SAnDReS 2.0: Development of machine-learning models to explore the scoring function space.

Classical scoring functions may exhibit low accuracy in determining ligand binding affinity for proteins. The availability of both protein-ligand structures and affinity data make it possible to develop machine-learning models focused on specific protein systems with superior predictive performance. Here, we report a new methodology named SAnDReS that combines AutoDock Vina 1.2 with 54 regression methods available in Scikit-Learn to calculate binding affinity based on protein-ligand structures. This approach allows exploration of the scoring function space. SAnDReS generates machine-learning models based on crystal, docked, and AlphaFold-generated structures. As a proof of concept, we examine the performance of SAnDReS-generated models in three case studies. For all three cases, our models outperformed classical scoring functions. Also, SAnDReS-generated models showed predictive performance close to or better than other machine-learning models such as KDEEP, CSM-lig, and ΔVinaRF20. SAnDReS 2.0 is available to download at https://github.com/azevedolab/sandres.

Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking.

Screening already approved drugs for activity against a novel pathogen can be an important part of global rapid-response strategies in pandemics. Such high-throughput repurposing screens have already identified several existing drugs with potential to combat SARS-CoV-2. However, moving these hits forward for possible development into drugs specifically against this pathogen requires unambiguous identification of their corresponding targets, something the high-throughput screens are not typically designed to reveal. We present here a new computational inverse-docking protocol that uses all-atom protein structures and a combination of docking methods to rank-order targets for each of several existing drugs for which a plurality of recent high-throughput screens detected anti-SARS-CoV-2 activity. We demonstrate validation of this method with known drug-target pairs, including both non-antiviral and antiviral compounds. We subjected 152 distinct drugs potentially suitable for repurposing to the inverse docking procedure. The most common preferential targets were the human enzymes TMPRSS2 and PIKfyve, followed by the viral enzymes Helicase and PLpro. All compounds that selected TMPRSS2 are known serine protease inhibitors, and those that selected PIKfyve are known tyrosine kinase inhibitors. Detailed structural analysis of the docking poses revealed important insights into why these selections arose, and could potentially lead to more rational design of new drugs against these targets.

Improved prediction of bilayer and monolayer properties using a refined BMW-MARTINI force field.

Coarse-grained (CG) models allow enlarging the size and time scales that are reachable by atomistic molecular dynamics simulations. A CG force field (FF) for lipids and amino acids that possesses a polarizable water model has been developed following the MARTINI parametrization strategy, the BMW-MARTINI [1]. We tested the BMW-MARTINI FF capability to describe some structural and thermodynamical properties of lipid monolayers and bilayers. We found that, since the surface tension values of oil/water interfaces calculated with the model are not correct, compression isotherms of lipid monolayers present artifacts. Also, this FF predicts DPPC and DAPC bilayers to remain in the Lα phase at temperatures as low as 283K, contrary to the expected from their experimental Tm values. Finally, simulations at constant temperature of bilayers of saturated lipids belonging to PC homologous, showed an increase in the mean molecular area (Mma) upon increasing the chain length, inversely to the experimental observation. We refined BMW-MARTINI FF by modifying as few parameters as possible in order to bring simulated and experimental measurements closer. We have also modified structural parameters of the lipid geometry that do not have direct influence in global properties of the bilayer membranes or monolayers, but serve to approach the obtained CG geometry to atomistic reference values. The refined FF is able to better reproduce phase transition temperatures and Mma for saturated PC bilayers than BMW-MARTINI and MARTINI FF. Finally, the simulated surface pressure-Mma isotherms of PC monolayers resemble the experimental ones and eliminate serious artifacts of previous models.

School shootings during 2013-2015 in the USA.

BACKGROUND: Data on the factors associated with school shootings in the USA are limited. The public conversation has often suggested several factors that may be linked to these events, however with little empirical support. Aiming to fill this gap, we describe the characteristics of school shooting incidents in the USA between 2013 and 2015 and explore whether four factors that represent domains of firearm policy, educational policy and epidemiological risk factors for intentional firearm injuries-background check (BC) policies, per capita mental health expenditures (MHE), K-12 education expenditure (KEE) and urbanicity-were associated with school shootings during this period. METHODS: We searched LexisNexis, a newspaper and broadcast media databases for school shooting incidents from 1 January 2013 to 31 December 2015. Presence of BC laws was extracted from legal information in LexisNexis. State-level covariates of per capita MHE (2013), KEE (2013) and urbanicity (2010) rates were obtained from publicly available data sources. We used negative binomial regression models accounting for clustering by state to explore unadjusted associations between the BC laws, state-level covariates and school shootings to report IRR and 95% CI. RESULTS: We documented 154 school shootings (35, 55 and 64 each year). In unadjusted models, BC for firearm purchase (IRR=0.55, 95% CI 0.39 to 0.76), ammunition purchase (IRR=0.11, 95% CI 0.05 to 0.27), log per capita MHE (IRR=0.58, 95% CI 0.37 to 0.90), log per-capita KEE (IRR=0.09, 9% CI 0.02 to 0.29) and urbanicity (IRR=0.97, 95% CI 0.96 to 0.99) were associated with school shooting. CONCLUSIONS: School shootings are less likely in states with BC laws, higher MHE and KEE, and with greater per cent urban population.

Gun ownership and social gun culture.

We assessed gun ownership rates in 2013 across the USA and the association between exposure to a social gun culture and gun ownership. We used data from a nationally representative sample of 4000 US adults, from 50 states and District of Columbia, aged >18 years to assess gun ownership and social gun culture performed in October 2013. State-level firearm policy information was obtained from the Brady Law Center and Injury Prevention and Control Center. One-third of Americans reported owning a gun, ranging from 5.2% in Delaware to 61.7% in Alaska. Gun ownership was 2.25-times greater among those reporting social gun culture (PR=2.25, 95% CI 2.02 to 2.52) than those who did not. In conclusion, we found strong association between social gun culture and gun ownership. Gun cultures may need to be considered for public health strategies that aim to change gun ownership in the USA.

Interactions of the fatty acid-binding protein ReP1-NCXSQ with lipid membranes. Influence of the membrane electric field on binding and orientation.

The regulatory protein of the squid nerve sodium calcium exchanger (ReP1-NCXSQ) is a 15kDa soluble, intracellular protein that regulates the activity of the Na(+)/Ca(2+) exchanger in the squid axon. It is a member of the cellular retinoic acid-binding proteins family and the fatty acid-binding proteins superfamily. It is composed of ten beta strands defining an inner cavity and a domain of two short alpha helix segments. In this work, we studied the binding and orientation of ReP1-NCXSQ in anionic and zwitterionic lipid membranes using molecular dynamics (MD) simulations. Binding to lipid membranes was also measured by filtration binding assay. ReP1-NCXSQ acquired an orientation in the anionic membranes with the positive end of the macrodipole pointing to the lipid membrane. Potential of mean force calculations, in agreement with experimental measurements, showed that the binding to the anionic interfaces in low ionic strength was stronger than the binding to anionic interfaces in high ionic strength or to zwitterionic membranes. The results of MD showed that the electrostatic binding can be mediated not only by defined patches or domains of basic residues but also by a global asymmetric distribution of charges. A combination of dipole-electric field interaction and local interactions determined the orientation of ReP1-NCXSQ in the interface.

Venlafaxine in management of hot flashes in women with breast cancer: a systematic review and meta-analysis.

Toxicity due to treatment causes a negative impact on quality of life in breast cancer survivors. Hot flash symptoms, described as intense sensations of heat, sweating and flushing occur in more than 50 % of breast cancer patients taking tamoxifen. We hypothesized that venlafaxine, a selective-norepinephrine reuptake inhibitor drug, was effective for reducing patient-reported hot flash scores among women treated for breast cancer compared to other non-hormonal treatments. We searched Medline, Scopus, and Cochrane Central Register of Controlled Trials from inception till May 2015 for venlafaxine (75 mg once daily or greater) with non-hormonal comparators for the treatment of hot flashes in female breast cancer patients. The primary outcome was hot flash score (derived from patient-reported hot flash severity and frequency) in randomized controlled trials. Standardized mean differences (SMD) were calculated for each study due to variation in the outcome measures. Heterogeneity was determined using I (2) statistics, and publication bias was assessed using a contour funnel plot and Egger's tests. Pooled analyses demonstrated that venlafaxine significantly reduced hot flash scores compared to the trial comparators (overall SMD 2.06; 95% confidence interval (CI) [0.40, 3.72]). There was significant heterogeneity among these studies (I (2) = 98.7%, P < 0.001). Asymmetry in the contour funnel plot suggests the presence of publication bias and a trend towards small study effects (Egger's test, P = 0.096). Venlafaxine is efficacious in managing hot flashes among women with breast cancer. This review highlights methodological issues that arise from eligible trials and recommends a collaborative approach in survivorship studies.

Metabolic effects of testosterone added to intensive lifestyle intervention in older men with obesity and hypogonadism.

BACKGROUND: Whether testosterone replacement therapy (TRT) conveys additional cardiometabolic benefit to an intensive lifestyle therapy (LT) in older men with obesity and hypogonadism remains unclear. OBJECTIVE: To determine whether TRT augments the effect of LT on metabolic outcomes in older men with obesity and hypogonadism. DESIGN: Secondary analysis of a randomized, double-blind, placebo-controlled trial. SETTING: Veterans Affairs Medical Center. PARTICIPANTS: 83 older (age ≥ 65 years) men with obesity (BMI ≥ 30 kg/m2) and persistently low AM testosterone (< 10.4 nmol/L) associated with frailty. INTERVENTIONS: LT (weight management and exercise training) plus either testosterone (LT+TRT) or placebo (LT+Pbo) for six months. OUTCOME MEASURES: Primary outcome was change in glycated hemoglobin (HbA1c). Secondary outcomes included changes in other glucometabolic and lipid profile components, liver enzymes, inflammatory markers, adipokines; subcutaneous, visceral, intramuscular, and hepatic fat; blood pressure, and metabolic syndrome score. RESULTS: HbA1c decreased similarly in LT+TRT and LT+Pbo groups (-0.5% vs. -0.6%, respectively; p= 0.35). While TRT showed no synergistic effect with LT on ameliorating secondary outcomes, it eliminated the augmentative effect of LT on high-density lipoprotein cholesterol concentration (5.4 ± 1.0 mg/dL in LT+Pbo group vs. 0.2 ± 1.1 mg/dL in LT+TRT group, p= 0.01) and adiponectin levels (-408 ± 489 ng/mL in TRT+LT group vs 1832 ± 468 ng/mL in LT+Pbo group, p= 0.02). CONCLUSION: In older men with obesity and hypogonadism, adding TRT for six months to LT does not result in further improved cardiometabolic profiles, and could potentially blunt some of the metabolic benefits induced by LT.

Thermodynamic and structural analysis of homodimeric proteins: model of ß-lactoglobulin.

The energetics of protein homo-oligomerization was analyzed in detail with the application of a general thermodynamic model. We have studied the thermodynamic aspects of protein-protein interaction employing ß-lactoglobulin A from bovine milk at pH=6.7 where the protein is mainly in its dimeric form. We performed differential calorimetric scans at different total protein concentration and the resulting thermograms were analyzed with the thermodynamic model for oligomeric proteins previously developed. The thermodynamic model employed, allowed the prediction of the sign of the enthalpy of dimerization, the analysis of complex calorimetric profiles without transitions baselines subtraction and the obtainment of the thermodynamic parameters from the unfolding and the association processes and the compared with association parameters obtained with Isothermal Titration Calorimetry performed at different temperatures. The dissociation and unfolding reactions were also monitored by Fourier-transform infrared spectroscopy and the results indicated that the dimer of ß-lactoglobulin (N(2)) reversibly dissociates into monomeric units (N) which are structurally distinguishable by changes in their infrared absorbance spectra upon heating. Hence, it is proposed that ß-lactoglobulin follows the conformational path induced by temperature:N(2)⇌2N⇌2D. The general model was validated with these results indicating that it can be employed in the study of the thermodynamics of other homo-oligomeric protein systems.

Exploring Scoring Function Space: Developing Computational Models for Drug Discovery.

BACKGROUND: The idea of scoring function space established a systems-level approach to address the development of models to predict the affinity of drug molecules by those interested in drug discovery. OBJECTIVE: Our goal here is to review the concept of scoring function space and how to explore it to develop machine learning models to address protein-ligand binding affinity. METHOD: We searched the articles available in PubMed related to the scoring function space. We also utilized crystallographic structures found in the protein data bank (PDB) to represent the protein space. RESULTS: The application of systems-level approaches to address receptor-drug interactions allows us to have a holistic view of the process of drug discovery. The scoring function space adds flexibility to the process since it makes it possible to see drug discovery as a relationship involving mathematical spaces. CONCLUSION: The application of the concept of scoring function space has provided us with an integrated view of drug discovery methods. This concept is useful during drug discovery, where we see the process as a computational search of the scoring function space to find an adequate model to predict receptor-drug binding affinity.

Insect RDL Receptor Models for Virtual Screening: Impact of the Template Conformational State in Pentameric Ligand-Gated Ion Channels.

The RDL receptor is one of the most relevant protein targets for insecticide molecules. It belongs to the pentameric ligand-gated ion channel (pLGIC) family. Given that the experimental structures of pLGICs are difficult to obtain, homology modeling has been extensively used for these proteins, particularly for the RDL receptor. However, no detailed assessments of the usefulness of homology models for virtual screening (VS) have been carried out for pLGICs. The aim of this study was to evaluate which are the determinant factors for a good VS performance using RDL homology models, specially analyzing the impact of the template conformational state. Fifteen RDL homology models were obtained based on different pLGIC templates representing the closed, open, and desensitized states. A retrospective VS process was performed on each model, and their performance in the prioritization of active ligands was assessed. In addition, the three best-performing models among each of the conformations were subjected to molecular dynamics simulations (MDS) in complex with a representative active ligand. The models showed variations in their VS performance parameters that were related to the structural properties of the binding site. VS performance tended to improve in more constricted binding cavities. The best performance was obtained with a model based on a template in the closed conformation. MDS confirmed that the closed model was the one that best represented the interactions with an active ligand. These results imply that different templates should be evaluated and the structural variations between their channel conformational states should be specially examined, providing guidelines for the application of homology modeling for VS in other proteins of the pLGIC family.

Identification of a site in Sar1 involved in the interaction with the cytoplasmic tail of glycolipid glycosyltransferases.

Glycolipid glycosyltransferases (GGT) are transported from the endoplasmic reticulum (ER) to the Golgi, their site of residence, via COPII vesicles. An interaction of a (R/K)X(R/K) motif at their cytoplasmic tail (CT) with Sar1 is critical for the selective concentration in the transport vesicles. In this work using computational docking, we identify three putative binding pockets in Sar1 (sites A, B, and C) involved in the interaction with the (R/K)X(R/K) motif. Sar1 mutants with alanine replacement of amino acids in site A were tested in vitro and in cells. In vitro, mutant versions showed a reduced ability to bind immobilized peptides with the CT sequence of GalT2. In cells, Sar1 mutants (Sar1(D198A)) specifically affect the exiting of GGT from the ER, resulting in an ER/Golgi concentration ratio favoring the ER. Neither the typical Golgi localization of GM130 nor the exiting and transport of the G protein of the vesicular stomatitis virus were affected. The protein kinase inhibitor H89 produced accumulation of Sec23, Sar1, and GalT2 at the ER exit sites; Sar1(D189A) also accumulated at these sites, but in this case GalT2 remained disperse along ER membranes. The results indicate that amino acids in site A of Sar1 are involved in the interaction with the CT of GGT for concentration at ER exiting sites.

Catalytic and glycan-binding abilities of ppGalNAc-T2 are regulated by acetylation.

Post-translational acetylation is an important molecular regulatory mechanism affecting the biological activity of proteins. Polypeptide GalNAc transferases (ppGalNAc-Ts) are a family of enzymes that catalyze initiation of mucin-type O-glycosylation. All ppGalNAc-Ts in mammals are type II transmembrane proteins having a Golgi lumenal region that contains a catalytic domain with glycosyltransferase activity, and a C-terminal R-type ("ricin-like") lectin domain. We investigated the effect of acetylation on catalytic activity of glycosyltransferase, and on fine carbohydrate-binding specificity of the R-type lectin domain of ppGalNAc-T2. Acetylation effect on ppGalNAc-T2 biological activity in vitro was studied using a purified human recombinant ppGalNAc-T2. Mass spectrometric analysis of acetylated ppGalNAc-T2 revealed seven acetylated amino acids (K103, S109, K111, K363, S373, K521, and S529); the first five are located in the catalytic domain. Specific glycosyltransferase activity of ppGalNAc-T2 was reduced 95% by acetylation. The last two amino acids, K521 and S529, are located in the lectin domain, and their acetylation results in alteration of the carbohydrate-binding ability of ppGalNAc-T2. Direct binding assays showed that acetylation of ppGalNAc-T2 enhances the recognition to αGalNAc residue of MUC1αGalNAc, while competitive assays showed that acetylation modifies the fine GalNAc-binding form of the lectin domain. Taken together, these findings clearly indicate that biological activity (catalytic capacity and glycan-binding ability) of ppGalNAc-T2 is regulated by acetylation.

Binding and interactions of L-BABP to lipid membranes studied by molecular dynamic simulations.

Chicken liver bile acid-binding protein (L-BABP) is a member of the fatty acid-binding proteins super family. The common fold is a beta-barrel of ten strands capped with a short helix-loop-helix motif called portal region, which is involved in the uptake and release of non-polar ligands. Using multiple-run molecular dynamics simulations we studied the interactions of L-BABP with lipid membranes of anionic and zwitterionic phospholipids. The simulations were in agreement with our experimental observations regarding the electrostatic nature of the binding and the conformational changes of the protein in the membrane. We observed that L-BABP migrated from the initial position in the aqueous bulk phase to the interface of anionic lipid membranes and established contacts with the head groups of phospholipids through the side of the barrel that is opposite to the portal region. The conformational changes in the protein occurred simultaneously with the binding to the membrane. Remarkably, these conformational changes were observed in the portal region which is opposite to the zone where the protein binds directly to the lipids. The protein was oriented with its macrodipole aligned in the configuration of lowest energy within the electric field of the anionic membrane, which indicates the importance of the electrostatic interactions to determine the preferred orientation of the protein. We also identified this electric field as the driving force for the conformational change. For all the members of the fatty acid-binding protein family, the interactions with lipid membranes is a relevant process closely related to the uptake, release and transfer of the ligand. The observations presented here suggest that the ligand transfer might not necessarily occur through the domain that directly interacts with the lipid membrane. The interactions with the membrane electric field that determine orientation and conformational changes described here can also be relevant for other peripheral proteins.

Kinetics of lipid-membrane binding and conformational change of L-BABP.

We designed an experimental approach to differentiate the kinetics of protein binding to a lipid membrane from the kinetics of the associated conformational change in the protein. We measured the fluorescence intensity of the single Trp6 in chicken liver bile acid-binding protein (L-BABP) as a function of time after mixing the protein with lipid membranes. We mixed the protein with pure lipid membranes, with lipid membranes in the presence of a soluble quencher, and with lipid membranes containing a fluorescence quencher attached to the lipid polar head group. We fitted simultaneously the experimental curves to a three-state kinetic model. We conclude that in a first step, the binding of L-BABP to the interfacial region of the anionic lipid polar head groups occurred simultaneously with a conformational change to the partly unfolded state. In a second slower step, Trp6 buried within the polar head group region, releasing contacts with the aqueous phase.

Effects of gabergic phenols on the dynamic and structure of lipid bilayers: A molecular dynamic simulation approach.

γ-Aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the vertebrate and invertebrate nervous system. GABAA receptors are activated by GABA and their agonists, and modulated by a wide variety of recognized drugs, including barbiturates, anesthetics, and benzodiazepines. The phenols propofol, thymol, chlorothymol, carvacrol and eugenol act as positive allosteric modulators on GABAA-R receptor. These GABAergic phenols interact with the lipid membrane, therefore, their anesthetic activity could be the combined result of their specific activity (with receptor proteins) as well as nonspecific interactions (with surrounding lipid molecules) modulating the supramolecular organization of the receptor environment. Therefore, we aimed to contribute to a description of the molecular events that occur at the membrane level as part of the mechanism of general anesthesia, using a molecular dynamic simulation approach. Equilibrium molecular dynamics simulations indicate that the presence of GABAergic phenols in a DPPC bilayer orders lipid acyl chains for carbons near the interface and their effect is not significant at the bilayer center. Phenols interacts with the polar interface of phospholipid bilayer, particularly forming hydrogen bonds with the glycerol and phosphate group. Also, potential of mean force calculations using umbrella sampling show that propofol partition is mainly enthalpic driven at the polar region and entropic driven at the hydrocarbon chains. Finally, potential of mean force indicates that propofol partition into a gel DPPC phase is not favorable. Our in silico results were positively contrasted with previous experimental data.

Music as a Therapy to Alleviate Anxiety During Inpatient Rehabilitation for Stroke.

PURPOSE: The aim of the study was to determine if listening to music may reduce anxiety experienced by stroke patients during acute rehabilitation. DESIGN: A prospective, nonblinded, randomized study in an inpatient rehabilitation setting. METHODS: Fifty participants were randomized into two groups: (1) 1 hour of music (intervention) or (2) no music (control). All participants completed pretest anxiety and depression screening and 44 completed the posttest anxiety screening. Differences between groups were determined using chi-square and t tests. FINDINGS: After listening to music for 1 hour, participants who completed the posttest (n = 44) reported significantly less anxiety (p < .0001) compared to before the intervention. The control group showed no difference in their pre- and posttest anxiety scores (p = .84). No differences were determined among age, gender, or diagnostic groups. CONCLUSIONS: These findings demonstrate that music intervention may help lessen anxiety in rehabilitation patients poststroke. CLINICAL RELEVANCE: Offering musical intervention to stroke patients in rehabilitation may lessen symptoms of anxiety.

Relevance of the protein macrodipole in the membrane-binding process. Interactions of fatty-acid binding proteins with cationic lipid membranes.

The fatty acid-binding proteins L-BABP and Rep1-NCXSQ bind to anionic lipid membranes by electrostatic interactions. According to Molecular Dynamics (MD) simulations, the interaction of the protein macrodipole with the membrane electric field is a driving force for protein binding and orientation in the interface. To further explore this hypothesis, we studied the interactions of these proteins with cationic lipid membranes. As in the case of anionic lipid membranes, we found that both proteins, carrying a negative as well as a positive net charge, were bound to the positively charged membrane. Their major axis, those connecting the bottom of the ß-barrel with the α-helix portal domain, were rotated about 180 degrees as compared with their orientations in the anionic lipid membranes. Fourier transform infrared (FTIR) spectroscopy of the proteins showed that the positively charged membranes were also able to induce conformational changes with a reduction of the ß-strand proportion and an increase in α-helix secondary structure. Fatty acid-binding proteins (FABPs) are involved in several cell processes, such as maintaining lipid homeostasis in cells. They transport hydrophobic molecules in aqueous medium and deliver them into lipid membranes. Therefore, the interfacial orientation and conformation, both shown herein to be electrostatically determined, have a strong correlation with the specific mechanism by which each particular FABP exerts its biological function.

Trastuzumab inhibits pituitary tumor cell growth modulating the TGFB/SMAD2/3 pathway.

In pituitary adenomas, early recurrences and resistance to conventional pharmacotherapies are common, but the mechanisms involved are still not understood. The high expression of epidermal growth factor receptor 2 (HER2)/extracellular signal-regulated kinase (ERK1/2) signal observed in human pituitary adenomas, together with the low levels of the antimitogenic transforming growth factor beta receptor 2 (TBR2), encouraged us to evaluate the effect of the specific HER2 inhibition with trastuzumab on experimental pituitary tumor cell growth and its effect on the antiproliferative response to TGFB1. Trastuzumab decreased the pituitary tumor growth as well as the expression of ERK1/2 and the cell cycle regulators CCND1 and CDK4. The HER2/ERK1/2 pathway is an attractive therapeutic target, but its intricate relations with other signaling modulators still need to be unraveled. Thus, we investigated possible cross-talk with TGFB signaling, which has not yet been studied in pituitary tumors. In tumoral GH3 cells, co-incubation with trastuzumab and TGFB1 significantly decreased cell proliferation, an effect accompanied by a reduction in ERK1/2 phosphorylation, an increase of SMAD2/3 activation. In addition, through immunoprecipitation assays, a diminution of SMAD2/3-ERK1/2 and an increase SMAD2/3-TGFBR1 interactions were observed when cells were co-incubated with trastuzumab and TGFB1. These findings indicate that blocking HER2 by trastuzumab inhibited pituitary tumor growth and modulated HER2/ERK1/2 signaling and consequently the anti-mitogenic TGFB1/TBRs/SMADs cascade. The imbalance between HER2 and TGFBRs expression observed in human adenomas and the response to trastuzumab on experimental tumor growth may make the HER2/ERK1/2 pathway an attractive target for future pituitary adenoma therapy.

Coalescence of Nanoclusters Analyzed by Well-Tempered Metadynamics. Comparison with Straightforward Molecular Dynamics.

The coalescence process of two nanoparticles to yield a core-shell structure is analyzed by a well-tempered metadynamics procedure. This methodology has been shown to be useful in understanding the present phenomenon in terms of two collective variables: the distance between the center of mass of the coalescing particles and the gyration radius of the resulting core element. The free-energy contour plots clearly show that the coalescence process involves the deformation of the core material, which is manifested in the residence of the system in regions with a larger gyration radius. Results from molecular dynamics for the same system were found helpful to reach the definition of this second collective variable. The advantages and limitations of the latter approach are discussed.