Separation and detection methods for covalent drug-protein adducts

Covalent binding of reactive metabolites of drugs to proteins has been a predominant hypothesis for the mechanism of toxicity caused by numerous drugs. The development of efficient and sensitive analytical methods for the separation, identification, quantification of drug-protein adducts have important clinical and toxicological implications. In the last few decades, continuous progress in analytical methodology has been achieved with substantial increase in the number of new, more specific and more sensitive methods for drug-protein adducts. The methods used for drug-protein adduct studies include those for separation and for subsequent detection and identification. Various chromatographic (e.g., affinity chromatography, ion-exchange chromatography, and high-performance liquid chromatography) and electrophoretic techniques [e.g., sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), two-dimensional SDS-PAGE, and capillary electrophoresis], used alone or in combination, offer an opportunity to purify proteins adducted by reactive drug metabolites. Conventionally, mass spectrometric (MS), nuclear magnetic resonance, and immunological and radioisotope methods are used to detect and identify protein targets for reactive drug metabolites. However, these methods are labor-intensive, and have provided very limited sequence information on the target proteins adducted, and thus the identities of the protein targets are usually unknown. Moreover, the antibody-based methods are limited by the availability, quality, and specificity of antibodies to protein adducts, which greatly hindered the identification of specific protein targets of drugs and their clinical applications. Recently, the use of powerful MS technologies (e.g., matrix-assisted laser desorption/ionization time-of-flight) together with analytical proteomics have enabled one to separate, identify unknown protein adducts, and establish the sequence context of specific adducts by offering the opportunity to search for adducts in proteomes containing a large number of proteins with protein adducts and unmodified proteins. The present review highlights the separation and detection technologies for drug-protein adducts, with an emphasis on methodology, advantages and limitations to these techniques. Furthermore, a brief discussion of the application of these techniques to individual drugs and their target proteins will be outlined.     

Photoaffinity labeling combined with mass spectrometric approaches as a tool for structural proteomics

Protein chemistry, such as crosslinking and photoaffinity labeling, in combination with modern mass spectrometric techniques, can provide information regarding protein-protein interactions beyond that normally obtained from protein identification and characterization studies. While protein crosslinking can make tertiary and quaternary protein structure information available, photoaffinity labeling can be used to obtain structural data about ligand-protein interaction sites, such as oligonucleotide-protein, drug-protein and protein-protein interaction. In this article, we describe mass spectrometry-based photoaffinity labeling methodologies currently used and discuss their current limitations. We also discuss their potential as a common approach to structural proteomics for providing 3D information regarding the binding region, which ultimately will be used for molecular modeling and structure-based drug design.     

Survey of binding properties of fatty acid-binding proteins. Chromatographic methods

Fatty acid-binding proteins (FABPs) are members of a super family of lipid-binding proteins, and occur intracellularly in vertebrates and invertebrates. This review briefly addresses the structural and molecular properties of the fatty acid binding proteins, together with their potential physiological role. Special attention is paid to the methods used to study the binding characteristics of FABPs. An overview of the conventional (Lipidex, the ADIFAB and ITC) and innovative separation-based techniques (chromatographic and electrophoretic methods) for the study of ligand-protein interactions is presented along with a discussion of their strengths, weak points and potential applications. The best conventional approaches with natural fatty acids have generally revealed only limited information about the interactions of fatty acid proteins. In contrast, high-performance affinity chromatography (HPAC) studies of several proteins provide full information on the binding characteristics. The review uses, as an example, the application of immobilized liver basic FABP as a probe for the study of ligand-protein binding by high-performance affinity chromatography. The FABP from chicken liver has been immobilized on aminopropyl silica and the developed stationary phase was used to examine the enantioselective properties of this protein and to study the binding of drugs to FABP. In order to clarify the retention mechanism, competitive displacement studies were also carried out by adding short chain fatty acids to the mobile phase as displacing agents and preliminary quantitative structure-retention relationship (QSRRs) correlations were developed to describe the nature of the interactions between the chemical structures of the analytes and the observed chromatographic results.The results of these studies may shed light on the proposed roles of these proteins in biological systems and may find applications in medicine and medicinal chemistry. This knowledge will yield a deeper insight into the mechanism of fatty acid binding in order to indisputably show the central role played by FABPs in cellular FA transport and utilization for a proper lipid metabolism.     

Exploring the energy landscapes of molecular recognition by a genetic algorithm: Analysis of the requirements for robust docking of HIV-1 protease and FKBP-12 complexes

Energy landscapes of molecular recognition are explored by performing “semi-rigid” docking of FK-506 and rapamycin with the Fukisawa binding protein (FKBP-12), and flexible docking simulations of the Ro-31-8959 and AG-1284 inhibitors with HIV-1 protease by a genetic algorithm. The requirements of a molecular recognition model to meet thermodynamic and kinetic criteria of ligand-protein docking simultaneously are investigated using a family of simple molecular recognition energy functions. The critical factor that determines the success rate in predicting the structure of ligand-protein complexes is found to be the roughness of the binding energy landscape, in accordance with a minimal frustration principle. The results suggest that further progress in structure prediction of ligand-protein complexes can be achieved by designing molecular recognition energy functions that generate binding landscapes with reduced frustration. © 1996 Wiley-Liss, Inc.     

Estimation of drug-protein binding parameters on assuming the validity of thermodynamic equilibrium

This contribution focuses the reader's attention on the pitfalls usually emerging during the phase of evaluation of experimental data of drug-protein binding studies. To overcome the occurrence of problem(s) apparently defying solution, the concept of "affinity spectra" is recommended to be implemented for data evaluation. A (general) "binding study protocol" is also suggested, which can prevent the formation of inadequate conclusions and the generation of unrealistic drug-protein binding parameters.     

The cytokine storm in COVID-19: Further advances in our understanding the role of specific chemokines involved

SARS-COV-2 infection represents the greatest pandemic of the world, counting daily increasing number of subjects positive to the virus and, sadly, increasing number of deaths. Current studies reported that the cytokine/chemokine network is crucial in the onset and maintenance of the “cytokine storm”, the event occurring in those patients in whom the progression of COVID-19 will progress, in most cases, to a very severe and potentially threatening disease. Detecting a possible “immune signature” in patients, as assessed by chemokines status in patients with COVID-19, could be helpful for individual risk stratification for developing a more or less severe clinical course of the disease. The present review is specifically aimed at overviewing current evidences provided by in vitro and in vivo studies addressing the issue of which chemokines seems to be involved, at least at present, in COVID-19. Currently available experimental and clinical studies regarding those chemokines more deeply studied in COVID-19, with a specific focus on their role in the cytokine storm and ultimately with their ability to predict the clinical course of the disease, will be taken into account. Moreover, similarities and differences between chemokines and cytokines, which both contribute to the onset of the pro-inflammatory loop characterizing SARS-COV-2 infection, will be briefly discussed. Future studies will rapidly accumulate in the next months and their results will hopefully provide more insights as to the complex physiopathology of COVID-19-related cytokine storm. This will likely make the present review somehow “dated” in a short time, but still the present review provides an overview of the scenario of the current knowledge on this topic.     

Recent advances in chromatographic and electrophoretic methods for the study of drug-protein interactions

Drug-protein binding is an important process in determining the activity and fate of a pharmaceutical agent once it has entered the body. This review examines various chromatographic and electrophoretic methods that have been developed to study such interactions. An overview of each technique is presented along with a discussion of its strengths, weaknesses and potential applications. Formats that are discussed include the use of both soluble and immobilized drugs or proteins, and approaches based on zonal elution, frontal analysis or vacancy peak measurements. Furthermore, examples are provided that illustrate the use of these methods in determining the overall extent of drug-protein binding, in examining the displacement of a drug by other agents and in measuring the equilibrium or rate constants for drug-protein interactions. Examples are also given demonstrating how the same methods, particularly when used in high-performance liquid chromatography or capillary electrophoresis systems, can be employed as rapid screening tools for investigating the binding of different forms of a chiral drug to a protein or the binding of different proteins and peptides to a given pharmaceutical agent.     

Social evaluation of municipal solid waste management systems from a life cycle perspective: a systematic literature review

Purpose

The social aspects of municipal solid waste management (MSWM) systems are underpinning their sustainability and effectiveness. The assessment of these systems from a life cycle perspective is widespread throughout environmental life cycle assessment (LCA), but few studies have used social life cycle assessment (S-LCA). The present study is an innovative review with the objective to analyse and describe the current level of development of S-LCA applications in MSWM, and to identify the main methodological challenges and best practices, aiming at recommending approaches to harmonise future S-LCA applications in MSWM.

Materials and methods

A systematic review of the literature found 36 relevant scientific articles. These were submitted to bibliometric and content analysis, which includes an analysis of how methodological aspects of the four phases of S-LCA were applied in comparison with best practice and existing guidelines.

Results and discussion

There was a predominance of case studies in developing countries (59%) and evaluation of the stages of collection/transportation, pre-processing (sorting) and landfilling (55%). There were more studies focusing on stakeholders, “workers” and “local communities” and in the impact subcategories “employment”, “working hours”, “health and safety/working conditions”, “community involvement/participation” and “health and safety/living conditions of community”. There was great variability in the application of the method (47% of the studies included methodological developments). However, the 39% based on UNEP guidelines were closer to a methodological consensus.

Conclusion

In general, studies need more detail and clarity in describing the methodological decisions used. Improvements are needed for issues that limit the S-LCA method, including the difficulties of covering the entire life cycle, relating impacts to the functional unit, standardizing impact assessment methods, addressing allocation and data quality issues and interpretation of results and their limitations. Improvements can be achieved by using participatory methods in the selection of categories, subcategories and impact indicators, as well as by clarifying the definition of a product system and detailing “cut-off criteria” of processes/organizations and the impact of these decisions on results.

     

转录调控研究的方法学进展

基因的表达在多个层次受到严格的控制,其中转录水平的调控是控制基因表达的重要环节之一。近几年,随着分子生物学研究方法的不断发展,转录调控的研究方法学也出现了新的变化。本文综述了基于作者所在课题组对链霉菌次级代谢调控研究过程中优化和改进的转录调控研究方法,如基于SYBR Gold的凝胶阻滞实验,基于荧光标记和毛细管电泳检测的足迹法,基于报告基因的直接调控关系分析等;同时也对研究调控蛋白和靶启动子相互作用的新方法进行了阐述,如表面等离子共振技术和等温滴定量热测定技术等。这些转录调控研究方法的优化和总结,能够帮助研究者开展相关研究。     

Bone morphogenetic protein-2 and tumor growth: Diverse effects and possibilities for therapy

Concern regarding safety with respect to the clinical use of human bone morphogenetic protein-2 (BMP-2) has become an increasingly controversial topic. The role of BMP-2 in carcinogenesis is of particular concern. Although there have been many studies of this topic, the results have been contradictory and confusing. We conducted a systematic review of articles that are relevant to the relationship or effect of BMP-2 on all types of tumors and a total of 97 articles were included. Studies reported in these articles were classified into three major types: “expression studies”, “in vitro studies”, and “in vivo studies”. An obvious pattern was that those works that hypothesize an inhibitory effect for BMP-2 most often examined only the proliferative properties of the tumor cells. This subset of studies also contained an extraordinary number of contradictory findings which made drawing a reliable general conclusion impossible. In general, we support a pro-tumorigenesis role for BMP-2 based on the data from these in vitro cell studies and in vivo animal studies, however, more clinical studies should be carried out to help make a firm conclusion.     

Participation of women medical Physicists in European scientific events: The European experience

PurposeThough the number of women scientists is increasing over the years, studies show that they are still under-represented in leadership roles. The purpose of this work is to establish the percentage of women Medical Physicists (wMPs) that have participated in European scientific events and evaluate it as an indication of the current position of women in the field of Medical Physics in Europe and to propose possible ways to encourage their participation.Materials and MethodsData regarding the participants in European scientific events of Medical Physics were collected. The participants were divided into categories according to the program of the events and their gender was identified. The percentage of wMPs in each category was evaluated.ResultsThe participation of wMPs attending courses is greater than 50%. The categories with the greatest participation are “Organizing Committees”, “Chairpersons-Moderators” and “Oral Presentations”. The categories with the lower participation of wMPs are “Scientific Committee”, “Symposiums” and “Invited Speakers”. None of wMPs were represented as “Course Directors”.ConclusionsThe attendance of wMPs in courses is slightly greater than average. However, wMPs do not have an equally important recognition in special invited roles in conferences. They are still under-represented in “Scientific Committees”, “Invited Speakers”, “Symposiums” and “Course directors”. wMPs should be encouraged to participate even more actively in European conferences and the organizing committees should invite more wMPs in special roles. More studies concerning the status of female MPs in each country separately should be encouraged as they will help in understanding the position of wMPS in Europe.     

Toward prediction of functional protein pockets using blind docking and pocket search algorithms

Location of functional binding pockets of bioactive ligands on protein molecules is essential in structural genomics and drug design projects. If the experimental determination of ligand-protein complex structures is complicated, blind docking (BD) and pocket search (PS) calculations can help in the prediction of atomic resolution binding mode and the location of the pocket of a ligand on the entire protein surface. Whereas the number of successful predictions by these methods is increasing even for the complicated cases of exosites or allosteric binding sites, their reliability has not been fully established. For a critical assessment of reliability, we use a set of ligand-protein complexes, which were found to be problematic in previous studies. The robustness of BD and PS methods is addressed in terms of success of the selection of truly functional pockets from among the many putative ones identified on the surfaces of ligand-bound and ligand-free (holo and apo) protein forms. Issues related to BD such as effect of hydration, existence of multiple pockets, and competition of subsidiary ligands are considered. Practical cases of PS are discussed, categorized and strategies are recommended for handling the different situations. PS can be used in conjunction with BD, as we find that a consensus approach combining the techniques improves predictive power.     

Extending Ethnoprimatology: Human–Alloprimate Relationships in Managed Settings

The majority of studies in ethnoprimatology focus on areas of sympatry where humans and nonhuman primates (hereafter, primates) naturally coexist. We argue that much can be gained by extending the field’s scope to incorporate settings where humans manage most aspects of primates’ lives, such as zoos, laboratories, sanctuaries, and rehabilitation centers (hereafter, managed settings). We suggest that the mixed-methods approach of ethnoprimatology, which facilitates examination of both humans’ and primates’ responses to one another, can reveal not only how humans’ ideas about primates shape management strategies, but also how those management strategies affect primates’ lives. Furthermore, we note that a greater focus on managed settings will strengthen links between ethnoprimatology and primate rights/welfare approaches, and will introduce new questions into discussions of ethics in primatology. For example, managed settings raise questions about when it might be justifiable to restrict primates’ freedom for a “greater good,” and the desirability of making primates’ lives more “natural” even if this would decrease their well-being. Finally, we propose that because ethnoprimatology is premised on challenging false dichotomies between categories of field site—specifically, between “natural” and “unnatural” free-ranging populations—it makes sense for ethnoprimatologists to examine settings in which humans exert considerable control over primates’ lives, given that the distinction between “wild” and “captive” is similarly unclear.     

Ultraviolet resonance Raman study of drug binding in dihydrofolate reductase, gyrase, and catechol O-methyltransferase.

This paper presents a study of the use of ultraviolet resonance Raman (UVRR) spectroscopic methods as a means of elucidating aspects of drug-protein interactions. Some of the RR vibrational bands of the aromatic amino acids tyrosine and tryptophan are sensitive to the microenvironment, and the use of UV excitation radiation allows selective enhancement of the spectral features of the aromatic amino acids, enabling observation specifically of their change in microenvironment upon drug binding. The three drug-protein systems investigated in this study are dihydrofolate reductase with its inhibitor trimethoprim, gyrase with novobiocin, and catechol O-methyltransferase with dinitrocatechol. It is demonstrated that UVRR spectroscopy has adequate sensitivity to be a useful means of detecting drug-protein interactions in those systems for which the electronic absorption of the aromatic amino acids changes because of hydrogen bonding and/or possible dipole-dipole and dipole-polarizability interactions with the ligand.     

Towards understanding the mechanisms of molecular recognition by computer simulations of ligand-protein interactions

The thermodynamic and kinetic aspects of molecular recognition for the methotrexate (MTX)-dihydrofolate reductase (DHFR) ligand-protein system are investigated by the binding energy landscape approach. The impact of 'hot' and 'cold' errors in ligand mutations on the thermodynamic stability of the native MTX-DHFR complex is analyzed, and relationships between the molecular recognition mechanism and the degree of ligand optimization are discussed. The nature and relative stability of intermediates and thermodynamic phases on the ligand-protein association pathway are studied, providing new insights into connections between protein folding and molecular recognition mechanisms, and cooperativity of ligand-protein binding. The results of kinetic docking simulations are rationalized based on the thermodynamic properties determined from equilibrium simulations and the shape of the underlying binding energy landscape. We show how evolutionary ligand selection for a receptor active site can produce well-optimized ligand-protein systems such as MTX-DHFR complex with the thermodynamically stable native structure and a direct transition mechanism of binding from unbound conformations to the unique native structure.     

ABCG2 Dysfunction Increases the Risk of Renal Overload Hyperuricemia

ATP-binding cassette transporter, sub-family G, member 2 (ABCG2/BCRP) is identified as a high-capacity urate exporter, and its dysfunction has an association with serum uric acid levels and gout/hyperuricemia risk. Generally, hyperuricemia has been classified into urate “overproduction type,” “underexcretion type,” and “combined type” based on only renal urate excretion, without considering an extra-renal pathway such as gut excretion. In this study, we investigated the effects of ABCG2 dysfunction on human urate handling and the mechanism of hyperuricemia.

Clinical parameters for urate handling including urinary urate excretion (UUE) were examined in 644 Japanese male outpatients with hyperuricemia. The severity of their ABCG2 dysfunction was estimated by genotype combination of two common ABCG2 variants, nonfunctional Q126X (rs72552713) and half-functional Q141K (rs2231142).

Contrary to the general understanding that ABCG2 dysfunction leads to decreased renal urate excretion, UUE was significantly increased by ABCG2 dysfunction (P = 3.60 × 10^?10). Mild, moderate, and severe ABCG2 dysfunctions significantly raised the risk of “overproduction” hyperuricemia including overproduction type and combined type, conferring risk ratios of 1.36, 1.66, and 2.35, respectively.

The present results suggest that common dysfunctional variants of ABCG2 decrease extra-renal urate excretion including gut excretion and cause hyperuricemia. Thus, “overproduction type” in the current concept of hyperuricemia should be renamed “renal overload type,” which is caused by two different mechanisms, “extra-renal urate underexcretion” and genuine “urate overproduction.”

Our new concept will lead to a more accurate diagnosis and more effective therapeutic strategy for hyperuricemia and gout.     

The Biological Applications of Two Aggregation‐Induced Emission Luminogens

Fluorescence imaging, as a commonly used scientific tool, is widely applied in various biomedical and material structures through visualization technology. Highly selective and sensitive luminescent biological probes, as well as those with good water solubility, are urgently needed for biomedical research. In contrast to the traditional aggregation‐caused quenching of fluorescence, in the unique phenomenon of aggregation‐induced emission (AIE), the individual luminogens have extremely weak or no emissivity because they each have free intramolecular motion; however, when they form aggregates, these components immediately “light up”. Since the discovery of “turn‐on” mechanism, researchers have been studying and applying AIE in a variety of fields to develop more sensitive, selective, and efficient strategies for the AIE dyes. There are numerous advantages to the use of AIE‐based methods, including low background interference, strong contrast, high performance in intracellular imaging, and the ability for long‐term monitoring in vivo. In this review, two typical examples of AIEgens, TPE‐Cy and TPE‐Ph‐In, are described, including their structure properties and applications. Recent progress in the biological applications is mainly focused on. Undoubtedly, in the near future, an increasing number of encouraging and practical ideas will promote the development of more AIEgens for broad use in biomedical applications.     

Mass spectrometry approaches to monitor protein-drug interactions

Recent advances in mass spectrometry-based approaches have enabled the investigation of drug-protein interactions in various ways including the direct detection of drug-target complexes, the examination of drug-induced changes in the target protein structure, and the monitoring of enzymatic target activity. Mass spectrometry-based proteomics methods also permit the unbiased analysis of changes in protein abundance and post-translational modifications induced by drug action. Finally, chemoproteomic affinity enrichment studies enable the deconvolution of drug targets under close to physiological conditions. This review provides an overview of current methods for the characterization of drug-target interactions by mass spectrometry and describes a protocol for chemoproteomic target binding studies using immobilized bioactive molecules.     

Sustainability indicators for municipalities of megacities: Integrating health,safety and environmental performance

The sustainability assessment of public sector organizations including municipalities, with a focus on the integration of health, safety, and environmental (HSE) issues in the context of sustainability performance indicators, has almost remained underexplored. Moreover, since a large number of the activities of megacities’ municipalities have directly to do with HSE issues, there seems to be a substantial gap in the study of megacities and corresponding local public administrations. The present study is aimed at developing a performance evaluation tool, supported by indicators, to monitor the HSE aspects of sustainable development in the municipalities of megacities. To put the proposed tool into practice, a set of performance evaluation indicators is proposed to be adopted in Iranian municipalities, integrated in the megacity of Tehran. The selection process was conducted by employing Delphi technique. In doing so, a 2-round questionnaire was responded by qualified experts to select the most robust indicators of HSE performance and evaluate the priority of each indicator. A total of 80 indicators were generated and grouped into 13 categories, 29 sub-categories, and 7 themes- (Health (H), Safety (S), Environment (E), Health-Safety (HS), Health-Environment (HE), Safety-Environment (SE), and Health, Safety and Environment (HSE)). Findings indicate that amongst the overall average score of the 13 categories, “Fire and emergency response” is the most important category, closely followed by “Waste”, “Transportation”, and “Natural systems” categories. Moreover, among the 7 proposed themes, the integrated “HSE theme”, nearly followed by “safety theme”, plays the most significant role in enhancing the HSE performance of sustainability in Tehran municipalities. It is concluded that in the HSE context of the megacities municipalities under scrutiny, social aspects of sustainability gain more attention in comparison with the environmental ones. Furthermore, in municipalities of megacities, the indicators related to health and safety could be considered as ‘key indicators’ and should be thus classified into independent categories so that their roles can be highlighted in the management and assessment of municipal sustainable development.