Searching glycolate oxidase inhibitors based on QSAR, molecular docking, and molecular dynamic simulation approaches

Using computer modeling to find new LRRK2 inhibitors for parkinson's disease

Parkinson's disease (PD) is a complex neurodegenerative disorder that affects multiple neurotransmitters, and its exact cause is still unknown. Developing new drugs for PD is a lengthy and expensive process, making it difficult to find new treatments. This study aims to create a detailed dataset to build strong predictive models with various machine learning algorithms. An ensemble modeling approach was employed to screen the DrugBank database, aiming to repurpose approved medications as potential treatments for Parkinson's disease (PD). The dataset was constructed using pIC50 values of various compounds targeting the inhibition of leucine-rich repeat kinase 2 (LRRK2). The best ensemble model showed exceptional predictive performance, with five-fold cross-validation and external validation metrics exceeding 0.8 (Q2cv = 0.864 and Q2ext = 0.873). The DrugBank screening resulted in three promising drugs-triamterene, phenazopyridine, and CRA_1801-with predicted pIC50 values greater than 7, warranting further investigation as novel PD treatments. Molecular docking and molecular dynamics simulations were performed to provide a comprehensive understanding of the interactions between LRRK2 and the inhibitors in the data set and best molecules of the screening. Free energy of binding calculation along with hydrogen bond occupancy analysis and RMSD of the ligand in the pocket show CRA_1801 as the best candidate to be repurposed as LRRK2 inhibitor.

The potential role of alkaline diets in prevention of calcium oxalate kidney stone formation

Formation of kidney stones is considered a major global problem. Diet plays an important role in the management of kidney stone formation. The main goal of the present research was to evaluate the protective role of fruit and vegetable mixtures as models of an alkaline diet on formation of kidney stones in rats and to conduct molecular docking study. The chemical compositions, phenolic compound profile, β-carotene content, vitamin C and antioxidant activity of both mixtures were assessed. Fruit (-42.419 ) and vegetable (-11.13) mixtures recorded a negative potential renal acid load in the presence of macro-/micro-nutrients, β-carotene and phenolic compounds; chlorogenic acid was the major content in both mixtures. Both mixtures exhibited high antioxidant activity. Molecular docking study proved that rutin displayed the highest binding affinities for glycolate oxidase (-11.8 kcal mol-1) and lactate dehydrogenase (-10.1 kcal mol-1). The kidney stone model in rats exhibited metabolic acidosis in the urinary profile through reduction of citrate; Ca, Mg and K excretion and elevation of oxalate, creatinine, creatinine clearance, uric acid, urea and protein. Additionally, there was a significant reduction in plasma Ca, Mg and K levels, while liver and kidney function parameters improved significantly. Fruit and vegetable mixtures as models of an alkaline diet proved improvement in all the parameters. Histopathological examination of kidney sections of the kidney stone model showed crystal deposition, inflammation, and severe necrosis. Kidney sections of alkaline diet models indicated mild and moderate changes. Conclusion: The results of this study proved that both alkaline diet models were effective in protecting against kidney stone formation in vivo and in molecular docking studies.

Opportunities in Primary and Enteric Hyperoxaluria at the Cross-Roads Between the Clinic and Laboratory

Hyperoxaluria is a condition in which there is a pathologic abundance of oxalate in the urine through either hepatic overproduction (primary hyperoxaluria [PH]) or excessive enteric absorption of dietary oxalate (enteric hyperoxaluria [EH]). Severity can vary with the most severe forms causing kidney failure and extrarenal manifestations. To address the current challenges and innovations in hyperoxaluria, the 14th International Hyperoxaluria Workshop convened in Perugia, Italy, bringing together international experts for focused presentation and discussion. The objective of the following report was to disseminate an overview of the proceedings and provide substrate for further thought. The format of this paper follows the format of the meeting, addressing, "PH type 1" (PH1) first, followed by "surgery, genetics, and ethics in PH", then "PH types 2 and 3," (PH2 and PH3) and, finally, "EH." Each session began with presentations of the current clinical challenges, followed by discussion of the latest advances in basic and translational research, and concluded with interactive discussions about prioritizing the future of research in the field to best serve the need of the patients.

Computational approaches for lead compound discovery in dipeptidyl peptidase-4 inhibition using machine learning and molecular dynamics techniques

The prediction of possible lead compounds from already-known drugs that may present DPP-4 inhibition activity imply a advantage in the drug development in terms of time and cost to find alternative medicines for the treatment of Type 2 Diabetes Mellitus (T2DM). The inhibition of dipeptidyl peptidase-4 (DPP-4) has been one of the most explored strategies to develop potential drugs against this condition. A diverse dataset of molecules with known experimental inhibitory activity against DPP-4 was constructed and used to develop predictive models using different machine-learning algorithms. Model M36 is the most promising one based on the internal and external performance showing values of Q2CV = 0.813, and Q2EXT = 0.803. The applicability domain evaluation and Tropsha's analysis were conducted to validate M36, indicating its robustness and accuracy in predicting pIC50 values for organic molecules within the established domain. The physicochemical properties of the ligands, including electronegativity, polarizability, and van der Waals volume were relevant to predict the inhibition process. The model was then employed in the virtual screening of potential DPP4 inhibitors, finding 448 compounds from the DrugBank and 9 from DiaNat with potential inhibitory activity. Molecular docking and molecular dynamics simulations were used to get insight into the ligand-protein interaction. From the screening and the favorable molecular dynamic results, several compounds including Skimmin (pIC50 = 3.54, Binding energy = -8.86 kcal/mol), bergenin (pIC50 = 2.69, Binding energy = -13.90 kcal/mol), and DB07272 (pIC50 = 3.97, Binding energy = -25.28 kcal/mol) seem to be promising hits to be tested and optimized in the treatment of T2DM. This results imply a important reduction in cost and time on the application of this drugs because all the information about the its metabolism is already available.

A molecular journey on the pathogenesis of primary hyperoxaluria

PURPOSE OF REVIEW

Primary hyperoxalurias (PHs) are rare disorders caused by the deficit of liver enzymes involved in glyoxylate metabolism. Their main hallmark is the increased excretion of oxalate leading to the deposition of calcium oxalate stones in the urinary tract. This review describes the molecular aspects of PHs and their relevance for the clinical management of patients.

RECENT FINDINGS

Recently, the study of PHs pathogenesis has received great attention. The development of novel in vitro and in vivo models has allowed to elucidate how inherited mutations lead to enzyme deficit, as well as to confirm the pathogenicity of newly-identified mutations. In addition, a better knowledge of the metabolic consequences in disorders of liver glyoxylate detoxification has been crucial to identify the key players in liver oxalate production, thus leading to the identification and validation of new drug targets.

SUMMARY

The research on PHs at basic, translational and clinical level has improved our knowledge on the critical factors that modulate disease severity and the response to the available treatments, leading to the development of new drugs, either in preclinical stage or, very recently, approved for patient treatment.

Navigating the Evolving Landscape of Primary Hyperoxaluria: Traditional Management Defied by the Rise of Novel Molecular Drugs

Primary hyperoxalurias (PHs) are inherited metabolic disorders marked by enzymatic cascade disruption, leading to excessive oxalate production that is subsequently excreted in the urine. Calcium oxalate deposition in the renal tubules and interstitium triggers renal injury, precipitating systemic oxalate build-up and subsequent secondary organ impairment. Recent explorations of novel therapeutic strategies have challenged and necessitated the reassessment of established management frameworks. The execution of diverse clinical trials across various medication classes has provided new insights and knowledge. With the evolution of PH treatments reaching a new milestone, prompt and accurate diagnosis is increasingly critical. Developing early, effective management and treatment plans is essential to improve the long-term quality of life for PH patients.