scholarly journals The Homology Modeling and Docking Investigation of Human Cathepsin B

2020 ◽  
Vol 10 (1) ◽  
pp. 26687
Author(s):  
Afshin Khara ◽  
Ehsan Jahangirian ◽  
Hossein Tarrahimofrad
Keyword(s):  
Amino Acids ◽  
Protease Inhibitors ◽  
Cystatin C ◽  
Active Site ◽  
Cathepsin B ◽  
Antigen Processing ◽  
3D Structure ◽  
Cysteine Proteases ◽  
Docking Studies ◽  
Alternative Methods

Background: Cathepsin B comprises a group of lysosomal cysteine proteases belonging to the Papain family; it has an intracellular function in the process of protein catabolism, antigen processing in the immune response, and Alzheimer’s disease. In cancers, cathepsin B interferes with autophagy and intracellular catabolism, and breaks down extracellular matrix, decreases protease inhibitors expression, and ultimately helps to accelerate metastasis, tumor malignancy, and reduce immune resistance. Methods: In this study, the 3D structure of cathepsin B was constructed using modeler and Iterative Threading ASSEmbly Refinement (I-TASSER), based on similarity to the crystallographic model of procathepsin B (1PBH). Then, the predicted cathepsin B model was evaluated using PROCHECK and PROSA for quality and reliability. Molecular studies suggested that the amino acids cysteine 108, histidine 189, and histidine 190 form the envelope of the active site of cathepsin B. The docking studies of cathepsin B was performed with protease inhibitors cystatin C, E-64 and leupeptin. Results: The lowest binding energy was related to the cathepsin B-E-64 complex. Accordingly, it was found that E64 interacts with the amino acid cysteine 108 of the active site of cathepsin B. Leupeptin made 2 hydrogen bonds with cathepsin B, but none with the active site of cathepsin amino acids. Cystatin C established a hydrogen bond with the arginine 18 of cathepsin B and made electrostatic bonds with aspartate 148 of cathepsin B. Conclusion: Therefore, the bioinformatics and docking studies of cathepsin B with its inhibitors could be used as reliable identification, treatment, and alternative methods for selecting the inhibitors and controllers of cancer progression.

scholarly journals Differential Localization of Cysteine Protease Inhibitors and a Target Cysteine Protease, Cathepsin B, by Immuno-Confocal Microscopy

1998 ◽  
Vol 46 (6) ◽  
pp. 745-751 ◽  
Author(s):  
Cathárine C. Calkins ◽  
Mansoureh Sameni ◽  
Jennifer Koblinski ◽  
Bonnie F. Sloane ◽  
Kamiar Moin
Keyword(s):  
Confocal Microscopy ◽  
Cell Line ◽  
Protease Inhibitors ◽  
Cystatin C ◽  
Cysteine Protease ◽  
Cathepsin B ◽  
Cysteine Proteases ◽  
Hepatoma Cells ◽  
Embryonic Liver ◽  
Cysteine Protease Inhibitors

The cystatin superfamily of cysteine protease inhibitors and target cysteine proteases such as cathepsin B have been implicated in malignant progression. The respective cellular/extracellular localization of cystatins and cysteine proteases in tumors may be critical in regulating activity of the enzymes. Confocal microscopy has enabled us to demonstrate the differential localization of cystatins and cathepsin B in an embryonic liver cell line and an invasive hepatoma cell line. In both, stefins A and B were distributed diffusely throughout the cytoplasm, whereas cystatin C was distributed in juxtanuclear vesicles. Stefin A and cystatin C, but not stefin B, were present on the cell surface. Cystatin C was found on the top surfaces of both cell lines, whereas stefin A was found only on the top surface of the embryonic liver cells. Cathepsin B staining was concentrated in perinuclear vesicles in the embryonic liver cells. In the hepatoma cells, staining for cathepsin B was also present in vesicles adjacent to the cell membrane and on localized regions of the bottom surface. Such a disparate distribution of cathepsin B and its endogenous inhibitors may facilitate proteolysis by the hepatoma cells and thereby contribute to their invasive phenotype.

scholarly journals Stroke in Icelandic patients with hereditary amyloid angiopathy is related to a mutation in the cystatin C gene, an inhibitor of cysteine proteases.

1989 ◽  
Vol 169 (5) ◽  
pp. 1771-1778 ◽  
Author(s):  
E Levy ◽  
C Lopez-Otin ◽  
J Ghiso ◽  
D Geltner ◽  
B Frangione
Keyword(s):  
Amino Acids ◽  
Cystatin C ◽  
Cerebral Hemorrhage ◽  
Signal Sequence ◽  
Genetic Defect ◽  
Cysteine Proteases ◽  
Amyloid Angiopathy ◽  
Primary Defect ◽  
Gene Encoding ◽  
The Brain

Cystatin C is an inhibitor of lysosomal cysteine proteases and consists of 120 amino acids. A variant of cystatin C lacking the first NH2-terminal residues and having one amino acid substitution at position 68 forms amyloid deposits mainly in the walls of brain arteries, causing fatal strokes in Icelandic patients with familial cerebral hemorrhage secondary to a form of an autosomal dominant amyloidosis. To understand the molecular basis of the genetic defect, the gene encoding cystatin C was isolated from genomic DNA libraries made from normal tissue and the brain of an Icelandic patient with hereditary cerebral hemorrhage with amyloidosis (HCHWA-I). The data indicate that the cystatin C gene encodes a polypeptide of 146 amino acids, of which the first 26 correspond to a secretory peptide signal sequence. The gene contains two intervening sequences that interrupt the coding region at amino acids 55 and 93. Comparison with genes encoding salivary cystatins and kininogen proteins show sequence homology and conservation of exon-intron structure. Except for a mutation in the second exon (CAG instead of CTG in the normal gene, resulting in the substitution of glutamine for a leucine residue), the gene cloned from the brain of the Icelandic patient is identical to the normal cystatin C gene. Thus, HCHWA-I is the first familial type of amyloidosis related to a point mutation in a gene encoding for an inhibitor. The mutation in the structural gene encoding cystatin C appears to be the primary defect in this inherited disorder causing amyloid fibril formation and accumulation followed by cerebral hemorrhage.

scholarly journals Binding site analysis of potential protease inhibitors of COVID-19 using AutoDock

2020 ◽  
Author(s):  
DIPTI MOTHAY ◽  
K.V. RAMESH
Keyword(s):  
Protease Inhibitor ◽  
Protease Inhibitors ◽  
Active Site ◽  
Molecular Interaction ◽  
3D Structure ◽  
Active Site Residues ◽  
Multiple Sequence ◽  
Site Analysis ◽  
Interaction Studies ◽  
Structural Insights

Abstract Recent outbreak of COVID-19 caused by SARS-CoV-2 in December 2019 raised global health concerns. Re-purposing the available protease inhibitor drugs for immediate use in treatment in SARS‐CoV‐2 infections could improve the currently available clinical management. The current study, aims to predict theoretical structure for protease of COVID-19 and to explore further whether this protein can serve as a target for protease inhibitor drugs such as remdesivir, nelfinavir, lopinavir, ritonavir and α –ketoamide. While the 3D structure of protease was predicted using SWISS MODEL server, molecular interaction studies between protein and ligands were performed using AutoDock software. The predicted protease model was reasonably good based on reports generated by different validation servers. The study further revealed that all the protease inhibitor drugs got docked with negative dock energy onto the target protein. Molecular interaction studies showed that protease structure had multiple active site residues for remdesivir, while for remaining ligands the structure had only one active site residue each. From the output of multiple sequence alignment, it is evident that ligand binding sites were conserved. The current in-silico study thus, provides structural insights about the protease of COVID-19 and also its molecular interactions with some of the known protease inhibitors.

scholarly journals Probing the specificity of cysteine proteinases at subsites remote from the active site: analysis of P4, P3, P2′ and P3′ variations in extended substrates

2000 ◽  
Vol 347 (1) ◽  
pp. 123-129 ◽  
Author(s):  
Fernada C. Vieira PORTARO ◽  
Ana Beatriz F. SANTOS ◽  
Maria Helena S. CEZARI ◽  
Maria Aparecida JULIANO ◽  
Luiz JULIANO ◽  
...  
Keyword(s):  
Amino Acids ◽  
Significant Influence ◽  
Active Site ◽  
Cathepsin B ◽  
Cathepsin L ◽  
Cysteine Proteinases ◽  
Aminobenzoic Acid ◽  
Site Analysis ◽  
Hydrophobic Amino Acids ◽  
Human Cathepsin

We have determined the kinetic parameters for the hydrolysis by papain, cathepsin B and cathepsin L of internally quenched fluorescent peptides derived from the lead peptides Abz-AAFRSAQ-EDDnp [in which Abz and EDDnp stand for o-aminobenzoic acid and N-(2,4-dinitrophenyl)ethylenediamine respectively], to map the specificity of S4 and S3 subsites, and Abz-AFRSAAQ-EDDnp, to identify the specificity of S2ʹ and S3ʹ. Abz and EDDnp were the fluorescent quencher pair. These two series of peptides were cleaved at the Arg-Ser bond and systematic modifications at P4, P3, P2ʹ and P3ʹ were made. The S4 to S2ʹ subsites had a significant influence on the hydrolytic efficiencies of the three enzymes. Only papain activity was observed to be dependent on S3ʹ, indicating that its binding site is larger than those of cathepsins B and L. Hydrophobic amino acids were accepted at S4, S3, S2ʹ and S3ʹ of the three enzymes. The best substrates for cathepsins L and B had Trp and Asn at P2ʹ respectively; variations at this position were less accepted by these enzymes. The best substrates for papain were peptides containing Trp, Tyr or Asn at P3ʹ. Basic residues at P3 and P4 were well accepted by cathepsin L and papain. We also explored the susceptibility of substrates Abz-AFRSXAQ-EDDnp, modified at P2ʹ (X), to human cathepsin B mutants from which one or two occluding loop contacts had been removed. The modifications at His111 (H111A) and His110 (H110A) of cathepsin B led to an increase in kcat values of one or two orders of magnitude. The hydrolytic efficiencies of these cathepsin B mutants became closer to those of papain or cathepsin L.

scholarly journals DOCKING STUDIES FOR VARIOUS ANTIBACTERIAL BENZILATE DERIVATIVES

2017 ◽  
Vol 10 (4) ◽  
pp. 268
Author(s):  
Sudha Rajendran ◽  
Brindha Devi P ◽  
Charles C Kanakam ◽  
Nithya G
Keyword(s):  
Infectious Disease ◽  
Amino Acids ◽  
Mycobacterium Tuberculosis ◽  
Active Site ◽  
Docking Studies ◽  
Antibacterial Drug ◽  
Structure Activity ◽  
Docking Tool ◽  
Excretion Study ◽  
Benzilic Acid

Objectives: In this study, we have focused on discovering the leads for the enzyme targets of infectious disease tuberculosis. We employed computeraided drug design docking tool,to discover new leads for Mycobacterium tuberculosis (MTB).Methods: Five compounds were synthesized and they are made to dock into the active site of the enzyme; retrieved from protein data bank.Results: The docking studies and structure–activity relationship reveals that the compound 2’-chloro-4-methoxy-3nitro benzilic acid after threedifferent docking strategies reveals that the score was found to be higher compared with others(−5.568 kcal/mol).Conclusion: On the closer analysis of this molecule, the molecule showed stacking interaction and the compound has also found to be surrounded by non-polar amino acids, which makes this molecule potent toward antibacterial drug discovery.Keywords: Antibacterials, Docking, Absorption, Distribution, Metabolism and excretion study, Resistance.

scholarly journals Molecular effects of mutated amino acids involved in Transmembrane and Domain regions on the BCR oncogene protein using In silico techniques

2020 ◽  
Vol 11 (4) ◽  
pp. 5850-5854
Author(s):  
Anuradha Manogharan ◽  
Regina Mary Rathina Samy ◽  
Ramadevi Mohan
Keyword(s):  
Amino Acids ◽  
Research Work ◽  
3D Structure ◽  
Docking Studies ◽  
Vital Role ◽  
Drug Binding ◽  
Functional Domains ◽  
Transmembrane Segments ◽  
Drug Designing ◽  
Oncogene Protein

BCR gene is expressed in patients with Philadelphia-positive Leukemias, known as chronic myeloid leukaemia (CML). Here, we focus on how the intramolecular domains and transmembrane segments are involved in the mutated sites of BCR. In this research work, we thoroughly analysed the transmembrane segments and the functional domains and predicted the 3D structure. We applied two kinds of techniques in our work. One is sequence-based, where we proved that the transmembrane segments in the functional domains contain the mutated sites. The second technique is structure-based, where we predicted the 3D structure of BCR gene-coded protein and visualised the transmembrane segments, which included the mutated sites. By using advanced molecular visualisation tools, the molecular structural properties of the respective transmembrane regions of amino acids will be determined. Both the techniques involved the use of advanced insilico tools and database. Our results elucidated that both the sequence and structure-based outcomes represented the identified transmembrane segments in the functional domains, which are potential candidates for drug docking studies. Hence, we finally concluded that this research work would play a vital role in clinical oncology and structure-based drug designing. Our research work is the first attempt to prove that potential drug binding sites are present in BCR oncogene-protein using insilico techniques. The results of this research investigation form a basic foundation for structure-based drug designing.

Identification of the mutated sites present in the transmembrane regions of SCN1A_HUMAN (Sodium Voltage-Gated Channel Alpha Subunit 1) using Insilico techniques

2020 ◽  
Vol 5 (1) ◽  
pp. 1-6
Author(s):  
Balaji Munivelan
Keyword(s):  
Amino Acids ◽  
Outer Membrane ◽  
Structure Prediction ◽  
Homology Modelling ◽  
Transmembrane Helix ◽  
3D Structure ◽  
Docking Studies ◽  
Alpha Subunit ◽  
Voltage Gated ◽  
Gated Channel

Mutations in numerous genes which encode for voltage-gated sodium channels give rise to various epilepsy syndromes in humans. Our research investigation mainly focuses on the identification of the integral membrane protein of the SCN1A (Sodium Voltage-Gated Channel Alpha Subunit 1) in humans. Secondary, we focus on the transmembrane membrane (TP) amino acids directly involved in the epilepsy-involved mutated regions. Using Insilico protocols, we identify the TP proteins and amino acids and elucidate the Transmembrane Helix and the inside and outside amino acids regions of the SCN1A. With the help of Insilico proteomics server, the amino acids in the mutated regions involved in the TP were identified. Finally, 3D structure prediction was performed using homology modelling server and the modelled structure was cross validated for the TP and validated. The identified results were validated using molecular visualization tools. We prove that the mutated amino acids are present in the outer membrane of the TP regions. Thus, the outer membrane of sodium channel and the amino acids present in the outer membrane (T875M, R859C, and R1648H) play a vital role in Structure-Based Drug Designing and Drug Docking studies.

Down-regulation of human extracellular cysteine protease inhibitors by the secreted staphylococcal cysteine proteases, staphopain A and B

2007 ◽  
Vol 388 (4) ◽  
pp. 437-446 ◽  
Author(s):  
Bjarne Vincents ◽  
Patrik Önnerfjord ◽  
Milosz Gruca ◽  
Jan Potempa ◽  
Magnus Abrahamson
Keyword(s):  
Cystatin C ◽  
Cathepsin B ◽  
Time Course ◽  
Cysteine Proteases ◽  
Normal Activity ◽  
Therapeutic Agents ◽  
Cysteine Protease Inhibitors ◽  
Protein Substrates ◽  
Cathepsin H

Abstract Of seven human cystatins investigated, none inhibited the cysteine proteases staphopain A and B secreted by the human pathogen Staphylococcus aureus. Rather, the extracellular cystatins C, D and E/M were hydrolyzed by both staphopains. Based on MALDI-TOF time-course experiments, staphopain A cleavage of cystatin C and D should be physiologically relevant and occur upon S. aureus infection. Staphopain A hydrolyzed the Gly11 bond of cystatin C and the Ala10 bond of cystatin D with similar K m values of approximately 33 and 32 μM, respectively. Such N-terminal truncation of cystatin C caused >300-fold lower inhibition of papain, cathepsin B, L and K, whereas the cathepsin H activity was compromised by a factor of ca. 10. Similarly, truncation of cystatin D caused alleviated inhibition of all endogenous target enzymes investigated. The normal activity of the cystatins is thus down-regulated, indicating that the bacterial enzymes can cause disturbance of the host protease-inhibitor balance. To illustrate the in vivo consequences, a mixed cystatin C assay showed release of cathepsin B activity in the presence of staphopain A. Results presented for the specificity of staphopains when interacting with cystatins as natural protein substrates could aid in the development of therapeutic agents directed toward these proteolytic virulence factors.

Abstract 2513: Intraventricular Administration of Cystatin C Attenuates White Matter Injury In Rat Chronic Ischemia

Stroke ◽  
2012 ◽  
Vol 43 (suppl_1) ◽  
Author(s):  
Shingo Mitaki ◽  
Atsushi Nagai ◽  
Abdullah Md. Sheikh ◽  
Shuhei Yamaguchi
Keyword(s):  
White Matter ◽  
Cystatin C ◽  
Cathepsin B ◽  
Experimental Studies ◽  
Cysteine Proteases ◽  
White Matter Injury ◽  
Cerebral Hypoperfusion ◽  
Cysteine Protease Inhibitor ◽  
Intraventricular Administration ◽  
Chronic Ischemia

Background and Purpose Cerebral white matter lesions (WMLs) contribute to elderly cognitive deterioration and are usually caused by chronic ischemic insult. Experimental studies have shown that proteases are highly expressed in activated astrocyte and microglia, which are thought to be crucial in the development of WMLs. Cystatin C (CSTC) functions as a major extracellular cysteine protease inhibitor in mammals. Since the concentration of CSTC is 5 times higher in CSF than in plasma, CSTC is thought to be a major inhibitor of cysteine proteases in the central nervous system. We have shown that polymorphisms in the CSTC gene, which results in a decrease of plasma CSTC level, are significantly associated with prevalence of WMLs. However, direct impact of CSTC on the development of WMLs has not been elucidated yet. Here we studied whether direct administration of CSTC into brain has a protective effect on the pathophysiology of WMLs produced by chronic cerebral hypoperfusion in a rat model of permanent bilateral common carotid artery occlusion. Methods Adult Wister rats underwent ligation of bilateral common carotid arteries (LBCCA) and were divided into three groups; the CSTC group in which CSTC was injected continuously into the ventricle 14 consecutive days after LBCCA (n=10), the PBS group in which PBS was injected continuously into the ventricle 14 consecutive days after LBCCA (n=10), and the sham group (n=10). All rats were perfused on 14 days after LBCCA. The severity of WMLs and accumulation of microglia and astrocytes in the corpus callosum (CC) and optic nerve (ON) were evaluated. Furthermore, the activity of cathepsin B, one of the major proteases, was measured in the tissue lysates of CC and ON using the assay kit. Results Continuous intraventricular infusion of CSTC significantly reduced the severity of WMLs (CC; p<0.001 vs. PBS, ON; p<0.001 vs. PBS) and inhibited the accumulation and activation of microglia (CC; p=0.03 vs. PBS, ON; p<0.001 vs. PBS) and astrocytes (CC; p=0.003 vs. PBS, ON; p=0.04 vs. PBS) both in CC and ON. There were no alterations in cathepsin B activity in these regions. Conclusions The present study indicates that CSTC could suppress chronic ischemia-induced WMLs and the inhibition of proteases other than cathepsin B may be implicated in this beneficial effect.

scholarly journals Computational Studies on Photolyase (Phr) Proteins of Cyanobacteria

2021 ◽  
Author(s):  
Rajneesh - ◽  
Soumila Mondal ◽  
Jainendra Pathak ◽  
Prashant R. Singh ◽  
Shailendra P. Singh ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Active Site ◽  
Binding Sites ◽  
Structural Information ◽  
Interaction Analysis ◽  
3D Structure ◽  
Length Distribution ◽  
Amino Acid Sequences ◽  
Ligand Interaction

Photolyases (Phrs) are enzymes that utilize blue/ultraviolet (UV-A) region of light for repairing UV-induced cyclopyramidine dimer. We have studied Phr groups by bioinformatic analyses as well as active-site and structural modeling. The analysis of 238 amino acid sequences from 85 completely sequenced cyanobacterial genomes revealed five classes of Phrs, i.e., CPD Gr I, 6-4 Phrs/cryptochrome, Cry-DASH, Fe-S bacteria Phrs, and a group having fewer number of amino acids (276-385) in length. Distribution of Phr groups in cyanobacteria belonging to the order Synechococcales was found to be influenced by the habitats of the organisms. Class V Phrs were exclusively present in cyanobacteria. Unique motif and binding sites were reported in Group II and III. Fe-S protein binding site was only present in Group V. Active site residues and putative CPD/6-4pp binding residues are charged amino acids which were present on the surface of the proteins. Majority of hydrophilic amino acid residues were present on surface of Phrs. Sequence analysis confirmed the diverse nature of Phrs, though, sequence diversity does not affect their overall 3D structure. Protein-ligand interaction analysis identified novel CPD/6-4PP binding sites on Phrs. This structural information of Phrs can be used for the preparation of efficient Phr based formulations.

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