Endoscopic submucosal dissection vs. endoscopic mucosal resection in the treatment of early Barrett's neoplasia: Systematic review and meta-analysis.

OBJECTIVES: Endoscopic resection is the preferred approach to treat early Barrett's neoplasia, reducing the need for surgical interventions. However, the best choice between endoscopic mucosal resection (EMR) or endoscopic submucosal dissection (ESD) remains unclear. The study aimed to compare the efficacy and safety of EMR vs. ESD for early Barrett's neoplasia. METHODS: An electronic search was conducted in MEDLINE, Central Cochrane, EMBASE, and LILACS until November 2023. Studies comparing ESD vs. EMR in the treatment of patients with early Barrett's neoplasia were included. This study was performed according to the Preferred Report Items for Systematic Reviews and Meta-Analyses guidelines. The ROBIN-I tool was used to analyze the risk of bias and GRADE to measure the quality of the evidence. RESULTS: A total of 9352 patients from 15 observational studies were included. Patients undergoing ESD had significantly higher rates of en-bloc (odds ratio [OR] 25.96, 95% confidence interval [CI] 13.82, 48.74; I2 = 52%; P < 0.00001) and R0 (OR 5.10, 95% CI 3.29, 7.91; I2 = 73%; P < 0.00001) with a higher risk of adverse events, including bleeding, stricture formation, and perforation. In a subgroup analysis of patients who did not receive radiofrequency ablation, ESD had a lower recurrence rate than EMR (OR 0.22, 95% CI 0.05, 0.94; I2 = 88%; P = 0.04). CONCLUSION: Endoscopic submucosal dissection is more effective than EMR in treating early Barrett's neoplasia at the expense of higher adverse events rates.

CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels.

MOTIVATION: Protein tunnels and channels are key transport pathways that allow ligands to pass between proteins' external and internal environments. These functionally important structural features warrant detailed attention. It is difficult to study the ligand binding and unbinding processes experimentally, while molecular dynamics simulations can be time-consuming and computationally demanding. RESULTS: CaverDock is a new software tool for analysing the ligand passage through the biomolecules. The method uses the optimized docking algorithm of AutoDock Vina for ligand placement docking and implements a parallel heuristic algorithm to search the space of possible trajectories. The duration of the simulations takes from minutes to a few hours. Here we describe the implementation of the method and demonstrate CaverDock's usability by: (i) comparison of the results with other available tools, (ii) determination of the robustness with large ensembles of ligands and (iii) the analysis and comparison of the ligand trajectories in engineered tunnels. Thorough testing confirms that CaverDock is applicable for the fast analysis of ligand binding and unbinding in fundamental enzymology and protein engineering. AVAILABILITY AND IMPLEMENTATION: User guide and binaries for Ubuntu are freely available for non-commercial use at https://loschmidt.chemi.muni.cz/caverdock/. The web implementation is available at https://loschmidt.chemi.muni.cz/caverweb/. The source code is available upon request. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A home-based multidisciplinary programme for Down syndrome adults with muscular temporomandibular disorder.

BACKGROUND: Patients with Down syndrome (DS) present functional and anatomical alterations that may negatively impact their health and quality of life. Down syndrome patients have been shown to have a high prevalence of temporomandibular disorder (TMD), but little is known about the diagnosis, treatment and prevention in these individuals. OBJECTIVE: To evaluate the impact of a home-based multidisciplinary programme on muscular TMD in DS adults. METHODS: After being diagnosed with TMD-related masticatory muscle disorder, 20 adult men and 20 adult women with DS received an educational material with instructions on how to perform daily home facial self-massage and exercises for orofacial and masticatory muscles. Participants were also provided with educational information on TMD. Those who failed to perform at least 50% of the programme (23 days) were considered non-adherent. Oral parafunctional behaviours, facial pressure-pain threshold and maximum mouth opening were assessed at baseline and after the intervention. RESULTS: Twenty-five patients adhered to the programme as opposed to 15 non-adherent patients. Statistically significant improvements in all parameters were observed among adherent patients, except for the number of parafunctions. CONCLUSION: The proposed home-based multidisciplinary programme seemed to be effective in improving some aspects related to muscular TMD in DS adults.

CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories.

Motivation: Studying the transport paths of ligands, solvents, or ions in transmembrane proteins and proteins with buried binding sites is fundamental to the understanding of their biological function. A detailed analysis of the structural features influencing the transport paths is also important for engineering proteins for biomedical and biotechnological applications. Results: CAVER Analyst 2.0 is a software tool for quantitative analysis and real-time visualization of tunnels and channels in static and dynamic structures. This version provides the users with many new functions, including advanced techniques for intuitive visual inspection of the spatiotemporal behavior of tunnels and channels. Novel integrated algorithms allow an efficient analysis and data reduction in large protein structures and molecular dynamic simulations. Availability and implementation: CAVER Analyst 2.0 is a multi-platform standalone Java-based application. Binaries and documentation are freely available at www.caver.cz. Supplementary information: Supplementary data are available at Bioinformatics online.

Arch of cricoid cartilage anatomical variation: morphological and radiological aspects.

The cricoid cartilage serves as an anatomical reference for several surgical procedures for access to the airway. Additionally, it serves as an attachment point for muscles that move the vocal folds. We present a case where the cricoid cartilage arch is divided into distinct superior and inferior arches, with a fibrous membrane between them. We did not find any similar description to this case in the literature, which makes it unique to date. This type of variation is important knowledge for clinicians and surgeons during airway management in the anterior neck region. The presence of this variation could induce an error during a palpation of the thyroid and cricoid cartilages, realized in clinical examination and surgical or emergency procedures.

Surviving a transfixing gunshot wound to the head 70 years ago.

Surviving a gunshot wound to the head is a rare event, particularly in the past when medical treatment was much less advanced than it is today. Moreover, the finding of such a case as an identified specimen within a museum collection is even more uncommon. This led us to report on this unique case in this paper as it poses a challenge to forensic anthropology and provides a unique educational oppourtunity. The skull from the Collection at the Cranium Museum in the Department of Morphology and Genetic at the Federal University of São Paulo (UNIFESP) dates back to 1946. For trauma registration the bone location, severity, trauma aetiology, trauma classification, description, callus formation, periosteal reaction, degree and success of repair, and an estimate of the time elapsed since the trauma, were all assessed. To explore the case radiologically a CT scan of the skull was performed. Considering the survival of the patient and the morphology of the wound it is likely that the injury was caused by a small calibre, low-velocity gunshot. The bullet path shows an almost vertical direction on the right side of the individual's splanchno and neurocranium. The path of the projectile is consistent with a suicide attempt, although the possibility of a homicide simulating a suicide cannot be discarded. This case highlights how informative such cases can be to the practice of forensic anthropology.

Synthesizing the role of epigenetics in the response and adaptation of species to climate change in freshwater ecosystems.

Freshwater ecosystems are amongst the most threatened ecosystems on Earth. Currently, climate change is one of the most important drivers of freshwater transformation and its effects include changes in the composition, biodiversity and functioning of freshwater ecosystems. Understanding the capacity of freshwater species to tolerate the environmental fluctuations induced by climate change is critical to the development of effective conservation strategies. In the last few years, epigenetic mechanisms were increasingly put forward in this context because of their pivotal role in gene-environment interactions. In addition, the evolutionary role of epigenetically inherited phenotypes is a relatively recent but promising field. Here, we examine and synthesize the impacts of climate change on freshwater ecosystems, exploring the potential role of epigenetic mechanisms in both short- and long-term adaptation of species. Following this wrapping-up of current evidence, we particularly focused on bringing together the most promising future research avenues towards a better understanding of the effects of climate change on freshwater biodiversity, specifically highlighting potential molecular targets and the most suitable freshwater species for future epigenetic studies in this context.

Transgenerational Inheritance of DNA Hypomethylation in Daphnia magna in Response to Salinity Stress.

Epigenetic mechanisms have been found to play important roles in environmental stress response and regulation. These can, theoretically, be transmitted to future unexposed generations, yet few studies have shown persisting stress-induced transgenerational effects, particularly in invertebrates. Here, we focus on the aquatic microcrustacean Daphnia, a parthenogenetic model species, and its response to salinity stress. Salinity is a serious threat to freshwater ecosystems and a relevant form of environmental perturbation affecting freshwater ecosystems. We exposed one generation of D. magna to high levels of salinity (F0) and found that the exposure provoked specific methylation patterns that were transferred to the three consequent nonexposed generations (F1, F2, and F3). This was the case for the hypomethylation of six protein-coding genes with important roles in the organisms' response to environmental change: DNA damage repair, cytoskeleton organization, and protein synthesis. This suggests that epigenetic changes in Daphnia are particularly targeted to genes involved in coping with general cellular stress responses. Our results highlight that epigenetic marks are affected by environmental stressors and can be transferred to subsequent unexposed generations. Epigenetic marks could therefore prove to be useful indicators of past or historic pollution in this parthenogenetic model system. Furthermore, no life history costs seem to be associated with the maintenance of hypomethylation across unexposed generations in Daphnia following a single stress exposure.

Effects of a herbicide and copper mixture on the quality of marine plankton.

Pesticides and metals are often used in agriculture and are therefore often simultaneously discharged to nearby estuarine and marine areas. The effects of this organic-inorganic chemical mixture on food quality of aquatic organisms are currently unknown. In this study we test if a mixture of copper (inorganic) and the herbicide Primextra® Gold TZ (organic) affects the quality of the diatom Thalassiosira weissflogii and the copepod Acartia tonsa - two key species that fuel the local food-web. We quantified quality (i.e. energy content as food for the next trophic level) in terms of fatty acids, proteins and thiobarbituric acid reacting substances. We found non-additive effects (positive and negative) of the metal-herbicide mixture on the diatom and copepod species. In general, nutritionally important biochemical parameters of Acartia tonsa were most sensitive to the chemical stressors.

Social representations of nurses concerning domestic violence against women: study with a structural approach. / Representações sociais de enfermeiras acerca da violência doméstica contra a mulher: estudo com abordagem estrutural.

OBJECTIVE: To analyse the structure and contents of the social representations of nurses concerning domestic violence against women. METHODS: This is a qualitative study conducted with 100 nurses between May and September 2014 in two hospitals of Rio Grande, RS, Brazil. Data were collected through evocations and semi-structured interviews. The data were processed in Evoc software and subjected to contextual analysis, respectively. RESULTS: A negative representation was identified with core elements alluding to forms of violence and its judgment, expressed as "physical aggression" and "contempt". In the periphery, "fear" is how the professionals and the victims feel toward the aggressor and "submission" is mentioned as a cause of violence. The term "verbal aggression" in the contrast zone suggests the possibility of a subgroup with a different representation. CONCLUSIONS: A centralised view regarding physical injuries and the culpabilisation of domestic abuse victims can limit care actions, revealing the need to discuss this subject with health workers.

Enzyme Tunnels and Gates As Relevant Targets in Drug Design.

Many enzymes contain tunnels and gates that are essential to their function. Gates reversibly switch between open and closed conformations and thereby control the traffic of small molecules-substrates, products, ions, and solvent molecules-into and out of the enzyme's structure via molecular tunnels. Many transient tunnels and gates undoubtedly remain to be identified, and their functional roles and utility as potential drug targets have received comparatively little attention. Here, we describe a set of general concepts relating to the structural properties, function, and classification of these interesting structural features. In addition, we highlight the potential of enzyme tunnels and gates as targets for the binding of small molecules. The different types of binding that are possible and the potential pharmacological benefits of such targeting are discussed. Twelve examples of ligands bound to the tunnels and/or gates of clinically relevant enzymes are used to illustrate the different binding modes and to explain some new strategies for drug design. Such strategies could potentially help to overcome some of the problems facing medicinal chemists and lead to the discovery of more effective drugs.

Narrow band imaging versus lugol chromoendoscopy to diagnose squamous cell carcinoma of the esophagus: a systematic review and meta-analysis.

BACKGROUND: In the early stage esophageal cancer, changes in the mucosa are subtle and pass unnoticed in endoscopic examinations using white light. To increase sensitivity, chromoscopy with Lugol's solution has been used. Technological advancements have led to the emergence of virtual methods of endoscopic chromoscopy, including narrow band imaging (NBI). NBI enhances the relief of the mucosa and the underlying vascular pattern, providing greater convenience without the risks inherent to the use of vital dye. The purpose of this systematic review and meta-analysis was to evaluate the ability of NBI to diagnose squamous cell carcinoma of the esophagus and to compare it to chromoscopy with Lugol's solution. METHODS: This systematic review included all studies comparing the diagnostic accuracy of NBI and Lugol chromoendoscopy performed to identify high-grade dysplasia and/or squamous cell carcinoma in the esophagus. In the meta-analysis, we calculated and demonstrated sensitivity, specificity, and positive and negative likelihood values in forest plots. We also determined summary receiver operating characteristic (sROC) curves and estimates of the areas under the curves for both per-patient and per-lesion analysis. RESULTS: The initial search identified 7079 articles. Of these, 18 studies were included in the systematic review and 12 were used in the meta-analysis, for a total of 1911 patients. In per-patient and per-lesion analysis, the sensitivity, specificity, and positive and negative likelihood values for Lugol chromoendoscopy were 92% and 98, 82 and 37%, 5.42 and 1.4, and 0.13 and 0.39, respectively, and for NBI were 88 and 94%, 88 and 65%, 8.32 and 2.62, and 0.16 and 0.12, respectively. There was a statistically significant difference in only specificity values, in which case NBI was superior to Lugol chromoendoscopy in both analyses. In the per-patient analysis, the area under the sROC curve for Lugol chromoendoscopy was 0.9559. In the case of NBI, this value was 0.9611; in the per-lesion analysis, this number was 0.9685 and 0.9587, respectively. CONCLUSIONS: NBI was adequate in evaluating the esophagus in order to diagnose high-grade dysplasia and squamous cell carcinoma. In the differentiation of those disorders from other esophageal mucosa alterations, the NBI was shown to be superior than Lugol.

Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling.

The anthropogenic toxic compound 1,2,3-trichloropropane is poorly degradable by natural enzymes. We have previously constructed the haloalkane dehalogenase DhaA31 by focused directed evolution ( Pavlova, M. et al. Nat. Chem. Biol. 2009 , 5 , 727 - 733 ), which is 32 times more active than the wild-type enzyme and is currently the most active variant known against that substrate. Recent evidence has shown that the structural basis responsible for the higher activity of DhaA31 was poorly understood. Here we have undertaken a comprehensive computational study of the main steps involved in the biocatalytic hydrolysis of 1,2,3-trichloropropane to decipher the structural basis for such enhancements. Using molecular dynamics and quantum mechanics approaches we have surveyed (i) the substrate binding, (ii) the formation of the reactive complex, (iii) the chemical step, and (iv) the release of the products. We showed that the binding of the substrate and its transport through the molecular tunnel to the active site is a relatively fast process. The cleavage of the carbon-halogen bond was previously identified as the rate-limiting step in the wild-type. Here we demonstrate that this step was enhanced in DhaA31 due to a significantly higher number of reactive configurations of the substrate and a decrease of the energy barrier to the SN2 reaction. C176Y and V245F were identified as the key mutations responsible for most of those improvements. The release of the alcohol product was found to be the rate-limiting step in DhaA31 primarily due to the C176Y mutation. Mutational dissection of DhaA31 and kinetic analysis of the intermediate mutants confirmed the theoretical observations. Overall, our comprehensive computational approach has unveiled mechanistic details of the catalytic cycle which will enable a balanced design of more efficient enzymes. This approach is applicable to deepen the biochemical knowledge of a large number of other systems and may contribute to robust strategies in the development of new biocatalysts.

Oxidative stress and genotoxicity of an organic and an inorganic nanomaterial to Eisenia andrei: SDS/DDAB nano-vesicles and titanium silicon oxide.

In the past few years the number of studies on the toxic effects of nanomaterials (NMs) in the environment increased significantly. Nonetheless, the data is still scarce, since there is a large number of NMs and new ones are being developed each day. Soils are extremely important for life, and are easily exposed to the released NMs, thus enhanced efforts are needed to study the impacts on soil biota. The objective of the present work was to determine if different concentrations of two NMs, one inorganic (TiSiO4) and other organic (nano-vesicles of sodium sodecyl sulfate/ didodecyl dimethylammonium bromide - SDS/DDAB), are genotoxic to soil invertebrates. Additionally, it was intended to understand whether, in the event of occurring, genotoxicity was caused by the incapability of the cells to deal with the oxidative stress caused by these NMs. With that purpose, Eisenia andrei were exposed for 30 days to the artificial OECD soil contaminated with different concentrations of the NMs being tested. After the exposure, coelomocytes were extracted from earthworms and DNA damage was measured by the comet assay. The activity of antioxidant enzymes (e.g. glutathione peroxidase, glutathione reductase and glutathione-S-Transferase) and lipid peroxidation were also assessed. The results showed that both NMs were genotoxic, particularly TiSiO4 for which significant DNA damages were recorded for concentrations above 444mg of TiSiO4-NM/kg of soildw. Since no statistically significant differences were found in the tested antioxidant enzymes and in lipid peroxidation, the mechanism of genotoxicity of these NMs seemed to be unrelated with oxidative stress.

[Social representation of domestic violence against women among Nursing Technicians and Community Agents]. / Representação social da violência doméstica contra a mulher entre Técnicos de Enfermagem e Agentes Comunitários.

OBJECTIVE: To analyze the social representations of the Nursing Technicians and Community Health Agents about domestic violence against women. METHOD: A qualitative study carried out in the city of Rio Grande, RS, in which evocations and interviews were collected between July and November 2013. For the treatment of data were used the EVOC 2005 software and the context analysis. RESULTS: It is a structured representation, in which the central nucleus contains conceptual, imaging and attitudinal elements, namely: abuse, aggression, physical aggression, cowardice and lack of respect. Such terms were present in the context of the interviews. The professionals acknowledged that violence is not limited to physical aspects and were judgemental about the acts of the aggressor. CONCLUSION: This knowledge may enable the problematization of the studied phenomenon with the team, and facilitate the search for prevention and intervention strategies for victims, offenders and managers of health services.

Risk factors associated with negative in-vivo diagnostic results in bovine tuberculosis-infected cattle in Spain.

BACKGROUND: Despite great effort and investment incurred over decades to control bovine tuberculosis (bTB), it is still one of the most important zoonotic diseases in many areas of the world. Test-and-slaughter strategies, the basis of most bTB eradication programs carried out worldwide, have demonstrated its usefulness in the control of the disease. However, in certain countries, eradication has not been achieved due in part to limitations of currently available diagnostic tests. In this study, results of in-vivo and post-mortem diagnostic tests performed on 3,614 animals from 152 bTB-infected cattle herds (beef, dairy, and bullfighting) detected in 2007-2010 in the region of Castilla y León, Spain, were analyzed to identify factors associated with positive bacteriological results in cattle that were non-reactors to the single intradermal tuberculin test, to the interferon-gamma (IFN-γ) assay, or to both tests applied in parallel (Test negative/Culture + animals, T-/C+). The association of individual factors (age, productive type, and number of herd-tests performed since the disclosure of the outbreak) with the bacteriology outcome (positive/negative) was analyzed using a mixed multivariate logistic regression model. RESULTS: The proportion of non-reactors with a positive post-mortem result ranged from 24.3% in the case of the SIT test to 12.9% (IFN-γ with 0.05 threshold) and 11.9% (95% CI 9.9-11.4%) using both tests in parallel. Older (>4.5 years) and bullfighting cattle were associated with increased odds of confirmed bTB infection by bacteriology, whereas dairy cattle showed a significantly lower risk. Ancillary use of IFN-γ assay reduced the proportion of T-/C + animals in high risk groups. CONCLUSIONS: These results demonstrate the likelihood of positive bacteriological results in non-reactor cattle is influenced by individual epidemiological factors of tested animals. Increased surveillance on non-reactors with an increased probability of being false negative could be helpful to avoid bTB persistence, particularly in chronically infected herds. These findings may aid in the development of effective strategies for eradication of bTB in Spain.

InVADo: Interactive Visual Analysis of Molecular Docking Data.

Molecular docking is a key technique in various fields like structural biology, medicinal chemistry, and biotechnology. It is widely used for virtual screening during drug discovery, computer-assisted drug design, and protein engineering. A general molecular docking process consists of the target and ligand selection, their preparation, and the docking process itself, followed by the evaluation of the results. However, the most commonly used docking software provides no or very basic evaluation possibilities. Scripting and external molecular viewers are often used, which are not designed for an efficient analysis of docking results. Therefore, we developed InVADo, a comprehensive interactive visual analysis tool for large docking data. It consists of multiple linked 2D and 3D views. It filters and spatially clusters the data, and enriches it with post-docking analysis results of protein-ligand interactions and functional groups, to enable well-founded decision-making. In an exemplary case study, domain experts confirmed that InVADo facilitates and accelerates the analysis workflow. They rated it as a convenient, comprehensive, and feature-rich tool, especially useful for virtual screening.

A short-term exposure to saxitoxin triggers a multitude of deleterious effects in Daphnia magna at levels deemed safe for human health.

Harmful algal blooms and the toxins produced during these events are a human and environmental health concern worldwide. Saxitoxin and its derivatives are potent natural aquatic neurotoxins produced by certain freshwater cyanobacteria and marine algae species during these bloom events. Saxitoxins effects on human health are well studied, however its effects on aquatic biota are still largely unexplored. This work aims at evaluating the effects of a pulse acute exposure (24 h) of the model cladoceran Daphnia magna to 30 µg saxitoxin L-1, which corresponds to the safety guideline established by the World Health Organization (WHO) for these toxins in recreational freshwaters. Saxitoxin effects were assessed through a comprehensive array of biochemical (antioxidant enzymes activity and lipid peroxidation), genotoxicity (alkaline comet assay), neurotoxicity (total cholinesterases activity), behavioral (swimming patterns), physiological (feeding rate and heart rate), and epigenetic (total 5-mC DNA methylation) biomarkers. Exposure resulted in decreased feeding rate, heart rate, total cholinesterases activity and catalase activity. Contrarily, other antioxidant enzymes, namely glutathione-S-transferases and selenium-dependent Glutathione peroxidase had their activity increased, together with lipid peroxidation levels. The enhancement of the antioxidant enzymes was not sufficient to prevent oxidative damage, as underpinned by lipid peroxidation enhancement. Accordingly, average DNA damage level was significantly increased in STX-exposed daphnids. Total DNA 5-mC level was significantly decreased in exposed organisms. Results showed that even a short-term exposure to saxitoxin causes significant effects on critical molecular and cellular pathways and modulates swimming patterns in D. magna individuals. This study highlights sub-lethal effects caused by saxitoxin in D. magna, suggesting that these toxins may represent a marked challenge to their thriving even at a concentration deemed safe for humans by the WHO.

Azobenzene-Based Photoswitchable Substrates for Advanced Mechanistic Studies of Model Haloalkane Dehalogenase Enzyme Family.

The engineering of efficient enzymes for large-scale production of industrially relevant compounds is a challenging task. Utilizing rational protein design, which relies on a comprehensive understanding of mechanistic information, holds significant promise for achieving success in this endeavor. Pre-steady-state kinetic measurements, obtained either through fast-mixing techniques or photoswitchable substrates, provide crucial mechanistic insights. The latter approach not only furnishes mechanistic clarity but also affords real-time structural elucidation of reaction intermediates via time-resolved femtosecond crystallography. Unfortunately, only a limited number of such valuable mechanistic probes are available. To address this gap, we applied a multidisciplinary approach, including computational analysis, chemical synthesis, physicochemical property screening, and enzyme kinetics to identify promising candidates for photoswitchable probes. We demonstrate the approach by designing an azobenzene-based photoswitchable substrate tailored for haloalkane dehalogenases, a prototypic class of enzymes pivotal in developing computational tools for rational protein design. The probe was subjected to steady-state and pre-steady-state kinetic analysis, which revealed new insights about the catalytic behavior of the model biocatalysts. We employed laser-triggered Z-to-E azobenzene photoswitching to generate the productive isomer in situ, opening avenues for advanced mechanistic studies using time-resolved femtosecond crystallography. Our results not only pave the way for the mechanistic understanding of this model enzyme family, incorporating both kinetic and structural dimensions, but also propose a systematic approach to the rational design of photoswitchable enzymatic substrates.

CoVAMPnet: Comparative Markov State Analysis for Studying Effects of Drug Candidates on Disordered Biomolecules.

Computational study of the effect of drug candidates on intrinsically disordered biomolecules is challenging due to their vast and complex conformational space. Here, we developed a comparative Markov state analysis (CoVAMPnet) framework to quantify changes in the conformational distribution and dynamics of a disordered biomolecule in the presence and absence of small organic drug candidate molecules. First, molecular dynamics trajectories are generated using enhanced sampling, in the presence and absence of small molecule drug candidates, and ensembles of soft Markov state models (MSMs) are learned for each system using unsupervised machine learning. Second, these ensembles of learned MSMs are aligned across different systems based on a solution to an optimal transport problem. Third, the directional importance of inter-residue distances for the assignment to different conformational states is assessed by a discriminative analysis of aggregated neural network gradients. This final step provides interpretability and biophysical context to the learned MSMs. We applied this novel computational framework to assess the effects of ongoing phase 3 therapeutics tramiprosate (TMP) and its metabolite 3-sulfopropanoic acid (SPA) on the disordered Aß42 peptide involved in Alzheimer's disease. Based on adaptive sampling molecular dynamics and CoVAMPnet analysis, we observed that both TMP and SPA preserved more structured conformations of Aß42 by interacting nonspecifically with charged residues. SPA impacted Aß42 more than TMP, protecting α-helices and suppressing the formation of aggregation-prone ß-strands. Experimental biophysical analyses showed only mild effects of TMP/SPA on Aß42 and activity enhancement by the endogenous metabolization of TMP into SPA. Our data suggest that TMP/SPA may also target biomolecules other than Aß peptides. The CoVAMPnet method is broadly applicable to study the effects of drug candidates on the conformational behavior of intrinsically disordered biomolecules.