Structural Insights into the Unique Activation Mechanisms of a Non-Classical Calpain and its Disease-Causing Variants

Vélez, Gabriel; Sun, Young Joo; Khan, Shaniya H.; Yang, Jing; Herrmann, Jonathan; Chemudupati, Teja; MacLaren, Robert E.; Gakhar, Lokesh; Wakatsuki, Soichi; Bassuk, Alexander G.; Mahajan, Vinit B.

doi:10.2139/ssrn.3469831

Cited by 5 publications

(17 citation statements)

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“…The models were in agreement and aligned well with minor variations in surface-exposed loop regions. The TMPRSS2-S1P model was then analyzed by ConSurf as previously described (31). The 600 sequences from our sequence-based phylogenetic analysis underwent MSA using MAFFT and conservation scores were calculated using the Bayesian method option in ConSurf.…”

Section: Structural Modeling Of Tmprss2-s1p Briefly a Blast Search mentioning

confidence: 99%

“…Structures were superimposed using PyMOL to calculate the pairwise root mean square deviation (RMSD) between protein alpha carbon atoms (Ca). A structural dissimilarity matrix (SDM) was constructed using the Ca RMSD values in order to generate a phylogenetic tree as previously described (31). To expedite the pairwise alignment process, we developed a Python-based script (named 3DPhyloFold) to perform the pairwise alignment of protein structures and generate an SDM.…”

Section: Structure-based Phylogenetic Analysismentioning

confidence: 99%

“…To expedite the pairwise alignment process, we developed a Python-based script (named 3DPhyloFold) to perform the pairwise alignment of protein structures and generate an SDM. The phylogenetic tree was constructed using the UPGMA (Unweighted Pair Group Method with Arithmetic Mean) method in MEGAX software as previously described (31). For comparison, the sequences from the corresponding structures were also analyzed by sequence-based phylogeny.…”

Section: Structure-based Phylogenetic Analysismentioning

confidence: 99%

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Structure-based phylogeny identifies avoralstat as a TMPRSS2 inhibitor that prevents SARS-CoV-2 infection in mice

Sun¹,

Vélez²,

Parsons³

et al. 2021

Journal of Clinical Investigation

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Drugs targeting host proteins can act prophylactically to reduce viral burden early in disease and limit morbidity, even with antivirals and vaccination. Transmembrane serine protease 2 (TMPRSS2) is a human protease required for SARS-CoV-2 viral entry and may represent such a target. We hypothesized that drugs selected from proteins related by their tertiary structure, rather than their primary structure, were likely to interact with TMPRSS2. We created a structure-based phylogenetic computational tool named 3DPhyloFold to systematically identify structurally similar serine proteases with known therapeutic inhibitors and demonstrated effective inhibition of SARS-CoV-2 infection in vitro and in vivo. Several candidate compounds, Avoralstat, PCI-27483, Antipain, and Soybean-Trypsin-Inhibitor, inhibited TMPRSS2 in biochemical and cell infection assays.Avoralstat, a clinically tested Kallikrein-related B1 inhibitor, inhibited SARS-CoV-2 entry and replication in human airway epithelial cells. In an in vivo proof of principle, Avoralstat significantly reduced lung tissue titers and mitigated weight-loss when administered prophylactically to SARS-CoV-2 susceptible mice indicating its potential to be repositioned for COVID-19 prophylaxis in humans.

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Section: Structural Modeling Of Tmprss2-s1p Briefly a Blast Search mentioning

confidence: 99%

Section: Structure-based Phylogenetic Analysismentioning

confidence: 99%

Section: Structure-based Phylogenetic Analysismentioning

confidence: 99%

See 1 more Smart Citation

Structure-based phylogeny identifies avoralstat as a TMPRSS2 inhibitor that prevents SARS-CoV-2 infection in mice

Sun¹,

Vélez²,

Parsons³

et al. 2021

Journal of Clinical Investigation

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“…Since the discovery of the first NIV-causing mutations, efforts have been taken to understand the structure, function, targets, and downstream signaling effectors of the CAPN5 protease (Bassuk et al, 2015;Gakhar et al, 2016;Mahajan et al, 2012;Schaefer et al, 2016;Wert et al, 2014Wert et al, , 2015Wert et al, , 2019. Our group solved the structure of the CAPN5 protease core domain (termed CAPN5-PC), a finding that furthers the study of NIV disease mechanisms (Velez et al, 2020). The wild-type CAPN5-PC structure revealed unique structural features compared with classical calpain cores and provided clues as to how NIV mutations would increase enzymatic activity (Figure 2A).…”

Section: Mechanistic Insights Into Niv Pathogenesismentioning

confidence: 99%

Molecular Surgery: Proteomics of a Rare Genetic Disease Gives Insight into Common Causes of Blindness

Vélez

Mahajan

2020

iScience

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Summary Rare diseases are an emerging global health priority. Although individually rare, the prevalence of rare “orphan” diseases is high, affecting approximately 300 million people worldwide. Treatments for these conditions are often inadequate, leaving the disease to progress unabated. Here, we review the clinical features and pathophysiology of neovascular inflammatory vitreoretinopathy (NIV), a rare inflammatory retinal disease caused by mutations in the CAPN5 gene. Although the prevalence of NIV is low (1 in 1,000,000 people), the disease mimics more common causes of blindness (e.g. uveitis, retinitis pigmentosa, proliferative diabetic retinopathy, and proliferative vitreoretinopathy) at distinct clinical stages. There is no cure for NIV to date. We highlight how personalized proteomics helped identify potential stage-specific biomarkers and drug targets in liquid vitreous biopsies. The NIV vitreous proteome revealed enrichment of molecular pathways associated with common retinal pathologies and implicated superior targets for therapeutic drug repositioning. In addition, we review our pipeline for collecting, storing, and analyzing ophthalmic surgical samples. This approach can be adapted to treat a variety of rare genetic diseases.

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“…7 Calpains are calcium-activated intracellular cysteine proteases. In mammals, there are so far 15 known members of the calpain family among which μ-calpain and m-calpain, also called calpain-1 and calpain 2, respectively, are recognized as abundantly and widely expressed species 8,9 For activation, μ-calpain and m-calpain require micro-and millimolar concentration of calcium ion in vitro, respectively. 10 Because the intracellular calcium ion concentration fluctuates at micromolar levels in vivo, it is proposed that phospholipids, a major component of cytoplasmic membranes, lower the [Ca 2+ ] required to activate calpain, and the proximity of the cytoplasmic membranes provides a favorable niche for calpain activation.…”

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confidence: 99%

The investigation of calpain in human placenta with fetal growth restriction

Goto

Ozaki

Ozawa

et al. 2020

American J Rep Immunol

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Problem The mechanism of fetal growth restriction (FGR) is not fully understood. In this study, we explored the contribution of the calpain‐calpastatin system and the activated states of calpains in human FGR placenta. Method of study The placentas were collected from patients of FGR (n = 17) and controls (n = 23) at elective cesarean sections in Nagoya City University Hospital and used for experiments upon informed consent. The existence and the expression of calpains and calpastatin in human placenta were compared between FGR and controls using immunohistochemistry, SDS‐PAGE, and Western blotting. Results Staining of calpains (pre‐, post‐μ‐calpain, pre‐, post‐m‐calpain, and calpain‐6) and calpastatin was observed in cytoplasm of trophoblast cells, both in FGR and control placenta. Pre‐μ‐calpain was located in the cytoplasm, and post‐μ‐calpain was located mainly in proximity to the cytoplasmic membrane. The expression of pre‐μ‐calpain was significantly higher (P < .001) and calpain‐6 was significantly lower (P = .01) in FGR placentas. The inactive μ‐calpain (80 kDa) was significantly elevated (P < .01), and active μ‐calpain (76 kDa) was significantly decreased (P = .01) in FGR placentas. Conclusion The results demonstrate that activation of μ‐calpain is suppressed in FGR placentas and that calpain‐6 in human placenta is involved in the pathology of FGR.

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Structural Insights into the Unique Activation Mechanisms of a Non-Classical Calpain and its Disease-Causing Variants

Cited by 5 publications

References 0 publications

Structure-based phylogeny identifies avoralstat as a TMPRSS2 inhibitor that prevents SARS-CoV-2 infection in mice

Structure-based phylogeny identifies avoralstat as a TMPRSS2 inhibitor that prevents SARS-CoV-2 infection in mice

Molecular Surgery: Proteomics of a Rare Genetic Disease Gives Insight into Common Causes of Blindness

The investigation of calpain in human placenta with fetal growth restriction

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