The design of a new truncated and engineered alpha1-antitrypsin based on theoretical studies: an antiprotease therapeutics for pulmonary diseases

Exploring Proteases as Alternative Molecular Targets to Tackle Inflammation in Cystic Fibrosis Respiratory Infections

Cystic fibrosis (CF) is characterized by chronic respiratory infections and excessive inflammation, driven by both host- and pathogen-derived proteases. The dysregulated activity of proteolytic enzymes such as neutrophil elastase (NE), cathepsin G, and matrix metalloproteases (MMPs) degrades lung tissue, exacerbates airway remodeling, and perpetuates inflammatory cycles. Concurrently, bacterial proteases from pathogens such as Pseudomonas aeruginosa and Staphylococcus aureus contribute to immune evasion and tissue destruction, compounding disease severity. Despite advances in antimicrobial and anti-inflammatory therapies, protease-driven lung damage remains a critical challenge. This review examines the dual role of host and bacterial proteases in CF pathophysiology, highlighting emerging protease-targeted therapies aimed at mitigating lung damage and inflammation. Strategies explored include the inhibition of NE, MMPs, and bacterial proteases, with a focus on innovative therapeutic approaches such as dual-function inhibitors, biologics, and advanced drug delivery systems. By restoring the protease-antiprotease balance, these interventions offer the potential to improve clinical outcomes and quality of life for CF patients.

Recent Advances of Proteomics in Management of Acute Kidney Injury

Acute Kidney Injury (AKI) is currently recognized as a life-threatening disease, leading to an exponential increase in morbidity and mortality worldwide. At present, AKI is characterized by a significant increase in serum creatinine (SCr) levels, typically followed by a sudden drop in glomerulus filtration rate (GFR). Changes in urine output are usually associated with the renal inability to excrete urea and other nitrogenous waste products, causing extracellular volume and electrolyte imbalances. Several molecular mechanisms were proposed to be affiliated with AKI development and progression, ultimately involving renal epithelium tubular cell-cycle arrest, inflammation, mitochondrial dysfunction, the inability to recover and regenerate proximal tubules, and impaired endothelial function. Diagnosis and prognosis using state-of-the-art clinical markers are often late and provide poor outcomes at disease onset. Inappropriate clinical assessment is a strong disease contributor, actively driving progression towards end stage renal disease (ESRD). Proteins, as the main functional and structural unit of the cell, provide the opportunity to monitor the disease on a molecular level. Changes in the proteomic profiles are pivotal for the expression of molecular pathways and disease pathogenesis. Introduction of highly-sensitive and innovative technology enabled the discovery of novel biomarkers for improved risk stratification, better and more cost-effective medical care for the ill patients and advanced personalized medicine. In line with those strategies, this review provides and discusses the latest findings of proteomic-based biomarkers and their prospective clinical application for AKI management.

Binding energy analysis and molecular dynamic simulation studies of the designed orally active, non-toxic GABARAP modulators

Epilepsy is a severe neurological disorder that occurs when the communication between the neurons is disturbed. Gamma-amino butyric acid-associated protein (GABARAP) plays a key role in balancing Gamma-aminobutyric acid-A (GABA(A)) receptor functions of inhibiting the neurotransmission and controlling the seizure. In this study, we introduce the derivatives of the selected anti-epileptic drugs, namely Felbamate and Clobazam, by substituting different hydrophilic and hydrophobic groups at the specified positions. Molecular docking studies between the derivatives and GABARAP were carried out using PyRx software. The interacting residues were identified from LigPlot⁺. Drug-likeness, drug-related properties, and toxic endpoints of each derivative were analyzed using the SwissADME, Osiris property explorer, and ProTox-II servers. After analyzing the binding energy, drug-properties, and toxicity, the best five derivatives of Felbamate and Clobazam were selected. Molecular Dynamic simulation studies involving the target-ligand interaction were carried out for 100 nanoseconds using GROMACS 2018. The root mean square deviation, root mean square fluctuation, radius of gyration, Solvent accessible area, Energy plots and trajectories of the ten GABARAP complexes of the derivatives, and two GABARAP complexes of parent drugs were compared and critically analyzed. Among the five Felbamate derivatives, F7 formed the most stable complex with GABARAP. Among the five Clobazam derivatives, C27, C33 and C32 showed stable GABARAP interaction. In light of the above systematic computational analysis, we propose F7, C27, C33, and C32 as the potential anti-epileptic drug candidates for developing novel therapeutics. The substitution of hydrophobic groups at para position on benzene ring has promoted strong binding to GABARAP. Communicated by Ramaswamy H. Sarma.

Augmentation therapy with alpha 1-antitrypsin: present and future of production, formulation, and delivery

Alpha 1-antitrypsin is one of the first protein therapeutics introduced on the market - more than 30 years ago - and, to date, it is indicated only for the treatment of the severe forms of a genetic condition known as alpha-1 antitrypsin deficiency. The only approved preparations are derived from plasma, posing potential problems associated with its limited supply and high processing costs. Moreover, augmentation therapy with alpha 1-antitrypsin is still limited to intravenous infusions, a cumbersome regimen for patients. Here, we review the recent literature on its possible future developments, focusing on i) the recombinant alternatives to the plasma-derived protein, ii) novel formulations, and iii) novel administration routes. Regulatory issues and the still unclear noncanonical functions of alpha 1-antitrypsin - possibly associated with the glycosylation pattern found only in the plasma-derived protein - have hindered the introduction of new products. However, potentially new therapeutic indications other than the treatment of alpha-1 antitrypsin deficiency might open the way to new sources and new formulations.

Reviewing the experimental and mathematical factors involved in tight binding inhibitors Ki values determination: The bi-functional protease inhibitor SmCI as a test model

Different methodologies for determining the dissociation equilibrium constant (K_i) of protein tight binding inhibitors are frequently found in the scientific literature. Taking into account that the K_i value is the main parameter characterizing the inhibition strength, its determination often represents the first step during the characterization of a potential drug. The purpose of this review is to summarize the current information related to tight binding inhibitors K_i values determination and discuss about the importance of different factors as the enzyme concentration, the inhibitor concentration dilution series, the enzyme-inhibitor incubation time and the dose-response data mathematical fitting. For this aim, the bi-functional SmCI protease inhibitor is used as a tool for exemplifying the experimental and mathematical steps performed during tight binding inhibitors K_i values determination. In addition, the natural and the different recombinant forms of SmCI were used to go deeply into the comparison of some mathematic approaches that are frequently used in the literature. Finally, other biochemical techniques that could be potentially used for tight binding inhibitors K_i values determination are also commented.

Computational modeling helps uncover mechanisms related to the progression of emphysema

Emphysema is a progressive disease characterized by deterioration of alveolar structure and decline in lung function. While morphometric and molecular biology studies have not fully uncovered the underlying mechanisms, they have produced data to advance computational modeling. In this review, we discuss examples in which modeling has led to novel insight into mechanisms related to disease progression. Finally, we propose a general scheme of multiscale modeling approach that could help unravel the progressive nature of emphysema and provide patient specific mechanisms perhaps suitable for use in treatment therapies.

Proteolytic and N-glycan processing of human α1-antitrypsin expressed in Nicotiana benthamiana

Plants are increasingly being used as an expression system for complex recombinant proteins. However, our limited knowledge of the intrinsic factors that act along the secretory pathway, which may compromise product integrity, renders process design difficult in some cases. Here, we pursued the recombinant expression of the human protease inhibitor α1-antitrypsin (A1AT) in Nicotiana benthamiana. This serum protein undergoes intensive posttranslational modifications. Unusually high levels of recombinant A1AT were expressed in leaves (up to 6 mg g(-1) of leaf material) in two forms: full-length A1AT located in the endoplasmic reticulum displaying inhibitory activity, and secreted A1AT processed in the reactive center loop, thus rendering it unable to interact with target proteinases. We found that the terminal protein processing is most likely a consequence of the intrinsic function of A1AT (i.e. its interaction with proteases [most likely serine proteases] along the secretory pathway). Secreted A1AT carried vacuolar-type paucimannosidic N-glycans generated by the activity of hexosaminidases located in the apoplast/plasma membrane. Notwithstanding, an intensive glycoengineering approach led to secreted A1AT carrying sialylated N-glycan structures largely resembling its serum-derived counterpart. In summary, we elucidate unique insights in plant glycosylation processes and show important aspects of postendoplasmic reticulum protein processing in plants.