GM-DockZn: a geometry matching-based docking algorithm for zinc proteins.

MOTIVATION: Molecular docking is a widely used technique for large-scale virtual screening of the interactions between small-molecule ligands and their target proteins. However, docking methods often perform poorly for metalloproteins due to additional complexity from the three-way interactions among amino-acid residues, metal ions and ligands. This is a significant problem because zinc proteins alone comprise about 10% of all available protein structures in the protein databank. Here, we developed GM-DockZn that is dedicated for ligand docking to zinc proteins. Unlike the existing docking methods developed specifically for zinc proteins, GM-DockZn samples ligand conformations directly using a geometric grid around the ideal zinc-coordination positions of seven discovered coordination motifs, which were found from the survey of known zinc proteins complexed with a single ligand. RESULTS: GM-DockZn has the best performance in sampling near-native poses with correct coordination atoms and numbers within the top 50 and top 10 predictions when compared to several state-of-the-art techniques. This is true not only for a non-redundant dataset of zinc proteins but also for a homolog set of different ligand and zinc-coordination systems for the same zinc proteins. Similar superior performance of GM-DockZn for near-native-pose sampling was also observed for docking to apo-structures and cross-docking between different ligand complex structures of the same protein. The highest success rate for sampling nearest near-native poses within top 5 and top 1 was achieved by combining GM-DockZn for conformational sampling with GOLD for ranking. The proposed geometry-based sampling technique will be useful for ligand docking to other metalloproteins. AVAILABILITY AND IMPLEMENTATION: GM-DockZn is freely available at www.qmclab.com/ for academic users. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Argonaute proteins: structures and their endonuclease activity.

Argonaute proteins are highly conserved and widely expressed in almost all organisms. They not only play a critical role in the biogenesis of small RNAs but also defend against invading nucleic acids via small RNA or DNA-mediated gene silencing pathways. One functional mechanism of Argonaute proteins is acting as a nucleic-acid-guided endonuclease, which can cleave targets complementary to DNA or RNA guides. The cleavage then leads to translational silencing directly or indirectly by recruiting additional silencing proteins. Here, we summarized the latest research progress in structural and biological studies of Argonaute proteins and pointed out their potential applications in the field of gene editing.

A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT.

Bacterial xenogeneic silencing proteins selectively bind to and silence expression from many AT rich regions of the chromosome. They serve as master regulators of horizontally acquired DNA, including a large number of virulence genes. To date, three distinct families of xenogeneic silencers have been identified: H-NS of Proteobacteria, Lsr2 of the Actinomycetes, and MvaT of Pseudomonas sp. Although H-NS and Lsr2 family proteins are structurally different, they all recognize the AT-rich DNA minor groove through a common AT-hook-like motif, which is absent in the MvaT family. Thus, the DNA binding mechanism of MvaT has not been determined. Here, we report the characteristics of DNA sequences targeted by MvaT with protein binding microarrays, which indicates that MvaT prefers binding flexible DNA sequences with multiple TpA steps. We demonstrate that there are clear differences in sequence preferences between MvaT and the other two xenogeneic silencer families. We also determined the structure of the DNA-binding domain of MvaT in complex with a high affinity DNA dodecamer using solution NMR. This is the first experimental structure of a xenogeneic silencer in complex with DNA, which reveals that MvaT recognizes the AT-rich DNA both through base readout by an "AT-pincer" motif inserted into the minor groove and through shape readout by multiple lysine side chains interacting with the DNA sugar-phosphate backbone. Mutations of key MvaT residues for DNA binding confirm their importance with both in vitro and in vivo assays. This novel DNA binding mode enables MvaT to better tolerate GC-base pair interruptions in the binding site and less prefer A tract DNA when compared to H-NS and Lsr2. Comparison of MvaT with other bacterial xenogeneic silencers provides a clear picture that nature has evolved unique solutions for different bacterial genera to distinguish foreign from self DNA.

Vitronectin: a promising breast cancer serum biomarker for early diagnosis of breast cancer in patients.

Breast cancer is the most common cancer in women worldwide, identification of new biomarkers for early diagnosis and detection will improve the clinical outcome of breast cancer patients. In the present study, we determined serum levels of vitronectin (VN) in 93 breast cancer patients, 30 benign breast lesions, 9 precancerous lesions, and 30 healthy individuals by enzyme-linked immunosorbent assays. Serum VN level was significantly higher in patients with stage 0-I primary breast cancer than in healthy individuals, patients with benign breast lesion or precancerous lesions, as well as those with breast cancer of higher stages. Serum VN level was significantly and negatively correlated with tumor size, lymph node status, and clinical stage (p < 0.05 in all cases). In addition, VN displayed higher area under curve (AUC) value (0.73, 95 % confidence interval (CI) [0.62-0.84]) than carcinoembryonic antigen (CEA) (0.64, 95 % CI [0.52-0.77]) and cancer antigen 15-3 (CA 15-3) (0.69, 95 % CI [0.58-0.81]) when used to distinguish stage 0-I cancer and normal control. Importantly, the combined use of three biomarkers yielded an improvement in receiver operating characteristic curve with an AUC of 0.83, 95 % CI [0.74-0.92]. Taken together, our current study showed for the first time that serum VN is a promising biomarker for early diagnosis of breast cancer when combined with CEA and CA15-3.

Discovery of a 4-aryloxy-1H-pyrrolo[3,2-c]pyridine and a 1-aryloxyisoquinoline series of TRPA1 antagonists.

A series of TRPA1 antagonists is described having a 4-aryloxy-1H-pyrrolo[3,2-c]pyridine or a 1-aryloxyisoquinoline scaffold. These compounds have high ligand efficiency and favorable physical properties and may thus serve as scaffolds for further optimization.

Multifunctional biocompatible Ni/Ni-P nanospheres for anti-tumor "neoadjuvant phototherapy" combining photothermal therapy and photodynamic therapy.

Gastric cancer, a gastrointestinal tumor with high morbidity and lethality, is often treated using strategies that are not as effective as they could be due to the locally advanced stage. Although pre-operative neoadjuvant chemotherapy can degrade the tumor stage to afford the possibility of surgery, it still possesses the problems of high systemic toxicity and low selectivity. In this work, we constructed an intelligent multi-functional nanoplatform (NNPIP NPs) with synergistic effects of photothermal therapy (PTT) and photodynamic therapy (PDT), which consisted of the nickel/nickel phosphide (Ni/Ni-P) nanosphere as the core, polyethyleneimine (PEI) as the shell, and the loaded indocyanine green (ICG). The mutual reinforcement of heat generated by the core and photosensitizer under 808 nm NIR laser irradiation is highly effective in the synergistic action of PTT. And co-delivery of ICG with nanoparticles into the cell enhances the PDT effect by reducing the consumption of singlet oxygen (1O2). Ultimately, this therapeutic strategy in vivo not only shrunk tumors but even eliminated tumors completely in a quarter of samples, which may be considered as a potential alternative to neoadjuvant chemotherapy and called "neoadjuvant phototherapy". In addition, as a nanoplatform based on transition metal nickel, NNPIP NPs could also be considered as a potential contrast agent for T1-weighted magnetic resonance imaging (MRI). Herein, we can diagnose and achieve pre-surgical downstaging of tumors and hope to improve R0 resection rates with lower toxicity and higher selectivity.

[Feasibility of sentinel lymph node biopsy peri-neoadjuvant chemotherapy in breast cancer].

OBJECTIVE: To explore the feasibility of sentinel lymph node biopsy in peri-neoadjuvant chemotherapy for breast cancer patients. METHODS: A total of 252 breast cancer patients underwent sentinel lymph node biopsy and axillary lymph node dissection from January 2005 to November 2011, including 150 patients in pre-neoadjuvant chemotherapy group and 102 in post-neoadjuvant chemotherapy group. The feasibility of sentinel lymph node biopsy under different clinical states of axillary lymph node was compared. RESULTS: No significant difference was found in the detection rate (98.5% vs 92.8%), false negative rate (6.7% vs 7.9%), accuracy (98.4% vs 91.9%) and negative sensitivity (97.9% vs 88.0%) of sentinel lymph node biopsy before neoadjuvant chemotherapy whether the axillary lymph node was negative or positive. However, the transfer rate of sentinel lymph node in the positive group was significantly higher than the negative group (28.8% vs 67.5%, P = 0.000). False negative rate of sentinel lymph node in biopsy was significantly higher in the post-neoadjuvant chemotherapy group than the pre-neoadjuvant chemotherapy group (7.5% vs 23.9%, P = 0.024) and the accuracy/negative sensitivity decreased significantly (95.1% vs 83.5%, P = 0.005/94.4% vs 75.0%, P = 0.003). No statistical difference existed in the detection rate, false negative rate, accuracy, negative sensitivity of sentinel lymph node in biopsy before and after neoadjuvant chemotherapy in patients with negative axillary lymph node for a preliminary diagnosis. The accuracy of sentinel lymph node decreased significantly in biopsy after neoadjuvant chemotherapy in patients with positive axillary lymph node confirmed pathologically for a preliminary diagnosis compared with before (98.4/83.7%, P = 0.010), the transfer rate of sentinel lymph node increased significantly (28.8/53.7%, P = 0.005) and negative sensitivity reduced significantly (97.9/68.0%, P = 0.007); Compared with pre-neoadjuvant chemotherapy, the negative sensitivity decreased significantly in patients with axillary lymph node positive confirmed pathologically and then turned negative (94.4% vs 57.1%, P = 0.005) while the transfer rate of sentinel lymph node increased significantly (28.8%/65.0%, P = 0.003). CONCLUSIONS: Sentinel lymph node before neoadjuvant chemotherapy may accurately predict axillary lymph node metastasis. The detection rate, false negative rate, accuracy, negative sensitivity of sentinel lymph node in biopsy after neoadjuvant chemotherapy in patients with negative axillary lymph node for preliminary diagnosis are the same before neoadjuvant chemotherapy. Patients with positive axillary lymph node for a preliminary diagnosis are unsuitable for sentinel lymph node biopsy whether axillary lymph node turns negative or not after neoadjuvant chemotherapy.

Insights into Coronavirus Papain-like Protease Structure, Function and Inhibitors.

The coronavirus family consists of pathogens that seriously affect human and animal health. They mostly cause respiratory or enteric diseases, which can be severe and life-threatening, such as coronavirus disease 2019 (COVID-19), severe acute respiratory syndrome (SARS), and Middle East Respiratory Syndrome (MERS) in humans. The conserved coronaviral papain-like protease is an attractive antiviral drug target because it is essential for coronaviral replication, and it also inhibits host innate immune responses. This review focuses on the latest research progress relating to the mechanism of coronavirus infection, the structural and functional characteristics of coronavirus papain-like protease, and the potent inhibitors of the protease.

Potent Uncompetitive Inhibitors of Nicotinamide N-Methyltransferase (NNMT) as In Vivo Chemical Probes.

NNMT uses SAM as a cofactor to catalyze the methylation of nicotinamide, producing 1-methylnicotinamide. Recent studies have shown that NNMT upregulation in cancer-associated fibroblasts (CAFs) is required to maintain the CAF phenotype in high-grade serous carcinoma. These observations suggest that NNMT should be evaluated as a therapeutic target, especially in cancer. Although several small-molecule inhibitors of NNMT have been identified, there remains a need for highly potent and selective inhibitors with excellent in vivo activity and ADME properties that can be used as reliable chemical probes. We have identified azaindoline carboxamide 38 as a selective and potent NNMT inhibitor with favorable PK/PD and safety profiles as well as excellent oral bioavailability and pharmaceutical properties. Our mechanistic studies indicate that 38 binds uncompetitively with SAM but competitively with nicotinamide consistent with its binding in the nicotinamide binding site and likely forming a positive interaction with SAM.

Discovery of mu-opioid selective ligands derived from 1-aminotetralin scaffolds made via metal-catalyzed ring-opening reactions.

A series of 1-aminotetralin scaffolds was synthesized via metal-catalyzed ring-opening reactions of heterobicyclic alkenes. Small libraries of amides and amines were made using the amino group of each scaffold as a handle. Screening of these libraries against human opioid receptors led to the identification of (S)-(S)-5.2a as a high-affinity selective mu ligand (IC(50)mu=5 nM, kappa=707 nM, delta=3,795 nM) displaying mu-agonist/antagonist properties due to its partial agonism (EC(50)=2.6 microM; E(max)=18%).

Variations in early gut microbiome are associated with childhood eczema.

We assessed the relationship between gut microbiome profile and childhood eczema in 172 subjects (age < 3 years, healthy group N = 123, eczema group N = 49) utilizing 16S rRNA gene sequencing. Lower relative abundance of Bifidobacterium was shown to be associated with childhood eczema. Considering that developmental and environmental factors could modify the state of children's gut microbiome, we divided the samples into four age groups: 0-0.5 years, 0.5-1 years, 1-2 years and 2-3 years for farther analyses. Data revealed significant inter-group differences between healthy and eczema samples in all age groups, and decreased microbial diversity was most significantly found in children with eczema of age 2-3 years old. Decreased abundance of Bifidobacterium was a major finding in eczema groups from 0.5-3 years compared to the age matched healthy controls, but not significant in children younger than 6 month old. Of note, Bifidobacterium operational taxonomic units were identified by Random Forest with highly predictive power of 0.83 (AUC = 0.83) in ROC analysis, which also confirmed its role as a key genus that is associated with eczema. To verify the sequencing results, we performed quantitative polymerase chain reaction of Bifidobacterium and Bacteroides in the same cohort, and in a new eczema cohort (N = 57) for validation. Significantly, lower Bifidobacterium quantities were found in both eczema groups with an age range of 0.5-3 years. These results suggest variations in early gut microbiome are associated with childhood eczema.

Clinical characteristics of Poland's syndrome associated with breast cancer: Two case reports and a literature review.

Poland's syndrome is a rare congenital malformation that is characterized by a congenital defect of the pectoralis major. It is associated with various ipsilateral upper extremity anomalies and homolateral breast hypoplasia. There have been reports of Poland's syndrome being associated with different malignancies. Here, we report two cases of Poland's syndrome associated with breast cancer (BC) and review the literature. To date, 21 cases (including our two cases) of Poland's syndrome associated with BC have been reported. The clinical characteristics of the disease are analyzed in this report.

CD147 functions as the signaling receptor for extracellular divalent copper in hepatocellular carcinoma cells.

Elevated copper levels in tumor microenvironment are directly correlated to cancer progression in a variety of malignancies. Copper is required in angiogenesis, and promotes the proliferation and metastasis of cancer cells. However, the molecular mechanism of copper in promoting cancer progression remains elusive. Here we report that CD147 serves as a signaling receptor for extracellular Cu2+ in hepatocellular carcinoma (HCC) cells. Cu2+ binds to the extracellular membrane-proximal domain of CD147 and mediates its self-association. Cu2+-mediated self-association of CD147 activates PI3K/Akt signaling pathway leading to the up-regulation of matrix metalloproteinase MMP-2 and MMP-14 in HCC cells. Cu2+-induced CD147 self-association also enhances the ability of HCC cells to stimulate MMP-2 expression from neighboring fibroblasts, as well as increases the invasiveness of HCC cells which is abolished by the copper chelator tetrathiomolybdate. We have mapped the interfaces and identified the key residues of CD147 involved in the Cu2+ induced self-association. The Cu2+ binding deficient CD147 mutant abolishes the stimulating effects of Cu2+ on HCC cells. Our study reveals a novel extracellular signaling role of copper in promoting cancer cell metastasis, which implies that targeting the Cu2+-induced self-association of CD147 is a new strategy for cancer treatment.

Discovery of agonists of cannabinoid receptor 1 with restricted central nervous system penetration aimed for treatment of gastroesophageal reflux disease.

Agonists of the cannabinoid receptor 1 (CB1) have been suggested as possible treatments for a range of medical disorders including gastroesophageal reflux disease (GERD). While centrally acting cannabinoid agonists are known to produce psychotropic effects, it has been suggested that the CB1 receptors in the periphery could play a significant role in reducing reflux. A moderately potent and highly lipophilic series of 2-aminobenzamides was identified through focused screening of GPCR libraries. Development of this series focused on improving potency and efficacy at the CB1 receptor, reducing lipophilicity and limiting the central nervous system (CNS) exposure while maintaining good oral absorption. Improvement of the series led to compounds having excellent potency at the CB1 receptor and high levels of agonism, good physical and pharmacokinetic properties, and low penetration into the CNS. A range of compounds demonstrated a dose-dependent inhibition of transient lower esophageal sphincter relaxations in a dog model.

Functionalized cross-linked poly(vinyl alcohol) resins as reaction scavengers and as supports for solid-phase organic synthesis.

New hydrophilic poly(vinyl alcohol) (PVA-OH) resins were prepared by an inverse suspension polymerization using epichlorohydrin as a cross-linker. These novel resins swell in a variety of solvents commonly used in solid-phase organic synthesis, such as dicholomethane, dioxane, methanol, tetrahydrofuran, and dimethylformamide. In addition, PVA-OH shows excellent swelling in water. The cross-linked PVA-OH beads were functionalized with an aldehyde group and were tested as scavengers for primary amines in three different reactions: amide bond formation, reductive amination reaction, and urea formation. With 1-2 equiv of the PVA aldehyde resin, all the excess primary amines were successfully scavenged. The utility of PVA-OH resins as solid supports in mono- and dipeptide synthesis was also investigated using symmetrical anhydride and MSNT/MeIm (2,4,6-mesitylenesulfonyl-3-nitro-1,2,4-triazolide in the presence of 1-methylimidazol) methods.