Browsing by Author "Wang, Bo"
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Item A novel decellularized matrix of Wnt signaling-activated osteocytes accelerates the repair of critical-sized parietal bone defects with osteoclastogenesis, angiogenesis, and neurogenesis(Elsevier, 2022-08-16) Wang, Xiaofang; Ma, Yufei; Chen, Jie; Liu, Yujiao; Liu, Guangliang; Wang, Pengtao; Wang, Bo; Taketo, Makoto M.; Bellido, Teresita; Tu, Xiaolin; Anatomy, Cell Biology and Physiology, School of MedicineCell source is the key to decellularized matrix (DM) strategy. This study compared 3 cell types, osteocytes with/without dominant active Wnt/β-catenin signaling (daCO and WTO) and bone marrow stromal cells (BMSCs) for their DMs in bone repair. Decellularization removes all organelles and >95% DNA, and retained >74% collagen and >71% GAG, maintains the integrity of cell basement membrane with dense boundaries showing oval and honeycomb structure in osteocytic DM and smooth but irregular shape in the BMSC-DM. DM produced higher cell survival rate (90%) and higher proliferative activity. In vitro, daCO-DM induces more and longer stress fibers in BMSCs, conducive to cell adhesion, spreading, and osteogenic differentiation. 8-wk after implantation of the critical-sized parietal bone defect model, daCO-DM formed tight structures, composed of a large number of densely-arranged type-I collagen under polarized light microscope, which is similar to and integrated with host bone. BV/TV (>54%) was 1.5, 2.9, and 3.5 times of WTO-DM, BMSC-DM, and none-DM groups, and N.Ob/T.Ar (3.2 × 102/mm2) was 1.7, 2.9, and 3.3 times. At 4-wk, daCO-DM induced osteoclastogenesis, 2.3 times higher than WTO-DM; but BMSC-DM or none-DM didn't. daCO-DM increased the expression of RANKL and MCSF, Vegfa and Angpt1, and Ngf in BMSCs, which contributes to osteoclastogenesis, angiogenesis, and neurogenesis, respectively. daCO-DM promoted H-type vessel formation and nerve markers β3-tubulin and NeuN expression. Conclusion: daCO-DM produces metabolic and neurovascularized organoid bone to accelerate the repair of bone defects. These features are expected to achieve the effect of autologous bone transplantation, suitable for transformation application.Item Design, synthesis and antimycobacterial activity of novel nitrobenzamide derivatives(Elsevier, 2018) Wang, Hongjian; Lv, Kai; Li, Xiaoning; Wang, Bo; Wang, Apeng; Tao, Zeyu; Geng, Yunhe; Wang, Bin; Huang, Menghao; Liu, Mingliang; Guo, Huiyuan; Lu, Yu; Medicine, School of MedicineWe report herein the design and synthesis of a series of novel nitrobenzamide derivatives. Results reveal that many of them display considerable in vitro antitubercular activity. Four N-benzyl or N-(pyridine-2-yl)methyl 3,5-dinitrobenzamides A6, A11, C1 and C4 have not only the same excellent MIC values of <0.016 μg/mL against both drug-sensitive MTB strain H37Rv and two drug-resistant clinical isolates as PBTZ169 and the lead 1, but also acceptable safety indices (SI > 1500), opening a new direction for further development.Item Enrichment of Chemical Libraries Docked to Protein Conformational Ensembles and Application to Aldehyde Dehydrogenase 2(American Chemical Society, 2014-07-28) Wang, Bo; Buchman, Cameron D.; Li, Liwei; Hurley, Thomas D.; Meroueh, Samy O.; Department of Biochemistry & Molecular Biology, IU School of MedicineMolecular recognition is a complex process that involves a large ensemble of structures of the receptor and ligand. Yet, most structure-based virtual screening is carried out on a single structure typically from X-ray crystallography. Explicit-solvent molecular dynamics (MD) simulations offer an opportunity to sample multiple conformational states of a protein. Here we evaluate our recently developed scoring method SVMSP in its ability to enrich chemical libraries docked to MD structures of seven proteins from the Directory of Useful Decoys (DUD). SVMSP is a target-specific rescoring method that combines machine learning with statistical potentials. We find that enrichment power as measured by the area under the ROC curve (ROC-AUC) is not affected by increasing the number of MD structures. Among individual MD snapshots, many exhibited enrichment that was significantly better than the crystal structure, but no correlation between enrichment and structural deviation from crystal structure was found. We followed an innovative approach by training SVMSP scoring models using MD structures (SVMSPMD). The resulting models were applied to two difficult cases (p38 and CDK2) for which enrichment was not better than random. We found remarkable increase in enrichment power, particularly for p38, where the ROC-AUC increased by 0.30 to 0.85. Finally, we explored approaches for a priori identification of MD snapshots with high enrichment power from an MD simulation in the absence of active compounds. We found that the use of randomly selected compounds docked to the target of interest using SVMSP led to notable enrichment for EGFR and Src MD snapshots. SVMSP rescoring of protein–compound MD structures was applied for the search of small-molecule inhibitors of the mitochondrial enzyme aldehyde dehydrogenase 2 (ALDH2). Rank-ordering of a commercial library of 50 000 compounds docked to MD structures of ALDH2 led to five small-molecule inhibitors. Four compounds had IC50s below 5 μM. These compounds serve as leads for the design and synthesis of more potent and selective ALDH2 inhibitors.Item Essential metabolic, anti-inflammatory, and anti-tumorigenic functions of miR-122 in liver(The Journal of Clinical Investigation, 2012-08-01) Hsu, Shu-hao; Wang, Bo; Kota, Janaiah; Yu, Jianhua; Costinean, Stefan; Kutay, Huban; Yu, Lianbo; Bai, Shoumei; La Perle, Krista; Chivukula, Raghu R.; Mao, Hsiaoyin; Wei, Min; Clark, K. Reed; Mendell, Jerry R.; Caligiuri, Michael A.; Jacob, Samson T.; Mendell, Joshua T.; Ghoshal, KalpanamiR-122, an abundant liver-specific microRNA (miRNA), regulates cholesterol metabolism and promotes hepatitis C virus (HCV) replication. Reduced miR-122 expression in hepatocellular carcinoma (HCC) correlates with metastasis and poor prognosis. Nevertheless, the consequences of sustained loss of function of miR-122 in vivo have not been determined. Here, we demonstrate that deletion of mouse Mir122 resulted in hepatosteatosis, hepatitis, and the development of tumors resembling HCC. These pathologic manifestations were associated with hyperactivity of oncogenic pathways and hepatic infiltration of inflammatory cells that produce pro-tumorigenic cytokines, including IL-6 and TNF. Moreover, delivery of miR-122 to a MYC-driven mouse model of HCC strongly inhibited tumorigenesis, further supporting the tumor suppressor activity of this miRNA. These findings reveal critical functions for miR-122 in the maintenance of liver homeostasis and have important therapeutic implications, including the potential utility of miR-122 delivery for selected patients with HCC and the need for careful monitoring of patients receiving miR-122 inhibition therapy for HCV.Item Exploring a structural protein-drug interactome for new therapeutics in lung cancer(Royal Society of Chemistry, 2014-03-04) Peng, Xiaodong; Wang, Fang; Li, Liwei; Bum-Erdene, Khuchtumur; Xu, David; Wang, Bo; Sinn, Tony; Pollok, Karen; Sandusky, George; Li, Lang; Turchi, John; Jalal, Shadia I.; Meroueh, Samy; Department of Biochemistry & Molecular Biology, IU School of MedicineThe pharmacology of drugs is often defined by more than one protein target. This property can be exploited to use approved drugs to uncover new targets and signaling pathways in cancer. Towards enabling a rational approach to uncover new targets, we expand a structural protein-ligand interactome () by scoring the interaction among 1000 FDA-approved drugs docked to 2500 pockets on protein structures of the human genome. This afforded a drug-target network whose properties compared favorably with previous networks constructed using experimental data. Among drugs with the highest degree and betweenness two are cancer drugs and one is currently used for treatment of lung cancer. Comparison of predicted cancer and non-cancer targets reveals that the most cancer-specific compounds were also the most selective compounds. Analysis of compound flexibility, hydrophobicity, and size showed that the most selective compounds were low molecular weight fragment-like heterocycles. We use a previously-developed screening approach using the cancer drug erlotinib as a template to screen other approved drugs that mimic its properties. Among the top 12 ranking candidates, four are cancer drugs, two of them kinase inhibitors (like erlotinib). Cellular studies using non-small cell lung cancer (NSCLC) cells revealed that several drugs inhibited lung cancer cell proliferation. We mined patient records at the Regenstrief Medical Record System to explore the possible association of exposure to three of these drugs with occurrence of lung cancer. Preliminary in vivo studies using the non-small cell lung cancer (NCLSC) xenograft model showed that losartan- and astemizole-treated mice had tumors that weighed 50 (p < 0.01) and 15 (p < 0.01) percent less than the treated controls. These results set the stage for further exploration of these drugs and to uncover new drugs for lung cancer therapy.Item Molecular Recognition in a Diverse Set of Protein-Ligand Interactions Studied with Molecular Dynamics Simulations and End-Point Free Energy Calculations(ACS Publications, 2013-10-28) Wang, Bo; Li, Liwei; Hurley, Thomas D.; Meroueh, Samy O.; Department of Biochemistry & Molecular Biology, School of MedicineEnd-point free energy calculations using MM-GBSA and MM-PBSA provide a detailed understanding of molecular recognition in protein-ligand interactions. The binding free energy can be used to rank-order protein-ligand structures in virtual screening for compound or target identification. Here, we carry out free energy calculations for a diverse set of 11 proteins bound to 14 small molecules using extensive explicit-solvent MD simulations. The structure of these complexes was previously solved by crystallography and their binding studied with isothermal titration calorimetry (ITC) data enabling direct comparison to the MM-GBSA and MM-PBSA calculations. Four MM-GBSA and three MM-PBSA calculations reproduced the ITC free energy within 1 kcal•mol−1 highlighting the challenges in reproducing the absolute free energy from end-point free energy calculations. MM-GBSA exhibited better rank-ordering with a Spearman ρ of 0.68 compared to 0.40 for MM-PBSA with dielectric constant (ε = 1). An increase in ε resulted in significantly better rank-ordering for MM-PBSA (ρ = 0.91 for ε = 10). But larger ε significantly reduced the contributions of electrostatics, suggesting that the improvement is due to the non-polar and entropy components, rather than a better representation of the electrostatics. SVRKB scoring function applied to MD snapshots resulted in excellent rank-ordering (ρ = 0.81). Calculations of the configurational entropy using normal mode analysis led to free energies that correlated significantly better to the ITC free energy than the MD-based quasi-harmonic approach, but the computed entropies showed no correlation with the ITC entropy. When the adaptation energy is taken into consideration by running separate simulations for complex, apo and ligand (MM-PBSAADAPT), there is less agreement with the ITC data for the individual free energies, but remarkably good rank-ordering is observed (ρ = 0.89). Interestingly, filtering MD snapshots by pre-scoring protein-ligand complexes with a machine learning-based approach (SVMSP) resulted in a significant improvement in the MM-PBSA results (ε = 1) from ρ = 0.40 to ρ = 0.81. Finally, the non-polar components of MM-GBSA and MM-PBSA, but not the electrostatic components, showed strong correlation to the ITC free energy; the computed entropies did not correlate with the ITC entropy.Item A new class of orthosteric uPAR·uPA small-molecule antagonists are allosteric inhibitors of the uPAR·vitronectin interaction(American Chemical Society, 2015-06-19) Liu, Degang; Zhou, Donghui; Wang, Bo; Knabe, William Eric; Meroueh, Samy O.; Department of Biochemistry & Molecular Biology, IU School of MedicineThe urokinase receptor (uPAR) is a GPI-anchored cell surface receptor that is at the center of an intricate network of protein-protein interactions. Its immediate binding partners are the serine proteinase urokinase (uPA), and vitronectin (VTN), a component of the extracellular matrix. uPA and VTN bind at distinct sites on uPAR to promote extracellular matrix degradation and integrin signaling, respectively. Here, we report the discovery of a new class of pyrrolone small-molecule inhibitors of the tight ∼1 nM uPAR·uPA protein-protein interaction. These compounds were designed to bind to the uPA pocket on uPAR. The highest affinity compound, namely 7, displaced a fluorescently labeled α-helical peptide (AE147-FAM) with an inhibition constant Ki of 0.7 μM and inhibited the tight uPAR·uPAATF interaction with an IC50 of 18 μM. Biophysical studies with surface plasmon resonance showed that VTN binding is highly dependent on uPA. This cooperative binding was confirmed as 7, which binds at the uPAR·uPA interface, also inhibited the distal VTN·uPAR interaction. In cell culture, 7 blocked the uPAR·uPA interaction in uPAR-expressing human embryonic kidney (HEK-293) cells and impaired cell adhesion to VTN, a process that is mediated by integrins. As a result, 7 inhibited integrin signaling in MDA-MB-231 cancer cells as evidenced by a decrease in focal adhesion kinase (FAK) phosphorylation and Rac1 GTPase activation. Consistent with these results, 7 blocked breast MDA-MB-231 cancer cell invasion with IC50 values similar to those observed in ELISA and surface plasmon resonance competition studies. Explicit-solvent molecular dynamics simulations show that the cooperativity between uPA and VTN is attributed to stabilization of uPAR motion by uPA. In addition, free energy calculations revealed that uPA stabilizes the VTNSMB·uPAR interaction through more favorable electrostatics and entropy. Disruption of the uPAR·VTNSMB interaction by 7 is consistent with the cooperative binding to uPAR by uPA and VTN. Interestingly, the VTNSMB·uPAR interaction was less favorable in the VTNSMB·uPAR·7 complex suggesting potential cooperativity between 7 and VTN. Compound 7 provides an excellent starting point for the development of more potent derivatives to explore uPAR biology.Item Structure-based computational studies of protein-ligand interactions(2014-12) Wang, Bo; Meroueh, Samy; Pu, Jingzhi; Boyd, Donald B.; Naumann, Christoph A.Molecular recognition plays an important role in biological systems. The purpose of this study was to get a better understanding of the process by incorporating computational tools.Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) method and Molecular Mechanics-Poisson Boltzmann Surface Area (MM-PBSA) method, the end-point free energy calculations provide the binding free energy the can be used to rank-order protein–ligand structures in virtual screening for compound or target identification. Free energy calculations were performed on a diverse set of 11 proteins bound to 14 small molecules was carried out for. A direct comparison was taken between the calculated free energy and the experimental isothermal titration calorimetry (ITC) data. Four and three systems in MM-GBSA and MM-PBSA calculations, respectively, reproduced the ITC free energy within 1 kcal•mol–1. MM-GBSA exhibited better rank-ordering with a Spearman ρ of 0.68 compared to 0.40 for MM-PBSA with dielectric constant (ε = 1). The rank-ordering performance of MM-PBSA improved with increasing ε (ρ = 0.91 for ε = 10), but the contributions of electrostatics became significantly lower at larger ε level, suggesting that the only nonpolar and entropy components contribute to the improved results. Our previously developed scoring function, Support Vector Regression Knowledge-Based (SVRKB), resulted in excellent rank-ordering (ρ = 0.81) when applied into MD simulations. Filtering MD snapshots by prescoring protein–ligand complexes with a machine learning-based approach (SVMSP) resulted in a significant improvement in the MM-PBSA results (ε = 1) from ρ = 0.40 to ρ = 0.81. Finally, the nonpolar components in the free energy calculations showed strong correlation to the ITC free energy while the electrostatic components did not; the computed entropies did not correlate with the ITC entropy. Explicit-solvent molecular dynamics (MD) simulations offer an opportunity to sample multiple conformational states of a protein-ligand system in molecular recognition. SVMSP is a target-specific rescoring method that combines machine learning with statistical potentials. We evaluate the performance of SVMSP in its ability to enrich chemical libraries docked to MD structures. Seven proteins from the Directory of Useful Decoys (DUD) were involved in the study. We followed an innovative approach by training SVMSP scoring models using MD structures (SVMSPMD). The resulting models remarkably improved enrichment in two cases. We also explored approaches for a prior identification of MD snapshots with high enrichment power from an MD simulation in the absence of active compounds. SVMSP rescoring of protein–compound MD structures was applied for the search of small-molecule inhibitors of the mitochondrial enzyme aldehyde dehydrogenase 2 (ALDH2). Rank-ordering of a commercial library of 50,000 compounds docked to MD optimized structures of ALDH2 led to five small-molecule inhibitors. Four compounds had IC50s below 5 μM. These compounds serve as leads for the design and synthesis of more potent and selective ALDH2 inhibitors.Item Tailored motivational interviewing (TMI): Translating basic science in skills acquisition into a behavioral intervention to improve community health worker motivational interviewing competence for youth living with HIV(APA, 2021-12) Naar, Sylvie; Pennar, Amy L.; Wang, Bo; Brogan-Hartlieb, Kathryn; Fortenberry, J. Dennis; Pediatrics, School of MedicineObjective: Interventions to promote evidence-based practices are particularly needed for paraprofessional staff working with minority youth with HIV who have higher rates of HIV infection but lower rates of linkage and retention in care compared to older adults. Utilizing the ORBIT model for behavioral intervention development, we defined and refined a behavioral intervention for providers, Tailored Motivational Interviewing (TMI), to improve provider competence in previous studies (Phase 1a and 1b). The current study focuses on ORBIT Phase 2a-proof of concept. We hypothesized that TMI would be acceptable and feasible and would show a signal of efficacy of improving and maintaining community health worker (CHW) MI competence scores using an innovative statistical method for small N proof-of-concept studies. Method: Longitudinal data were collected from 19 CHWs at 16 youth HIV agencies. CHWs from 8 sites were assigned to the TMI group per the cofunders request. The remaining 8 sites were randomly assigned to TMI or services as usual. MI competence was assessed at baseline and up to 15 times over 2 years. Random coefficient models were utilized to examine time trajectories of competence scores and the impact of the intervention on competence trajectories. Semistructured interviews were conducted to determine barriers and facilitators of TMI. Results: Competence scores in the TMI group significantly increased while the scores of the control group significantly decreased. Further analysis of the intervention group demonstrated that scores significantly increased during the first 3 months after initial workshop and was sustained through the end of the study. Qualitative findings revealed insufficient time and competing priorities as perceived barriers whereas integrating MI into routine agency practices and ongoing training might facilitate implementation. Conclusions: Following a successful proof-of-concept, the next step is a fully randomized pilot study of TMI relative to a control condition in preparation for a stepped-wedge cluster randomized full scale trial.Item Ti3C2Tx solid lubricant coatings in rolling bearings with remarkable performance beyond state-of-the-art materials(Elsevier, 2021-12) Marian, Max; Feile, Klara; Rothammer, Benedict; Bartz, Marcel; Wartzack, Sandro; Seynstahl, Armin; Tremmel, Stephan; Krauß, Sebastian; Merle, Benoit; Böhm, Thomas; Wang, Bo; Wyatt, Brian C.; Anasori, Babak; Rosenkranz, Andreas; Mechanical and Energy Engineering, School of Engineering and TechnologyTwo-dimensional (2D) transition metal carbides, nitrides, and carbonitrides, known as MXenes, are a growing class of 2D materials, which offer great solid lubrication ability for low friction applications due to their weakly bonded multi-layer structure and tribo-layer formation with self-lubricating characteristics. To date, most studies have assessed their tribological response in basic laboratory tests. However, these tests do not adequately reflect the complex geometries, kinematics, and stresses present in machine components. Here, we aim at bridging this gap through assessment of the friction and wear performance of multi-layer Ti3C2Tx MXene solid lubricant coatings used in rolling bearings. MXenes’ tribological response is compared with state-of-the art solid lubricant coatings, which include molybdenum disulfide (MoS2), tungsten-doped hydrogenated amorphous carbon (a-C:H:W), and hydrogen-free, more graphite-like amorphous carbon (a–C). Multi-layer Ti3C2Tx MXene coatings reduce wear on the bearing washers by up to 94%, which can be attributed to the transfer of the lubricious MXene nano-sheets to secondary tribo-contacts of the bearing. While the frictional torque of all solid lubricant coatings is similar during steady-operation, the MXene-coated bearings extend the service life by 30% and 55% compared to MoS2 and DLC, respectively. This contribution demonstrates the ability of MXene solid lubricant coatings to outperform state-of-the-art solid lubricants in dry-running machine components such as rolling bearings.