Advances in protein chemistry and structural biology最新文献

Protein molecules organize into an intricate alphabet of twenty amino acids and five architecture levels. The jargon "one structure, one functionality" has been challenged, considering the amount of intrinsically disordered proteins in the human genome and the requirements of hierarchical hetero- and homo-protein complexes in cell signaling. The assembly of large protein structures in health and disease is now viewed through the lens of phase separation and transition phenomena. What drives protein misfolding and aggregation? Or, more fundamentally, what hinders proteins from maintaining their native conformations, pushing them toward aggregation? Here, we explore the principles of protein folding, phase separation, and aggregation, which hinge on crucial events such as the reorganization of solvents, the chemical properties of amino acids, and their interactions with the environment. We focus on the dynamic shifts between functional and dysfunctional states of proteins and the conditions that promote protein misfolding, often leading to disease. By exploring these processes, we highlight potential therapeutic avenues to manage protein aggregation and reduce its harmful impacts on health.

Insulin and its analogue formulations are the main components in the therapy of insulin-dependent forms of diabetes. Insulin and its analogues can form amyloid-like aggregates during long-term storage and local concentration increases, leading to reduced therapeutic efficacy and potential side effects such as insulin amyloidosis. The aim of this study was to identify and propose new non-toxic inhibitors and preservatives to replace phenol in insulin formulations. The peptide FVNQH and phenol red were studied as promising inhibitors of fibril formation of insulin, lispro, and glargine in vitro using the specific amyloid dye thioflavin T. The peptide FVNQH and phenol red (0.5-1 mg/mL) showed a bacteriostatic effect on the E. coli K-12 strain after 24 h. The fibril-inhibiting and antimicrobial effects of these substances were similar to the effect of phenol at a concentration of 0.5 mg/mL. Thus, the identified inhibitors can potentially replace phenolic components in slowing amyloid aggregation and increase the stability of insulin and its analogues.

CD5 is a pan T-cell marker expressed by all T-cells and a subset of B-cells, i.e., B1a cells. The significance of CD5 is evident from its functions, starting from T-cell development, antigen priming, activation, and effector response to the maintenance of tolerance. Varying CD5 expression and signaling in response to TCR-pMHC complex avidity is associated with thymic selection, competency, and effector response. Altered CD5 expression is associated with immunological and diseased conditions such as CD5^-/low infiltrating T-cells in solid tumors, CD5^hi T-cells in anergy conditions, CD5^-/low phenotype of leukemic T-cells, high CD5 expression by regulatory T-cells, CD5^lowphenotype of autoreactive T-cells, etc. A low CD5 expression triggers activation-induced cell death upon antigenic stimulation. There are three forms of CD5: membrane CD5 (mCD5), intracellular CD5 (cCD5) and soluble CD5 (sCD5). mCD5 and cCD5 are generated from conventional and non-conventional mRNA variants, i.e., E1A and E1B, respectively. E1B variant encoding cCD5 is derived from a human endogenous retrovirus segment inserted 8.2 kb upstream to conventional E1A exon. Various conditions, such as leukemia, exposure to hydrocarbon, hypoxia, etc., can trigger E1B transcription and, thus, cCD5 expression. Blocking mCD5 with mAb can restore immune response, effectively targeting cancer. Understanding cCD5, linked to leukemogenesis, can offer new avenues of immunotherapy.

Cancer appears to be a significant global public health concern and most prevalent leading cause of death worldwide. Delays in the diagnosis and treatment may lead to an increase in the prevalence of advanced-stage disease and death. Therefore, creating innovative diagnostic instruments and treatments that demonstrate high effectiveness is imperative. The majority of malignancies have dysfunction in the p53 pathway. In addition, p53 becomes dysfunctional and tends to undergo misfolding and aggregation, resulting in the creation of amyloid aggregates. Efforts are underway to investigate methods for reinstating the regular functioning and manifestation of p53. In this study, we have investigated Heat shock proteins (HSPs), which are molecular chaperones that play a significant role in various cellular processes such as intercellular transportation, formation or disintegration of complex protein, stabilisation or degradation of aggregated or misfolded proteins and protein folding. HSP40, also known as JDPs, are distinguished by their highly conserved J-domains. These domains facilitate the ability to bind to HSP70 and as a co-chaperone enhance the activity of ATPase. Emerging evidence indicates that HSP70/JDPs can influence the levels and/or functions of both wild-type and mutant p53. Only a small number of HSP40/JDPs, including C7, C2, B9, B1, A3, and DNAJA1, have been seen to influence the functions of both WT-p53 and Mut-p53. However, out of the sixteen members, only these handful are implicated in the advancement of cancer. Therefore, studying other HSP40/JDPs that are involved in the advancement of cancer and the activities of p53 (both mutant and wild type), together with their related processes, would enhance our understanding of how cancer progresses, we might potentially speed up the development of innovative treatments for cancer. It is expected that pharmacological molecules and their analogues that specifically target p53 aggregation might be utilised with other anticancer drugs to address the issue of p53 aggregation.

Within the cellular milieu, protein molecules must fold into precise three-dimensional structures to attain functionality. Protein chains can assume many misfolded states during this critical process. Such errant configurations are unstable and can aggregate into toxic misfolded conformations. In protein misfolding disorders, polypeptides are folded in an aberrant manner, resulting in non-functional and often pathogenic states. Protein folding is fundamental to biological function, and disruption of the process can result in toxic aggregates, such as oligomers and amyloid fibrils, which are implicated in a variety of diseases, particularly neurodegenerative diseases such as Alzheimer's and Parkinson's. Here, we examine the delicate interplay of forces that determine the native conformation of proteins and how perturbations in this balance lead to disease. A critical aspect of our discussion is the cell's proteostasis network, a complex network of molecular chaperones and regulators responsible for regulating protein folding and maintaining the health of the cell. In this chapter, we discuss how intrinsic protein properties, post-translational modifications, and extrinsic environmental factors can destabilize proteins, thereby resulting in their misfolding. Several pathogenic mechanisms will be elucidated, including the progression from a misfolded protein to the development of disease phenotypes. Next, the chapter will present an overview of the current therapeutic approaches to mitigate the diseases caused by protein misfolding. Using the latest findings in clinical and experimental research, we will evaluate the therapeutic landscape, ranging from small-molecule inhibitors to chaperone-based therapies.

Protein aggregation research stands at the cutting edge of biomedical science, offering crucial insights into the molecular underpinnings of neurodegenerative and amyloid-associated diseases. Significant advancements in deciphering the structural, biophysical, and molecular intricacies of protein misfolding are driving the development of innovative therapies. Emerging approaches, from small molecule inhibitors to sophisticated polymer-based therapeutics, hold great promise for alleviating the toxic impacts of aggregation with the potential to prevent, delay, or even reverse disease progression. Despite these advances, the field contends with substantial challenges. The polymorphic and complex nature of protein aggregates poses major obstacles to both research and therapeutic design. Yet, interdisciplinary methodologies-integrating advanced spectroscopic, imaging, and computational tools-are creating new pathways to address these complexities, effectively bridging molecular breakthroughs and practical therapeutic applications. The rapid shift of foundational discoveries to clinical trials marks a pivotal step forward, instilling new hope for patients with protein aggregation disorders. Each breakthrough propels us closer to life-changing therapies that may reshape the outlook for these patients. The promise of precise and effective treatments is driving a transformative shift in medical science, establishing protein aggregation research as a crucial pillar in combating these challenging diseases and offering a beacon of hope for the future of neurodegenerative care.

Antibodies are a class of biomolecules armed with extraordinary diversity, unmatched in the biological world by any other class of molecules. This characteristic feature equips antibodies to recognize, bind, and eliminate an infinite number of pathogens/antigens facilitated by their effector functions. The repertoire of natural binding specificities of antibodies (Abs) is greater than the calculated estimate of ∼10¹² in humans, as a naive, single antigen-binding site may bind more than one antigen employing the plasticity in antigen-antibody interactions, potentiating Abs to fight infinite pathogenic insults and restrict the development of cancers. Additionally, advanced technological interventions, by allowing manipulation of the germline and acquired specificities of human/animal immunoglobulins (Ig) have contributed immensely to broaden their existing repertoire and scope of clinical applications. The available natural repertoire of Ig and Ig-like molecules in other animals, e.g., mice, horses, cows, pigs, rabbits, camels, llamas, etc., further diversified the source of unique antigen-binding specificities. The recombinant DNA technology, in association with hybridoma , transgenic, and phage display technologies, has helped create a parallel repertoire of unique antibody molecules [animal Abs, camelid heavy chain Abs (hcAbs), chimeric Abs, chimeric hcAbs, humanized Abs, humanized nanobody (Nb)-hcAbs, human Abs, etc.], monoclonal Ab (mAb) derived fragments [antigen-binding-fragment (Fab), single-chain-variable-fragment (scFv), variable-fragement (Fv), single-variable-domain of hcAbs (V_HH), bispecific scFv, diabodies, triabodies, intrabodies, bispecific Fabs, tri-specific Fabs, etc.), and immunoconjugates generated by fusing/conjugating mAb fragments with enzyme, toxin, prodrug etc., molecules. The current chapter provides a detailed description of the natural and engineered antibody repertoires and discusses various strategies using which these molecules are being inducted as novel immunotherapeutics for treating a significant number of human diseases.

Immunotherapy has emerged as a hallmark of hope in the formidable battle against solid tumors such as breast cancer, colorectal cancer, etc., with antibody-drug conjugates (ADCs) starting a new era of precision medicine. This chapter delves into the dynamic landscape of immunotherapeutic strategies, focusing on the transformative potential of ADCs. ADCs represent a combination of chemotherapy and immunotherapy, more innovative chemotherapy. We emphasize the intricate interplay between tumor biology and therapeutic intervention, uncovering the mechanisms underlying ADC efficacy and the hurdles they must overcome. Each facet of ADC development is carefully examined, from the delicate balance between payload potency and safety to the quest for enhanced tumor penetration. We also elucidate the synergistic potential of combining ADCs with existing modalities, including chemotherapy and radiation therapy, to amplify therapeutic outcomes while mitigating adverse effects. As we navigate the complexities of solid tumor oncology, a profound understanding of the immunotherapeutic potential of ADCs is gained, offering hope for a cure for patients and clinicians alike. Henceforth, we delve into this transformative journey as we advance in solid tumor treatment regimens using immunotherapy with ADCs, poised at the forefront of oncological innovation.

Nuclear receptors (NRs) are ligand-activated transcription factors that regulate gene expression in response to physiological signals, such as hormones and other chemical messengers. These receptors either activate or repress the transcription of target genes, which in turn promotes or suppresses physiological processes governing growth, differentiation, and homeostasis. NRs bind to specific DNA sequences and, in response to ligand binding, either promote or hinder the assembly of the transcriptional machinery, thereby influencing gene expression at the transcriptional level. These receptors are involved in a wide range of pathological conditions, including cancer, metabolic disorders, chronic inflammatory diseases, and immune system-related disorders. Modulation of NR function through targeted drugs has shown therapeutic benefits in treating such conditions. NR-targeted drugs, which either completely or selectively activate or block receptor function, represent a significant class of clinically valuable therapeutics. However, the pathways of NR-mediated gene expression and the resulting physiological effects are complex, involving crosstalk between various biomolecular components. As a result, NR-targeted drug discovery is challenging. With improved understanding of how NRs regulate physiological functions and deeper insights into their molecular structure, the process of NR-targeted drug discovery has evolved. While many traditional NR-targeting drugs are associated with side effects of varying severity, new drug candidates are being designed to minimize these adverse effects. Given that NR activity varies according to the tissue in which they are expressed and the specific isoform that is activated or repressed, achieving selectivity in targeting specific tissues and isoform classes may help reduce systemic side effects. In a recent breakthrough, the isoform-selective, hepato-targeted thyroid hormone-β agonist, Resmetirom (marketed as Rezdiffra), was approved for the treatment of non-alcoholic steatohepatitis. This chapter explores the structural and mechanistic principles guiding NR-targeted drug discovery and provides insights into recent developments in this field.

Research on the Alzheimer's disease (AD) has been going on for over 100 years, but there is yet to be found an effective cure that has passed all the clinical trials. However, many compounds have been explored for their effects on AD patients, compounds that could help ease the disease symptoms or help slow down the disease progression or reverse the effects of the disease. Small molecules like toluidine blue and melatonin are seen to be useful against AD. Natural compounds were seen to have an exceptional potential as therapeutics for AD. Highly branched polymers, dendrimers were also seen to be effective Tau and AD therapeutics as drug-delivery systems and on their own. Metal complexes and metal nanoparticles also showed success against AD. Synthesis of a bifunctional compound that was an effective chelating agent for Cu, useful against Tau and Amyloid-β (Aβ) and was catalysed by excess Cu metal present in association with Aβ was also done. It is necessary to take forward the effective therapeutics to further levels of clinical trials.