Peeping into human renal calcium oxalate stone matrix: characterization of novel proteins involved in the intricate mechanism of urolithiasis

Targeting protein receptors and enzymes for precision management of urolithiasis: A comprehensive review

Urolithiasis, characterized by the formation of solid crystalline structures within the urinary tract, presents a significant global health burden with high recurrence rates and limited treatment efficacy. Recent research has identified various protein receptors and enzymes implicated in the pathogenesis of urolithiasis, offering potential targets for therapeutic intervention. Protein receptors such as the calcium-sensing receptor and vasopressin V2 receptor play crucial roles in regulating urinary calcium excretion and water reabsorption, respectively, influencing stone formation. Additionally, modulation of receptors like the angiotensin II receptor and aldosterone receptor can impact renal function and electrolyte balance, contributing to stone prevention. Furthermore, enzymes such as urease inhibitors and xanthine oxidase inhibitors offer targeted approaches to prevent the formation of specific stone types. This review discusses the potential of targeting these receptors and enzymes for the treatment of urolithiasis, exploring associated drugs and their mechanisms of action. Despite promising avenues for personalized and precision medicine approaches, challenges such as the need for robust clinical evidence and ensuring cost-effectiveness must be addressed for the translation of these interventions into clinical practice. By overcoming these challenges, receptor-targeted therapies and enzyme inhibitors hold promise for revolutionizing the management of urolithiasis and reducing its global burden.

Protective Role of Rosmarinic Acid in Experimental Urolithiasis: Understanding Its Impact on Renal Parameters

This study aimed to assess the ability of rosmarinic acid (RA) to prevent kidney stone formation in an ethylene glycol and ammonium chloride (EG/AC) model. There was an increase in diuresis in the normotensive (NTRs) and hypertensive rats (SHRs) treated with hydrochlorothiazide (HCTZ) and exposed to EG/AC, while RA restored urine volume in NTRs. The EG/AC groups exhibited lower urine pH and electrolyte imbalance; these parameters were not affected by any of the treatments. Both HCTZ+EG/AC and RA+EG/AC reduced calcium oxalate crystal formation in NTR and SHR urine. Kidney tissue analysis revealed alterations in oxidative stress and inflammation parameters in all EG/AC-receiving groups, with RA enhancing antioxidant defenses in SHRs. Additionally, crystals were found in the kidney histology of all EG/AC-exposed groups, with reduced Bowman's capsule areas in NTRs and SHRs. The NTR VEH+EG/AC group showed intense renal damage, while the others maintained their structures, where treatments with HCTZ and RA were fundamental for kidney protection in the NTRs. Docking analysis showed that RA exhibited good binding affinity with matrix metalloproteinase-9, phosphoethanolamine cytidylyltransferase, and human glycolate oxidase enzymes. The data disclosed herein underscore the importance of further research to understand the underlying mechanisms better and validate the potential of RA for clinical use.

Identification of novel inhibitor against human phosphoethanolamine cytidylyltransferase from phytochemicals of Citrus sinensis peel extract by in vitro and in silico approach

Kidney stone is a major global menace that demands research on nonsurgical treatment involving biological compounds for the benefit of the patients. Among the biological extracts, citric acid is traditionally used to dissolve kidney stones. The current research focuses on evaluating the in vitro anti-urolithiatic activity and in silico study of ethanolic extract of Citrus sinensis (ECS) peel against c: phosphoethanolamine cytidylyltransferase (PCYT). The diuretic activity was evaluated using in vitro model against the synthesized calcium oxalate crystals and cytotoxicity study in Madin-Darby canine kidney cell lines. The phytochemicals were identified using gas chromatography-mass spectroscopy. The interaction mechanism was studied using computational docking studies to confirm their involvement in the dissolution of calcium oxalate kidney stones. Further molecular properties, drug-likeness, ADME (absorption, distribution, metabolism, and excretion), and toxicity analysis were followed for the ligands using software tools. 5-Hydroxymethylfurfural, 2,4-di-tert-butylphenol, 2-methoxy-4-vinylphenol, 6-octen-1-ol, 3,7-dimethyl-, acetate (citronellyl acetate), 3',5'-dimethoxyacetophenone, and ethyl alpha-d-glucopyranoside showed good binding affinities against PCYT. Moreover, the docking studies showed the ligand 3',5'-dimethoxyacetophenone has the highest binding energy (-6.68 kcal/mol) for human CTP. The present investigation concludes that these compounds of C. sinensis peel extract compounds are responsible as novel inhibitors against human CTP and extend their use in the pharmaceutical drug development process.

Inhibitory activity of Enhydra fluctuans Lour. on calcium oxalate crystallisation through in silico and in vitro studies

The decoction of the whole plant of Enhydra fluctuans is used ethno medicinally by various tribes for the treatment of kidney stones and urinary problems. However, no scientific studies were carried out to delineate its influence on urinary stone formation and crystallisation. Hence, the present study is proposed to investigate the effect of the aqueous extract of Enhydra fluctuans extract on in vitro crystallisation of calcium oxalate. The present study also evaluated. in silico studies of the metabolites with the target proteins present in the renal calcium oxalate stone matrix. The plant material was subjected to decoction to obtain an aqueous extract. The effect of the extract on calcium oxalate crystallization was evaluated by in vitro nucleation and aggregation assays. Further, the metabolites present in E. fluctuans were mined from the existing literature and their number was found to be 35. The selected 35 metabolites of E. fluctuans were subjected to molecular docking with the 5 proteins which are known to be responsible for calcium oxalate crystal growth. Results of in vitro studies indicated that the extract (50, 100, and 200 μg/mL) and standard drug cystone (1,000 μg/mL) exhibited an inhibitory role in the nucleation process where the percentage inhibitions were 52.69, 43.47, 21.98, and 31.67 μg/mL respectively. The results of molecular docking studies revealed that 2 out of 35 metabolites i.e. Baicalein-7-O-diglucoside and 4',5,6,7-Tetrahydroxy-8-methoxy isoflavone-7-O-beta-D- galactopyranosyl-(1→3)-O-beta-D-xylopyranosyl-(1→4)- O-alpha-L-rhamnopyranoside showed modulatory effects on the four renal stone matrix-associated protein (Human CTP: Phosphoethanolamine Cytidylyltransferase (Protein Data Bank ID: 3ELB), UDP glucose: glycoprotein glucosyltransferase 2 (Gene: UGGT2) (AlphaFold) and RIMS-binding protein 3A (Gene: RIMBP3) (AlphaFold), and Ras GTPase activating-like protein (PDB: 3FAY) based on their docking scores which indicates that they may inhibit the crystallization process. Findings from this study show that Enhydra fluctuans may be effective in the prevention of the crystallization of calcium oxalate. However, further, in vivo studies as well as molecular studies are needed to be conducted to confirm and strengthen its anti-urolithiatic activity and to elucidate the possible mechanism of action involved therein.

Comparison of cat and human calcium oxalate monohydrate kidney stone matrix proteomes

Despite its critical nature, the role of matrix in calcium oxalate stone formation is poorly understood. The wide diversity of proteins comprising matrix has contributed to the ambiguity. This study compares the protein distributions measured by mass spectrometry in human calcium oxalate stone matrix to that observed in cat stone matrix, because cats share many clinical characteristics of their stone disease with humans. The observed protein distributions were analyzed in the context of a recent model based on the aggregation of strongly anionic and strongly cationic proteins which includes selective adsorption of other proteins based on total charge. Matrix protein distributions shared many common features between species, including enrichment of both strongly anionic and strongly cationic proteins, increased total charge in matrix proteins compared to urine proteins, and a high degree of similarity of prominent strongly anionic proteins in the matrix of both species. However, there was weaker overlap of the specific dominant proteins in other regions of the net charge distribution. Collectively, these observations support the conceptual model where the strongly anionic proteins associate most strongly with the calcium oxalate crystal surfaces, while the other proteins associate with the strongly anionic proteins through non-specific, charge interactions with each other to create stones. Also, cats appear to be the best animal model of human stone disease identified to date based on these similarities.

On the protein content of kidney stones: an explorative study

OBJECTIVES

Kidney stone formation is complex; urinary protein inhibitors play a major role in natural defense against stone formation. Using attenuated total-reflectance Fourier-transform infrared (ATR-FTIR) spectroscopy of kidney stones, proteins are usually not quantified and often reported as 'organic matrix', for which there is little attention: treatment of urolithiasis is based on the nature of the major organic/inorganic stone compound. Literature no longer regards urinary proteins as innocent bystander, but highlights the role of proteins as urolithiasis modulators. We explored the potential significance of the protein content of kidney stones.

METHODS

800 stones were analyzed using ATR-FTIR spectroscopy; spectra were corrected for protein content. The ratio of the amide I peak (1655 cm^-1) divided by the maximum peak was calculated. A subgroup of stones (n = 43) was weighed; protein concentration was assayed. Kidney stone composition was taken into account when calculating protein concentration. Electrophoresis was implemented to investigate the protein bands. Multiple regression analysis was carried out to study the influence of various demographic variables (age, gender, stone type) on protein concentration.

RESULTS

Protein concentration showed a marked variation according to the stone composition. High relative protein content (>0.4% stone mass) was found in mixed calcium apatite/calcium oxalate dihydrate stones, mixed calcium oxalate dihydrate/calcium oxalate monohydrate/calcium apatite stones, and mixed calcium oxalate monohydrate/brushite stones, whereas lower protein percentages were found in cystine, urate, and calcium oxalate monohydrate stones. Protein concentration was dependent of the patient's age.

CONCLUSION

ATR-FTIR is a practical way for assessing protein concentration in kidney stones.

LIST OF ABBREVIATIONS

A: absorbance; as, asymmetric vibrations; ATR-FTIR, attenuated total-reflectance Fourier-transform infrared; β, standardized regression coefficient; CAP, calcium apatite; COD, calcium oxalate dihydrate; COM, calcium oxalate monohydrate; CV, coefficient of variation; δ, bending vibrations; ELISA, enzyme-linked immunosorbent assay; IQR, interquartile range; IR, infrared; LOD, limit of detection; LOQ, limit of quantification; MIR, mid-infrared; N or n, amount; r, correlation; r², coefficient of determination; s, symmetric vibrations; SD, standard deviation; SE, standard error; THP, Tamm-Horsfall protein; UA, uric acid; V, stretching vibrations; VIF: variance inflation factor; ZnSe, zinc selenide.

Oxidative Modifications Switch Modulatory Activities of Urinary Proteins From Inhibiting to Promoting Calcium Oxalate Crystallization, Growth, and Aggregation

The incidence/prevalence of kidney stone disease has been increasing around the globe, but its pathogenic mechanisms remained unclear. We evaluated effects of oxidative modifications of urinary proteins on calcium oxalate (CaOx) stone formation processes. Urinary proteins derived from 20 healthy individuals were modified by performic oxidation, and the presence of oxidatively modified urinary proteins was verified, quantified, and characterized by Oxyblot assay and tandem MS (nanoLC-electrospray ionization-linear trap quadrupole-Orbitrap-MS/MS). Subsequently, activities of oxidatively modified urinary proteins on CaOx stone formation processes were examined. Oxyblot assay confirmed the marked increase in protein oxidation level in the modified urine. NanoLC-electrospray ionization-linear trap quadrupole-Orbitrap-MS/MS identified a total of 193 and 220 urinary proteins in nonmodified and modified urine samples, respectively. Among these, there were 1121 and 5297 unambiguous oxidatively modified peptides representing 42 and 136 oxidatively modified proteins in the nonmodified and modified urine samples, respectively. Crystal assays revealed that oxidatively modified urinary proteins significantly promoted CaOx crystallization, crystal growth, and aggregation. By contrast, the nonmodified urinary proteins had inhibitory activities. This is the first direct evidence demonstrating that oxidative modifications of urinary proteins increase the risk of kidney stone disease by switching their modulatory activities from inhibiting to promoting CaOx crystallization, crystal growth, and aggregation.

Protein primary structure correlates with calcium oxalate stone matrix preference

Despite the apparent importance of matrix proteins in calcium oxalate kidney stone formation, the complexity of the protein mixture continues to elude explanation. Based on a series of experiments, we have proposed a model where protein aggregates formed from a mixture containing both strongly charged polyanions and strongly charged polycations could initiate calcium oxalate crystal formation and crystal aggregation to create a stone. These protein aggregates also preferentially adsorb many weakly charged proteins from the urine to create a complex protein mixture that mimics the protein distributions observed in patient samples. To verify essential details of this model and identify an explanation for phase selectivity observed in weakly charged proteins, we have examined primary structures of major proteins preferring either the matrix phase or the urine phase for their contents of aspartate, glutamate, lysine and arginine; amino acids that would represent fixed charges at normal urine pH of 6-7. We verified enrichment in stone matrix of proteins with a large number of charged residues exhibiting extreme isoelectric points, both low (pI<5) and high (pI>9). We found that the many proteins with intermediate isoelectric points exhibiting preference for stone matrix contained a smaller number of charge residues, though still more total charges than the intermediate isoelectric point proteins preferring the urine phase. While other sources of charge have yet to be considered, protein preference for stone matrix appears to correlate with high total charge content.

Kidney stone proteomics: an update and perspectives

INTRODUCTION

Main problems of kidney stone disease are its increasing prevalence and high recurrence rate after calculi removal in almost all areas around the globe. Despite enormous efforts in the past, its pathogenic mechanisms remain unclear and need further elucidations. Proteomics has thus become an essential tool to unravel such sophisticated disease mechanisms at cellular, subcellular, molecular, tissue, and whole organism levels.

AREAS COVERED

This review provides abrief overview of kidney stone disease followed by updates on proteomics for investigating urinary stone modulators, matrix proteins, cellular responses to different types/doses of calcium oxalate (CaOx) crystals, sex hormones and other stimuli, crystal-cell interactions, crystal receptors, secretome, and extracellular vesicles (EVs), all of which lead to better understanding of the disease mechanisms. Finally, the future challenges and translation of these obtained data to the clinic are discussed.

EXPERT OPINION

Knowledge from urinary proteomics for exploring the important stone modulators (either inhibitors or promoters) will be helpful for early detection of asymptomatic cases for prompt prevention of symptoms, complications, and new stone formation. Moreover, these modulators may serve as the new therapeutic targets in the future for successful treatment and prevention of kidney stone disease by medications or other means of intervention.

Human kidney stone matrix proteins alleviate hyperoxaluria induced renal stress by targeting cell-crystal interactions

Increased levels of urinary oxalate also known as hyperoxaluria, increase the likelihood of kidney stone formation through enhanced calcium oxalate (CaOx) crystallization. The management of lithiatic renal pathology requires investigations at the initial macromolecular stages. Hence, the current study was designed to unravel the protein make-up of human kidney stones and its impact on renal cells' altered proteome, induced as the consequence of CaOx injury. CaOx kidney stones were collected from patients; stones were pooled for entire cohort, followed by protein extraction. Immunocytochemistry, RT-PCR and flow-cytometric analysis revealed the promising antilithiatic activity of kidney stone matrix proteins. The iTRAQ analysis of renal cells showed up-regulation of 12 proteins and down-regulation of 41 proteins due to CaOx insult, however, this differential expression was normalized in the presence of kidney stone matrix proteins. Protein network analysis revealed involvement of up-regulated proteins in apoptosis, calcium-binding, inflammatory and stress response pathways. Moreover, seven novel antilithiatic proteins were identified from human kidney stones' matrix: Tenascin-X-isoform2, CCDC-144A, LIM domain kinase-1, Serine/Arginine receptor matrix protein-2, mitochondrial peptide methionine sulfoxide reductase, volume-regulated anion channel subunit-LRRC8A and BMPR2. In silico analysis concluded that these proteins exert antilithiatic potential through crystal binding, thereby inhibiting the crystal-cell interaction, a pre-requisite to initiate inflammatory response. Thus, the outcomes of this study provide insights into the molecular events of CaOx induced renal toxicity and subsequent progression into nephrolithiasis.

Inhibitive Effects of Huashi Pill on Formation of Renal Stones by Modulating Urine Biochemical Indexes and Osteopontin in Renal Stone Rat Models

Background

Renal stones are the accumulated or deposited crystals that form and appear in supersaturated urine. This study aimed to the investigate the therapeutic effects of Huashi Pill on clearance of renal stones.

Material/Methods

Sprague Dawley rats were divided into normal control, positive control, low-dosage Huashi Pill, medium-dosage Huashi Pill, and high-dosage Huashi Pill groups. A renal rat model was established by using ethylene glycol, ammonium chloride, and calcium gluconate. The urinary pH, urine protein, and uric acid levels, as well as the calcium, magnesium, and phosphorus levels were examined. The blood urea nitrogen (BUN) and creatinine (Cr) levels were also evaluated. Aspartate aminotransferase (AST), alanine aminotransferase (ALT), and total bilirubin (TBIL) levels were evaluated. Crystal formation and calcium deposits were examined using hematoxylin and eosin (H and E) staining and von Kossa staining, respectively. Osteopontin (OPN) expression was evaluated with quantitative real-time polymerase chain reaction assay and immunohistochemical assay.

Results

A renal stone rat model was successfully established. Huashi Pill significantly improved water and food intake and enhanced pH value of urine (P<0.05). Huashi Pill significantly improved the liver functions by decreasing ALT and TBIL levels (P<0.05). Huashi Pill regulated the amounts of microelements. Huashi Pill significantly decreased the urine protein, uric acid, and Cr levels (P<0.05). Huashi Pill inhibited formation of stone crystals and reduced the insoluble calcium deposition. Huashi Pill significantly downregulated expression of OPN in the kidney tissues of renal rat models (P<0.05).

Conclusions

Huashi Pill inhibited stone formation by regulating urine biochemical indexes and reducing OPN expression in kidney tissue in a renal stone rat model.

The role of macromolecules in the formation of kidney stones

The formation of crystal aggregates, one of the critical processes in kidney stone pathogenesis, involves interactions between crystals (predominantly calcium oxalate monohydrate, COM) and urinary constituents (e.g., proteins), which serve as an adhesive "glue" between crystals in stones. To develop a better understanding of the protein-crystal interactions that lead to crystal aggregation, we have measured the effect of model proteins on bulk COM crystal properties as well as their adsorption on crystal surfaces using three synthetic polyanions: poly(aspartic acid) (polyD), poly(glutamic acid) (polyE), and poly(acrylic acid) (polyAA). These anionic macromolecules reduced the amount of COM crystal aggregation in bulk solution to an extent similar to that observed for mixture of proteins from normal urine, with little difference between the polymers. In contrast, the polymers exhibited differences in measures of COM crystal growth. Polycations such as poly(arginine) (polyR) and poly(lysine) (polyK) reduced aggregation weakly and exerted negligible effects on crystal growth. All polyions were found to associate with COM crystal surfaces, as evidenced by changes in the zeta potential of COM crystals in electrophoretic mobility measurements. On the other hand, COM aggregation and possibly growth can be promoted by many binary mixtures of polycations and polyanions, which appeared to be mediated by polymer aggregate formation rather than loss of crystal charge stabilization. Similarly, crystal aggregation promotion behavior can be driven by forming aggregates of weakly charged polyanions, like Tamm-Horsfall protein, suggesting that polymer (protein) aggregation may play a critical role in stone formation. Sensitivity of polyanion-COM crystal surface interactions to the chemical composition of polymer side groups were demonstrated by large differences in crystal aggregation behavior between polyD and polyE, which correlated with atomic force microscopy (AFM) measurements of growth inhibition on various COM surfaces and chemical force microscopy (CFM) measurements of unbinding forces between COM crystal surfaces and AFM tips decorated with either carboxylate or amidinium moieties (mimicking polyanion and polyR side chains, respectively). The lack of strong interaction for polyE at the COM (100) surface compared to polyD appeared to be the critical difference. Finally, the simultaneous presence of polyanions and polycations appeared to alter the ability of polycations to mediate unbinding forces in CFM and promote crystal growth. In summary, polyanions strongly associated with COM surfaces and influenced crystallization, while polycations did not, though important differences were observed based on the physicochemical properties of polyanions. Observations suggest that COM aggregation with both polyanion-polycation mixtures and weakly charged polyanions is promoted by polymer aggregate formation, which plays a critical role in bridging crystal surfaces.

Natural promoters of calcium oxalate monohydrate crystallization

Crystallization is often facilitated by modifiers that interact with specific crystal surfaces and mediate the anisotropic rate of growth. Natural and synthetic modifiers tend to function as growth inhibitors that hinder solute attachment and impede the advancement of layers on crystal surfaces. There are fewer examples of modifiers that operate as growth promoters, whereby modifier-crystal interactions accelerate the kinetic rate of crystallization. Here, we examine two proteins, lysozyme and lactoferrin, which are observed in the organic matrix of three types of pathological stones: renal, prostatic, and pancreatic stones. This work focuses on the role of these proteins in the crystallization of calcium oxalate monohydrate (COM), the most prominent constituent of human kidney stones. Using a combination of experimental techniques, we show that these proteins, which are rich in l-arginine and l-lysine amino acids, promote COM growth. The synthesis and testing of peptides derived from contiguous segments of lysozyme's primary amino acid sequence revealed subdomains within the protein that operate either as an inhibitor or promoter of COM growth, with the latter exhibiting efficacies that nearly match that of the protein. We observed that cationic proteins promote COM growth over a wide range of modifier concentration, which differs from calcification promoters in the literature that exhibit dual roles as promoters and inhibitors at low and high concentration, respectively. This seems to suggest a unique mechanism of action for lysozyme and lactoferrin. Possible explanations for their effects on COM growth and crystal habit are proposed on the basis of classical colloidal theories and the physicochemical properties of peptide subdomains, including the number and spatial location of charged or hydrogen-bonding moieties.