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1.
BMC Genomics ; 25(1): 643, 2024 Jun 27.
Article in English | MEDLINE | ID: mdl-38937673

ABSTRACT

BACKGROUND: The CBM13 family comprises carbohydrate-binding modules that occur mainly in enzymes and in several ricin-B lectins. The ricin-B lectin domain resembles the CBM13 module to a large extent. Historically, ricin-B lectins and CBM13 proteins were considered completely distinct, despite their structural and functional similarities. RESULTS: In this data mining study, we investigate structural and functional similarities of these intertwined protein groups. Because of the high structural and functional similarities, and differences in nomenclature usage in several databases, confusion can arise. First, we demonstrate how public protein databases use different nomenclature systems to describe CBM13 modules and putative ricin-B lectin domains. We suggest the introduction of a novel CBM13 domain identifier, as well as the extension of CAZy cross-references in UniProt to guard the distinction between CAZy and non-CAZy entries in public databases. Since similar problems may occur with other lectin families and CBM families, we suggest the introduction of novel CBM InterPro domain identifiers to all existing CBM families. Second, we investigated phylogenetic, nomenclatural and structural similarities between putative ricin-B lectin domains and CBM13 modules, making use of sequence similarity networks. We concluded that the ricin-B/CBM13 superfamily may be larger than initially thought and that several putative ricin-B lectin domains may display CAZyme functionalities, although biochemical proof remains to be delivered. CONCLUSIONS: Ricin-B lectin domains and CBM13 modules are associated groups of proteins whose database semantics are currently biased towards ricin-B lectins. Revision of the CAZy cross-reference in UniProt and introduction of a dedicated CBM13 domain identifier in InterPro may resolve this issue. In addition, our analyses show that several proteins with putative ricin-B lectin domains show very strong structural similarity to CBM13 modules. Therefore ricin-B lectin domains and CBM13 modules could be considered distant members of a larger ricin-B/CBM13 superfamily.


Subject(s)
Lectins , Phylogeny , Protein Domains , Ricin , Ricin/chemistry , Ricin/genetics , Lectins/chemistry , Lectins/genetics , Lectins/metabolism , Databases, Protein , Amino Acid Sequence , Sequence Homology, Amino Acid
2.
Toxins (Basel) ; 16(6)2024 May 26.
Article in English | MEDLINE | ID: mdl-38922138

ABSTRACT

A certified reference material of ricin (CRM-LS-1) was produced by the EuroBioTox consortium to standardise the analysis of this biotoxin. This study established the N-glycan structures and proportions including their loci and occupancy of ricin CRM-LS-1. The glycan profile was compared with ricin from different preparations and other cultivars and isoforms. A total of 15 different oligomannosidic or paucimannosidic structures were identified in CRM-LS-1. Paucimannose was mainly found within the A-chain and oligomannose constituted the major glycan type of the B-chain. Furthermore, the novel primary structure variants E138 and D138 and four different C-termini of the A-chain as well as two B-chain variants V250 and F250 were elucidated. While the glycan proportions and loci were similar among all variants in CRM-LS-1 and ricin isoforms D and E of all cultivars analysed, a different stoichiometry for isoforms D and E and the amino acid variants were found. This detailed physicochemical characterization of ricin regarding the glycan profile and amino acid sequence variations yields unprecedented insight into the molecular features of this protein toxin. The variable attributes discovered within different cultivars present signature motifs and may allow discrimination of the biotoxin's origin that are important in molecular forensic profiling. In conclusion, our data of in-depth CRM-LS-1 characterization combined with the analysis of other cultivars is representative for known ricin variants.


Subject(s)
Polysaccharides , Ricin , Ricin/genetics , Ricin/chemistry , Ricin/analysis , Polysaccharides/chemistry , Polysaccharides/analysis , Reference Standards , Protein Isoforms/genetics , Protein Isoforms/chemistry
3.
Anal Biochem ; 692: 115580, 2024 Sep.
Article in English | MEDLINE | ID: mdl-38825159

ABSTRACT

Ricin is one of the most toxic substances known and a type B biothreat agent. Shiga toxins (Stxs) produced by E. coli (STEC) and Shigella dysenteriae are foodborne pathogens. There is no effective therapy against ricin or STEC and there is an urgent need for inhibitors. Ricin toxin A subunit (RTA) and A1 subunit of Stx2a (Stx2A1) bind to the C-terminal domain (CTD) of the ribosomal P-stalk proteins to depurinate the sarcin/ricin loop. Modulation of toxin-ribosome interactions has not been explored as a strategy for inhibition. Therefore, development of assays that detect inhibitors targeting toxin-ribosome interactions remains a critical need. Here we describe a fluorescence anisotropy (FA)-based competitive binding assay using a BODIPY-TMR labeled 11-mer peptide (P11) derived from the P-stalk CTD to measure the binding affinity of peptides ranging from 3 to 11 amino acids for the P-stalk pocket of RTA and Stx2A1. Comparison of the affinity with the surface plasmon resonance (SPR) assay indicated that although the rank order was the same by both methods, the FA assay could differentiate better between peptides that show nonspecific interactions by SPR. The FA assay detects only interactions that compete with the labeled P11 and can validate inhibitor specificity and mechanism of action.


Subject(s)
Fluorescence Polarization , Ribosomes , Ricin , Ricin/antagonists & inhibitors , Ricin/metabolism , Ricin/chemistry , Fluorescence Polarization/methods , Ribosomes/metabolism , Surface Plasmon Resonance , Shiga Toxin/antagonists & inhibitors , Shiga Toxin/metabolism , Shiga Toxin/chemistry , Binding, Competitive , Protein Binding , Shiga Toxin 2/antagonists & inhibitors , Shiga Toxin 2/metabolism , Shiga Toxin 2/chemistry
4.
Biomol NMR Assign ; 18(1): 85-91, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38642265

ABSTRACT

Ricin is a potent plant toxin that targets the eukaryotic ribosome by depurinating an adenine from the sarcin-ricin loop (SRL), a highly conserved stem-loop of the rRNA. As a category-B agent for bioterrorism it is a prime target for therapeutic intervention with antibodies and enzyme blocking inhibitors since no effective therapy exists for ricin. Ricin toxin A subunit (RTA) depurinates the SRL by binding to the P-stalk proteins at a remote site. Stimulation of the N-glycosidase activity of RTA by the P-stalk proteins has been studied extensively by biochemical methods and by X-ray crystallography. The current understanding of RTA's depurination mechanism relies exclusively on X-ray structures of the enzyme in the free state and complexed with transition state analogues. To date we have sparse evidence of conformational dynamics and allosteric regulation of RTA activity that can be exploited in the rational design of inhibitors. Thus, our primary goal here is to apply solution NMR techniques to probe the residue specific structural and dynamic coupling active in RTA as a prerequisite to understand the functional implications of an allosteric network. In this report we present de novo sequence specific amide and sidechain methyl chemical shift assignments of the 267 residue RTA in the free state and in complex with an 11-residue peptide (P11) representing the identical C-terminal sequence of the ribosomal P-stalk proteins. These assignments will facilitate future studies detailing the propagation of binding induced conformational changes in RTA complexed with inhibitors, antibodies, and biologically relevant targets.


Subject(s)
Nitrogen Isotopes , Nuclear Magnetic Resonance, Biomolecular , Ricin , Ricin/chemistry , Protein Subunits/chemistry , Amino Acid Sequence
5.
Biochemistry ; 63(7): 893-905, 2024 Apr 02.
Article in English | MEDLINE | ID: mdl-38467020

ABSTRACT

Shiga toxin 2a (Stx2a) is the virulence factor of Escherichia coli (STEC), which is associated with hemolytic uremic syndrome, the leading cause of pediatric kidney failure. The A1 subunit of Stx2a (Stx2A1) binds to the conserved C-terminal domain (CTD) of the ribosomal P-stalk proteins to remove an adenine from the sarcin-ricin loop (SRL) in the 28S rRNA, inhibiting protein synthesis. There are no antidotes against Stx2a or any other ribosome-inactivating protein (RIP). The structural and functional details of the binding of Stx2A1 to the P-stalk CTD are not known. Here, we carry out a deletion analysis of the conserved P-stalk CTD and show that the last eight amino acids (P8) of the P-stalk proteins are the minimal sequence required for optimal affinity and maximal inhibitory activity against Stx2A1. We determined the first X-ray crystal structure of Stx2A1 alone and in complex with P8 and identified the exact binding site. The C-terminal aspartic acid of the P-stalk CTD serves as an anchor, forming key contacts with the conserved arginine residues at the P-stalk binding pocket of Stx2A1. Although the ricin A subunit (RTA) binds to the P-stalk CTD, the last aspartic acid is more critical for the interaction with Stx2A1, indicating that RIPs differ in their requirements for the P-stalk. These results demonstrate that the catalytic activity of Stx2A1 is inhibited by blocking its interactions with the P-stalk, providing evidence that P-stalk binding is an essential first step in the recruitment of Stx2A1 to the SRL for depurination.


Subject(s)
Ricin , Shiga Toxin 2 , Humans , Child , Shiga Toxin 2/analysis , Shiga Toxin 2/metabolism , Ribosomes/metabolism , Ricin/chemistry , Ricin/genetics , Ricin/metabolism , Aspartic Acid , Binding Sites , Peptides/metabolism , Escherichia coli/metabolism
6.
Biochemistry (Mosc) ; 88(11): 1956-1969, 2023 Nov.
Article in English | MEDLINE | ID: mdl-38105212

ABSTRACT

Euphorbiaceae, also known as the spurge family, is a large group of flowering plants. Despite being tropical natives, they are now widespread. Due to its medicinal and commercial importance, this family of plants attracted a lot of attention in the scientific community. The distinctive characteristic of the family is production of milky latex, which is a rich source of several lectins, the proteins that bind carbohydrates. Although their function is unclear, they are believed to defend plants against damaging phytopathogenic microorganisms, insects, and predatory animals. Additionally, they serve as crucial metabolic regulators under a variety of stressors. Detection, separation, purification, and characterization of lectins from the Euphorbiaceae family - mostly from the latex of plants - began over 40 years ago. This effort produced over 35 original research papers that were published. However, no systematic review that compiles these published data has been presented yet. This review summarizes and describes several procedures and protocols employed for extraction and purification of lectins belonging to this family. Physicochemical properties and biological activities of the lectins, along with their medicinal and pharmacological properties, have also been analyzed. Additionally, using examples of ricin and ricin agglutinin, we have structurally analyzed characteristics of the lectin known as Ribosome Inactivating Protein Type II (RIP-Type II) that belongs to this family. We anticipate that this review article will offer a useful compendium of information on this important family of lectins, show the scientists involved in lectin research the gaps in our knowledge, and offer insights for future research.


Subject(s)
Euphorbiaceae , Ricin , Animals , Ricin/chemistry , Plant Lectins/pharmacology , Latex/chemistry , Plants
7.
Infect Immun ; 91(11): e0033223, 2023 Nov 16.
Article in English | MEDLINE | ID: mdl-37877711

ABSTRACT

Many AB toxins contain an enzymatic A moiety that is anchored to a cell-binding B moiety by a disulfide bridge. After receptor-mediated endocytosis, some AB toxins undergo retrograde transport to the endoplasmic reticulum (ER) where reduction of the disulfide bond occurs. The reduced A subunit then dissociates from the holotoxin and enters the cytosol to alter its cellular target. Intoxication requires A chain separation from the holotoxin, but, for many toxins, it is unclear if reduction alone is sufficient for toxin disassembly. Here, we examined the link between reduction and disassembly for several ER-translocating toxins. We found disassembly of the reduced Escherichia coli heat-labile enterotoxin (Ltx) required an interaction with one specific ER-localized oxidoreductase: protein disulfide isomerase (PDI). In contrast, the reduction and disassembly of ricin toxin (Rtx) and Shiga toxin 1 (Stx1) were coupled events that did not require PDI and could be triggered by reductant alone. PDI-deficient cells accordingly exhibited high resistance to Ltx with continued sensitivity to Rtx and Stx1. The distinct structural organization of each AB toxin thus appears to determine whether holotoxin disassembly occurs spontaneously upon disulfide reduction or requires the additional input of PDI.


Subject(s)
Ricin , Ricin/toxicity , Ricin/chemistry , Ricin/metabolism , Shiga Toxin 1 , Protein Disulfide-Isomerases/metabolism , Disulfides
8.
Biochemistry ; 62(22): 3181-3187, 2023 11 21.
Article in English | MEDLINE | ID: mdl-37903428

ABSTRACT

Monoclonal antibodies, JB4 and SylH3, neutralize ricin toxin (RT) by inhibiting the galactose-specific lectin activity of the B subunit of the toxin (RTB), which is required for cell attachment and entry. It is not immediately apparent how the antibodies accomplish this feat, considering that RTB consists of two globular domains (D1, D2) each divided into three homologous subdomains (α, ß, γ) with the two functional galactosyl-specific carbohydrate recognition domains (CRDs) situated on opposite poles (subdomains 1α and 2γ). Here, we report the X-ray crystal structures of JB4 and SylH3 Fab fragments bound to RTB in the context of RT. The structures revealed that neither Fab obstructed nor induced detectable conformational alterations in subdomains 1α or 2γ. Rather, JB4 and SylH3 Fabs recognize nearly identical epitopes within an ancillary carbohydrate recognition pocket located in subdomain 1ß. Despite limited amino acid sequence similarity between SylH3 and JB4 Fabs, each paratope inserts a Phe side chain from the heavy (H) chain complementarity determining region (CDR3) into the 1ß CRD pocket, resulting in local aromatic stacking interactions that potentially mimic a ligand interaction. Reconciling the fact that stoichiometric amounts of SylH3 and JB4 are sufficient to disarm RTB's lectin activity without evidence of allostery, we propose that subdomain 1ß functions as a "coreceptor" required to stabilize glycan interactions principally mediated by subdomains 1α and 2γ. Further investigation into subdomain 1ß will yield fundamental insights into the large family of R-type lectins and open novel avenues for countermeasures aimed at preventing toxin uptake into vulnerable tissues and cells.


Subject(s)
Ricin , Toxins, Biological , Ricin/chemistry , Ricin/metabolism , Antibodies, Monoclonal , Epitopes , Molecular Conformation , Carbohydrates
9.
Gene ; 877: 147547, 2023 Aug 15.
Article in English | MEDLINE | ID: mdl-37286020

ABSTRACT

Ribosome-inactivating proteins (RIPs) are RNA N-glycosidases that depurinate an adenine residue in the conserved alpha-sarcin/ricin loop (SRL) of rRNA, inhibiting protein synthesis. Previously, we reported the existence of these toxins in insects, whose presence is restricted to mosquitoes from the Culicinae subfamily (e.g., Aedes aegypti) and whiteflies from the Aleyrodidae family (e.g., Bemisia tabaci). Both groups of genes are derived from two independent horizontal gene transfer (HGT) events and are evolving under purifying selection. Here, we report and characterize the occurrence of a third HGT event in the Sciaroidea superfamily, which supports the recurrent acquisition of RIP genes by insects. Transcriptomic experiments, available in databases, allowed us to describe the temporal and spatial expression profiles for these foreign genes in these organisms. Furthermore, we found that RIP expression is induced after infection with pathogens and provided, for the first time, transcriptomic evidence of parasite SRL depurination. This evidence suggests a possible role of these foreign genes as immune effectors in insects.


Subject(s)
Hemiptera , Ricin , Animals , Ribosome Inactivating Proteins/genetics , Ribosome Inactivating Proteins/metabolism , Gene Transfer, Horizontal , Insecta/genetics , Protein Biosynthesis , RNA, Ribosomal , Ricin/chemistry , Ricin/genetics , Ricin/metabolism , Hemiptera/genetics , Hemiptera/metabolism , Plant Proteins/genetics
10.
J Enzyme Inhib Med Chem ; 38(1): 2219038, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37259593

ABSTRACT

Ricin toxin A chain (RTA), from Ricinus communis, is a deadly protein that inactivates ribosomes by degrading an adenine residue at position 4324 in 28S rRNA. Recently, we have demonstrated that pterin-7-carboxamides with peptide pendants were potent RTA inhibitors. Among these, N-(pterin-7-carbonyl)glycyl-L-tyrosine (7PCGY) is the most potent RTA inhibitor as a small organic molecule. However, despite this fascinating inhibitory activity, the mode of interaction of 7PCGY with RTA remains elusive. This study aimed to elucidate the factors responsible for the high RTA inhibitory activity of 7PCGY based on X-ray crystallographic analysis. Herein, we report the successfully resolved X-ray crystal structure of 7PCGY/RTA complexes, revealing that the interaction between the phenolic hydroxy group in 7PCGY and Asn78 of RTA through a hydrogen bonding and the conformational change of Tyr80 and Asn122 are responsible for the high RTA inhibitory activity of 7PCGY.


Subject(s)
Ricin , Ricin/chemistry , Ricin/genetics , Ricin/metabolism , Pterins/chemistry , Pterins/pharmacology , Crystallography, X-Ray , Peptides
11.
Sud Med Ekspert ; 66(3): 34-39, 2023.
Article in Russian | MEDLINE | ID: mdl-37192457

ABSTRACT

THE AIM OF THE STUDY: Is to suggest the method of ricin determination in biological liquids during forensic medical and chemicotoxicological examination. This research describes the optimal conditions of sample processing of biological liquids, allowing to extract the components (ricinine and ricinoleic acid) of castor seeds. The recommended analysis conditions allow to perform research for 15 minutes by high resolution mass spectrometry method combined with high-value liquid chromatography on a chromato-mass spectrometer to detect ricinine and ricinoleic acid. The chromatographic (retention time) and mass-spectrometric parameters (mass spectra) were established for the exact high-quality determination of ricinine and ricinoleic acid.


Subject(s)
Ricin , Ricinus communis , Ricin/toxicity , Ricin/analysis , Ricin/chemistry , Tandem Mass Spectrometry , Chromatography, High Pressure Liquid , Ricinus communis/chemistry , Forensic Medicine
12.
PLoS One ; 17(12): e0277770, 2022.
Article in English | MEDLINE | ID: mdl-36508422

ABSTRACT

The Ricin toxin A chain (RTA), which depurinates an adenine base at a specific region of the ribosome leading to death, has two adjacent specificity pockets in its active site. Based on this structural information, many attempts have been made to develop small-molecule RTA inhibitors that simultaneously block the two pockets. However, no attempt has been successful. In the present study, we synthesized pterin-7-carboxamides with tripeptide pendants and found that one of them interacts with both pockets simultaneously to exhibit good RTA inhibitory activity. X-ray crystallographic analysis of the RTA crystal with the new inhibitor revealed that the conformational change of Tyr80 is an important factor that allows the inhibitors to plug the two pockets simultaneously.


Subject(s)
Ricin , Ricin/chemistry , Pterins/metabolism , Catalytic Domain , Crystallography, X-Ray , Ribosomes/metabolism
13.
Int J Mol Sci ; 23(17)2022 Aug 24.
Article in English | MEDLINE | ID: mdl-36076961

ABSTRACT

Plukenetia volubilis is a highly promising plant with high nutritional and economic values. In our previous studies, the expression levels of ricin encoded transcripts were the highest in the maturation stage of P. volubilis seeds. The present study investigated the transcriptome and proteome profiles of seeds at two developmental stages (Pv-1 and Pv-2) using RNA-Seq and iTRAQ technologies. A total of 53,224 unigenes and 6026 proteins were identified, with functional enrichment analyses, including GO, KEGG, and KOG annotations. At two development stages of P. volubilis seeds, 8815 unique differentially expressed genes (DEGs) and 4983 unique differentially abundant proteins (DAPs) were identified. Omics-based association analysis showed that ribosome-inactivating protein (RIP) transcripts had the highest expression and abundance levels in Pv-2, and those DEGs/DAPs of RIPs in the GO category were involved in hydrolase activity. Furthermore, 21 RIP genes and their corresponding amino acid sequences were obtained from libraries produced with transcriptome analysis. The analysis of physicochemical properties showed that 21 RIPs of P. volubilis contained ricin, the ricin_B_lectin domain, or RIP domains and could be divided into three subfamilies, with the largest number for type II RIPs. The expression patterns of 10 RIP genes indicated that they were mostly highly expressed in Pv-2 and 4 transcripts encoding ricin_B_like lectins had very low expression levels during the seed development of P. volubilis. This finding would represent valuable evidence for the safety of oil production from P. volubilis for human consumption. It is also notable that the expression level of the Unigene0030485 encoding type I RIP was the highest in roots, which would be related to the antiviral activity of RIPs. This study provides a comprehensive analysis of the physicochemical properties and expression patterns of RIPs in different organs of P. volubilis and lays a theoretical foundation for further research and utilization of RIPs in P. volubilis.


Subject(s)
Ribosome Inactivating Proteins , Ricin , Humans , Plant Proteins/chemistry , Proteome/metabolism , Ribosome Inactivating Proteins/genetics , Ricin/chemistry , Seeds/metabolism , Transcriptome
14.
Biochem Biophys Res Commun ; 627: 1-4, 2022 10 30.
Article in English | MEDLINE | ID: mdl-35998389

ABSTRACT

Ricin toxin A-chain (RTA), a toxic protein from Ricinus communis, inactivates ribosomes to induce toxicity. The active site of RTA consists of two binding pockets. Many studies have focused on developing RTA inhibitors that can simultaneously bind to these critical pockets; however, almost all the inhibitors developed so far interact with only one pocket. In the present study, we discovered that pterin-7-carboxamides with aromatic l-amino acid pendants interacted with the active site of the enzyme in a 2-to-1 mode, where one inhibitor molecule bound to the primary pocket and the second one entered the secondary pocket in the active site of RTA. X-ray crystallographic analysis of inhibitor/RTA complexes revealed that the conformational changes of Tyr80 and Asn122 in RTA were critical for triggering the entry of inhibitor molecules into the secondary pocket of the RTA active site.


Subject(s)
Ricin , Crystallography, X-Ray , Ribosomes/metabolism , Ricin/chemistry , Ricin/metabolism , Ricin/toxicity
15.
Immunohorizons ; 6(6): 324-333, 2022 06 13.
Article in English | MEDLINE | ID: mdl-35697476

ABSTRACT

Inhalation of ricin toxin (RT) elicits profuse inflammation and cell death within the upper and lower airways, ultimately culminating in acute respiratory distress syndrome. We previously reported that the effects of pulmonary RT exposure in mice are nullified by intranasal administration of an mAb mixture consisting of PB10, directed against ricin's enzymatic subunit (RTA), and SylH3, directed against ricin's binding subunit (RTB). We now report that delivery of PB10 and SylH3 as an RT-mAb immune complex (RIC) to mice by the intranasal or i.p. routes stimulates the rapid onset of RT-specific serum IgG that persists for months. RIC administration also induced high-titer, toxin-neutralizing Abs. Moreover, RIC-treated mice were immune to a subsequent 5 × LD50 RT challenge on days 30 or 90. Intranasal RIC administration was more effective than i.p. delivery at rendering mice immune to intranasal RT exposure. Finally, we found that the onset of RT-specific serum IgG following RIC delivery was independent of FcγR engagement, as revealed through FcγR knockout mice and RICs generated with PB10/SylH3 LALA (leucine to alanine) derivatives. In conclusion, a single dose of RICs given intranasally to mice was sufficient to stimulate durable protective immunity to RT by an FcγR-independent pathway.


Subject(s)
Ricin , Animals , Antibodies, Monoclonal , Antigen-Antibody Complex , Immunoglobulin G , Mice , Receptors, IgG , Ricin/chemistry , Ricin/metabolism
16.
J Biol Chem ; 298(4): 101742, 2022 04.
Article in English | MEDLINE | ID: mdl-35182523

ABSTRACT

During ricin intoxication in mammalian cells, ricin's enzymatic (RTA) and binding (RTB) subunits disassociate in the endoplasmic reticulum. RTA is then translocated into the cytoplasm where, by virtue of its ability to depurinate a conserved residue within the sarcin-ricin loop (SRL) of 28S rRNA, it functions as a ribosome-inactivating protein. It has been proposed that recruitment of RTA to the SRL is facilitated by ribosomal P-stalk proteins, whose C-terminal domains interact with a cavity on RTA normally masked by RTB; however, evidence that this interaction is critical for RTA activity within cells is lacking. Here, we characterized a collection of single-domain antibodies (VHHs) whose epitopes overlap with the P-stalk binding pocket on RTA. The crystal structures of three such VHHs (V9E1, V9F9, and V9B2) in complex with RTA revealed not only occlusion of the ribosomal P-stalk binding pocket but also structural mimicry of C-terminal domain peptides by complementarity-determining region 3. In vitro assays confirmed that these VHHs block RTA-P-stalk peptide interactions and protect ribosomes from depurination. Moreover, when expressed as "intrabodies," these VHHs rendered cells resistant to ricin intoxication. One VHH (V9F6), whose epitope was structurally determined to be immediately adjacent to the P-stalk binding pocket, was unable to neutralize ricin within cells or protect ribosomes from RTA in vitro. These findings are consistent with the recruitment of RTA to the SRL by ribosomal P-stalk proteins as a requisite event in ricin-induced ribosome inactivation.


Subject(s)
Ribosomal Proteins , Ricin , Single-Domain Antibodies , Animals , Epitopes/metabolism , Mammals/metabolism , Peptides/metabolism , RNA, Ribosomal, 28S/metabolism , Ribosomal Proteins/chemistry , Ribosomal Proteins/metabolism , Ribosomes/metabolism , Ricin/chemistry , Single-Domain Antibodies/metabolism
17.
J Biomol Struct Dyn ; 40(12): 5309-5319, 2022 08.
Article in English | MEDLINE | ID: mdl-33410376

ABSTRACT

Ricin is a potent cytotoxin with no available antidote. Its catalytic subunit, RTA, damages the ribosomal RNA (rRNA) of eukaryotic cells, preventing protein synthesis and eventually leading to cell death. The combination between easiness of obtention and high toxicity turns ricin into a potential weapon for terrorist attacks, urging the need of discovering effective antidotes. On this context, we used computational techniques, in order to identify potential ricin inhibitors among approved drugs. Two libraries were screened by two different docking algorithms, followed by molecular dynamics simulations and MM-PBSA calculations in order to corroborate the docking results. Three drugs were identified as potential ricin inhibitors: deferoxamine, leucovorin and plazomicin. Our calculations showed that these compounds were able to, simultaneously, form hydrogen bonds with residues of the catalytic site and the secondary binding site of RTA, qualifying as potential antidotes against intoxication by ricin.Communicated by Ramaswamy H. Sarma.


Subject(s)
Ricin , Antidotes , Drug Repositioning , Molecular Docking Simulation , Molecular Dynamics Simulation , Ricin/chemistry , Ricin/metabolism , Ricin/pharmacology
18.
J Biomol Struct Dyn ; 40(12): 5427-5445, 2022 08.
Article in English | MEDLINE | ID: mdl-33526002

ABSTRACT

Ricin is a potent toxin derived from the castor bean plant and comprises two subunits, RTA and RTB. Because of its cytotoxicity, ricin has alarmed world authorities for its potential use as a chemical weapon. Ricin also affects castor bean agribusiness, given the risk of animal and human poisoning. Over the years, many groups attempted to propose small-molecules that bind to the RTA active site, the catalytic chain. Despite such efforts, there is still no effective countermeasure against ricin poisoning. The computational study carried out in the present work renews the discussion about small-molecules that may inhibit this toxin. Here, a structure-based virtual screening protocol capable of discerning active RTA inhibitors from inactive ones was performed to screen over 2 million compounds from the ZINC database to find novel scaffolds that strongly bind into the active site of the RTA. Besides, a novel score method based on ligand undocking force profiles and semi-empirical quantum chemical calculations provided insights into the rescore of docking poses. Summing up, the filtering steps pointed out seven main compounds, with the SCF00-451 as a promising candidate to inhibit the killing activity of such potent phytotoxin.


Subject(s)
Ricin , Toxins, Biological , Animals , Humans , Ligands , Molecular Dynamics Simulation , Ricin/chemistry , Ricin/metabolism , Ricin/pharmacology
19.
Toxins (Basel) ; 13(12)2021 12 03.
Article in English | MEDLINE | ID: mdl-34941700

ABSTRACT

Kirkiin is a new type 2 ribosome-inactivating protein (RIP) purified from the caudex of Adenia kirkii with a cytotoxicity compared to that of stenodactylin. The high toxicity of RIPs from Adenia genus plants makes them interesting tools for biotechnology and therapeutic applications, particularly in cancer therapy. The complete amino acid sequence and 3D structure prediction of kirkiin are here reported. Gene sequence analysis revealed that kirkiin is encoded by a 1572 bp open reading frame, corresponding to 524 amino acid residues, without introns. The amino acid sequence analysis showed a high degree of identity with other Adenia RIPs. The 3D structure of kirkiin preserves the overall folding of type 2 RIPs. The key amino acids of the active site, described for ricin and other RIPs, are also conserved in the kirkiin A chain. Sugar affinity studies and docking experiments revealed that both the 1α and 2γ sites of the kirkiin B chain exhibit binding activity toward lactose and D-galactose, being lower than ricin. The replacement of His246 in the kirkiin 2γ site instead of Tyr248 in ricin causes a different structure arrangement that could explain the lower sugar affinity of kirkiin with respect to ricin.


Subject(s)
Amino Acid Sequence , Binding Sites , Ribosome Inactivating Proteins, Type 2/chemistry , Ribosome Inactivating Proteins, Type 2/genetics , Catalytic Domain , Molecular Docking Simulation , Passifloraceae/chemistry , Passifloraceae/genetics , Plant Proteins/chemistry , Protein Domains , Ricin/chemistry , Sequence Analysis, DNA
20.
mSphere ; 6(6): e0075021, 2021 12 22.
Article in English | MEDLINE | ID: mdl-34730377

ABSTRACT

The development of vaccines against biothreat toxins like ricin (RT) is considered an integral component of the U.S. national security efforts. RiVax is a thermostable, lyophilized RT subunit vaccine adsorbed to aluminum salt adjuvant intended for use by military personnel and first responders. Phase 1 studies indicated that RiVax is safe and immunogenic, while a three-dose intramuscular vaccination regimen in nonhuman primates elicited protection against lethal dose RT challenge by aerosol. Here, we investigated, in a mouse model, the durability of RiVax-induced antibody responses and corresponding immunity to lethal dose RT challenge. Groups of mice were subcutaneously administered 3 or 1 µg of RiVax on days 0 and 21 and challenged with 10× 50% lethal dose (LD50) RT by injection at six different intervals over the course of 12 months. Serum antibody titers and epitope-specific competition assays were determined prior to each challenge. We report that the two-dose, 3-µg regimen conferred near-complete protection against RT challenge on day 35 and complete protection thereafter (challenge days 65, 95, 125, 245, and 365). The two-dose, 3-µg regimen was superior to the 1-µg regimen as revealed by slight differences in survival and morbidity scores (e.g., hypoglycemia, weight loss) on challenge days 35 and 365. In separate experiments, a single 3-µg RiVax vaccination proved only marginally effective at eliciting protective immunity to RT, underscoring the necessity of a prime-boost regimen to achieve full and long-lasting protection against RT. IMPORTANCE Ricin toxin (RT) is a notorious biothreat, as exposure to even trace amounts via injection or inhalation can induce organ failure and death within a matter of hours. In this study, we advance the preclinical testing of a candidate RT vaccine known as RiVax. RiVax is a recombinant nontoxic derivative of RT's enzymatic subunit that has been evaluated for safety in phase I clinical trials and efficacy in a variety of animal models. We demonstrate that two doses of RiVax are sufficient to protect mice from lethal dose RT challenge for up to 1 year. We describe kinetics and other immune parameters of the antibody response to RiVax and discuss how these immune factors may translate to humans.


Subject(s)
Epitopes/chemistry , Ricin/chemistry , Vaccines, Subunit/administration & dosage , Vaccines/administration & dosage , Aerosols , Animals , Bioterrorism , Female , Freeze Drying , Injections, Intramuscular , Lethal Dose 50 , Mice , Mice, Inbred BALB C
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