[Delay in the diagnosis and treatment of five types of cancer in two urban health centres]. / Demora en el diagnóstico y tratamiento de 5 tipos de cáncer en 2 centros de salud urbanos.

OBJECTIVES: To assess the diagnostic (ID) and treatment (IT) intervals of the most prevalent cancers in patients attached to two health centres and to analyse the influence of sociodemographic, clinical and health system (HS) organisational factors. DESIGN: Observational, retrospective, analytical cohort study. SITE: Primary care. Two urban health centres. PARTICIPANTS: Three hundred sixty-five patients diagnosed with colorectal cancer (CRC), breast, lung, prostate or bladder cancer between 1/1/2012 and 31/12/2017. MAIN MEASURES: The medians of ID and IT and the risk (OR) of ID and IT above those medians according to the above factors are compared. The contribution of each process step to ID is analysed. RESULTS: Median ID was 92 days, maximum in prostate cancer (395 days) and minimum in lung (54 days). Factors associated with prolonged ID (OR>92 days) were female sex, CRC or prostate location, localised stage, index primary care (AP) consultation and outpatient diagnostic pathway. Prolonged IT (OR>56 days) was related to CRC or prostate location and outpatient diagnostic route. ID components with the greatest influence on delay were: Primary Care Interval (IAP), Secondary Care Delay (DAS) and Secondary Care Adjunctive Test Delay (DPAS). The contribution of IAP was highest in patients with CRC, lung and bladder. CONCLUSIONS: ID and IT were 92 and 56 days respectively. The ID components with the highest contribution to delay were IAP, DAS and DPAS. Increasing diagnostic capacity in PC and organising specific diagnostic and treatment pathways would shorten these intervals and allow earlier detection.

FoxO1 negatively regulates leptin-induced POMC transcription through its direct interaction with STAT3.

FoxO1, which is up-regulated during early stages of diet-induced leptin resistance, directly interacts with STAT3 and prevents STAT3 from binding to specificity protein 1 (SP1)-pro-opiomelanocortin (POMC) promoter complex, and thereby inhibits STAT3-mediated regulation of POMC transcription. FoxO1 also binds directly to the POMC promoter and negatively regulates its transcription. The present study aims to understand the relative contribution of the two interactions in regulating POMC expression. We studied the structural requirement of FoxO1 for its interaction with STAT3 and POMC promoter, and tested the inhibitory action of FoxO1 mutants by using biochemical assays, molecular biology and computer modelling. FoxO1 mutant with deletion of residues Ala137-Leu160 failed to bind to STAT3 or inhibit STAT3-mediated POMC activation, although its binding to the POMC promoter was unaffected. Further analysis mapped Gly140-Leu160 to be critical for STAT3 binding. The identified region Gly140-Leu160 was conserved among mammalian FoxO1 proteins, and showed a high degree of sequence identity with FoxO3, but not FoxO4. Consistently, FoxO3 could interact with STAT3 and inhibit POMC promoter activity, whereas FoxO4 could not bind to STAT3 or affect POMC promoter activity. We further identified that five residues (Gln145, Arg147, Lys148, Arg153 and Arg154) in FoxO1 were necessary in FoxO1-STAT3 interaction, and mutation of these residues abolished its interaction with STAT3 and inhibition of POMC promoter activity. Finally, a FoxO1-STAT3 interaction interface model generated by computational docking simulations confirmed that the identified residues of FoxO1 were in close proximity to STAT3. These results show that FoxO1 inhibits STAT3-mediated leptin signalling through direct interaction with STAT3.

mAb806 binding to epidermal growth factor receptor: a computational study.

The epidermal growth factor receptor (EGFR) is an important target in the treatment of cancer. A very potent antibody, mAb806, has been developed against overexpressed EGFR and was found to be particularly active in brain tumors. Structural studies reveal that it binds to an epitope on the extracellular region of the EGFR. However, this epitope is cryptic/buried in crystal structures of the active (untethered) and inactive (tethered) EGFR, and it is unclear as to how the antibody interacts with this region. To explore this interaction, we combined molecular docking, steered molecular dynamics, and equilibrium molecular dynamics simulations. Our computational models reveal that the antibody induces local unfolding around the epitope to form the antibody-EGFR complex. In addition, regions in the vicinity of the epitope also modulate the interaction, which are in accordance with several other known antibody-antigen interactions, and offers new possibilities for the design of antibodies with increased potency and specificity for this receptor.

Exploiting protein intrinsic flexibility in drug design.

Molecular recognition in biological systems relies on the existence of specific attractive interactions between two partner molecules. Structure-based drug design seeks to identify and optimize such interactions between ligands and their protein targets. The approach followed in medicinal chemistry follows a combination of careful analysis of structural data together with experimental and/or theoretical studies on the system. This chapter focuses on the fact that a protein is not fully characterized by a single structure, but by an ensemble of states, some of them represent "hidden conformations" with cryptic binding sites. We highlight case studies where both experimental and computational methods have been used to mutually drive each other in an attempt to improve the success of the drug design approaches.Advances in both experimental techniques and computational methods have greatly improved our physico-chemical understanding of the functional mechanisms in biomolecules and opened a debate about the interplay between molecular structure and biomolecular function. The beautiful static pictures of protein structures may have led to neglecting the intrinsic protein flexibility, however we are entering a new era where more sophisticated methods are used to exploit this ability of macromolecules, and this will definitely lead to the inclusion of the notion in the pharmaceutical field of drug design.

[A randomised clinical trial to evaluate the effectiveness of an educational intervention developed for adult asthmatics in a primary care centre]. / Ensayo clínico aleatorio para evaluar la eficacia de una intervención educativa desarrollada en atención primaria sobre asmáticos adultos.

OBJECTIVE: To assess the effect of an educational intervention on asthma control and quality of life. DESIGN: A randomised clinical trial of patients with asthma, with an intervention group (IG) and a control (GC). Asthma control and quality of life was measured in both groups at baseline and every three months for one a year. Blinding was only possible in the collection and analysis of data. LOCATION: Two urban Primary Care Health Centres PARTICIPANTS: A total of 163 patients aged 18 to 55 years were included: 84 were assigned to the IG and 79 to the CG. The follow-up was completed by 104 patients (GI: 55 and GC 49). INTERVENTION GI: Three educational sessions in small interactive groups. The first session was at the beginning of spring, the second 15 days later, and the third 6 months later, to recall the knowledge. MAIN MEASUREMENTS: Asthma control level and quality of life using ACT(Asthma Control Test) and the AQLQ (Asthma Quality of life Questionnaire). RESULTS: In the third month, statistically significant differences were detected in the percentage of patients with good control [(P=.0002), 75% in the GI, and 48.5% in the GC, Relative Risk (RR)=1.6 [1.2 to 2.1], Number Needed to Treat (NNT)=3.8 [2.4 to 9.4], and an improvement in levels of quality of life from baseline (P=.005), RR=2.3 [1.3 to 4.1], NNT: 4.3 [2.6 to 12.4]. No differences were detected in the remaining sessions. CONCLUSIONS: These interventions are effective in improving the control and quality of life in short-term, which can guide us in choosing the best time to do it.

Ras classical effectors: new tales from in silico complexes.

Components of signal transduction pathways have evolved as connected hubs, recognizing several binding partners with remarkable affinities and specificities. Ras is one of these hubs, sensitive to rapid and subtle changes, thus enabling the correct transfer of information. The dynamic nature of such systems makes their structural characterization challenging, despite the vast amount of experimental data available. These data, however, can be used as a restraint for generating comprehensive models of the association of Ras with its effectors. We believe that by following this type of approach, the derived 3D models can provide atomistic understanding of important biological issues, such as how Ras discriminates between the Ras binding domains of its various effectors. The modeled binding interfaces could be used as the starting points for selective modulations of interactions and pathways using small molecules, peptides or mutagenesis.

Evidence of Ongoing Transmission of Zika Virus in Mérida, Mexico.

Since the Zika virus (ZIKV) pandemic in 2015-2017, there has been a near absence of reported cases in the Americas outside of Brazil. However, the conditions for Aedes-borne transmission persist in Latin America, and the threat of ZIKV transmission is increasing as population immunity wanes. Mexico has reported only 70 cases of laboratory-confirmed ZIKV infection since 2020, with no cases recorded in the Yucatán peninsula. Here, we provide evidence of active ZIKV transmission, despite the absence of official case reports, in the city of Mérida, Mexico, the capital of the state of Yucatán. Capitalizing on an existing cohort, we detected cases in participants with symptoms consistent with flavivirus infection from 2021 to 2022. Serum samples from suspected cases were tested for ZIKV RNA by polymerase chain reaction or ZIKV-reactive IgM by ELISA. To provide more specific evidence of exposure, focus reduction neutralization tests were performed on ELISA-positive samples. Overall, we observed 25 suspected ZIKV infections for an estimated incidence of 2.8 symptomatic cases per 1,000 persons per year. Our findings emphasize the continuing threat of ZIKV transmission in the setting of decreased surveillance and reporting.

Educational intervention for the control of Aedes aegypti with Wolbachia in Yucatan, Mexico.

The implementation of new control strategies for Aedes aegypti (Ae. Aegpyti), a vector of dengue, chikungunya, and Zika viruses, requires communities to adopt specific behaviors to achieve the success of these innovations. AIM: We evaluated the effect of an educational intervention based on the Precede-Proceed Model (PPM) and the Diffusion of Innovations Theory (DIT) for the control and prevention of diseases transmitted by Ae. aegypti through release of male mosquitoes infected with Wolbachia bacteria in a suburban town in Yucatan, Mexico. MATERIAL AND METHODS: From July 2019 to February 2020, a quasi-experimental study was carried out through an educational intervention (pre- and post-measurements) using quantitative-qualitative techniques, in a Yucatan suburban town where male mosquitoes with Wolbachia were released for the suppression of Ae. aegypti populations. Eleven educational workshops were attended by heads of household (n = 19) and schoolchildren (n = 11). Other 136 heads of household not attending the workshops received information individually. RESULTS: The educational intervention had a significant effect on the mean scores of the contributing and behavioral factors for adoption of innovation (p < 0.05) in the pre- and post-intervention measurements. CONCLUSION: Innovative methods for the control and prevention of diseases related to Aedes aegypti can be strengthened through educational interventions supported by sound methodologies. DESCRIPTORS: Community health education, Aedes aegypti, Wolbachia, Mexico.

Towards the prediction of protein interaction partners using physical docking.

Deciphering the whole network of protein interactions for a given proteome ('interactome') is the goal of many experimental and computational efforts in Systems Biology. Separately the prediction of the structure of protein complexes by docking methods is a well-established scientific area. To date, docking programs have not been used to predict interaction partners. We provide a proof of principle for such an approach. Using a set of protein complexes representing known interactors in their unbound form, we show that a standard docking program can distinguish the true interactors from a background of 922 non-redundant potential interactors. We additionally show that true interactions can be distinguished from non-likely interacting proteins within the same structural family. Our approach may be put in the context of the proposed 'funnel-energy model'; the docking algorithm may not find the native complex, but it distinguishes binding partners because of the higher probability of favourable models compared with a collection of non-binders. The potential exists to develop this proof of principle into new approaches for predicting interaction partners and reconstructing biological networks.

Macrostate identification from biomolecular simulations through time series analysis.

This paper builds upon the need for a more descriptive and accurate understanding of the landscape of intermolecular interactions, particularly those involving macromolecules such as proteins. For this, we need methods that move away from the single conformation description of binding events, toward a descriptive free energy landscape where different macrostates can coexist. Molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methods provide an excellent approach for such a dynamic description of the binding events. An alternative to the standard method of the statistical reporting of such results is proposed.

SARS-CoV-2 antibody prevalence in a pediatric cohort of unvaccinated children in Mérida, Yucatán, México.

The prevalence of SARS-CoV-2 exposure in children during the global COVID-19 pandemic has been underestimated due to lack of testing and the relatively mild symptoms in adolescents. Understanding the exposure rates in the pediatric population is essential as children are the last to receive vaccines and can act as a source for SARS-CoV-2 mutants that may threaten vaccine escape. This cross-sectional study aims to quantify the prevalence of anti-SARS-CoV-2 serum antibodies in children in a major city in México in the Spring of 2021 and determine if there are any demographic or socioeconomic correlating factors. We obtained socioeconomic information and blood samples from 1,005 children from 50 neighborhood clusters in Mérida, Yucatán, México. We then tested the sera of these participants for anti-SARS-CoV-2 IgG and IgM antibodies using lateral flow immunochromatography. We found that 25.5% of children in our cohort were positive for anti-SARS-CoV-2 antibodies and there was no correlation between age and antibody prevalence. Children that lived with large families were statistically more likely to have antibodies against SARS-CoV-2. Spatial analyses identified two hotspots of high SARS-CoV-2 seroprevalence in the west of the city. These results indicate that a large urban population of unvaccinated children has been exposed to SARS-CoV-2 and that a major correlating factor was the number of people within the child's household with a minor correlation with particular geographical hotspots. There is also a larger population of children that may be susceptible to future infection upon easing of social distancing measures. These findings suggest that in future pandemic scenarios, limited public health resources can be best utilized on children living in large households in urban areas.

A comparison of the dynamics of pantothenate synthetase from M. tuberculosis and E. coli: computational studies.

Pantothenate synthetase (PS) catalyzes the final step of the pantothenate pathway, in which pantothenate is formed from pantoate and ß-alanine in an ATP-dependent reaction. Mycobacterium tuberculosis PS (MTB PS) is functionally a dimer and a potential target for novel antitubercular drugs. Molecular dynamics simulations show that the functional dynamics of the enzyme are dominated by motions of a flexible gate loop in the N-terminal domain and of the C-terminal domain. The gate loop motions dominate in MTB PS while the C-terminal domain motion dominates in Escherichia coli PS. Simulations also show that the correlated motions of the domains are severely compromised in the monomeric forms. Mutations that reduce the mobility of the gate loop in MTB PS and increased it in E. coli PS were designed and validated through simulations.

Synergy between trastuzumab and pertuzumab for human epidermal growth factor 2 (Her2) from colocalization: an in silico based mechanism.

INTRODUCTION: Human epidermal growth factor 2 (Her2), a receptor tyrosine kinase, is overexpressed in breast cancers. It has been successfully targeted by small molecule kinase inhibitors and by antibodies. Recent clinical data show a synergistic response in patients when two antibodies, trastuzumab and pertuzumab, are given in combination. METHODS: This unexpected effect is rationalized through computer models and molecular dynamic simulations by hypothesizing that the two antibodies can co-localize on the same molecule of the Her2 extracellular domain. RESULTS: Simulations suggest that the clinical synergism observed for the two antibodies arises partly from enhanced affinity that originates in cooperative interactions between these two antibodies when they are co-localized on Her2 and "clamp" it; this may inhibit dimerization and possibly higher oligomerizations with neighboring receptors. In the presence of trastuzumab, the receptor becomes highly plastic, especially domains I to III, and this appears to promote increased association with pertuzumab. Further, the presence of pertuzumab evokes novel interactions between the receptor and trastuzumab. Indeed, splicing out of this region in silico results in a big reduction in the interactions of the antibody with the receptor. CONCLUSIONS: If validated, these findings will bring about a new direction in the design of antibodies whereby different epitopes on the same antibody may be targeted to lead to synergistic/cooperative inhibition and contribute to generate more potent therapeutics and to increase clinical efficacy.

An isoform-specific PDZ-binding motif targets type I PIP5 kinase beta to the uropod and controls polarization of neutrophil-like HL60 cells.

Type I phosphatidylinositol 4-phosphate 5-kinase (PIP5KI)-beta participates in establishing polarity during leukocyte chemotaxis. Its final 83 amino acids localize PIP5KIbeta to the uropod of chemotaxing neutrophils and T cells, and interact with ezrin-radixin-moesin (ERM) proteins and EBP50 (4.1-ERM-binding phosphoprotein 50), a scaffold protein with 2 PDZ (PSD-95, disc large, ZO-1) domains. The structural motifs at the PIP5KIbeta C terminus that confer signaling specificity are, nonetheless, unknown. We show that the last 4 residues of PIP5KIbeta constitute an atypical PDZ-binding motif, which steers PIP5KIbeta to the uropod by binding to both EBP50 PDZ domains. Molecular modeling and mutagenesis indicated that PDZ-binding motif is necessary for PIP5KIbeta localization and for chemoattractant-induced neutrophil polarization. Polarity in cells that express PIP5KIbeta mutants lacking the PDZ-binding motif was restored by overexpression of PIP5KIbeta, but not of PIP5KIgamma_i2, another isoform that localizes to the neutrophil uropod. Our results identify an isoform-specific PDZ-binding motif in PIP5KIbeta, which confers specificity for PIP5KIbeta signaling at the uropod during leukocyte chemotaxis.

Insights into the DNA cleavage mechanism of human LINE-1 retrotransposon endonuclease.

The human LINE-1 endonuclease (L1-EN) contributes in defining the genomic integration sites of the abundant human L1 and Alu retrotransposons. LINEs have been considered as possible vehicles for gene delivery and understanding the mechanism of L1-EN could help engineering them as genetic tools. We tested the in vitro activity of point mutants in three L1-EN residues--Asp145, Arg155, Ile204--that are key for DNA cleavage, and determined their crystal structures. The L1-EN structure remains overall unaffected by the mutations, which change the enzyme activity but leave DNA cleavage sequence specificity mostly unaffected. To better understand the mechanism of L1-EN, we performed molecular dynamics simulations using as model the structures of wild type EN-L1, of two betaB6-betaB5 loop exchange mutants we have described previously to be important for DNA recognition, of the R155A mutant from this study, and of the homologous TRAS1 endonuclease: all confirm a rigid scaffold. The simulations crucially indicate that the betaB6-betaB5 loop shows an anticorrelated motion with the surface loops betaA6-betaA5 and betaB3-alphaB1. The latter loop harbors N118, a residue that alters DNA cleavage specificity in homologous endonucleases, and implies that the plasticity and correlated motion of these loops has a functional importance in DNA recognition and binding. To further explore how these loops are possibly involved in DNA binding, we docked computationally two DNA substrates to our structure, one involving a flipped-out nucleotide downstream the scissile phosphodiester; and one not. The models for both scenarios are feasible and agree with the hypotheses derived from the dynamic simulations. The reduced cleavage activity we have observed for the I204Y mutant above however, favors the flipped out nucleotide model.

MINOES: a new approach to select a representative ensemble of structures in NMR studies of (partially) unfolded states. Application to Delta25-PYP.

In nature, some proteins partially unfold under specific environmental conditions. These unfolded states typically consist of a large ensemble of conformations; their proper description is therefore a challenging problem. NMR spectroscopy is particularly well suited for this task: information on conformational preferences can be derived, for example, from chemical shifts or residual dipolar couplings. This information, which is measured as a time- and ensemble-average, can be used to model these states by generating large ensembles of conformations. The challenge is then to select a minimum representative set of conformations out of a large ensemble to represent the unfolded state. We have developed for this purpose an algorithm called MINOES (MINimum Optimal Ensemble Selection), which is based on an iterative procedure based on a driven expansion/contraction selection process. MINOES aims at selecting an optimal and minimal ensemble of conformations that, on average, maximizes the agreement between back-calculated and experimental (NMR) data, without any a-priori assumption about the required ensemble size. This approach is demonstrated by modeling the partially unfolded state of a deletion mutant of the Photoactive Yellow Protein, Delta25-PYP, which has been previously characterized by NMR (Bernard et al., Structure 2005;13:953-962).

Nuclear magnetic resonance-based modeling and refinement of protein three-dimensional structures and their complexes.

Nuclear magnetic resonance (NMR) has become a well-established method to characterize the structures of biomolecules in solution. High-quality structures are now produced, thanks to both experimental and computational developments, allowing the use of new NMR parameters and improved protocols and force fields in structure calculation and refinement. In this chapter, we give a short overview of the various types of NMR data that can provide structural information, and then focus on the structure calculation methodology itself. We discuss and illustrate with tutorial examples both "classical" structure calculation and refinement approaches as well as more recently developed protocols for modeling biomolecular complexes.

Epidemiology of dengue and other arboviruses in a cohort of school children and their families in Yucatan, Mexico: Baseline and first year follow-up.

Dengue is the most prevalent mosquito-borne viral disease of humans and is caused by the four serotypes of dengue virus. To estimate the incidence of dengue and other arboviruses, we analyzed the baseline and first year follow-up of a prospective school-based cohort study and their families in three cities in the state of Yucatan, Mexico. Through enhanced surveillance activities, acute febrile illnesses in the participants were detected and yearly blood samples were collected to evaluate dengue infection incidence. A Cox model was fitted to identify hazard ratios of arboviral infections in the first year of follow-up of the cohort. The incidence of dengue symptomatic infections observed during the first year of follow-up (2015-2016) was 3.5 cases per 1,000 person-years (95% CI: 1.9, 5.9). The incidence of dengue infections was 33.9 infections per 1,000 person-years (95% CI: 31.7, 48.0). The majority of dengue infections and seroconversions were observed in the younger age groups (≤ 14 years old). Other arboviruses were circulating in the state of Yucatan during the study period. The incidence of symptomatic chikungunya infections was 8.6 per 1,000 person-years (95% CI: 5.8, 12.3) and the incidence of symptomatic Zika infections was 2.3 per 1,000 person-years (95% CI: 0.9, 4.5). Our model shows that having a dengue infection during the first year of follow-up was significantly associated with being female, living in Ticul or Progreso, and being dengue naïve at baseline. Age was not significantly associated with the outcome, it was confounded by prior immunity to dengue that increases with age. This is the first report of a cohort in Latin America that provides incidence estimates of the three arboviruses co-circulating in all age groups. This study provides important information for understanding the epidemiology of dengue and other arboviruses and better informing public health policies.

Dengue seroprevalence in a cohort of schoolchildren and their siblings in Yucatan, Mexico (2015-2016).

BACKGROUND: The implementation of vector control interventions and potential introduction new tools requires baseline data to evaluate their direct and indirect effects. The objective of the study is to present the seroprevalence of dengue infection in a cohort of children 0 to 15 years old followed during 2015 to 2016, the risk factors and the role of enhanced surveillance strategies in three urban sites (Merida, Ticul and Progreso) in Yucatan, Mexico. METHODS: A cohort of school children and their family members was randomly selected in three urban areas with different demographic, social conditions and levels of transmission. We included results from 1,844 children aged 0 to 15 years. Serum samples were tested for IgG, NS1 and IgM. Enhanced surveillance strategies were established in schools (absenteeism) and cohort families (toll-free number). RESULTS: Seroprevalence in children 0 to 15 years old was 46.8 (CI 95% 44.1-49.6) with no difference by sex except in Ticul. Prevalence increased with age and was significantly lower in 0 to 5 years old (26.9%, 95% CI:18.4-35.4) compared with 6 to 8 years old (43.9%, 95% CI:40.1-47.7) and 9 to 15 years old (61.4%, 95% CI:58.0-64.8). Sharing the domestic space with other families increased the risk 1.7 times over the individual families that own or rented their house, while risk was significantly higher when kitchen and bathroom were outside. Complete protection with screens in doors and windows decreased risk of infection. Seroprevalence was significantly higher in the medium and high risk areas. CONCLUSIONS: The prevalence of antibodies in children 0 to 15 years in three urban settings in the state of Yucatan describe the high exposure and the heterogenous transmission of dengue virus by risk areas and between schools in the study sites. The enhanced surveillance strategy was useful to improve detection of dengue cases with the coincident transmission of chikungunya and Zika viruses.

Prediction of protein loop geometries in solution.

The ability to determine the structure of a protein in solution is a critical tool for structural biology, as proteins in their native state are found in aqueous environments. Using a physical chemistry based prediction protocol, we demonstrate the ability to reproduce protein loop geometries in experimentally derived solution structures. Predictions were run on loops drawn from (1)NMR entries in the Protein Databank (PDB), and from (2) the RECOORD database in which NMR entries from the PDB have been standardized and re-refined in explicit solvent. The predicted structures are validated by comparison with experimental distance restraints, a test of structural quality as defined by the WHAT IF structure validation program, root mean square deviation (RMSD) of the predicted loops to the original structural models, and comparison of precision of the original and predicted ensembles. Results show that for the RECOORD ensembles, the predicted loops are consistent with an average of 95%, 91%, and 87% of experimental restraints for the short, medium and long loops respectively. Prediction accuracy is strongly affected by the quality of the original models, with increases in the percentage of experimental restraints violated of 2% for the short loops, and 9% for both the medium and long loops in the PDB derived ensembles. We anticipate the application of our protocol to theoretical modeling of protein structures, such as fold recognition methods; as well as to experimental determination of protein structures, or segments, for which only sparse NMR restraint data is available.