Advances in protein chemistry and structural biology最新文献

Design of nanobodies have emerged as a new trend in antibody engineering, leveraging their unique properties including high stability, solubility, and the ability to bind to challenging targets such as membrane proteins. The application of computational strategies is pivotal for refining the efficacy of protein binders like nanobodies by broadening the sequence diversity, forecasting and bolstering their binding potency, selectivity, and overall performance. Recent advancements in computational techniques, such as machine learning algorithms and physics-based molecular modeling have significantly improved the design and development of nanobodies. These techniques allow for the precise modeling of nanobody-target interactions, enabling the identification of key residues responsible for binding and the prediction of potential conformational changes. In this study, five parental nanobodies binding to GPCRs and transporters were first used as template to create in silico nanobody libraries with the SCHEMA algorithm. Then, their binding potential and function to GPCRs or transporters were predicted by pre-trained machine learning models. The sequences above a threshold were processed with Rosetta and AlphaFold2 for 3D structural predictions. To further identify optimal conformations of specific nanobodies theoretically binding to 5-HT1AR or SERT, protein-protein docking by RosettaDock were performed. Finally, based on these model complexes, new nanobodies were redesigned, resulting in 21 and 18 candidates with enhanced binding to 5-HT1AR and SERT, respectively.

Immunotherapy is emerging as a novel and reliable therapeutic technique for treating diseases such as autoimmunity, HIV/AIDS, allergy and cancers. This approach works by modulating the patient's immune system, activating both the innate and humoral branches to combat life-threatening diseases. The foundation of immunotherapy began with the discovery and development of "serum therapy" by German physiologist Emil Von Behring who received the Nobel Prize in 1901 for his contributions to the treatment of diphtheria. Around the same time, Dr. William Coley expanded the field for cancer treatment by developing the first immune based cure for sarcomas using attenuated strains of bacteria injected directly into patient's tumours. As medical science advanced, a broader understanding of the immune system and its components led to the emergence of different immunotherapeutic techniques. These include adoptive cell transfer therapy, cytokine therapy, cancer vaccines, and antibody-drug conjugates. The chapter provides a comprehensive understanding of the history and the current techniques used in immunotherapy, detailing the principles behind their mechanisms and the types of diseases tackled by each immunotherapeutic technique. By examining the journey from early discoveries to modern advancements, the chapter highlights the transformative impact of immunotherapy on medical science and patient care.

Protein misfolding is a process in which an amino acid chain fails to attain its correct three-dimensional conformation, leading to structural abnormalities and functional impairment. This phenomenon plays a crucial role in various pathological conditions, including cancer, where it contributes to disease progression and cellular dysfunction. Cancer cells often secrete misfolded proteins, which actively interact with the tumor microenvironment (TME)-a complex network of stromal cells, immune cells, fibroblasts, and tumor cells-to influence key oncogenic processes. The consequences of protein misfolding extend beyond mere structural anomalies; they can drive tumorigenesis by enhancing cell proliferation, promoting metastasis, suppressing immune responses, and inducing chemoresistance. Given these critical implications, understanding the interplay between misfolded proteins and the TME offers valuable insights for therapeutic advancements. This chapter explores the molecular basis of protein misfolding, its role in modulating the TME, its impact on cancer progression, and emerging therapeutic strategies. Additionally, selected case studies are presented to highlight real-world applications of these concepts in cancer treatment and research.

Heat shock proteins (HSPs) are a conserved family of molecular chaperones that play a fundamental role in maintaining cellular homeostasis by facilitating protein folding, preventing aggregation, and mediating proteostasis under stress conditions. In cancer, HSPs are frequently overexpressed, contributing to tumor initiation, progression, metastasis, and therapeutic resistance. Their ability to stabilize oncoproteins, regulate apoptosis, and modulate immune responses makes them key players in tumorigenesis and promising therapeutic targets. This article comprehensively explores the classification and functional diversity of HSPs, highlighting their interactions with oncogenic pathways such as PI3K/AKT, MAPK, and p53. We discuss the dysregulation of prominent HSP families, including HSP27, HSP40, HSP60, HSP70, HSP90, and HSP110 across various cancer types, emphasizing their roles in promoting malignancy and modulating treatment responses. The chapter further elucidates how HSPs facilitate metabolic reprogramming in cancer cells, primarily through their interactions with key metabolic regulators, such as HIF-1α, c-Myc, and AKT, thereby sustaining the Warburg effect and promoting tumor cell survival. We examine their potential applications in precision oncology, including the development of HSP inhibitors, immunotherapies, and personalized treatment strategies. Additionally, we discuss novel therapeutic approaches, including chaperone-mediated autophagy modulation, HSP-based vaccines, and the integration of nanoparticle-mediated drug delivery systems. While HSP-targeted therapies offer significant promise, challenges such as drug resistance, toxicity, and compensatory upregulation of other chaperones remain formidable obstacles. Future research should focus on refining therapeutic selectivity, optimizing combination regimens, and utilizing advanced technologies, such as CRISPR-based gene editing and nanotechnology, to enhance treatment efficacy.

The concept of tumors as prion-like diseases similar to neurodegenerative disorders has gained attraction in recent years. p53, the most well-known tumor suppressor, has been extensively studied for its expression, mutations, and functions in various cancers. Recent findings reveal that p53 undergoes prion-like aggregation in tumors, leading to pathological amyloid fibril formation, functional alterations, and tumor progression. The mechanisms of p53 aggregation involve mutations, structural domains, isoforms, and external factors such as Zn²⁺ concentrations, pH, temperature, and chaperone abnormalities. While the role of p53 aggregation in tumors is increasingly recognized, controversies remain regarding its precise pathogenic mechanisms. This chapter reviews the structural features of p53 amyloid fibrils, its aggregation characteristics and effects, and the molecular mechanisms driving this phenomenon. Additionally, this chapter summarizes current therapeutic approaches targeting p53 aggregation and prion-like behavior, including small molecules and peptides designed to inhibit aggregation and restore p53's tumor suppressive function. By illuminating these aspects, this chapter aims to deepen our comprehension of how p53 aggregation disrupts its physiological functions. It also highlights the potential of targeting these aggregates as a novel therapeutic strategy in cancer treatment.

The nuclear pore complex, a large multimeric structure consists of numerous protein components, serves as a crucial gatekeeper for the transport of macromolecules across the nuclear envelope in eukaryotic cells. Dysfunction of the NPC has been implicated in various neurodegenerative diseases, including Alzheimer's disease. In AD, Tau aggregates interact with NPC proteins, known as nucleoporins, leading to disruptions in nuclear transport. Hyperphosphorylated Tau, a hallmark of AD pathology, interacts with central channel NUPs such as Nup62 and Nup98, causing cytoplasmic mis-localization of these proteins and impairing nuclear transport. Furthermore, Tau-NUP interactions promote Tau aggregation and the formation of neurofibrillary tangles, exacerbating neurodegeneration. Oligomeric Tau adheres to the lamin B receptor as well as nuclear lamin, preventing nucleocytoplasmic transport and resulting in heterochromatin unwinding, DNA damage, and neuronal death. The decrease in lamin B and increasing levels of lamin A along with C in AD-affected brain areas highlight the disease's intricacy. Furthermore, Tau internalization in the nucleus and interaction with nuclear pore complexes worsen NPC dysfunction, which contributes to neurotoxicity. Tau-DNA interactions suggest a chaperone-like role for Tau in DNA organization and repair, highlighting its involvement in maintaining genomic integrity. This review explores the intricate relationships between Tau, NPC components, and nuclear lamin in the context of AD, providing insights into the mechanisms underlying Tau-induced neurodegeneration and potential therapeutic targets.

Alzheimer's disease (AD) is associated with numerous risk factors, many of them attributed to exposure to harmful chemical substances at levels higher than recommended. The exposure can happen through sources like food, water and the environment. A significant number of the risk factors are modifiable, that is; their effects can be altered by minor modifications kept under consideration. This article describes four such modifiable risk factors- exposure to metals, high levels of the amino acid homocysteine in the plasma, exposure to pesticides and chronic consumption of alcohol. Heavy metals can enter our bodies through various sources like water, food (through the soil), and through sources like cigarette smoke. They can alter normal brain functioning and increase the risk for neurodegenerative diseases, including AD. High levels of plasma homocysteine can also be a risk factor, with various proposed potential mechanisms. Pesticide use may have some alarming consequences. The effects of many pesticides on increasing the chances for AD are proven by many studies, which also show that occupational exposure to them is a great risk. Another risk factor discussed is the heavy consumption of alcohol, which plays a role in altering the neurotransmitter release, which may lead to it being a risk factor for AD. The type of alcohol consumed also had varied effects. Some strategies to mitigate the risk of the modifiable risk factors have been discussed.

The structural landscape of proteins serves as a molecular blueprint for drug discovery, offering critical insights into target interactions, binding mechanisms, and rational drug design. Advances in structural biology, including X-ray crystallography, cryo-electron microscopy, and computational modeling, have revolutionized the understanding of protein conformations and dynamics. By integrating structural insights with computational drug design, researchers can predict ligand-binding affinities, optimize drug candidates, and enhance target specificity in an effective manner. This approach has proven instrumental in developing novel therapeutics for diseases ranging from cancer to neurodegenerative disorders. Furthermore, techniques like structure-based drug discovery (SBDD), Ligand based drug design (LBDD), Pharmacophore based drug discovery and molecular dynamics enables the identification of allosteric sites, fostering the development of selective modulators with improved efficacy and reduced off-target effects. This review highlights the pivotal role of protein structure analysis in modern drug discovery, emphasizing its applications in hit identification, lead optimization, and the design of precision therapeutics. Understanding protein structure at atomic resolution remains the cornerstone of rational drug design, paving the way for more effective and personalized therapeutics.

Antibodies are important functional proteins widely used in the prevention, diagnosis, and treatment of diseases. Heavy-chain single-domain antibodies (VHHs) derived from camels, also known as nanobodies (Nbs), are gradually becoming alternative options to full-length antibodies (VHHs) due to their small molecular weight, high stability, and good affinity. The structure of Nb includes framework regions (FRs) and complementarity-determining regions (CDRs). Currently, the prediction of CDRs structures in Nbs remains a challenge. Based on the different lengths and residue arrangements of CDR3, which form different antigen-binding surfaces, Nbs can be classified into three major categories: concave, loop, and convex. In this study, we selected representative Nbs with known structures from each category (Nb32, Nb80, and Nb35) and systematically studied their structures, especially the prediction accuracy of CDR3, using two strategies: physics-based simulations (homology modeling + molecular dynamics simulation) and deep learning (AlphaFold2 and RoseTTAFold). By comparing and analyzing the prediction results with experimental structures, we provided suggestions for accurately predicting the structures of different categories of Nbs and proposed the viewpoint that the formation of the binding surface between Nbs and target proteins requires proteins through an induced fit mechanism.

Klebsiella pneumoniae, a Gram-negative bacterium, poses a significant public health threat due to its resistance to various antibiotics, including β-lactams and carbapenems. This resistance is mainly due to the production of Klebsiella pneumoniae carbapenemases (KPCs). The issue of KPC-2 and its variant, KPC-3, by K. pneumoniae strains, results in resistance to the substrate imipenem and β-lactamase inhibitors. Using Schrodinger software, we performed a high-throughput virtual screening of 374 compounds from the ChemDiv natural compound library in this study, targeting KPC-2 and KPC-3. The top compounds were identified using Extra Precision (XP) mode. Molecular dynamics simulations (MDS) were performed for 500 ns using GROMACS. Among the compounds, N075-0013 and N098-0051 for KPC-2 and N025-0014 and N099-0011 for KPC-3 exhibited binding energies ranging from -5.40 to -7.01 kcal/mol against both KPC-2 and KPC-3. The complexes formed with these compounds remained stable in their dynamic environments, suggesting their potential as effective inhibitors of KPC-2 and KPC-3. These results underscore the potential therapeutic promise of these compounds, justifying further in vitro and in vivo validation for their development as inhibitors of Klebsiella pneumoniae carbapenemases.