1
|
França TCC, Botelho FD, Drummond ML, LaPlante SR. Theoretical Investigation of Repurposed Drugs Potentially Capable of Binding to the Catalytic Site and the Secondary Binding Pocket of Subunit A of Ricin. ACS OMEGA 2022; 7:32805-32815. [PMID: 36120038 PMCID: PMC9476511 DOI: 10.1021/acsomega.2c04819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
Recently, we reported a library of 82 compounds, selected from different databanks through virtual screening and docking studies, and pointed to 6 among them as potential repurposed dual binders to both the catalytic site and the secondary binding pockets of subunit A of ricin (RTA). Here, we report additional molecular modeling studies of an extended list of compounds from the original library. Rounds of flexible docking followed by molecular dynamics simulations and further rounds of MM-PBSA calculations using a more robust protocol, enabled a better investigation of the interactions of these compounds inside RTA, the elucidation of their dynamical behaviors, and updating the list of the most important residues for the ligand binding. Four compounds were pointed as potential repurposed ricin inhibitors that are worth being experimentally investigated.
Collapse
Affiliation(s)
- Tanos C. C. França
- Université
de Québec, INRS—Centre Armand-Frappier Santé
Biotechnologie, Laval, Quebec H7V 1B7, Canada
- Laboratory
of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro 22290-270, Brazil
- Department
of Chemistry, Faculty of Science, University
of Hradec Kralove, Rokitanskeho
62, Hradec Kralove 50003, Czech Republic
| | - Fernanda D. Botelho
- Laboratory
of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro 22290-270, Brazil
| | | | - Steven R. LaPlante
- Université
de Québec, INRS—Centre Armand-Frappier Santé
Biotechnologie, Laval, Quebec H7V 1B7, Canada
| |
Collapse
|
2
|
Liang L, Xia J, Liu C, Liu S. [Highly toxic type Ⅱ ribosome-inactivating proteins ricin and abrin and their detection methods: a review]. Se Pu 2021; 39:260-270. [PMID: 34227307 PMCID: PMC9403808 DOI: 10.3724/sp.j.1123.2020.10001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Ⅱ型核糖体失活蛋白(RIPs)是一类重要的蛋白毒素,该类毒素大都具有一对二硫键连接的A-B链结构特征,B链具有半乳糖结合特性,能够与真核细胞膜表面受体特异性结合,将具有N-糖苷酶活性的A链导入细胞,与核糖体特定位点发生脱嘌呤作用使核糖体失活,最终通过抑制蛋白质合成而展现出细胞毒性。Ⅱ型RIPs毒素毒性极强,来源于植物的蓖麻毒素(ricin)和相思子毒素(abrin)的毒性分别是神经性毒剂维埃克斯(Vx)的385倍和2885倍。同时,该类毒素来源广泛、易于制备、稳定性好,成为一类潜在化生恐怖战剂,受到国内外广泛关注,其中蓖麻毒素作为唯一的蛋白毒素被收录于禁止化学武器公约禁控清单。近年来发生的多次蓖麻毒素邮件恐怖事件,进一步促进了有关Ⅱ型RIPs毒素的准确、灵敏、快速的检测鉴定技术的发展。剧毒性Ⅱ型RIPs毒素的检测鉴定方法主要涉及免疫分析法为代表的特异性识别和生物质谱分析为主的定性定量检测方法,以及基于脱嘌呤反应活性和细胞毒性的毒素活性检测方法。基于抗原-抗体作用的免疫检测法及基于寡核苷酸适配体的特异性识别检测法具有速度快、灵敏度高的优势,但对于复杂样品中高度同源蛋白的检测,易产生假阳性结果。随着生物质谱技术的快速发展,电喷雾离化(ESI)或基质辅助激光解吸离化(MALDI)等技术广泛应用于蛋白质的准确鉴定,不仅能够提供蛋白毒素的准确分子量和结构序列信息,而且能够实现准确定量。酶解质谱法是应用最为广泛的检测鉴定方法,通过酶解肽指纹谱分析,实现蛋白毒素的准确鉴定;对于复杂样品中蛋白毒素的分析,通过多种蛋白酶酶解策略获得丰富的特异性肽段标志物,然后进行肽段标志物的靶向质谱分析从而获得准确的定性及定量信息,方法有效提升了Ⅱ型RIPs毒素鉴定的准确度和灵敏度。免疫分析法和生物质谱法能够准确鉴定Ⅱ型RIPs毒素,但无法识别毒素是否还保持毒性。对于Ⅱ型RIPs毒素的活性分析,主要包括基于N-糖苷酶活性的脱嘌呤反应测定法和细胞毒性测定法,两种方法均可实现毒素毒性的简便、快速、灵敏的分析检测,是Ⅱ型RIPs毒素检测方法的有效补充。由于该类毒素的高度敏感性,国际禁止化学武器组织(OPCW)对相关样品中Ⅱ型RIPs毒素的分析提出了唯一性鉴定的技术要求。该文引用了Ⅱ型RIPs毒素及其检测方法相关的70篇文献,综述了以上Ⅱ型RIPs毒素的结构性质、中毒机理及典型剧毒性Ⅱ型RIPs毒素检测方法的研究进展,对不同检测方法的特点和应用潜力进行了总结,并结合OPCW对Ⅱ型RIPs毒素唯一性鉴定的技术需求,展望了未来Ⅱ型RIPs毒素检测技术研究的发展趋势。
Collapse
Affiliation(s)
- Longhui Liang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.,The Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing 102205, China
| | - Junmei Xia
- The Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing 102205, China
| | - Changcai Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.,The Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing 102205, China
| | - Shilei Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.,The Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing 102205, China
| |
Collapse
|
3
|
Yang J, Wang C, Luo L, Li Z, Xu B, Guo L, Xie J. Highly sensitive MALDI-MS measurement of active ricin: insight from more potential deoxynucleobase-hybrid oligonucleotide substrates. Analyst 2021; 146:2955-2964. [PMID: 33949380 DOI: 10.1039/d0an02205e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Herein, we report an improved MALDI-MS method for active ricin to contribute toward countermeasures against its real threat to the public. Compared with commonly used DNA or RNA substrates, the deoxynucleobase-hybrid oligonucleotide (RNA_dA, Rd) substrate containing functional Gd[combining low line]A[combining low line]GA loop was revealed as a substrate with more potential and used for the first time in ricin measurement via MALDI-MS. The Rd sequence greatly prompted ricin to exhibit its catalytic activity as rRNA N-glycosylase in ex vitro condition, which was supported by molecular docking simulation and enzymatic parameters depicted in MALDI-MS. Furthermore, we discovered that a highly pure matrix was the most crucial parameter for enhancing the sensitivity, which addressed the major obstacle encountered in the oligo(deoxy)nucleotide measurement, i.e., the interfering alkali metal ion-adducted signals in MALDI-MS. After the optimization of pH and enzymatic reaction buffer composition in this ex vitro condition, this method can provide a wide linearity of up to three orders of magnitude, i.e., 1-5000 ng mL-1, and a high sensitivity of 1 ng mL-1 without any enrichment. Denatured and active ricin could be distinctly differentiated, and the application to practical samples from one international exercise and a soft drink proved the feasibility of this new method. We believe this MALDI-MS method can contribute to the first response to ricin occurrence events in public safety and security, as well as pave a new way for a deep understanding of ricin and other type II ribosome inactivating proteins involved toxicology.
Collapse
Affiliation(s)
- Jiewei Yang
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing, 100850, China.
| | - Chenyu Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing, 100850, China. and School of Pharmacy, Minzu University, Beijing, 100081, China
| | - Li Luo
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing, 100850, China. and School of Public Health, Hebei Medical University, Shijiazhuang, Hebei Province 050017, China
| | - Zhi Li
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing, 100850, China.
| | - Bin Xu
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing, 100850, China.
| | - Lei Guo
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing, 100850, China.
| | - Jianwei Xie
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing, 100850, China.
| |
Collapse
|
4
|
Livet S, Worbs S, Volland H, Simon S, Dorner MB, Fenaille F, Dorner BG, Becher F. Development and Evaluation of an Immuno-MALDI-TOF Mass Spectrometry Approach for Quantification of the Abrin Toxin in Complex Food Matrices. Toxins (Basel) 2021; 13:toxins13010052. [PMID: 33450857 PMCID: PMC7828309 DOI: 10.3390/toxins13010052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 11/16/2022] Open
Abstract
The toxin abrin found in the seeds of Abrus precatorius has attracted much attention regarding criminal and terroristic misuse over the past decade. Progress in analytical methods for a rapid and unambiguous identification of low abrin concentrations in complex matrices is essential. Here, we report on the development and evaluation of a MALDI-TOF mass spectrometry approach for the fast, sensitive and robust abrin isolectin identification, differentiation and quantification in complex food matrices. The method combines immunoaffinity-enrichment with specific abrin antibodies, accelerated trypsin digestion and the subsequent MALDI-TOF analysis of abrin peptides using labeled peptides for quantification purposes. Following the optimization of the workflow, common and isoform-specific peptides were detected resulting in a ~38% sequence coverage of abrin when testing ng-amounts of the toxin. The lower limit of detection was established at 40 ng/mL in milk and apple juice. Isotope-labeled versions of abundant peptides with high ionization efficiency were added. The quantitative evaluation demonstrated an assay variability at or below 22% with a linear range up to 800 ng/mL. MALDI-TOF mass spectrometry allows for a simple and fast (<5 min) analysis of abrin peptides, without a time-consuming peptide chromatographic separation, thus constituting a relevant alternative to liquid chromatography-tandem mass spectrometry.
Collapse
Affiliation(s)
- Sandrine Livet
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, SPI, 91191 Gif-sur-Yvette, France; (S.L.); (H.V.); (S.S.); (F.F.)
| | - Sylvia Worbs
- Biological Toxins, Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (S.W.); (M.B.D.); (B.G.D.)
| | - Hervé Volland
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, SPI, 91191 Gif-sur-Yvette, France; (S.L.); (H.V.); (S.S.); (F.F.)
| | - Stéphanie Simon
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, SPI, 91191 Gif-sur-Yvette, France; (S.L.); (H.V.); (S.S.); (F.F.)
| | - Martin B. Dorner
- Biological Toxins, Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (S.W.); (M.B.D.); (B.G.D.)
| | - François Fenaille
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, SPI, 91191 Gif-sur-Yvette, France; (S.L.); (H.V.); (S.S.); (F.F.)
| | - Brigitte G. Dorner
- Biological Toxins, Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (S.W.); (M.B.D.); (B.G.D.)
| | - François Becher
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, SPI, 91191 Gif-sur-Yvette, France; (S.L.); (H.V.); (S.S.); (F.F.)
- Correspondence: ; Tel.: +33-1-69-08-13-15
| |
Collapse
|
5
|
Botelho FD, Santos MC, Gonçalves AS, França TCC, LaPlante SR, de Almeida JSFD. Identification of novel potential ricin inhibitors by virtual screening, molecular docking, molecular dynamics and MM-PBSA calculations: a drug repurposing approach. J Biomol Struct Dyn 2021; 40:5309-5319. [PMID: 33410376 DOI: 10.1080/07391102.2020.1870154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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.
Collapse
Affiliation(s)
- Fernanda D Botelho
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro/RJ, Brazil
| | - Marcelo C Santos
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro/RJ, Brazil
| | - Arlan S Gonçalves
- Federal Institute of Education Science and Technology - unit Vila Velha/ES, Brazil.,PPGQUI (Graduate Program in Chemistry), Federal University of Espirito Santo - Unit Goiabeiras, Vitória/ES, Brazil
| | - Tanos C C França
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro/RJ, Brazil.,INRS, Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, QC, Canada.,Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Steven R LaPlante
- INRS, Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, QC, Canada
| | - Joyce S F D de Almeida
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro/RJ, Brazil
| |
Collapse
|
6
|
Liang LH, Cheng X, Yu HL, Yang Y, Mu XH, Chen B, Li XS, Wu JN, Yan L, Liu CC, Liu SL. Quantitative detection of ricin in beverages using trypsin/Glu-C tandem digestion coupled with ultra-high-pressure liquid chromatography-tandem mass spectrometry. Anal Bioanal Chem 2020; 413:585-597. [PMID: 33184759 DOI: 10.1007/s00216-020-03030-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 10/26/2020] [Indexed: 12/16/2022]
Abstract
The toxic protein of ricin has drawn wide attention in recent years as a potential bioterrorism agent due to its high toxicity and wide availability. For the verification of the potential anti-terrorism activities, it is urgent for the quantification of ricin in food-related matrices. Here, a novel strategy of trypsin/Glu-C tandem digestion was introduced for quantitative detection of ricin marker peptides in several beverage matrices using isotope-labeled internal standard (IS)-mass spectrometry. The ricin in beverages was captured and enriched by biotinylated anti-ricin polyclonal antibodies conjugated to streptavidin magnetic beads. The purified ricin was cleaved using the developed trypsin/Glu-C tandem digestion method and then quantitatively detected by ultra-high-pressure liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) with isotope-labeled T7A and TG11B selected as IS. The use of trypsin/Glu-C digestion allows shorter peptides, which are more suitable for MS detection, to be obtained than the use of single trypsin digestion. Under the optimized tandem digestion condition, except for T7A in the A-chain, two resulting specific peptides of TG13A, TG28A from the A-chain and two of TG11B, TG33B from the B-chain were chosen as novel marker peptides with high MS response. The uniqueness of the selected marker peptides allows for unambiguous identification of ricin among its homologous proteins in a single run. The MS response of the four novel marker peptides is increased by more than 10 times compared with that of individual corresponding tryptic peptides. Both the marker peptides of A-chain T7A and B-chain TG11B were selected as quantitative peptides based on the highest MS response among the marker peptides from their individual chains. The limit of detection (LOD) of ricin is 0.1 ng/mL in PBS and 0.5 ng/mL in either milk or orange juice. The linear range of calibration curves for ricin were 0.5-300 ng/mL in PBS, 1.0-400 ng/mL in milk, and 1.0-250 ng/mL in orange juice. The method accuracy ranged between 82.6 and 101.8% for PBS, 88.9-105.2% for milk, and 95.3-118.7% for orange juice. The intra-day and inter-day precision had relative standard deviations (%RSD) of 0.3-9.4%, 0.7-8.9%, and 0.2-6.9% in the three matrices respectively. Furthermore, whether T7A or TG11B is used as a quantitative peptide, the quantitative results of ricin are consistent. This study provides not only a practical method for the absolute quantification of ricin in beverage matrices but also a new strategy for the investigation of illegal use of ricin in chemical weapon verification tasks such as OPCW biotoxin sample analysis exercises.
Collapse
Affiliation(s)
- Long-Hui Liang
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
- The Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing, 102205, China
| | - Xi Cheng
- The Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing, 102205, China
| | - Hui-Lan Yu
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
- The Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing, 102205, China
| | - Yang Yang
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
- The Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing, 102205, China
| | - Xi-Hui Mu
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Bo Chen
- The Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing, 102205, China
| | - Xiao-Sen Li
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
- The Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing, 102205, China
| | - Ji-Na Wu
- The Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing, 102205, China
| | - Long Yan
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
- The Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing, 102205, China
| | - Chang-Cai Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China.
- The Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing, 102205, China.
| | - Shi-Lei Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China.
- The Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing, 102205, China.
| |
Collapse
|
7
|
Tumer NE. Introduction to the Toxins Special Issue "Ricin Toxins". Toxins (Basel) 2019; 12:E13. [PMID: 31892170 PMCID: PMC7020407 DOI: 10.3390/toxins12010013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 12/24/2019] [Indexed: 12/28/2022] Open
Abstract
Ricin toxin isolated from the castor bean (Ricinus communis) is one of the most potent and lethal molecules known [...].
Collapse
Affiliation(s)
- Nilgun E Tumer
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901-8520, USA
| |
Collapse
|