood ALL. Methods: Clinical data of pediatric patients who received consolidation therapy between August 2012 and July 2018 were collected. Characteristics (incidences and patterns) of DILI at different stratifications were determined. Risks of DILI were evaluated using binary logistic regression analysis. Drug causality assessment was carried out by the updated Roussel Uclaf Causality Assessment Method (RUCAM). Results: Patients with high risk (HR) and standard risk (SR)/intermediate risk (IR) received 270 and 1539 courses of consolidation therapy, respectively; among these courses, 15 (5.6%) and 38 (2.5%) developed DILI. The occurrences of DILI in SR/IR patients were primarily associated with age (≤5.2 years), treatment course (≥5), and baseline serum parameters before treatment (cystatin C > 0.79 mg/L, albumin ≤45 g/L, and gamma-glutamyl transpeptidase (GGT) > 17 U/L). The ROC curve generated using the parameters assigned to specific values achieved an area under the curve (AUC) of 0.846 (95% CI 0.827-0.863) with a cutoff value of 3, and the sensitivity and specificity were 94.7% and 62.3%, respectively. For HR patients, a decrease in baseline albumin and elevation of baseline liver enzymes (GGT and aspartate aminotransferase) were observed in DILI cases compared with the non-DILI subjects. In the SR/IR group with DILI, the causality gradings for high-dose methotrexate (HD-MTX) were highly probable in 5 (13.2%) cases, probable in 31 (81.6%) cases, and possible in 2 (5.3%) cases. Among the DILI cases in HR-1, HR-2, and HR-3 groups, high causality gradings (probable + highly probable) were detected in "100% of HD-MTX + 57% of high-dose cytarabine (HD-Ara-C)," "100% of HD-MTX + 20% of pegylated asparaginase (PEG-ASP)," and "100% of HD-Ara-C + 33.3% of PEG-ASP," respectively. Conclusion: Incidence of DILI in HR patients was significantly higher than that in SR/IR patients. A number of potential risk factors were identified, among which the preexisting liver conditions were suggested as shared risk factors in all stratification groups. HD-MTX, HD-Ara-C, and PEG-ASP were the main causative agents of DILI. The knowledge generated from this study will be helpful for understanding characteristics of DILI during consolidation treatment in childhood ALL.

Predicting Protein-Peptide Complex Structures by Accounting for Peptide Flexibility and the Physicochemical Environment.

Predicting protein-peptide complex structures is crucial to the understanding of a vast variety of peptide-mediated cellular processes and to peptide-based drug development. Peptide flexibility and binding mode ranking are the two major challenges for protein-peptide complex structure prediction. Peptides are highly flexible molecules, and therefore, brute-force modeling of peptide conformations of interest in protein-peptide docking is beyond current computing power. Inspired by the fact that the protein-peptide binding process is like protein folding, we developed a novel strategy, named MDockPeP2, which tries to address these challenges using physicochemical information embedded in abundant monomeric proteins with an exhaustive search strategy, in combination with an integrated global search and a local flexible minimization method. Only the peptide sequence and the protein crystal structure are required. The method was systemically assessed using a newly constructed structural database of 89 nonredundant protein-peptide complexes with the peptide sequence length ranging from 5 to 29 in which about half of the peptides are longer than 15 residues. MDockPeP2 yielded a total success rate of 58.4% (70.8, 79.8%) for the bound docking (i.e., with the bound receptor and fully flexible peptides) and 19.0% (44.8, 70.7%) for the challenging unbound docking when top 10 (100, 1000) models were considered for each prediction. MDockPeP2 achieved significantly higher success rates on two other datasets, peptiDB and LEADS-PEP, which contain only short- and medium-size peptides (≤ 15 residues). For peptiDB, our method obtained a success rate of 62.0% for the bound docking and 35.9% for the unbound docking when the top 10 models were considered. For LEADS-PEP, MDockPeP2 achieved a success rate of 69.8% when the top 10 models were considered. The program is available at https://zougrouptoolkit.missouri.edu/mdockpep2/download.html.

A Selective Tether Recruits Activated Response Regulator CheB to Its Chemoreceptor Substrate.

Methylesterase/deamidase CheB is a key component of bacterial chemotaxis systems. It is also a prominent example of a two-component response regulator in which the effector domain is an enzyme. Like other response regulators, CheB is activated by phosphorylation of an aspartyl residue in its regulatory domain, creating an open conformation between its two domains. Studies of CheB in Escherichia coli and related organisms have shown that its enzymatic action is also enhanced by a pentapeptide-binding site for the enzyme at the chemoreceptor carboxyl terminus. Related carboxyl-terminal pentapeptides are found on >25,000 chemoreceptor sequences distributed across 11 bacterial phyla and many bacterial species, in which they presumably play similar roles. Yet, little is known about the interrelationship of CheB phosphorylation, pentapeptide binding, and interactions with its substrate methylesters and amides on the body of the chemoreceptor. We investigated by characterizing the binding kinetics of CheB to Nanodisc-inserted chemoreceptor dimers. The resulting kinetic and thermodynamic constants revealed a synergy between CheB phosphorylation and pentapeptide binding in which a phosphorylation mimic enhanced pentapeptide binding, and the pentapeptide served not only as a high-affinity tether for CheB but also selected the activated conformation of the enzyme. The basis of this selection was revealed by molecular modeling that predicted a pentapeptide-binding site on CheB which existed only in the open, activated enzyme. Recruitment of activated enzyme by selective tethering represents a previously unappreciated strategy for regulating response regulator action, one that may well occur in other two-component systems. IMPORTANCE Two-component signal transduction systems are a primary means by which bacteria sense and respond to their environment. Response regulators are key components of these systems. Phosphorylation of response regulators by cognate histidine kinases generate active conformations which act on specific targets, DNA sequences or proteins. The targets have been considered passive in this process. Our characterization of interaction between response regulator CheB and its target chemoreceptor revealed active participation of the target in response regulator action. We found that a pentapeptide sequence at the carboxyl terminus of Escherichia coli chemoreceptors is a selective tether that binds only phosphorylated CheB, thus selecting the form of this two-component enzyme active for covalent modification of the selecting chemoreceptor. Analogous pentapeptides are found on chemoreceptors in many bacterial species and are presumably also selective tethers. There may well be other, uncharacterized examples of active participation of target molecules in response to regulator action.

Panax notoginseng saponins reduces the cisplatin-induced acute renal injury by increasing HIF-1α/BNIP3 to inhibit mitochondrial apoptosis pathway.

Cisplatin (CDDP) may induce apoptosis of renal tubular epithelial cells (RTEC) and cause CDDP-induced acute kidney injury (CAKI) during cancer treatment, but yet lack of preventive measures and effective treatment. As a new Chinese herbal preparation, Panax notoginseng saponins (PNS) has been found to mitigate CDDP-induced CAKI through elevating the expression of HIF-1α in the rat model, according to the data from our previous works. However, the underlying link between HIF-1α and apoptosis has not been well elucidated. The current study as a follow-up work, was aimed to reveal if PNS improves CAKI through HIF-1α-dependent apoptosis. A stably HIF-1α-knockdown human proximal tubular epithelial cell (HK-2) line was established by transfecting a HIF-1α-siRNA into HK-2 cells. Cell viability, mitochondrial function, cell apoptosis ratio and the expression of apoptosis-associated proteins (Cyt C, Bcl2, Bax, caspases 3) were determined. In order to elucidate the underlying mechanism, the expression of HIF-1α and BNIP3 were assessed. Our results showed that treatment of PNS rescued the cell viability of CDDP-injured HK-2 or HIF-1α-knockdown HK-2 cells, and increased the expression levels of ATP and MMP in HK-2 or HIF-1α-knockdown HK-2 cells which were reduced by CDDP. Moreover, PNS treatment decreased the CDDP or CDDP plus HIF-1α-knockdown-induced elevation of apoptosis and apoptosis-associated protein expressions. These findings demonstrate that PNS reduces CAKI through increasing HIF-1α to inhibit mitochondrial apoptosis pathway. Hence, we suggest PNS as a protective and therapeutic new drug for CDDP treatment of cancers, which might have significant meaning of further research and application potential.

Drug-containing serum of rhubarb-astragalus capsule inhibits the epithelial-mesenchymal transformation of HK-2 by downregulating TGF-ß1/p38MAPK/Smad2/3 pathway.

ETHNOPHARMACOLOGICAL RELEVANCE: Rheum palmatum L; Astragalus membranaceus (Fisch.), is referred to as 'Dahuang, Huangqi' in China. As an important medicinal plant, the rhizome of rhubarb and astragalus is traditionally used in the treatment of kidney diseases associated with renal failure, inflammation and tumors. AIM OF THE STUDY: This study aimed to investigate the effect of a drug-containing serum of rhubarb-astragalus capsules (composed of rhubarb and astragalus) and to elucidate its mechanism in the epithelial-mesenchymal transformation of renal tubular epithelial cells. MATERIALS AND METHODS: Epithelial-mesenchymal transformation (EMT) of HK-2 cells was induced by TGF-ß1, and rhubarb-astragalus and losartan drug-containing serum from rats, as well as SB203580 (a specific inhibitor of p38 MAPK), were used. High-performance liquid chromatography analysis was performed to determine the main components of the drug-containing serum of rhubarb-astragalus from rats. Western blotting and immunofluorescence analysis were used to determine the levels of protein expression, and real-time quantitative PCR analysis was used to detect the levels of gene expression. RESULTS: The drug-containing serum of rhubarb-astragalus contained emodin (0.36 µg/ml) and danthraquinone (0.96 µg/ml). Rhubarb-astragalus significantly decreased the protein expression levels of α-SMA, FN, vimentin and N-cadherin in HK-2 cells that were increased by TGF-ß1, while it significantly increased the E-cadherin protein expression level that was decreased by TGF-ß1. Rhubarb-astragalus also significantly decreased the protein expression levels of TGF-ß1 and p38 MAPK and the mRNA expression levels of α-SMA, vimentin, TGF-ß1, p38 MAPK, Smad2 and Smad3 in HK-2 cells that were increased by TGF-ß1. It is worth noting that SB203580 (a p38 MAPK inhibitor) had similar effects as rhubarb-astragalus in this study. CONCLUSION: The drug-containing serum of rhubarb-astragalus can inhibit EMT in HK-2 cells by downregulating the TGF-ß1/p38 MAPK/Smad2/3 pathway.

The three-way junction structure of the HIV-1 PBS-segment binds host enzyme important for viral infectivity.

HIV-1 reverse transcription initiates at the primer binding site (PBS) in the viral genomic RNA (gRNA). Although the structure of the PBS-segment undergoes substantial rearrangement upon tRNALys3 annealing, the proper folding of the PBS-segment during gRNA packaging is important as it ensures loading of beneficial host factors. DHX9/RNA helicase A (RHA) is recruited to gRNA to enhance the processivity of reverse transcriptase. Because the molecular details of the interactions have yet to be defined, we solved the solution structure of the PBS-segment preferentially bound by RHA. Evidence is provided that PBS-segment adopts a previously undefined adenosine-rich three-way junction structure encompassing the primer activation stem (PAS), tRNA-like element (TLE) and tRNA annealing arm. Disruption of the PBS-segment three-way junction structure diminished reverse transcription products and led to reduced viral infectivity. Because of the existence of the tRNA annealing arm, the TLE and PAS form a bent helical structure that undergoes shape-dependent recognition by RHA double-stranded RNA binding domain 1 (dsRBD1). Mutagenesis and phylogenetic analyses provide evidence for conservation of the PBS-segment three-way junction structure that is preferentially bound by RHA in support of efficient reverse transcription, the hallmark step of HIV-1 replication.

MDock: A Suite for Molecular Inverse Docking and Target Prediction.

Molecular docking is commonly used for identification of drug candidates targeting a specified protein of known structure. With the increasing emphasis on drug repurposing over recent decades, molecular inverse docking has been widely applied to prediction of the potential protein targets of a specified molecule. In practice, inverse docking has many advantages, including early supervision of drugs' side effects and toxicity. MDock developed from our laboratory is a protein-ligand docking software based on a knowledge-based scoring function and has numerous applications to lead identification. In addition to its computational efficiency on ensemble docking for multiple protein conformations, MDock is well suited for inverse docking. In this chapter, we focus on introducing the protocol of inverse docking with MDock. For academic users, the MDock package is freely available at http://zoulab.dalton.missouri.edu/mdock.htm .

Identification of the fatty acid synthase interaction network via iTRAQ-based proteomics indicates the potential molecular mechanisms of liver cancer metastasis.

BACKGROUND: Fatty acid synthase (FASN) is highly expressed in various types of cancer and has an important role in carcinogenesis and metastasis. To clarify the mechanisms of FASN in liver cancer invasion and metastasis, the FASN protein interaction network in liver cancer was identified by targeted proteomic analysis. METHODS: Wound healing and Transwell assays was performed to observe the effect of FASN during migration and invasion in liver cancer. Isobaric tags for relative and absolute quantitation (iTRAQ)-based mass spectrometry were used to identify proteins interacting with FASN in HepG2 cells. Differential expressed proteins were validated by co-immunoprecipitation, western blot analyses and confocal microscopy. Western blot and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) were performed to demonstrate the mechanism of FASN regulating metastasis. RESULTS: FASN knockdown inhibited migration and invasion of HepG2 and SMMC7721 cells. A total of, 79 proteins interacting with FASN were identified. Additionally, gene ontology term enrichment analysis indicated that the majority of biological regulation and cellular processes that the FASN-interacting proteins were associated with. Co-precipitation and co-localization of FASN with fascin actin-bundling protein 1 (FSCN1), signal-induced proliferation-associated 1 (SIPA1), spectrin ß, non-erythrocytic 1 (SPTBN1) and CD59 were evaluated. Knockdown of FASN in liver cancer reduced the expression of FSCN1, SIPA1, SPTBN1 and CD59. Furthermore, inhibition of FASN, FSCN1 or SPTBN1 expression in liver cancer resulted in alterations of epithelial-mesenchymal transition (EMT)-associated markers E-cadherin, N-cadherin, vimentin and transcription factors, Snail and Twist, at the mRNA level, and changes in matrix metallopeptidase (MMP)-2 and MMP-9 protein expression. CONCLUSION: The results suggested that the FASN-interacting protein network produced by iTRAQ-based proteomic analyses may be involved in regulating invasion and metastasis in liver cancer by influencing EMT and the function of MMPs.

MDockPeP: A Web Server for Blind Prediction of Protein-Peptide Complex Structures.

Protein-peptide interactions mediate a wide range of important cellular tasks. In silico prediction of protein-peptide complex structure is highly desirable for mechanistic investigation of these processes and for therapeutic design. Recently, we developed a docking-based method for predicting protein-peptide complex structures, which starts with the peptide sequence and globally docks the all-atom, flexible peptide onto the protein structure. The produced modes are then evaluated with a statistical potential-based scoring function. The method has been implemented into an online server, MDockPeP server, which is freely available at http://zougrouptoolkit.missouri.edu/mdockpep . The server can be used for protein-peptide complex structure prediction. The server can also be used for initial-stage sampling of the protein-peptide binding modes for computational-demanding simulation or docking methods.

Structural basis of prostate-specific membrane antigen recognition by the A9g RNA aptamer.

Prostate-specific membrane antigen (PSMA) is a well-characterized tumor marker associated with prostate cancer and neovasculature of most solid tumors. PSMA-specific ligands are thus being developed to deliver imaging or therapeutic agents to cancer cells. Here, we report on a crystal structure of human PSMA in complex with A9g, a 43-bp PSMA-specific RNA aptamer, that was determined to the 2.2 Å resolution limit. The analysis of the PSMA/aptamer interface allows for identification of key interactions critical for nanomolar binding affinity and high selectivity of A9g for human PSMA. Combined with in silico modeling, site-directed mutagenesis, inhibition experiments and cell-based assays, the structure also provides an insight into structural changes of the aptamer and PSMA upon complex formation, mechanistic explanation for inhibition of the PSMA enzymatic activity by A9g as well as its ligand-selective competition with small molecules targeting the internal pocket of the enzyme. Additionally, comparison with published protein-RNA aptamer structures pointed toward more general features governing protein-aptamer interactions. Finally, our findings can be exploited for the structure-assisted design of future A9g-based derivatives with improved binding and stability characteristics.

Performance of human and server prediction in CAPRI rounds 38-45.

CAPRI challenges offer a variety of blind tests for protein-protein interaction prediction. In CAPRI Rounds 38-45, we generated a set of putative binding modes for each target with an FFT-based docking algorithm, and then scored and ranked these binding modes with a proprietary scoring function, ITScorePP. We have also developed a novel web server, Rebipp. The algorithm utilizes information retrieval to identify relevant biological information to significantly reduce the search space for a particular protein. In parallel, we have also constructed a GPU-based docking server, MDockPP, for protein-protein complex structure prediction. Here, the performance of our protocol in CAPRI rounds 38-45 is reported, which include 16 docking and scoring targets. Among them, three targets contain multiple interfaces: Targets 124, 125, and 136 have 2, 4, and 3 interfaces, respectively. In the predictor experiments, we predicted correct binding modes for nine targets, including one high-accuracy interface, six medium-accuracy binding modes, and six acceptable-accuracy binding modes. For the docking server prediction experiments, we predicted correct binding modes for eight targets, including one high-accuracy, three medium-accuracy, and five acceptable-accuracy binding modes.

RETRACTED: Interleukin-36 receptor antagonist is associated with the progression of renal cell carcinoma.

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been retracted at the request of the Editor-in-Chief. This article has similarities to seven other papers that have been published. They have similar Kaplan-Meier curves, and tables and table values. These similar graphics and tables apply to different disease states, target mediators and numbers of patients in different studies. After the comments of Dr Elisabeth Bik https://pubpeer.com/publications/39A1613F4546DA16064BA441B29A0F regarding this article, the journal requested the author to provide the raw data. However, the author did not respond. Dr Elisabeth Bik is acknowledged for pointing out the irregularities in these papers.

PepPro: A Nonredundant Structure Data Set for Benchmarking Peptide-Protein Computational Docking.

We present a nonredundant benchmark, coined PepPro, for testing peptide-protein docking algorithms. Currently, PepPro contains 89 nonredundant experimentally determined peptide-protein complex structures, with peptide sequence lengths ranging from 5 to 30 amino acids. The benchmark covers peptides with distinct secondary structures, including helix, partial helix, a mixture of helix and ß-sheet, ß-sheet formed through binding, ß-sheet formed through self-folding, and coil. In addition, unbound proteins' structures are provided for 58 complexes and can be used for testing the ability of a docking algorithm handling the conformational changes of proteins during the binding process. PepPro should benefit the docking community for the development and improvement of peptide docking algorithms. The benchmark is available at http://zoulab.dalton.missouri.edu/PepPro_benchmark. © 2019 Wiley Periodicals, Inc.

Identifying the molecular target sites for CFTR potentiators GLPG1837 and VX-770.

The past two decades have witnessed major breakthroughs in developing compounds that target the chloride channel CFTR for the treatment of patients with cystic fibrosis. However, further improvement in affinity and efficacy for these CFTR modulators will require insights into the molecular interactions between CFTR modulators and their binding targets. In this study, we use in silico molecular docking to identify potential binding sites for GLPG1837, a CFTR potentiator that may share a common mechanism and binding site with VX-770, the FDA-approved drug for patients carrying mutations with gating defects. Among the five binding sites predicted by docking, the two top-scoring sites are located at the interface between CFTR's two transmembrane domains: site I consists of D924, N1138, and S1141, and site IIN includes F229, F236, Y304, F312, and F931. Using mutagenesis to probe the importance of these sites for GLPG187 binding, we find that disruption of predicted hydrogen-bonding interactions by mutation of D924 decreases apparent affinity, while hydrophobic amino acids substitutions at N1138 and introduction of positively charged amino acids at S1141 improve the apparent affinity for GLPG1837. Alanine substitutions at Y304, F312, and F931 (site IIN) decrease the affinity for GLPG1837, whereas alanine substitutions at F229 and F236 (also site IIN), or at residues in the other three lower-scoring sites, have little effect. In addition, current relaxation analysis to assess the apparent dissociation rate of VX-770 yields results consistent with the dose-response experiments for GLPG8137, with the dissociation rate of VX-770 accelerated by D924N, F236A, Y304A, and F312A, but decelerated by N1138L and S1141K mutations. Collectively, these data identify two potential binding sites for GLPG1837 and VX-770 in CFTR. We discuss the pros and cons of evidence for these two loci and the implications for future drug design.

Constructing Connected Paths between UiO-66 and PIM-1 to Improve Membrane CO2 Separation with Crystal-Like Gas Selectivity.

Most metal-organic-framework- (MOF-) based hybrid membranes face the challenge of low gas permeability in CO2 separation. This study presents a new strategy of interweaving UiO-66 and PIM-1 to build freeways in UiO-66-CN@sPIM-1 membranes for fast CO2 transport. In this strategy, sPIM-1 is rigidified via thermal treatment to make polymer voids permanent, and concurrently polymer chains are mutually linked onto UiO-66-CN crystals to minimize interfacial defects. The pore chemistry of UiO-66-CN is kept intact in hybrid membranes, allowing full utilization of MOF pores and selective adsorption for CO2 . Separation results show that UiO-66-CN@sPIM-1 membranes possess exceptionally high CO2 permeability (15433.4-22665 Barrer), approaching to that of UiO-66-NH2 crystal (65-75% of crystal-derived permeability). Additionally, the CO2 /N2 permeation selectivity for a representative membrane (23.9-28.6) moves toward that of single crystal (24.6-29.6). The unique structure and superior CO2 /N2 separation performance make UiO-66-CN@sPIM-1 membranes promising in practical CO2 separations.