[Application value of CT examination of lymph node short diameter in evaluating cardia-left gastric lymph node metastasis in thoracic esophageal squamous cell carcinoma].

Objective: To investigate the application value of computed tomography (CT) examination of lymph node short diameter in evaluating cardia-left gastric lymph node metastasis in thoracic esophageal squamous cell carcinoma (ESCC). Methods: A total of 477 patients with primary thoracic ESCC who underwent surgical treatment in the Affiliated Cancer Hospital of Zhengzhou University from January 2013 to December 2017 were collected. All of them underwent McKeown esophagectomy plus complete two-field or three-field lymph node dissection. Picture archiving and communication system were used to measure the largest cardia-left gastric lymph node short diameter in preoperative CT images. The postoperative pathological diagnosis results of cardia-left gastric lymph node were used as the gold standard. Receiver operating characteristic (ROC) curve was used to evaluate the efficacy of CT lymph node short diameter in detecting the metastasis of cardia-left gastric lymph node in thoracic ESCC, and determine the optimal cut-off value. Results: The median short diameter of the largest cardia-left gastric lymph node was 4.1 mm in 477 patients, and the largest cardia-left gastric lymph node short diameter was less than 3 mm in 155 cases (32.5%). Sixty-eight patients had cardia-left gastric lymph node metastases, of which 38 had paracardial node metastases and 41 had left gastric node metastases. The lymph node ratios of paracardial node and left gastric node were 4.0% (60/1 511) and 3.3% (62/1 887), respectively. ROC curve analysis showed that the area under the curve of CT lymph node short diameter for evaluating cardia-left gastric lymph node metastasis was 0.941 (95% CI: 0.904-0.977; P<0.05). The optimal cut-off value of CT examination of the cardia-left gastric lymph node short diameter was 6 mm, and the corresponding sensitivity, specificity and accuracy were 85.3%, 91.7%, and 90.8%, respectively. Conclusion: CT examination of lymph node short diameter can be a good evaluation of cardia-left gastric lymph node metastasis in thoracic ESCC, and the optimal cut-off value is 6 mm.

Forensic Application of Plant Evidence.

ABSTRACT: With the increasingly obvious role of plant evidence in case detection, forensic botany, which provides clues and evidence in crime scene investigation by using botanical research method has attracted growing attention. The common experimental techniques used in forensic botany are morphological examination, physical and chemical examination, molecular genetic examination, and so on. This paper briefly expounds the advantages and disadvantages of different test methods, summarizes the problems that need to be paid attention to in the application of forensic botany by arranging the related literatures and cases of forensic botanical research, in order to provide reference for scene investigation of cases.

[Clinical and pathologic analysis of 414 cases of renal angiomyolipomain in a single institution].

Objective: To study the different clinicopathological characteristics between classic and epithelioid renal angiomyolipoma, and the relationships between clinicopathological characteristics and biological behaviors as basis for clinical treatment. Methods: The clinicopathological and follow-up data for the patients diagnosed with renal angiomyolipoma between 2004 and 2011 were retrospectively reviewed and analyzed. Results: There were 414 cases of renal angiomyolipoma diagnosed over 8 years ago, accounting for 8.1% (414/5 287) of all renal parenchymal tumors. The patients included 122 male and 292 female (male-to-female ratio of 1.0∶2.4), mean age 44.0 years (range 15-74 years). Of these, 195(47.1%) tumors occurred in the left kidney, 212(51.2%) in the right kidney and seven (1.7%) were bilateral. Clinically, some cases presented with hypochondrial pain, hematuria or palpable masses. Histologically, 394(95.2%) were classic angiomyolipoma, 20(4.8%) were epithelioid angiomyolipoma; 54, 23 and 7 cases had hemorrhage, necrosis and cystic degeneration, respectively; and 5, 30 and 14 cases had perirenal fat invasion, atypical cells and polymorphic/giant tumor cell. There was a positive correlation between atypical cells and epithelioid tumor type, respectively. The other clinicopathological parameters did not correlate with histological type. Follow-up data was available in 360 patients, with follow-up period of 3 to 99 months. One case died from other causes. The remaining patients were free of disease. Conclusions: Angiomyolipoma is a common renal parenchyma tumor. Clinically, it is usually biologically benign. Histologically, it can be either classic or epithelioid types. The epithelioid type should be differentiated from the classic renal cell carcinoma, Mit family translocation renal tumor and renal hemangioblastoma. Atypical cells, more commonly found in the epithelioid angiomyolipoma, do not affect the clinical prognosis of patients.

Strain-induced mechanotransduction through primary cilia, extracellular ATP, purinergic calcium signaling, and ERK1/2 transactivates CITED2 and downregulates MMP-1 and MMP-13 gene expression in chondrocytes.

OBJECTIVE: To determine the strain-induced signaling pathways involved in regulating the transactivation of the transcription regulator Cbp/p300 Interacting Transactivator with ED-rich tail 2 (CITED2) and downstream targets in chondrocytes. METHODS: Primary human chondrocytes or C28/I2 chondrocytic cells were subjected to various strain regimes. C57BL/6 mice were subjected to treadmill running. Loss-of-function was carried out using siRNA or inhibitors specific for targeted molecules. mRNA levels were assayed by RT-qPCR, and proteins by western blotting, immunofluorescence, and/or immunohistochemical staining. CITED2 promoter activity was assayed in chondrocytes using wild-type or mutant constructs. RESULTS: Cyclic strain at 5%, 1 Hz induced CITED2 expression and suppressed expression of matrix metalloproteinase (MMP)-1 and -13 at the messenger RNA (mRNA) and protein levels in human chondrocytes. Abolishing primary cilia through knockdown of intraflagellar transport protein (IFT88) attenuated CITED2 gene expression and decreased protein levels. Similar effects were observed with inhibitors of extracellular adenosine triphosphate (ATP) or P2 purinergic receptors, or antagonists of Ca(2+) signaling. Knockdown of IFT88 in articular chondrocytes in vivo diminished treadmill induced-CITED2 expression and upregulated MMPs. Knockdown of hypoxia-inducible factor (HIF)1α, specificity protein 1 (Sp1), or deletion of the shear stress response element (SSRE) in the CITED2 promoter limited cyclic strain-induced transactivation of CITED2. However, the strain induced-transactivation of CITED2 was abolished only on knockdown of HIF1α, Sp1, and SSRE or by loss-of-function of IFT88 or extracellular-signal-regulated kinases (ERK)1/2. CONCLUSIONS: CITED2 transactivation is a critical event in signaling generated by strain and transduced by primary cilia, extracellular ATP, P2 purinergic receptors, and Ca(2+) signaling. Strain-induced CITED2 transactivation requires HIF1α, Sp1, and an intact SSRE and leads to the downregulation of MMPs such as MMP-1 and MMP-13.

Randomized phase III trial of prophylactic cranial irradiation versus observation in patients with fully resected stage IIIA-N2 nonsmall-cell lung cancer and high risk of cerebral metastases after adjuvant chemotherapy.

BACKGROUND: This study compared prophylactic cranial irradiation (PCI) with observation in patients with resected stage IIIA-N2 non-small-cell lung cancer (NSCLC) and high risk of cerebral metastases after adjuvant chemotherapy. PATIENTS AND METHODS: In this open-label, randomized, phase III trial, patients with fully resected postoperative pathologically confirmed stage IIIA-N2 NSCLC and high cerebral metastases risk without recurrence after postoperative adjuvant chemotherapy were randomly assigned to receive PCI (30 Gy in 10 fractions) or observation. The primary end point was disease-free survival (DFS). The secondary end points included the incidence of brain metastases, overall survival (OS), toxicity and quality of life. RESULTS: This trial was terminated early after the random assignment of 156 patients (81 to PCI group and 75 to control group). The PCI group had significantly lengthened DFS compared with the control group, with a median DFS of 28.5 months versus 21.2 months [hazard ratio (HR), 0.67; 95% confidence interval (CI) 0.46-0.98; P = 0.037]. PCI was associated with a decrease in risk of brain metastases (the actuarial 5-year brain metastases rate, 20.3% versus 49.9%; HR, 0.28; 95% CI 0.14-0.57; P < 0.001). The median OS was 31.2 months in the PCI group and 27.4 months in the control group (HR, 0.81; 95% CI 0.56-1.16; P = 0.310). While main toxicities were headache, nausea/vomiting and fatigue in the PCI group, they were generally mild. CONCLUSION: In patients with fully resected postoperative pathologically confirmed stage IIIA-N2 NSCLC and high risk of cerebral metastases after adjuvant chemotherapy, PCI prolongs DFS and decreases the incidence of brain metastases.

Binding modes of GDP, GTP and GNP to NRAS deciphered by using Gaussian accelerated molecular dynamics simulations.

Probing binding modes of GDP, GTP and GNP to NRAS are of significance for understanding the regulation mechanism on the activity of RAS proteins. Four separate Gaussian accelerated molecular dynamics (GaMD) simulations were performed on the apo, GDP-, GTP- and GNP-bound NRAS. Dynamics analyses suggest that binding of three ligands highly affects conformational states of the switch domains from NRAS, which disturbs binding of NRAS to its effectors. The analyses of free energy landscapes (FELs) indicate that binding of GDP, GTP and GNP induces more energetic states of NRAS compared to the apo NRAS but the presence of GNP makes the switch domains more ordered than binding of GDP and GNP. The information of interaction networks of ligands with NRAS reveals that the π-π interaction of residue F28 and the salt bridge interactions of K16 and D119 with ligands stabilize binding of GDP, GTP and GNP to NRAS. Meanwhile magnesium ion plays a bridge role in interactions of ligands with NRAS, which is favourable for associations of GDP, GTP and GNP with NRAS. This work is expected to provide useful information for deeply understanding the function and activity of NRAS.

High resolution micro arthrography of hard and soft tissues in a murine model.

OBJECTIVE: Recent developments on high resolution micro computed tomography (µCT) allow imaging of soft tissues in small animal joints. Nevertheless, µCT images cannot distinguish soft tissues from synovial fluid due to their similar mass density, limiting the 3D assessment of soft tissues volume and thickness. This study aimed to evaluate a lead chromate contrast agent for µCΤ arthrography of rat knee joints ex vivo. DESIGN: Intact tibiofemoral rat joints were injected with the contrast agent at different concentrations and imaged using a µCT at 2.7 µm isotropic voxel size. Cartilage thickness was measured using an automated procedure, validated against histological measurements, and analyzed as a function of µCT image resolution. Changes in hard and soft tissues were also analyzed in tibiofemoral joints 4 weeks after surgical destabilization of the medial meniscus (DMM). RESULTS: The contrast agent diffused well throughout the whole knee cavity without penetrating the tissues, therefore providing high contrast at the boundaries between soft tissues and synovial fluid space. Thickness analysis of cartilage demonstrated a high similarity between histology and µ-arthrography approaches (R(2) = 0.90). Four weeks after surgical DMM, the development of osteophytes (Oph) and cartilage ulcerations was recognizable with µCT, as well as a slight increase in trabecular bone porosity, and decrease in trabecular thickness. CONCLUSIONS: A lead chromate-based contrast agent allowed discriminating the synovial fluid from soft tissues of intact knee joints, and thus made possible both qualitative and quantitative assessment of hard and soft tissues in both intact and DMM tibiofemoral joints using high resolution µCT.

Highly flexible and efficient top-emitting organic light-emitting devices with ultrasmooth Ag anode.

We demonstrate highly flexible and efficient top-emitting organic light-emitting devices (TOLEDs) by using an ultrasmooth Ag anode. A template-stripping process has been employed to create the ultrasmooth Ag anode on a photopolymer substrate. The flexible TOLEDs obtained by this method keep good electroluminescence properties under a small bending radius and after repeated bending. The efficiency of the flexible TOLEDs is improved by 60% compared with the conventional TOLEDs deposited on Si substrate due to the enhanced hole injection from the ultrasmooth anode.

Decoding drug resistant mechanism of V32I, I50V and I84V mutations of HIV-1 protease on amprenavir binding by using molecular dynamics simulations and MM-GBSA calculations.

Mutations V32I, I50V and I84V in the HIV-1 protease (PR) induce drug resistance towards drug amprenavir (APV). Multiple short molecular dynamics (MSMD) simulations and molecular mechanics generalized Born surface area (MM-GBSA) method were utilized to investigate drug-resistant mechanism of V32I, I50V and I84V towards APV. Dynamic information arising from MSMD simulations suggest that V32I, I50V and I84V highly affect structural flexibility, motion modes and conformational behaviours of two flaps in the PR. Binding free energies calculated by MM-GBSA method suggest that the decrease in binding enthalpy and the increase in binding entropy induced by mutations V32I, I50V and I84V are responsible for drug resistance of the mutated PRs on APV. The energetic contributions of separate residues on binding of APV to the PR show that V32I, I50V and I84V highly disturb the interactions of two flaps with APV and mostly drive the decrease in binding ability of APV to the PR. Thus, the conformational changes of two flaps in the PR caused by V32I, I50V and I84V play key roles in drug resistance of three mutated PR towards APV. This study can provide useful dynamics information for the design of potent inhibitors relieving drug resistance.

Percutaneous vertebral augmentation for osteoporotic vertebral compression fractures will increase the number of subsequent fractures at adjacent vertebral levels: a systematic review and meta-analysis.

OBJECTIVE: This study aimed to investigate whether percutaneous vertebral augmentation (PVA) was associated with clinical and radiological subsequent adjacent fractures in patients with osteoporotic vertebral compression fractures. MATERIALS AND METHODS: The systematic review was performed following PRISMA guidelines. Data were retrieved from PubMed, EMBASE, Cochrane Library, Google Scholar, Web of Science, and ClinicalTrial.gov, from database inception to March 2020. Eligible studies were those that assessed subsequent adjacent fractures after PVA in comparison with conservative treatment (CT). The number of patients with adjacent secondary vertebral fractures was calculated, and the pooled risk ratio (RR) with its 95% confidence intervals (95% CI) was used. Moreover, heterogeneity, sensitivity, and publication bias analyses were performed. RESULTS: Twenty-four studies were included finally. Moreover, 20/421 (4.75%) patients from the PVA group and 25/359 (6.96%) patients from the CT group had clinical subsequent adjacent fractures, and 46/440 (10.45%) patients from the PVA group and 36/444 (8.10%) patients from the CT group had radiological subsequent adjacent fractures. Both had no significant difference between the two groups (RR = 0.67, 95% CI [0.38, 1.19], p = 0.17)/(RR = 1.13, 95% CI [0.75, 1.70], p = 0.576). However, the number of fractured vertebrae was higher in the PVA group than in the CT group (RR = 1.41, 95% CI [1.03, 1.93], p = 0.03). A sensitivity analysis did not identify specific trials that seriously deflected. No obvious publication bias was identified. CONCLUSIONS: The systematic review revealed that PVA did not increase the incidence for subsequent adjacent fractures regardless of whether they were clinical or radiological fractures. However, PVA can increase the number of subsequent fractures at adjacent vertebral levels.

Insights into interaction mechanism of inhibitors E3T, E3H and E3B with CREB binding protein by using molecular dynamics simulations and MM-GBSA calculations.

CREB binding protein (CBP) and its paralog E1A binding protein (p300) are related to the development of inflammatory diseases, cancers and other diseases, and have been potential targets for the treatment of human diseases. In this work, interaction mechanism of three small molecules E3T, E3H, and E3B with CBP was investigated by employing molecular dynamics (MD) simulations, principal component analysis (PCA), and molecular mechanics/generalized born surface area (MM-GBSA) method. The results indicate that inhibitor bindings cause the changes of movement modes and structural flexibility of CBP, and van der Waals interactions mostly drive associations of inhibitors with CBP. In the meantime, the results based on inhibitor-residue interactions not only show that eight residues of CBP can strongly interact with E3T, E3H and E3B but also verify that the CH-CH, CH-π, and π-π interactions are responsible for vital contributions in associations of E3T, E3H and E3B with CBP. In addition, the H-O radial distribution functions (RDFs) were computed to assess the stability of hydrogen bonding interactions between inhibitors and CBP, and the obtained information identifies several key hydrogen bonds playing key roles in bindings of E3T, E3H and E3B to CBP. Potential new inhibitors have been proposed.

Insights into effect of the Asp25/Asp25' protonation states on binding of inhibitors Amprenavir and MKP97 to HIV-1 protease using molecular dynamics simulations and MM-GBSA calculations.

The protonation states of two aspartic acids in the catalytic strands of HIV-1 protease (PR) remarkably affect bindings of inhibitors to PR. It is requisite for the design of potent inhibitors towards PR to investigate the influences of Asp25/Asp25' protonated states on dynamics behaviour of PR and binding mechanism of inhibitors to PR. In this work, molecular dynamics (MD) simulations, MM-GBSA method and principal component (PC) analysis were coupled to explore the effect of Asp25/Asp25' protonation states on conformational changes of PR and bindings of Amprenavir and MKP97 to PR. The results show that the Asp25/Asp25' protonation states exert different impacts on structural fluctuations, flexibility and motion modes of PR. Dynamics analysis verifies that Asp25/Asp25' protonated states highly affect conformational dynamics of two flaps in PR. The binding free energy calculations results suggest that the Asp25/Asp25' protonated states obviously strengthen bindings of inhibitors to PR compared to the non-protonation state. Calculations of residue-based free energy decomposition indicate that the Asp25/Asp25' protonation not only disturbs the interaction network of inhibitors with PR but also stabilizes bindings of inhibitors to PR by cancelling the electrostatic repulsive interaction. Therefore, special attentions should be paid to the Asp25/Asp25' protonation in the design of potent inhibitors towards PR.

Decoding molecular mechanism underlying binding of drugs to HIV-1 protease with molecular dynamics simulations and MM-GBSA calculations.

HIV-1 protease (PR) is thought to be efficient targets of anti-AIDS drug design. Molecular dynamics (MD) simulations and multiple post-processing analysis technologies were applied to decipher molecular mechanism underlying binding of three drugs Lopinavir (LPV), Nelfinavir (NFV) and Atazanavir (ATV) to the PR. Binding free energies calculated by molecular mechanics generalized Born surface area (MM-GBSA) suggest that compensation between binding enthalpy and entropy plays a vital role in binding of drugs to PR. Dynamics analyses show that binding of LPV, NFV and ATV highly affects structural flexibility, motion modes and dynamics behaviour of the PR, especially for two flaps. Computational alanine scanning and interaction network analysis verify that although three drugs have structural difference, they share similar binding modes to the PR and common interaction clusters with the PR. The current findings also confirm that residues located interaction clusters, such as Asp25/Asp25', Gly27/Gly27', Ala28/Ala28', Asp29, Ile47/Ile47', Gly49/Gly49', Ile50/Ile50', Val82/Val82' and Ile84/Ile84, can be used as efficient targets of clinically available inhibitors towards the PR.

Polyoxometalate SbW9 regulates proliferation and apoptosis of NSCLC cells via PTEN-dependent AKT signaling pathway.

The article "Polyoxometalate SbW9 regulates proliferation and apoptosis of NSCLC cells via PTEN-dependent AKT signaling pathway, by H.-B. Sun, L. Xu, Z.-X. Wang, Y. Zheng, Y. Zhao, Y.-Y. Yin, X.-L. Han, Z.-N. Xu, published in Eur Rev Med Pharmacol Sci 2019; 23 (18): 7959-7967-PMID: 31599421" has been withdrawn from the authors due to some technical reasons (there are some evident errors and incorrect data). The Publisher apologizes for any inconvenience this may cause. https://www.europeanreview.org/article/19012.

MicroRNA-218 regulates the epithelial-to-mesenchymal transition and the PI3K/Akt signaling pathway to suppress lung adenocarcinoma progression by directly targeting BMI-1.

The article "MicroRNA-218 regulates the epithelial-to-mesenchymal transition and the PI3K/Akt signaling pathway to suppress lung adenocarcinoma progression by directly targeting BMI-1, by L. Xu, H.-B. Sun, Z.-N. Xu, X.-L. Han, Y.-Y. Yin, Y. Zheng, Y. Zhao, Z.-X. Wang, published in Eur Rev Med Pharmacol Sci 2019; 23 (18): 7978-7988-DOI: 10.26355/eurrev_201909_19014-PMID: 31599423" has been withdrawn from the authors due to some technical reasons (there are some errors and  incorrect data). The Publisher apologizes for any inconvenience this may cause. https://www.europeanreview.org/article/19014.

LINC01093 promotes proliferation and invasion of non-small cell lung cancer cells via targeting akt signaling pathway.

The article "LINC01093 promotes proliferation and invasion of non-small cell lung cancer cells via targeting akt signaling pathway, by Z.-X. Wang, Z.-N. Xu, H.-B. Sun, Y. Wang, Z.-F. Han, Y. Yu, X.-L. Han, Y.-Y. Yin, L. Xu, published in Eur Rev Med Pharmacol Sci 2020; 24 (1): 222-229- DOI: 10.26355/eurrev_202001_19914-PMID: 31957835" has been withdrawn from the authors due to some technical reasons (there are some errors and incorrect data). The Publisher apologizes for any inconvenience this may cause. https://www.europeanreview.org/article/19914.

Probing molecular mechanism of inhibitor bindings to bromodomain-containing protein 4 based on molecular dynamics simulations and principal component analysis.

It is well known that bromodomain-containing protein 4 (BRD4) has been thought as a promising target utilized for treating various human diseases, such as inflammatory disorders, malignant tumours, acute myelogenous leukaemia (AML), bone diseases, etc. For this study, molecular dynamics (MD) simulations, binding free energy calculations, and principal component analysis (PCA) were integrated together to uncover binding modes of inhibitors 8P9, 8PU, and 8PX to BRD4(1). The results obtained from binding free energy calculations show that van der Waals interactions act as the main regulator in bindings of inhibitors to BRD4(1). The information stemming from PCA reveals that inhibitor associations extremely affect conformational changes, internal dynamics, and movement patterns of BRD4(1). Residue-based free energy decomposition method was wielded to unveil contributions of independent residues to inhibitor bindings and the data signify that hydrogen bonding interactions and hydrophobic interactions are decisive factors affecting bindings of inhibitors to BRD4(1). Meanwhile, eight residues Trp81, Pro82, Val87, Leu92, Leu94, Cys136, Asn140, and Ile146 are recognized as the common hot interaction spots of three inhibitors with BRD4(1). The results from this work are expected to provide a meaningfully theoretical guidance for design and development of effective inhibitors inhibiting of the activity of BRD4.

Linc00703 suppresses non-small cell lung cancer progression by modulating CyclinD1/CDK4 expression.

OBJECTIVE: The aim of this study was to detect the expression of linc00703 in non-small cell lung cancer (NSCLC), and to explore the biological function and potential molecular mechanism of linc00703 in NSCLC using in vitro experiments. PATIENTS AND METHODS: The carcinoma tissues and para-carcinoma tissues were collected from 32 patients diagnosed with NSCLC, from which the RNA was extracted. The relative expression of linc00703 in NSCLC tissues was detected via quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The NSCLC cells and normal human bronchial epithelial cells were selected, in which the relative expression of linc00703 was determined via qRT-PCR. Next, the linc00703 overexpression plasmids were designed and synthesized, and then transiently transfected into NSCLC cells. After 48 h, the overexpression efficiency was detected. Finally, the changes in cell proliferation, apoptosis, cycle distribution and expressions of downstream molecular markers were determined using cell counting kit-8 (CCK8) assay, colony formation assay, flow cytometry and Western blotting, respectively, after overexpression of linc00703 in NSCLC cells. RESULTS: The results of qRT-PCR revealed that the expression of linc00703 was down-regulated by 5.14 times on average in 29 out of 32 cases of NSCLC tissues, and it was also down-regulated in NSCLC cells. Besides, it was found through CCK-8 assay, colony formation assay and flow cytometry that after overexpression of linc00703 in NSCLC cells, the cell proliferation was inhibited, the apoptosis was enhanced, and the cell cycle was arrested in G1/G0 phase. Furthermore, the results of Western blotting showed that after overexpression of linc00703, the protein expressions of cyclinD1 and cyclin-dependent kinase 4 (CDK4) declined, while those of cyclinE1 and CDK2 did not change. CONCLUSIONS: The expression of linc00703 is down-regulated in NSCLC, and it suppresses the occurrence and development of NSCLC via mediating the expression of cyclinD1/CDK4.

Molecular mechanism of inhibitor bindings to bromodomain-containing protein 9 explored based on molecular dynamics simulations and calculations of binding free energies.

Recently, bromodomain-containing protein 9 (BRD9) has been a prospective therapeutic target for anticancer drug design. Molecular dynamics (MD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method were adopted to explore binding modes of three inhibitors (5SW, 5U2, and 5U6) to BRD9 and identify the hot spot of the inhibitor-BRD9 binding. The results indicate that the inhibitor 5SW has the strongest binding ability to BRD9 among the current three inhibitors. Furthermore, the rank of the binding free energies predicted by MM-GBSA approach agrees with that determined by the experimental values. In addition, inhibitor-residue interactions were computed by using residue-based free-energy decomposition method and the results suggest that residue His42 produces the CH-H interactions, residues Asn100, Ile53 and Val49 produce the CH-[Formula: see text] interactions with three inhibitors and Tyr106, Phe45 and Phe44 generate the π-π interactions with inhibitors. Notably, the residue Asn140 forms hydrogen bonding interactions with three inhibitors. This research is expected to provide useful molecular basis and dynamics information at atomic levels for the design of potent inhibitors inhibiting the activity of BRD9.

Revealing binding selectivity of inhibitors toward bromodomain-containing proteins 2 and 4 using multiple short molecular dynamics simulations and free energy analyses.

Emerging evidences indicate bromodomain-containing proteins 2 and 4 (BRD2 and BRD4) play critical roles in cancers, inflammations, cardiovascular diseases and other pathologies. Multiple short molecular dynamics (MSMD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method were applied to investigate the binding selectivity of three inhibitors 87D, 88M and 89G towards BRD2 over BRD4. The root-mean-square fluctuation (RMSF) analysis indicates that the structural flexibility of BRD4 is stronger than that of BRD2. Moreover the calculated distances between the Cα atoms in the centres of the ZA_loop and BC_loop of BRD4 are also bigger than that of BRD2. The rank of binding free energies calculated using MM-GBSA method agrees well with that determined by experimental data. The results show that 87D can bind more favourably to BRD2 than BRD4, while 88M has better selectivity on BRD4 over BRD2. Residue-based free-energy decomposition method was utilized to estimate the inhibitor-residue interaction spectrum and the results not only identify the hot interaction spots of inhibitors with BRD2 and BRD4, but also demonstrate that several common residues, including (W370, W374), (P371, P375), (V376, V380) and (L381, L385) belonging to (BRD2, BRD4), generate significant binding difference of inhibitors to BRD2 and BRD4.