Different Types Of Molecules Research Articles

Hydrogen Isotope Labeling of Pharmaceuticals Via Dual Hydrogen Isotope Exchange Pathways Using CdS Quantum Dot Photocatalyst.

Isotopic labeling is a powerful technique extensively used in the pharmaceutical industry. By tracking isotope-labeled molecules, researchers gain unique and invaluable insights into the pharmacokinetics and pharmacodynamics of new drug candidates. Hydrogen isotope labeling is particularly important as hydrogen is ubiquitous in organic molecules in biological systems, and it can be introduced effectively through late-stage hydrogen isotope exchange (HIE). However, hydrogen isotope methods that simultaneously label multiple sites with varying types of C-H bonds in the different types of molecules are still lacking. Herein, we demonstrate a heterogeneous photocatalytic system using a CdS quantum dot catalyst that proceeds via a unique dual HIE pathway mechanism─one occurs in the reaction solution and the other on the catalytic surface─to address it. This unique mechanism unlocked several unique labeling capabilities, including simultaneous labeling of multiple and challenging sites such as secondary α-amino, α-ethereal, allyl, and vinyl sites, providing great versatility in practical uses for pharmaceutical labeling.

Molecular Components and Molecular Modelling for Asphalt: A Review

AbstractAsphalt is a complex, heterogeneous organic mixture increasingly used in modern pavement. With the rising traffic load and sustainable strategies, developing high‐performance asphalt materials becomes crucial, which relies on the understanding of the relationship between the physical chemical properties of asphalt and its constituent molecular components. This work aims to review the progress on the identification of asphalt molecular components, as well as different types of molecules being employed in various molecular dynamics simulations to assess the physical properties of asphalt. The state‐of‐the‐art techniques for the separation of molecular components for asphalt materials are first introduced, followed by common characterization techniques for asphalt molecules and microstructural features, which serve as the foundations for molecular modeling for asphalt materials. Various asphalt molecular models being employed in molecular dynamics simulations are summarised, covering pristine asphalt, modified asphalt, and aged asphalt. Different factors that impact the physical properties of asphalt as uncovered from these simulations are also discussed. This work provides a comprehensive overview on the molecular components of asphalt and the corresponding modeling as atomistic scale, which can guide the preparation of asphalt materials with on‐demand properties for sustainable development.

BioRxToolbox: A computational framework to streamline genetic circuit design in molecular data communications

ABSTRACT Developments in bioengineering and nanotechnology have ignited the research on biological and molecular communication systems. Despite potential benefits, engineering communication systems to carry data signals using biological messenger molecules and engineered cells is challenging. Diffusing molecules may fall behind their schedule to arrive at the receiver, interfering with symbols of subsequent time slots and distorting the signal. Existing theoretical molecular communication models often focus solely on the characteristics of a communication channel and fail to provide an end-to-end system response since they assume a simple thresholding process for a receiver cell and overlook how the receiver can detect the incoming distorted molecular signal. In this paper, we present a model-based and computational framework called BioRxToolbox for designing diffusion-based and end-to-end molecular communication systems coupled with synthetic genetic circuits. We describe a novel framework to encode information as a sequence of bits, each transmitted from the sender as a burst of molecules, control cellular behavior at the receiver, and minimize cellular signal interference by employing equalization techniques from communication theory. This approach allows the encoding and decoding of data bits efficiently using two different types of molecules that act as the data carrier and the antagonist to cancel out the heavy tail of the former. Here, BioRxToolbox is demonstrated using a biological design and computational simulations for various communication scenarios. This toolbox facilitates automating the choice of communication parameters and identifying the best communication scenarios that can produce efficient cellular signals.

High Expression of Immune Checkpoint Molecules in Different Types of Thyroid Cancer.

This study aimed to investigate the expression of programmed cell death protein-1 (PD-1) and its ligand (PD-L1) immune checkpoint molecules in thyroid carcinomas and determine their association with the clinicopathological characteristics of patients. Thyroid tissue specimens from100 patients diagnosed with primary thyroid carcinomas including papillary thyroid carcinoma (PTC), follicular thyroid carcinoma (FTC), medullary thyroid carcinoma (MTC), and anaplastic thyroid carcinoma (ATC) were collected. Sections were prepared from formalin-fixed paraffin-embedded samples, and PD-1 and PD-L1 expressions were examined using immunohistochemistry. PD-1 was detected in tumor-infiltrating lymphocytes (TILs) in 88% of the patients and tumor cells in 28% of the patients with 10% in PTC, 5% in FTC, 5% in MTC, and 8% in ATC). PD-L1 was found in tumor cells and TILs in 30% and 79% of the patients, respectively. Moreover, a significant difference was observed in PD-1 and PD-L1 expression between tumor cells and TILs across different tumor types. However, their expression in tumor cells and TILs was significantly higher in ATC compared to other tumor types. Additionally, the expression of PD-1 and PD-L1 was significantly associated with an advanced stage, higher tumor size, tumor necrosis, and mitosis. A significant positive correlation was also observed between the expression of PD-1 and PD-L1 in tumor cells and TILs. The higher expression of PD-1 and PD-L1 may contribute to tumor progression. Therefore, combinational immunotherapy by these immune checkpoint inhibitors might be a promising strategy for clinical improvement in patients with thyroid cancer, especially those with ATC.

Membrane-localized magnetic hyperthermia promotes intracellular delivery of cell-impermeant probes.

In this work, we report the disruptive use of membrane-localized magnetic hyperthermia to promote the internalization of cell-impermeant probes. Under an alternating magnetic field, magnetic nanoparticles (MNPs) immobilized on the cell membrane via bioorthogonal click chemistry act as nanoheaters and lead to the thermal disruption of the plasma membrane, which can be used for internalization of different types of molecules, such as small fluorescent probes and nucleic acids. Noteworthily, no cell death, oxidative stress and alterations of the cell cycle are detected after the thermal stimulus, although cells are able to sense and respond to the thermal stimulus through the expression of different types of heat shock proteins (HSPs). Finally, we demonstrate the utility of this approach for the transfection of cells with a small interference RNA (siRNA), revealing a similar efficacy to a standard transfection method based on the use of cationic lipid-based reagents (such as Lipofectamine), but with lower cell toxicity. These results open the possibility of developing new procedures for "opening and closing" cellular membranes with minimal disturbance of cellular integrity. This on-demand modification of cell membrane permeability could allow the direct intracellular delivery of biologically relevant (bio)molecules, drugs and nanomaterials, thus overcoming traditional endocytosis pathways and avoiding endosomal entrapment.

Mechanism simulation of polar and nonpolar organic solvent vapor adsorption on a multiwall carbon nanotubes paper gas sensor.

We investigate the adsorption behavior of polar and nonpolar molecules on carbon nanotube interfaces through computational simulations. Gaussian 16 was utilized to calculate the total energy of each possible molecular structure and analyze the adsorption mechanisms in stacked and inline configurations. The study reveals that nonpolar molecules favor stacked adsorption on two graphene interfaces, while polar molecules prefer inline adsorption. The findings suggest that inline adsorption of polar molecules results in minimal changes to the local dielectric constant, which may explain the absence of multi-step adsorption isotherms. The research examines the stability and energetics of molecular adsorption on graphene layers simulating CNT interfaces. Different types of molecules (polar and nonpolar) exhibit distinct adsorption behaviors, with nonpolar molecules aligning with the IUPAC type VI isotherm model and polar molecules following the Langmuir isotherm model (IUPAC type I). This study provides insight into how molecules are likely to adsorb on CNT surfaces and the impact on the local dielectric constant. This understanding has implications for the design and optimization of CNT-based sensors, particularly in detecting organic solvents and gases in various environments.

Dynamic Change Characteristics and Main Controlling Factors of Pore Gas and Water in Tight Reservoir of Yan’an Gas Field in Ordos Basin

Tight sandstone gas has become an important field of natural gas development in China. The tight sandstone gas resources of Yan’an gas field in Ordos Basin have made great progress. However, due to the complex gas–water relationship, its exploration and development have been seriously restricted. The occurrence state of water molecules in tight reservoirs, the dynamic change characteristics of gas–water two-phase seepage and its main controlling factors are still unclear. In this paper, the water-occurrence state, gas–water two-phase fluid distribution and dynamic change characteristics of different types of tight reservoir rock samples in Yan’an gas field were studied by means of water vapor isothermal adsorption experiment and nuclear magnetic resonance methane flooding experiment, and the main controlling factors were discussed. The results show that water molecules in different types of tight reservoirs mainly occur in clay minerals and their main participation is in the formation of fractured and parallel plate pores. The adsorption characteristics of water molecules conform to the Dent model; that is, the adsorption is divided into single-layer adsorption, multi-layer adsorption and capillary condensation. In mudstone, limestone and fine sandstone, water mainly occurs in small-sized pores with a diameter of 0.001 μm–0.1 μm. The dynamic change characteristics of gas and water are not obvious and no longer change under 7 MPa displacement pressure, and the gas saturation is low. The gas–water dynamic change characteristics of conglomerate and medium-coarse sandstone are obvious and no longer change under 9 MPa displacement pressure. The gas saturation is high, and the water molecules mainly exist in large-sized pores with a diameter of 0.1 μm–10 μm. The development of organic matter in tight reservoir mudstone is not conducive to the occurrence of water molecules. Clay minerals are the main reason for the high water saturation of different types of tight reservoir rocks. Tight rock reservoirs with large pore size and low clay mineral content are more conducive to natural gas migration and occurrence, which is conducive to tight sandstone gas accumulation.

Design of targeted antiviral polypeptides specific to SARS-CoV-2. Challenges and prospects

The COVID-19 epidemic demanded the rapid development of high-affinity molecules of different types aimed at a single target, the S-protein of SARS-CoV-2. The simultaneous development and testing of such molecules provide a unique opportunity to compare the features of biotechnological platforms for creating therapeutic proteins. This review considers classical antibodies, variable lymphocyte receptors, single-domain antibodies, and artificial scaffolds (DARPins, affibodies, VH), that are compared in terms of affinity, neutralizing activity, size and compatibility with different delivery methods. It can be concluded that all platforms used have produced high-affinity proteins that specifically bind to the coronavirus S-protein. The highest affinity of the targeting molecules with the virus protein was achieved by developing classical antibodies, nanobodies and by combining several binding modules into multivalent constructs with high avidity. Based on the results of <i>in vivo</i> experiments, it can be concluded that a high affinity of the therapeutic protein for the surface antigens of SARS-CoV-2 is a necessary but not sufficient condition for suppression of COVID-19 due to the peculiarities of the biology of this virus. The experience gained in the development of therapeutic agents against coronavirus will be useful for design of effective targeted drugs for the treatment of known and new viral infections.<br>The bibliography includes 126 references.

Magnetically Active Bicontinuous Polymer Structures for Multiple Controlled Drug Delivery.

The targeted delivery of drugs using wireless navigable magnetic robots allows the delivery of drug molecules to be controlled non only in time but also in space, improving medical outcomes. The main disadvantages behind their use lies in the low amount of drug that can be transported and the single nature of drug that can be loaded (hydrophilic or hydrophobic). These considerations limit their use in co-delivery systems, now recognized to be very promising for many different pathologies. A magnetic bijel-like structure is developed to load and release different types of molecules (hydrophilic and hydrophobic). In this work, the use of ε-caprolactone is explored, which can polymerize, forming hydrophobic domains (oil phase). After mixing with iron oxide nanoparticles (NPs), the water dispersion creates a magnetic biphasic porous structure without phase separation. The resulting device shows good performance both in magnetic actuation and as a drug delivery system.

Gap-Δenergy, a New Metric of the Bond Energy State, Assisting to Predict Molecular Toxicity.

Molecular toxicity is a critical feature of drug development. It is thus very important to develop computational models to evaluate the toxicity of small molecules. The accuracy of toxicity prediction largely depends on the quality of molecular representation; however, current methods for this purpose do not address this issue well. Here, we introduce a new metric, gap-Δenergy, which is designed to quantify the intermolecular bond energy difference with atom distance. We next find significant variations in the gap-Δenergy distribution among different types of molecules. Moreover, we show that this metric is able to distinguish the toxic small molecules. We collected data sets of toxic and exogenous small molecules and presented a novel index, namely, global toxicity, to evaluate the overall toxicity of molecules. Based on molecular descriptors and the proposed gap-Δenergy metric, we further constructed machine learning models that were trained with 7816 small molecules. The XGBoost-based model achieved the best performance with an AUC score of 0.965 and an F1 score of 0.849 on the test set (1954 small molecules), which outperformed the model that did not use gap-Δenergy features, with a sensitivity score increase of 3.2%.

A REVIEW ON MOLECULAR DOCKING AND ITS APPLICATION

Molecular Docking is powerful computer strategy, critical in drug development, structural biology, and biomolecular interaction researchproviding a thorough grasp of its importance in modern scientific study. Molecular docking involves forecasting how a small molecule, often a potential medication, will interact with a target biomolecule like DNA or a protein. This process examines the spatial and energetic compatibility of the ligand with the active site of the receptor, assisting in the discovery of new drug candidates, refining existing compounds, and understanding the intricate interactions between drugs and receptors. Molecular Docking a computational tool that evaluates and ranks different ligand-receptor conformations based on their binding energies. An accurate scoring function is imperative for distinguishing high-affinity ligands from low-affinity ones, this makes it possible to identify potential medication candidates for validation in experiments. Molecular docking finds application in various domains of Drug Progress, comprisingstructure-based medication development, virtual screening,lead optimization.When creating a medicine based on structure, the target biomolecules three-dimensional structure is employed to guide the ligand selection that will communicate with the region that is active. Virtual examination accelerates the discovery of potential drug properties by rapidly evaluating large compound libraries. Lead optimization, on the other hand, is facilitated through iterative docking studies aimed at enhancing binding affinity and pharmacological properties. The field of molecular docking has seen a proliferation of diverse techniques designed to address the unique challenges of structure-based drug design and biomolecular interaction analysis. This report provides an in-depth examination of thedistinct methodologies of docking, its principles, applications, and their importance in advancing our understanding of molecular interactions in different contexts.The diversity of docking methods arises from the need to accommodate different types of molecules, target structures, and research objectives.

The Chemical Reactivity of Membrane Lipids.

It is well-known that aqueous dispersions of phospholipids spontaneously assemble into bilayer structures. These structures have numerous applications across chemistry and materials science and form the fundamental structural unit of the biological membrane. The particular environment of the lipid bilayer, with a water-poor low dielectric core surrounded by a more polar and better hydrated interfacial region, gives the membrane particular biophysical and physicochemical properties and presents a unique environment for chemical reactions to occur. Many different types of molecule spanning a range of sizes, from dissolved gases through small organics to proteins, are able to interact with membranes and promote chemical changes to lipids that subsequently affect the physicochemical properties of the bilayer. This Review describes the chemical reactivity exhibited by lipids in their membrane form, with an emphasis on conditions where the lipids are well hydrated in the form of bilayers. Key topics include the following: lytic reactions of glyceryl esters, including hydrolysis, aminolysis, and transesterification; oxidation reactions of alkenes in unsaturated fatty acids and sterols, including autoxidation and oxidation by singlet oxygen; reactivity of headgroups, particularly with reactive carbonyl species; and E/Z isomerization of alkenes. The consequences of reactivity for biological activity and biophysical properties are also discussed.

Endocrine Disrupting Effects of Flame Retardants on Thyroid System

Accumulating scientific evidence shows that thyroid hormone synthesis and signaling are now recognized as one of the important targets of environmental chemicals, especially chemicals called endocrine disruptors. Endocrine disrupting chemicals (EDCs) are man-made chemicals and consist of different types of molecules, for instance some pesticides, plasticizers, flame retardants (FRs), surfactants, many of which can interfere with thyroid hormone synthesis or their actions. FRs, important members of endocrine disruptors, share similarities in their chemical structures when compared with thyroid hormones, and there is accumulating scientific findings pointing out that they may take part in the dysfunction of thyroid hormone homeostasis. The primary aim of using FRs is to minimize the risk of fire and prevention of its spreading. The potential effects of exposure to FRs on the thyroid and thyroid hormones have gained importance since they may easily migrate into the surrounding environment and are especially found in house dust. Within the framework of the results of some experimental animal and in vitro studies, as well as limited human studies researching the consequences of FRs on the thyroid system, this paper aims to make a general assessment of whether these chemicals have a role in some thyroid diseases. Although the information that FRs with endocrine disrupting properties may have an effect on thyroid hormone levels and cause disruption in the thyroid system is still in its infancy, there is emerging evidence that some members of FRs may have thyroid disrupting properties.

Review of: "(Nanobiosensors) The human sense of smell and taste, which detects different smells and tastes, or the body's immune system, which detects millions of different types of molecules, are examples of natural biosensors"

Review of: "(Nanobiosensors) The human sense of smell and taste, which detects different smells and tastes, or the body's immune system, which detects millions of different types of molecules, are examples of natural biosensors"

Extracellular Vesicles in Domestic Animals: Cellular Communication in Health and Disease.

Apoptotic and healthy cells of domestic animals release membrane-enclosed particles from their plasma membrane. These special structures, called extracellular vesicles, play an important role in intercellular communication. In the past, it was believed that their function was mainly to dispose unwanted cell contents and to help maintain cell homeostasis. However, we now know that they have important roles in health and disease and have diagnostic value as well as great potential for therapy in veterinary medicine. Extracellular vesicles facilitate cellular exchanges by delivering functional cargo molecules to nearby or distant tissues. They are produced by various cell types and are found in all body fluids. Their cargo reflects the state of the releasing parent cell, and despite their small size, this cargo is extraordinarily complex. Numerous different types of molecules contained in vesicles make them an extremely promising tool in the field of regenerative veterinary medicine. To further increase research interest and discover their full potential, some of the basic biological mechanisms behind their function need to be better understood. Only then will we be able to maximize the clinical relevance for targeted diagnostic and therapeutic purposes in various domestic animal species.

Photodynamic therapy of cervical cancer: a scoping review on the efficacy of various molecules.

Cervical cancer poses a considerable worldwide health issue, where infection with the human papillomavirus (HPV) plays a vital role as a risk factor. Photodynamic therapy (PDT) is a minimally invasive treatment for HPV-related cervical lesions, which uses photosensitizers and light to selectively destroy abnormal cells. Our objective is to present a comprehensive overview of the different types of molecules employed in PDT to reduce the occurrence and fatality rates associated with cervical cancer. Scoping review and bibliometric analysis. The article explores clinical trials investigating the efficacy of PDT in treating low-grade squamous intraepithelial lesion and high-grade squamous intraepithelial lesion, as well as preclinical approaches utilizing various molecules for PDT in cervical cancer. Furthermore, the article sheds light on potential molecules for PDT enhancement, examining their properties through computer modeling simulations, molecular docking, and assessing their advantages and disadvantages. Our findings demonstrate that PDT holds promise as a therapeutic approach for treating cervical lesions associated with HPV and cervical cancer. Additionally, we observe that the utilization of diverse dye classes enhances the anticancer effects of PDT. Among the various molecules employed in PDT, functionalized fullerene exhibits a notable inclination toward overexpressed receptors in cervical cancer cells, making it a potential candidate for intensified use in PDT. However, further research is needed to evaluate its long-term effectiveness and safety.

Ratio Shift Keying Modulation for Time-Varying Molecular Communication Channels.

Molecular Communications (MC) is a bio-inspired communication technique that uses molecules to encode and transfer information. Many efforts have been devoted to developing novel modulation techniques for MC based on various distinguishable characteristics of molecules, such as their concentrations or types. In this paper, we investigate a particular modulation scheme called Ratio Shift Keying (RSK), where the information is encoded in the concentration ratio of two different types of molecules. RSK modulation is hypothesized to enable accurate information transfer in dynamic MC scenarios where the time-varying channel characteristics affect both types of molecules equally. To validate this hypothesis, we first conduct an information-theoretical analysis of RSK modulation and derive the capacity of the end-to-end MC channel where the receiver estimates concentration ratio based on ligand-receptor binding statistics in an optimal or suboptimal manner. We then analyze the error performance of RSK modulation in a practical time-varying MC scenario, that is mobile MC, in which both the transmitter and the receiver undergo diffusion-based propagation. Our numerical and analytical results, obtained for varying levels of similarity between the ligand types used for ratio-encoding, and varying number of receptors, show that RSK can significantly outperform the most commonly considered MC modulation technique, concentration shift keying (CSK), in dynamic MC scenarios.

Recent Advances in Modeling Membrane β-Barrel Proteins Using Molecular Dynamics Simulations: From Their Lipid Environments to Their Assemblies.

Spurred by advances in AI-driven modeling and experimental methods, molecular dynamics simulations are now acting as a platform to integrate these different approaches. This combination of methods is especially useful to understand β-barrel proteins from the molecular level, e.g., identifying specific interactions with lipids or small molecules, up to assemblies comprised of hundreds of proteins and thousands of lipids. In this minireview, we will discuss recent advances, mainly from the last 5years, in modeling β-barrel proteins and their assemblies. These approaches require specific kinds of modeling and potentially different model resolutions that we will first describe in Subheading 1. We will then focus on different aspects of β-barrel protein modeling: how different types of molecules can diffuse through β-barrel proteins (Subheading 2); how lipids can interact with these proteins (Subheading 3); how β-barrel proteins can interact with membrane partners (Subheading 4) or periplasmic extensions and partners (Subheading 5) to form large assemblies.

PHOTODYNAMIC THERAPY FOR CERVICAL CANCER: A LITERATURE REVIEW

Relevance: Cervical cancer is a major public health problem worldwide, with human papillomavirus infection playing a vital role as a risk factor. Photodynamic therapy is a minimally invasive treatment for HPV-related cervical lesions that uses photosensitizers and light to selectively destroy abnormal cells.
 The study aimed to comprehensively review the different types of molecules used in PDT to reduce the morbidity and mortality associated with cervical cancer.
 Methods: A comprehensive search was conducted for all relevant articles investigating the efficacy and safety of PDT in the treatment of HPV-associated cervical cancer. PICO scores were determined for the review, and a literature search of the PubMed database was performed. An examination of the PubMed online database using keyword combinations identified 71 studies conducted between 2013 and 2023 that investigated using PDT to treat RSM cells.
 This article reviews ongoing clinical trials examining the efficacy of PDT in treating low-grade squamous cell intraepithelial neoplasia and high-grade squamous cell intraepithelial lesions, as well as preclinical approaches using different molecules for PDT in cervical cancer
 Results: Potential molecules for PDT are described, their advantages and disadvantages evaluated, and solutions to improve their compatibility with antitumor treatment are proposed. Our review shows that PDT is a promising therapeutic approach for diagnosing and treating HPV-related cervical lesions. At the same time, we observe that using different classes of dyes enhances the anticancer effects of PDT
 Conclusion: Fullerene and ALA-PDT are potential leaders for more intensive use in PDT, which will further help reduce the global incidence and mortality from cervical cancer. However, further studies are needed to evaluate its long-term efficacy and safety.

PHOTODYNAMIC THERAPY FOR CERVICAL CANCER:
 A LITERATURE REVIEW

Relevance: Cervical cancer is a major public health problem worldwide, with human papillomavirus infection playing a vital role as a risk
 factor. Photodynamic therapy is a minimally invasive treatment for HPV-related cervical lesions that uses photosensitizers and light to selectively
 destroy abnormal cells.
 The study aims to comprehensively review the different types of molecules used in PDT to reduce the morbidity and mortality associated with
 cervical cancer.
 Methods: A comprehensive search was conducted for all relevant articles investigating the efficacy and safety of PDT in the treatment of
 HPV-associated cervical cancer. PICO scores were determined for the review, and a literature search of the PubMed database was performed. An
 examination of the PubMed online database using keyword combinations identified 71 studies conducted between 2013 and 2023 that investigated
 using PDT to treat RSM cells.
 This article reviews ongoing clinical trials examining the efficacy of PDT in treating low-grade squamous cell intraepithelial neoplasia and
 high-grade squamous cell intraepithelial lesions, as well as preclinical approaches using different molecules for PDT in cervical cancer.
 Results: Potential molecules for PDT are described, their advantages and disadvantages evaluated, and solutions to improve their compatibility with antitumor treatment are proposed. Our review shows that PDT is a promising therapeutic approach for diagnosing and treating HPV-related
 cervical lesions. At the same time, we observe that using different classes of dyes enhances the anticancer effects of PDT.
 Conclusion: Fullerene and ALA-PDT are potential leaders for more intensive use in PDT, which will further help reduce the global incidence
 and mortality from cervical cancer. However, further studies are needed to evaluate its long-term efficacy and safety.