Abstract: Liposomes are hollow spheres composed of lipids bilayer membranes, which can encapsulate and deliver hydrophilic and hydrophobic substances. Liposomes are promising nano-drug delivery systems due to low immunogenicity, good stability, low toxicity and cost. Currently, a variety of liposome drugs for tumor treatment have been listed. Liposomes can accumulate in tumor tissues via enhanced permeability and retention effect (EPR) and are internalized into tumor cells by endocytosis or pinocytosis. Subsequently, liposomes are intracellularly cleaved to release drugs, thereby killing tumor cells. Liposomes that rely on the EPR effect are called passive targeting liposomes, which lack the ability to specifically recognize target tissues. However, active targeting liposomes can achieve targeting delivery via the specific binding between the targeting modifiers on the surface of liposomes and receptors on the surface of tumor cells. These receptors such as peptides, carbohydrates, ligands, antibodies and nucleic acid aptamers on the surface of tumor cells overexpress due to rapid growth of tumor cells and needs of nutrients and related growth factors. Thus, liposomes can be reasonably designed according to these specific receptors. Recent years, some studies have reported biomimetic liposomes by coating the cell membrane on the surface of liposomes, however, the research on biomimetic liposomes is still in its infancy, and there are still many problems to be solved. Additionally, since the length is limited, biomimetic liposomes are not reviewed in this paper. Taken together, liposomes as potential drug carriers, not only protect drugs, but also reduce side effects, importantly, they can precisely target tumor tissues through introducing targeting modifiers. In this work, we review the improvement of targeting function of liposome by five targeting modifiers including peptides, carbohydrates, ligands, antibodies and nucleic acid aptamers, and summarize the existing advantages and challenges of various targeted modifications. Finally, this review is expected to provide scientific reference for the LPs drug delivery system study and theoretical basis for the drug development.
Abstract: Objective To study the anti-breast cancer effects and molecular mechanisms of syringin, and to provide a theoretical basis for the clinical application of syringin.Methods The inhibitory effect of syringin on the proliferation of breast cancer cells was measured with MTT assay. Trypan blue, TdT-mediated dUTP nick-end labeling (TUNEL), and Annexin V-FITC/PI staining were used to detect apoptosis. Caspase-3 activation was detected via Western blot to determine whether apoptosis occurred. The expression of apoptosis-associated protein B-cell lymphoma-2 (Bcl-2) was detected and the effect of syringin on the mitochondrial apoptosis pathway was investigated via JC-1 staining. The PI3K agonist Recilisib was used for comparison. qRT-PCR and Western blot were used to assess the role of syringin in regulating the PI3K/Akt/mTOR pathway and inducing the apoptosis of cancer cells.Results Syringin had a time- and dose-dependent inhibitory effect on the proliferation of breast cancer cells and induced their apoptosis. A further study showed that after syringin treatment, Caspase-3 was activated, Bcl-2 expression decreased, the mitochondrial membrane potential was significantly reduced, and the mRNA and protein expressions of PI3K, Akt, and mTOR were not significantly changed, but the protein phosphorylation levels were significantly decreased. Recilisib partially limits the effect of syringin on the apoptosis of breast cancer cells.Conclusion Syringin has a good inhibitory effect on MDA-MB-231 and MCF-7 breast cancer cells. It can inhibit cell proliferation and induce mitochondrial apoptosis by inhibiting the activation of the PI3K/Akt/mTOR signaling pathway. Syringin is a potential anti-breast cancer drug.
Abstract: The CRISPR/Cas system consists of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (Cas). The system forms an adaptive immune system in archaea and bacteria. The inherent defense mechanism enables these microorganisms to protect themselves against the invasion of foreign genetic material. The system functions of immune response including three main stages: adaptation, expression/maturation, and interference, each stage needs specific Cas proteins encoded by Cas gene located near the CRISPR sequences, along with other auxiliary proteins. In 2015, Zhang et al. reported Cas12a (Cpf1) as a member of the Class II type V CRISPR/Cas12a system, which possesses endonuclease activity. This finding holds great promise for its application in the field of biotechnology. In 2018, Doudna’s team first applied the CRISPR/Cas12a system for detecting HPV nucleic acid. The system comprises the following essential components in vitro detection: Cas12a, the crRNA sequence complementary to the target DNA, the PAM sequence, and the ssDNA reporter. Cas12a possesses a typical RuvC domain, displaying a canonical bilobed architecture that consists of a recognition (REC) lobe and a nuclease (NUC) lobe. The REC lobe contains the REC1 and REC2 domains, and the NUC lobe includes RuvC, PAM-interacting (PI), Wedge (WED), and bridge helix (BH) domains. The mature crRNA for Cas12a has a length of 42-44 nt, consists of repeat sequence (19/ 20 nt) and spacer sequence (23-25 nt). The crRNA spacer sequence has been found to require a length of 18 nt to achieve complete cleavage activity in vitro. Additionally, mutation in the bases of crRNA can indeed affect the activity of Cas12a. The PAM sequence plays a critical role in the recognition and degradation of DNA by the CRISPR/Cas system, enabling the system to distinguish between self and non-self genomic materials. Cas12a can effectively target the spacer sequence downstream of a T-rich PAM sequence at the 5" end. LbCas12a and AsCas12a both recognize the PAM sequences of 5"-TTTN-3", while FnCas12a recognizes the PAM sequences of 5"-TTN-3". All of these PAM sequences are located upstream on the non-template strand (NTS) at the 5" end. Cas12a (Cpf1), guided by the crRNA, binds to the target DNA by recognizing the PAM sequence. It exhibits the ability to induce arbitrary cleavage of ssDNA within the system while cleaving the target ssDNA or dsDNA. According to this feature, an array of nucleic acid detection methods has been developed for tumor detection and infection diagnostics, such as the DETECTR (RPA-CRISPR/Cas12a method) and HOLMES (PCR-CRISPR/Cas12a method) in 2018. Then, in 2019, Cas12aVDet (one-step detection method), where Cas12a protein was immobilized on the upper wall of the reaction tube. This not only prevented contamination from opening the tube but also reduced the detection reaction time. In 2021, the dWS-CRISPR (digital warm-start CRISPR) was developed as a one-pot detection method. It serves as an accurate approach for quantitatively detecting SARS-CoV-2 in clinical specimens. With the innovation of scientific technology, the high-sensitivity signal transduction technology has also been integrated with the CRISPR/Cas12a system, enabling direct detection of nucleic acids, and eliminating the need for nucleic acid amplification steps. Here, we elaborated the detection principles of CRISPR/Cas12a in in vitro detection. We discussed the different stages leading to the catalytic pathway of target DNA, and the practical applications of Cas12a in nucleic acid detection. These findings revealed a target interference mechanism that originates from the binding of Cas12a-guided RNA complex to complementary DNA sequences within PAM-dependent (dsDNA) regions. The crRNA-DNA binding activates Cas12a, enabling site-specific dsDNA cleavage and non-specific ssDNA trans-cleavage. The release of Cas12a ssDNase activity provides a novel approach to enhance the sensitivity and specificity of molecular diagnostic applications. Before these CRISPR/Cas12a-based nucleic acid detection methods can be introduced into clinical use, substantial work is still required to ensure the accuracy of diagnosis. Nevertheless, we believe that these innovative detection tools based on CRISPR/Cas will revolutionize future diagnostic technologies, particularly offering significant assistance in pathogen infection diagnosis for developing countries with relatively poor healthcare conditions and high prevalence of infectious diseases.
Abstract: Mass spectrometry-based proteomics aims to identify peptides and proteins to give direct proofs of gene expressions, analyze structures and functions of proteins, study the relationship between proteins and diseases, and provide targeted treatment options. All these studies are based on the credibility of identified peptides and proteins. However, it is impossible to manually check all identified peptides because a large number of identifications can be collected from one mass spectrometry experiment. Thus, target-decoy approach (TDA) is proposed and always used to control the quality of identified peptides and proteins, and has been expanded to subclasses of peptides (including ordinary subclasses of peptides, variant peptides, and modified peptides) and cross-linking peptides. However, TDA still has two limitations: (1) the estimation of false discovery rate (FDR) is inaccurate and (2) validation of single identification cannot be supported. Thus, the identification results that passed the TDA-based FDR control need to be further validated and other validation methods which are used after TDA-FDR filtration (referred to as Beyond-TDA methods) have been developed to enhance peptide validation. This paper reviews TDA and its extensions as well as Beyond-TDA methods and discusses the advantages and disadvantages of each method. In the first part of this paper, we introduce the goal of proteomics, the process of mass spectrometry acquisition and analysis, the validation problem, and the early statistical methods to evaluate the identification credibility. Then, in the second part of this paper, we describe in detail the ordinary TDA-FDR method, including the assumption that random matches are equally likely to appear in target and decoy databases, the construction methods to generate the decoy database, and the computational formula of TDA-FDR. We also introduce the extensions of TDA-FDR on ordinary subclasses of peptides, variant peptides, modified peptides, proteogenomics peptides, cross-linking peptides, and glycopeptides. However, TDA cannot model the homologous incorrect peptides, thus TDA-FDR underestimates the actual false rate. So, after TDA-FDR filtration, it is necessary to use more strict validation methods, i.e., Beyond-TDA methods, which are reviewed in detail in the third part of this paper, to control validation credibility. In this part, four kinds of methods are introduced, including validation methods based on search space (trap database validation and open search validation), spectra similarity (synthetic peptide validation and theoretical spectra prediction), chemical information (retention time prediction and stable isotopic labeling validation) and machine learning technology (Percolator, pValid, and DeepRescore). Lastly, we summarize the content of this paper and discuss the future improvement directions of validation methods.
Abstract: Antibody drug conjugate (ADC) is typically composed of a monoclonal antibody conjugated with a cytotoxic small molecule drug via a linker. It is an emerging and promising class of targeted cancer therapeutics, combining both the highly cytotoxic activity of chemical drugs and highly targeting ability and specificity of monoclonal antibody. Fourteen ADCs have been approved for marketing so far worldwide, and more than 140 ADC drug candidates have been investigated in clinical studies. Various ADC technologies have been well developed to manufacture these ADC drugs in commercial scale as well as clinical scale. In this review, we describe the molecular structure, mechanisms of action and development history of ADCs. We then provide an overview of the current landscape and recent advances in each key element of ADCs, including antibody, linker, payload and conjugation, and their advantages and disadvantages. Future directions in ADC development may encompass smaller sized forms of antibodies such as antibody fragments and nanobodies to improve the penetration and accumulation of ADCs in the solid tumors. Novel linkers are also being tested to enhance the stability in circulation systems and reduce off-target toxicities. Emerging payloads of new functional mechanisms are also explored in the construction of ADCs to overcome the drug resistance resulted from currently used payloads of marketed ADCs. Various site-specific conjugation technologies have been adopted to reduce the heterogeneity of drug-load species and optimize the pharmacokinetic properties of ADCs. This review article aims to enhance systemic understanding and careful considerations in designing an ADC drug with improved efficacy and safety.
Abstract: Peroxisome is a kind of organelle conserved in eukaryotes, which is involved in many biochemical metabolic processes, including β-oxidation of fatty acids, production and degradation of reactive oxygen species, etc. Peroxisome biogenesis has growth and division model and de novo biogenesis model, which involves the import of peroxisome matrix and membrane proteins. Under normal physiological conditions, the proliferation and degradation of peroxisomes are balanced. While the matrix protein and membrane proteins in the peroxisome are misfolded and excessively accumulated, or the peroxisome is under environmental stress, such as high reactive oxygen species (ROS) concentration was exhibited, the peroxisomes homeostasis will be unbalanced. In order to maintain homeostasis in the biogenesis process and environmental stress, the peroxisome through division and degradation for quality control. What’s more, peroxisome has evolved multiple degradation pathways, including pexophagy, the receptor accumulation and degradation in the absence of recycling (RADAR) depending on ubiquitin-proteasome system (UPS) and so on. These pathways of peroxisomal degradation are significant for maintaining the integrity of cell structure and function. As the metabolic hub of eukaryotic cells, peroxisomes exchange substances and transmits signals with other organelles through peroxisomal membrane contact sites (MCSs), such as mitochondria, endoplasmic reticulum, lysosome and so on. These peroxisomal MCSs play a vital role in metabolic functions and homeostasis regulation, including lipid metabolism, peroxisome division, autophagy and other biological processes. In recent years, the maintenance of peroxisome homeostasis and MCSs have become research hotspots at home and abroad. The quantity change and spatio-temporal distribution of peroxisome are regularly dynamic to maintain the organism’s normal life activities, while the homeostasis imbalance of peroxisome will result in serious physiological dysfunction of cells. In humans, more and more diseases have been confirmed to be related to the imbalance of peroxisome homeostasis or mutations of peroxisome membrane contact sites, including cancer, diabetes, Alzheimer’s disease and Parkinson’s disease. In plant pathogenic fungi, recent studies have proved that the key genes of peroxisome biogenesis play an important role in pathogenicity, such as of rice blast fungus. This paper reviews the recent advances in the mechanism of peroxisome homeostasis and MCSs.
Abstract: Transient receptor potential vanilloid subfamily member 1 (TRPV1), also known as capsaicin receptor (VR1), is a kind of ligand gated non-selective cation channel which can be activated by capsaicin, heat (>43℃) and H+ (pH<6.0). TRPV1 is highly permeable to Ca2+. Previous studies found that TRPV1 mainly distributes in nervous system and mediates pruritus and pain response. Recent studies have shown that TRPV1 also widely distributes in non-nervous cells such as mast cells, bladder epithelial cells, monocytes, skin keratinized epithelial cells, islet cells and so on. TRPV1 has a wide range of functions and can mediate beneficial or harmful biological effects on the body. In the nervous system, TRPV1 related signal pathway mainly mediates itching and pain response. Relevant studies in pancreatic cells have shown that the upregulation of TRPV1 can alleviate the process of diabetes, but studies in pulmonary epithelial cells, pulmonary vascular endothelial cells, bronchial smooth muscle cells, etc. have shown that the upregulation of TRPV1 can accelerate the development of respiratory diseases. In addition, TRPV1 has dual effects of promotion or inhibition on the disease progression in cardiovascular system, digestive system and skin system. In cancer research, it was also found that the upregulation of TRPV1 played an important antineoplastic effect, which could inhibit the proliferation, invasion and migration of tumor cells in human tongue squamous cell carcinoma, prostate cancer, breast cancer and so on, arrest the cell cycle and induce cell apoptosis. At present, many studies have been carried out on the mechanism of TRPV1, among which the mechanism of TRPV1 mediating itching and pain is relatively in depth. TRPV1 has become a promising therapeutic target due to its extensive functions. New drugs targeted to TRPV1 have been developed to ameliorate diabetes, cardiovascular diseases, and some kinds of cancers. This paper introduces the latest progress in the distribution, structural characteristics and functions of TRPV1, and focuses on the research progress of pruritus and pain related signaling pathways mediated by TRPV1. We also introduced the Chinese herbal medicine with TRPV1 as the target, looking forward to providing theoretical guidance for taking TRPV1 as a potential therapeutic target by combination of traditional Chinese medicine and modern medicine.
Abstract: Nucleic acid aptamers are a class of single-stranded DNA or RNA molecules with specific molecular recognition capability, obtained by a process called systematic evolution of ligands by exponential enrichment (SELEX). They have the advantages of high thermal stability, ease of chemical synthesis and modification, and low immunogenicity compared to antibodies, and have attracted widespread interest in many fields such as bioanalysis, biomedicine, and biotechnology. High-quality aptamers are the basis of applications, however, the number of them that meet requirements of practical applications is very limited. How to obtain aptamers with high affinity, high specificity, and high in vivo stability is the technical bottleneck in the field of aptamers. Firstly, this review briefly introduces the basic theory of SELEX and its critical experimental steps including design of nucleic acid library, monitoring selection process, preparation of secondary library, sequencing and screening of candidate aptamers. The six main research directions of SELEX during the past thirty years are then concluded. They are respectively (1) how to improve the specificity of aptamers, (2) how to improve the stability of aptamers against nuclease degradation, (3) rapid SELEX, (4) how to isolate aptamers for complex targets, (5) how to isolate small molecule-binding aptamers, and (6) how to isolate high affinity aptamers. The development of rapid SELEX technologies has attracted tremendous attention and almost all physical separation methods have been applied to improve the SELEX efficiency. Very recently, several methods involving the highly efficient chemical reactions have been reported, providing novel strategies for the rapid isolation of aptamers. The key research progresses of SELEX technologies suitable for the isolation of small molecule-binding aptamers are subsequently reviewed and the challenges of each method are critically commented. There are three types of SELEX methods including the target-immobilized SELEX, library-immobilized SELEX (Capture-SELEX), and homogeneous SELEX (GO-SELEX). Even though the target-immobilized SELEX suffers from many issues such as steric hindrance, it is still a popularly used method due to its simplicity. In recent years, Capture-SELEX has been widely applied. The experimental conditions of Capture-SELEX (concentration of positive-SELEX target, choice of negative-SELEX targets and their concentrations) and the affinity (KD,dissociation constant) and the specificity of the isolated aptamers for the 36 targets are listed in a table. Based on the information from the table, the effect of the experimental conditions on the affinity and the specificity is discussed. The statistical data indicates that the lower concentration of the positive-SELEX targets favors the isolation of the higher affinity aptamers, while it is not a necessary condition. Negative-SELEX is currently the dominant strategy to improve the specificity of aptamers. However, the specificity of many aptamers cannot meet the requirement for practical applications. The choice of negative-SELEX targets and their concentrations in each case are quite different. In 20 out of the 36 targets, no negative-SELEX was performed for the aptamer isolation. How to obtain the aptamers with high specificity is the most difficult challenge for small molecule targets. It is in urgent need to establish novel strategies beyond negative-SELEX to improve the specificity of aptamers. The experimental conditions of GO-SELEX and the KD and the specificity of the isolated aptamers for the 13 small molecule targets are also list for comparison. The comparison data shows the less numbers of the enrichment cycles required for GO-SELEX than Capture-SELEX, while the obtained aptamers all commonly have KD in the nanomolar range. The lower enrichment efficiency of Capture-SELEX should be due to the self-dissociation of the immobilized library. The affinity evaluation is the important part of the characterization of aptamer structure and performance. More than ten affinity assays are frequently used for aptamer characterization, which are roughly divided into three categories: separation-based, immobilization-based, and homogeneous methods. All techniques could generate false-positive and false-negative results. Taking gold nanoparticle-based colorimetric assay and isothermal thermal titration as examples, we review the technical progresses and comment on the fundamental reasons resulting in the inconsistent results when the different affinity assays are conducted. The final part of this review provides an outlook on the future trends of aptamer isolation technologies, affinity characterization techniques, and the technical standardization.
Abstract: Natriuretic peptides (NPs) have been discovered for 30 years, and the clinical use of B-type natriuretic peptides (BNP) and N-terminal pro-B type natriuretic peptide (NT-proBNP) precursors have been a landmark in the management of cardiovascular disease, particularly in heart failure. The BNP has a powerful cardioprotective effect, but the BNP that rises dramatically after heart failure does not show corresponding activity, which is known as the “natriuretic peptide paradox”. In recent years, with the use of mass spectrometry and nuclear magnetic resonance techniques, “natriuretic peptide paradox” is being revealed through novel metabolic findings and testing technology. There are many different biologically active BNP isoforms in the peripheral circulation, and BNP metabolism after heart failure is different from that in the physiological state. Although the significant increase of BNP is detected after heart failure, it is essentially false positive due to bottlenecks in conventional the assay reagents of cross-react to various BNP isoforms, and therefore the bioactive levels of BNPs have been overestimated. So, we believe that it is necessary to strengthen the understanding of BNP in different pathophysiological conditions , and establish sensitive and specific detection methods by biochemical means to identify BNP1-32, BNP1-30, BNP3-32 and pro-B-type natriuretic peptide (proBNP). Accurate detection of BNPs will help us understand the deeper pathophysiological mechanisms of heart failure, and make precise clinical decision on the diagnosis and treatment.
Abstract: Autoradiography generally involves in metallic silver stain formation through irradiation to photosensitive materials (such as X-ray film) with further development and fixation steps using a radiolabeled probe, and the stain density indicates the relative amount of its target molecules and its distribution in tissue slices. This traditional method has a wide range of applications both in biological studies and preclinical drug researches. Phosphor film imaging has significantly shortened the autoradiography’s experimental intervals, and the positron nuclides with short-half-lives can also be performed. The purpose of this paper focuses on the frontier of some experimental works that can’t be completely replaced by non-radioactive labeled methods, such as some enzymatic activity assays, protein or peptide phosphorylation site analyses, nucleic acid assays with low concentrations, and the target (such as receptors) molecule distributions in tissue slices by radiolabeled selective ligands. Thus the technological platform should be reformulated to adapt to the current trends of experimental works.
Abstract: The structure of protein is determined by the sequence, and the function of protein is determined by its structure. The advent of accurate protein structure prediction tools has created new opportunities and challenges in the fields of structural biology, structural bioinformatics, drug discovery and many other fields of life sciences. The accuracy of single-chain protein structure prediction has reached a level comparable to that of experimental methods. In this review, we provide an overview of the theoretical basis, development history, and recent advances in the field of protein structure prediction. Additionally, we discuss how the large number of predicted protein structures and artificial intelligence-based methods affect experimental structural biology. Open questions and future research directions in the field of protein structure prediction are analyzed.
Abstract: R-loops are formed during transcription when the nascent RNA generated by RNA polymerases hybridizes with its complementary DNA template, giving rise to a region of DNA∶RNA hybrid and a displaced single-stranded DNA. R-loops are stable structures that have important beneficial physiological functions, but also could pose a threat to genomic stability. Unscheduled R-loops induce cell cycle checkpoint activation, DNA damage, and chromosome rearrangement in mammalian cells. R-loops expose unstable single-stranded DNA, which is prone to transcription-related mutations and recombination. R-loops may also directly block DNA replication, leading to DNA double strand breaks. Abnormal accumulations of R-loops have been found in some syndromes, human neurological disorders, and cancers. On the other hand, R-loops also play positive roles in physiological processes, such as epigenetic modification, DNA repair, gene regulation and mitochondrial stability. R-loops forming on transcription-termination regions, promote RNA polymerase pausing before termination. R-loops are regulated delicately in cells. Collisions between replication and transcription cause accumulation of R-loops. Replication stress, DNA damage and RNA Pol II pausing also induce R-loop formation. To resolve R-loops when they form, cell evolve numerous dissolution mechanisms. Ribonuclease RNase H1 and RNase H2 bind to R-loops and then catalyze the cleavage of RNA. Helicases, such as SETX, DHX9, DDX21, unwind the RNA from the R-loops. Defects in RNA processing factors, chromatin modulators, DNA repair proteins, cause accumulation of R-loops, suggesting they are involved in R-loop regulations. To detect R-loops, several methods have been developed and are mainly based on the S9.6 antibody and the HBD domain of RNase H1, however, both of them possess some issues. Understanding the regulatory mechanisms of R-loop formation and clearance could help us better know how cells maintain genomic stability and prevent disease development. In this review article, we summarized functions and regulations of R-loops. We also discussed methodologies used to detect R-loops. Finally, we proposed some future perspectives of R-loop research.
Abstract: Molecular medicine focus on understanding the diseases based on molecular level, and developing personalized medicine strategies for diagnostics and therapeutics. However, powerful molecular recognition tool is still limited for cancer diagnosis and therapy, which impeding cancer research. Aptamers are generated from systematic evolution of ligands by exponential enrichment (SELEX) also known as in vitro selection, ranging from synthetic single-stranded DNA, RNA or XNA (enhanced modified nucleotides), HNA (nucleotides of specific structures such as G quadruplex). The main advantages of aptamers including high specificity, high affinity, simple and rapid synthesis, easy chemical modification, wide target range, good tissue penetration and low immunogenicity. As a molecular recognition tool in molecular medicine, aptamer shows wide applications in developing personalized prediction, diagnosis and therapeutics for its high specificity and high affinity against target. This review discusses the applications of aptamers in disease diagnosis, including aptamer-based tumor marker discovery, liquid biopsy, and molecular imaging, Moreover, the applications of aptamer-based cancer therapy are reviewed, including aptamer-based inhibitors, aptameric drug conjugates, nanomedicines, and aptamer-mediated immunotherapy. Finally, it is promising aptamer will be extensively employed in the future including fundamental research, diagnosis and therapeutics. However, following issues are still need to be addressed. First, the application scenarios-dependent SELEX procedures lack studying which limits the clinical applications of aptamers. Second, the structure of aptamer-target complex has not been fully elucidated, which restricts the precise regulation of aptamers. Third, aptamer is easily degraded by enzymes in vivo and has a short half-life period, which hinders the applications of aptamer-drug conjugates in the development of targeted drugs. With the advancement of screening technology and the further enhancement of aptamer performance, it is expected that aptamers will find more extensive utilization in the field of molecular medicine in the future.
Abstract: Cerebral ischemia refers to the lack of blood supply in all parts of the brain leading to brain tissue ischemia and hypoxia, which leads to irreversible damage and necrosis of in dense ischemic areas. Its high disability and high mortality rate will cause serious harm to patients and their families. The key to the prognosis of cerebral ischemia is to take some measures to restore blood flow and oxygen supply, control the size of the infarct and save the cells in the penumbra. Hyperbaric oxygen therapy refers to letting patients inhale 100% oxygen under the environmental pressure higher than one atmosphere absolute to increase the oxygen content in the body. It can provide enough oxygen for ischemic hypoxic brain tissue and prevent the further aggravation of injury. Clinical trials have demonstrated that hyperbaric oxygen therapy can improve motor, sensory and cognitive dysfunction in patients with cerebral ischemia and can also be used as an adjuvant therapy. The mechanisms of hyperbaric oxygen therapy in the treatment of cerebral ischemia mainly include increasing the oxygen content, inducing neuroplasticity, regulating cerebral blood flow, regulating the expression level of cytokines, and reducing oxidative stress. It is worth noting that there are some prominent problems in the current research, such as adverse reactions during treatment, uncertainty of the effective therapeutic time window, a certain degree of difference between the results of basic research and clinical research, and the unportability of hyperbaric oxygen chamber. These problems severely limit the clinical application of hyperbaric oxygen therapy. In the future more basic and clinical research are needed to develop a more secure and reliable hyperbaric oxygen therapy protocol, reduce the toxic side effects and adverse reactions that may occur during the treatment, and provide new ideas for the treatment and prognosis of patients with cerebral ischemia
Abstract: The human brain receives a lot of visual information all the time, due to the limited ability of the human brain to process information, it is crucial to allocate attention to relevant information in a larger visual field and suppress irrelevant information that causes attention distraction in order to perform goal-oriented behavior. This process of selective and active processing of visual information to adapt to the current target is called visual attention, visual attention can be divided into two different functions: top-down attention and bottom-up attention. Since neural oscillations from brain electrical signals play an important role in cognitive processing, the close relationship between visual attention and neural oscillations has been reviewed, but the relationship between different attentional functions and neural oscillations has not been discussed. In this paper, we investigated the relationship between different attentional functions and neural oscillations. We found that the theta oscillations in the fronto-parietal region reflected top-down cognitive control, while the theta oscillations in the posterior brain region correlated with bottom-up attention. Lateralization of alpha oscillations in the parietal-occipital region contributes to attention allocation, while large-scale synchronization of alpha oscillations contributes to top-down effects of attention on the visual cortex. Beta oscillations mediate the interaction between top-down information and bottom-up information, and as information carriers promote visual information processing. Gamma oscillations may be related to top-down and bottom-up inter-attention integration. This paper reviews the research status of the relationship between visual attention function and neural oscillations in order to reveal the role of different neural oscillations in specific visual attention function.
Abstract: The high specificity and sustainability of enzymes make them widely used as green catalysts, and their stability and catalytic activity are vital for their practical applicability. Recently, enzymes have been endowed with desired physical and catalytic properties via using protein structural modification. From the protein structural point of view, enzyme thermal stability has been improved by modulation of non-covalent/covalent interactions (hydrophobic interaction, hydrogen bonding, salt bridges, aromatic interaction and disulfide bonds), loop truncation, C-/N-terminal engineering, introduction of proline with highest conformational rigidity in the flexible region, and substitution of glycine with highest conformational entropy. Meanwhile, the catalytic function has been enhanced or altered by various methods, including reducing steric hindrance, widening the binding pocket, moderating substrate binding affinity and active site flexibility. While, the generation of new features or improvement of the existing features often comes at the expense of the other ones. Thus, strategies include screening suitable mutation sites, co-selection for stability and activity, and using highly stable proteins as the parental backbones are also discussed to overcome the stability-activity trade-off. This review summarized recent advances in structural modification to improve the stability or/and catalytic activity of enzymes and further provided a brief prospect in the future developments.
Abstract: Marine macroalgae (including brown algae, red algae, and green algae) exhibit several features of an excellent feedstock for biorefinery, such as high yield of biomass, no occupation of arable land, and no requirement of fresh water. In 2021, the production of brown algae in China was 1.9 million tons, which was much higher than other economic algae. It is worth noting that the carbohydrate content of brown algae is as high as 60%, and three sugars, including alginate, fucoidan and laminarin are unique to brown algae. Amongst them, alginate is a linear anionic polysaccharide which consists of 1,4-linked C-5-epimers β-D-mannuronic acid (M) and α-L-guluronic acid (G). The decomposition of alginate is catalyzed by alginate lyases via β-elimination of glycosidic bonds. They produce various oligosaccharides with unsaturated uronic acid at the non-reducing end, or 4,5-unsaturated uronic acid monomers mannuronate (ΔManUA) and guluronate (ΔGulUA). Fucoidans usually consist of a backbone of α-1,3-L-fucopyranose residues or alternating α-1,3-linked and α-1,4-linked L-fucopyranosyls, and side branches containing glucose, galactose, rhamnose, xylose, mannose or glucuronic acid. The fucopyranose residues may be substituted with sulfate. The highly modified structure of fucoidans can significantly affect the cleavage of glycosidic linkages. Therefore, hydrolases that act on a branched chain and sulfatases are required for the primary degradation. Subsequently, L-fucoses are produced by a series of sulfatases and fucosidases belonging to GH29, GH95, GH107, GH141, GH151, or GH168 families. Laminarin, the storage polysaccharide in algae, is composed of a linear backbone of 20-30 residues of β-1,3-linked-D-glucopyranose and a branched chain of β-1,6-linked-D-glucopyranose. The glycosidic bond in its backbone can be broken by endo-β-1,3-laminarinases (EC 3.2.1.6 and EC 3.2.1.39) and exo-β-1,3-glucanases (EC 3.2.1.58). The β-1,6-glucanase (EC 3.2.1.75) releases glucose by breaking the glycosidic bond in the branched chain of laminarin. Algae-derived polysaccharides and their oligosaccharides have shown health beneficial effects, such as immunomodulatory, antitumor, anti-inflammatory, and other activities, which possess great potential as alternative, renewable resources in cosmetics and functional foods. In this review, we mainly focus on the efficient degradation of brown algae, and summarize the mechanisms adopted by these enzymes for catalysis and conformation changes of substrate specific recognition. Furthermore, it will provide insights for the precise customization of oligosaccharides and the construction of industrial biorefinery platform, thereby promoting the efficient conversion of brown algae.
Abstract: Transient receptor potential vanilloid 1 (TRPV1) channel, belonging to transient receptor potential (TRP) channel superfamily, is a ligand gated non-selective cation channel which can be activated by multiple physical and chemical stimuli. The abnormal irritation and expression of TRPV1 is involved in pathogenesis of various diseases, so that TRPV1 channel is one of the important targets for drug research and development. For a long time, TRPV1 channel has attracted much attention because of the excellent analgesic effect of TRPV1 modulators. Due to the recognition of the research work of receptors for temperature and touch by the 2021 Nobel Prize in physiology or medicine, TRPV1 channel has become the focus of attention once again. It has been more than 20 years of the research for TRPV1, but the gating mechanism and drug development are still the difficulties. TRPV1 agonists can only be used for topical administration, and the antagonists could be used for oral administration. However, the problem with antagonists is that they cause hyperthermia and damage to noxious heat detection, which is the result of TRPV1 antagonists simultaneously affecting capsaicin, H+ and heat gating. Studies have shown that there are common processes of the three gating mechanisms, but no way to affect a single gating mechanism. From the angles of physiological function, gating mechanism and drug discovery, this paper reviews the distribution and expression, functions and features as well as structural characteristics of TRPV1 channel. This paper focuses on three gating mechanisms and the progress of TRPV1 modulators in drug discovery. TRPV1 modulators are a exceptional analgesia drug, and have been studied in cardiovascular diseases, itch, cough, psychiatric disorders and diabetes. With the emerging of artificial intelligence (AI)-assisted drug design and the continuous exploration of gating mechanism, we should have confidence in the future of TRPV1 modulators.
Abstract: Mitochondria are semi-autonomous cellular organelles responsible for oxidative phosphorylation (OXPHOS) and adenosine triphosphate (ATP) synthesis and are the powerhouses of cellular metabolism. Mitochondria are present in almost all eukaryotic organisms and are involved in apoptosis, calcium homeostasis, and regulation of the innate immune responses, which play a vital role in normal physiological processes. Mitochondria contain their own DNA that encodes 37 genes, including 2 rRNAs, 13 mRNA, and 22 tRNAs genes. Gene expression in mitochondria involves complex transcriptional and post-transcriptional processes, including cleavage of polycistronic RNA, RNA modification, and terminal processing of RNA. These processes require the coordinated spatiotemporal action of several enzymes, and many different factors are involved in the regulation and control of protein synthesis to maintain the stability and turnover of mitochondrial RNA. Disorders in mitochondrial RNA processing lead to changes in RNA expression profiles, interfere with protein translation, cause mitochondrial dysfunction, and result in a variety of mitochondria-related diseases. Although substantial progress has been made in the field of mitochondrial RNA processing and regulation, there are still many controversies and unknowns. This article reviews the latest research progress on mitochondrial DNA transcription, RNA post-transcriptional processing, and factors affecting RNA processing.
Abstract: With the development of biopharmacology, many therapeutic enzymes have been developed for treatment of various diseases, including metabolic diseases, thrombotic cardiovascular diseases and cancers. Most of the approved therapeutic enzymes are hydrolases, which are used to clean the toxic organic compounds and biomacromolecules in vivo, such as saccharides, lipids, proteins and their aggregates. Due to the high catalytic activity, affinity and specificity of enzyme towards substrate, enzyme therapy has a shorter time frame and fewer side reactions compared to other therapeutic approaches. However, there are several critical bottlenecks that limit the effectiveness of therapeutic enzymes, including immunogenicity, short circulation time, and lack of tissue specificity. Many approaches have been used to overcome these challenges. Several second generation therapeutic enzymes with significantly improved effectiveness have been developed using molecular engineering technologies such as glycan modification and pegylation. In addition, enzyme gene therapy becomes an emerging approach for treatment of diseases caused by enzymes deficiencies. Here, we reviewed the current enzyme-based therapeutics, and discussed its advantages, challenges and future perspectives.