1
|
Yang X, Wei A, Cao X, Wang Z, Wan H, Wang B, Peng H. Identification and Biological Evaluation of a Novel Small-Molecule Inhibitor of Ricin Toxin. Molecules 2024; 29:1435. [PMID: 38611715 PMCID: PMC11012547 DOI: 10.3390/molecules29071435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
The plant-derived toxin ricin is classified as a type 2 ribosome-inactivating protein (RIP) and currently lacks effective clinical antidotes. The toxicity of ricin is mainly due to its ricin toxin A chain (RTA), which has become an important target for drug development. Previous studies have identified two essential binding pockets in the active site of RTA, but most existing inhibitors only target one of these pockets. In this study, we used computer-aided virtual screening to identify a compound called RSMI-29, which potentially interacts with both active pockets of RTA. We found that RSMI-29 can directly bind to RTA and effectively attenuate protein synthesis inhibition and rRNA depurination induced by RTA or ricin, thereby inhibiting their cytotoxic effects on cells in vitro. Moreover, RSMI-29 significantly reduced ricin-mediated damage to the liver, spleen, intestine, and lungs in mice, demonstrating its detoxification effect against ricin in vivo. RSMI-29 also exhibited excellent drug-like properties, featuring a typical structural moiety of known sulfonamides and barbiturates. These findings suggest that RSMI-29 is a novel small-molecule inhibitor that specifically targets ricin toxin A chain, providing a potential therapeutic option for ricin intoxication.
Collapse
Affiliation(s)
- Xinran Yang
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100850, China; (X.Y.)
- Department of Operational Medicine, Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin 300050, China
| | - Aili Wei
- Department of Operational Medicine, Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin 300050, China
| | - Xiyuan Cao
- Department of Operational Medicine, Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin 300050, China
| | - Zicheng Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100850, China; (X.Y.)
| | - Hongzhi Wan
- Department of Operational Medicine, Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin 300050, China
| | - Bo Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100850, China; (X.Y.)
| | - Hui Peng
- Department of Operational Medicine, Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin 300050, China
| |
Collapse
|
2
|
Rudolph MJ, Dutta A, Tsymbal AM, McLaughlin JE, Chen Y, Davis SA, Theodorous SA, Pierce M, Algava B, Zhang X, Szekely Z, Roberge JY, Li XP, Tumer NE. Structure-based design and optimization of a new class of small molecule inhibitors targeting the P-stalk binding pocket of ricin. Bioorg Med Chem 2024; 100:117614. [PMID: 38340640 PMCID: PMC11418912 DOI: 10.1016/j.bmc.2024.117614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Abstract
Ricin, a category-B agent for bioterrorism, and Shiga toxins (Stxs), which cause food poisoning bind to the ribosomal P-stalk to depurinate the sarcin/ricin loop. No effective therapy exists for ricin or Stx intoxication. Ribosome binding sites of the toxins have not been targeted by small molecules. We previously identified CC10501, which inhibits toxin activity by binding the P-stalk pocket of ricin toxin A subunit (RTA) remote from the catalytic site. Here, we developed a fluorescence polarization assay and identified a new class of compounds, which bind P-stalk pocket of RTA with higher affinity and inhibit catalytic activity with submicromolar potency. A lead compound, RU-NT-206, bound P-stalk pocket of RTA with similar affinity as a five-fold larger P-stalk peptide and protected cells against ricin and Stx2 holotoxins for the first time. These results validate the P-stalk binding site of RTA as a critical target for allosteric inhibition of the active site.
Collapse
Affiliation(s)
- Michael J Rudolph
- New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, United States
| | - Arkajyoti Dutta
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, United States
| | - Anastasiia M Tsymbal
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Rd, Piscataway, NJ 08854, United States
| | - John E McLaughlin
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, United States
| | - Yang Chen
- New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, United States
| | - Simon A Davis
- New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, United States
| | - Sophia A Theodorous
- New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, United States
| | - Michael Pierce
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, United States
| | - Benjamin Algava
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, United States
| | - Xiaoyu Zhang
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, United States
| | - Zoltan Szekely
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Rd, Piscataway, NJ 08854, United States
| | - Jacques Y Roberge
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Rd, Piscataway, NJ 08854, United States
| | - Xiao-Ping Li
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, United States.
| | - Nilgun E Tumer
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, United States.
| |
Collapse
|
3
|
Botelho FD, Franca TCC, LaPlante SR. The Search for Antidotes Against Ricin. Mini Rev Med Chem 2024; 24:1148-1161. [PMID: 38350844 DOI: 10.2174/0113895575270509231121060105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/30/2023] [Accepted: 10/18/2023] [Indexed: 02/15/2024]
Abstract
The castor plant (Ricinus communis) is primarily known for its seeds, which contain a unique fatty acid called ricinoleic acid with several industrial and commercial applications. Castor seeds also contain ricin, a toxin considered a chemical and biological warfare agent. Despite years of investigation, there is still no effective antidote or vaccine available. However, some progress has been made, and the development of an effective treatment may be on the horizon. To provide an updated overview of this issue, we have conducted a comprehensive review of the literature on the current state of research in the fight against ricin. This review is based on the reported research and aims to address the challenges faced by researchers, as well as highlight the most successful cases achieved thus far. Our goal is to encourage the scientific community to continue their efforts in this critical search.
Collapse
Affiliation(s)
- Fernanda Diniz Botelho
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Praça General Tibúrcio 80, 22290-270, Rio de Janeiro, RJ, Brazil
| | - Tanos Celmar Costa Franca
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Praça General Tibúrcio 80, 22290-270, Rio de Janeiro, RJ, Brazil
- Université de Québec, INRS - Centre Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, Québec, H7V 1B7, Canada
- Department of Chemistry, Faculty of Science, University of Hradec Králové, Hradec Králové, Czech Republic
| | - Steven R LaPlante
- Université de Québec, INRS - Centre Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, Québec, H7V 1B7, Canada
| |
Collapse
|
4
|
Saito R, Goto M, Katakura S, Ohba T, Kawata R, Nagatsu K, Higashi S, Kurisu K, Matsumoto K, Ohtsuka K. Pterin-based small molecule inhibitor capable of binding to the secondary pocket in the active site of ricin-toxin A chain. PLoS One 2022; 17:e0277770. [PMID: 36508422 PMCID: PMC9744275 DOI: 10.1371/journal.pone.0277770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/03/2022] [Indexed: 12/14/2022] Open
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.
Collapse
Affiliation(s)
- Ryota Saito
- Department of Chemistry, Faculty of Science, Toho University, Funabashi, Chiba, Japan
- Research Center for Materials with Integrated Properties, Toho University, Funabashi, Chiba, Japan
| | - Masaru Goto
- Department of Molecular Bioscience, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Shun Katakura
- Department of Chemistry, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Taro Ohba
- Department of Molecular Bioscience, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Rena Kawata
- Department of Molecular Bioscience, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Kazuki Nagatsu
- Department of Molecular Bioscience, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Shoko Higashi
- Department of Chemistry, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Kaede Kurisu
- Department of Chemistry, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Kaori Matsumoto
- Department of Chemistry, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Kouta Ohtsuka
- Department of Chemistry, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| |
Collapse
|
5
|
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
|
6
|
Goto M, Higashi S, Ohba T, Kawata R, Nagatsu K, Suzuki S, Anslyn EV, Saito R. Conformational change in ricin toxin A-Chain: A critical factor for inhibitor binding to the secondary pocket. Biochem Biophys Res Commun 2022; 627:1-4. [PMID: 35998389 DOI: 10.1016/j.bbrc.2022.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/03/2022] [Indexed: 11/28/2022]
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.
Collapse
Affiliation(s)
- Masaru Goto
- Department of Molecular Bioscience, Faculty of Science, Toho University, Funabashi, Chiba, 274-8510, Japan
| | - Shoko Higashi
- Department of Chemistry, Faculty of Science, Toho University, Funabashi, Chiba, 274-8510, Japan
| | - Taro Ohba
- Department of Molecular Bioscience, Faculty of Science, Toho University, Funabashi, Chiba, 274-8510, Japan
| | - Rena Kawata
- Department of Molecular Bioscience, Faculty of Science, Toho University, Funabashi, Chiba, 274-8510, Japan
| | - Kazuki Nagatsu
- Department of Molecular Bioscience, Faculty of Science, Toho University, Funabashi, Chiba, 274-8510, Japan
| | - Saori Suzuki
- Department of Chemistry, Faculty of Science, Toho University, Funabashi, Chiba, 274-8510, Japan
| | - Eric V Anslyn
- Department of Chemistry, The University of Texas at Austin, Austin, TX, 78712, United States
| | - Ryota Saito
- Department of Chemistry, Faculty of Science, Toho University, Funabashi, Chiba, 274-8510, Japan; Research Center for Materials with Integrated Properties, Toho University, Funabashi, Chiba, 274-8510, Japan.
| |
Collapse
|
7
|
Bennett Z, Grumbles K, Pruet J. Comparative routes to 7-carboxymethyl-pterin: A useful medicinal chemistry building block. Pteridines 2022. [DOI: 10.1515/pteridines-2022-0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Pterins, such as folate and biopterin, and their derivatives hold significant importance given their biological relevance, as well as the numerous pterin-based inhibitors developed for targeting various biological targets. For this reason, pterins can be viewed as a privileged scaffold, as the discovery of new pterin analogs gives rise to a vast array of potential drug candidates. 7-carboxymethyl-pterin (7-CMP) represents a useful scaffold for the rapid generation of structurally diverse pterin amides and has been a key building block in medicinal chemistry. In an effort to facilitate rapid generation of this pterin scaffold, we have explored multiple routes towards 7-CMP to assess the most efficient method of generation. Methods were evaluated based on yield, regioselectivity, reaction time, and hazardous reaction conditions. This work can aide in the synthesis and discovery of new pterin-based drug candidates.
Collapse
Affiliation(s)
- Zachary Bennett
- Department of Chemistry, Valparaiso University , Valparaiso , IN , USA
| | - Kassidy Grumbles
- Department of Chemistry, Valparaiso University , Valparaiso , IN , USA
| | - Jeffrey Pruet
- Department of Chemistry, Valparaiso University , Valparaiso , IN , USA
| |
Collapse
|
8
|
Li XP, Harijan RK, Cao B, Kahn JN, Pierce M, Tsymbal AM, Roberge JY, Augeri D, Tumer NE. Synthesis and Structural Characterization of Ricin Inhibitors Targeting Ribosome Binding Using Fragment-Based Methods and Structure-Based Design. J Med Chem 2021; 64:15334-15348. [PMID: 34648707 PMCID: PMC10704857 DOI: 10.1021/acs.jmedchem.1c01370] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ricin toxin A subunit (RTA) is the catalytic subunit of ricin, which depurinates an adenine from the sarcin/ricin loop in eukaryotic ribosomes. There are no approved inhibitors against ricin. We used a new strategy to disrupt RTA-ribosome interactions by fragment screening using surface plasmon resonance. Here, using a structure-guided approach, we improved the affinity and inhibitory activity of small-molecular-weight lead compounds and obtained improved compounds with over an order of magnitude higher efficiency. Four advanced compounds were characterized by X-ray crystallography. They bind at the RTA-ribosome binding site as the original compound but in a distinctive manner. These inhibitors bind remotely from the catalytic site and cause local conformational changes with no alteration of the catalytic site geometry. Yet they inhibit depurination by ricin holotoxin and inhibit the cytotoxicity of ricin in mammalian cells. They are the first agents that protect against ricin holotoxin by acting directly on RTA.
Collapse
Affiliation(s)
- Xiao-Ping Li
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Rajesh K Harijan
- Department of Biochemistry, Albert Einstein College of Medicine, Jack and Pearl Resnick Campus, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Bin Cao
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Jennifer N Kahn
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Michael Pierce
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Anastasiia M Tsymbal
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Jacques Y Roberge
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - David Augeri
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Nilgun E Tumer
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States
| |
Collapse
|
9
|
Rocha-Santos A, Chaves EJ, Grillo IB, de Freitas AS, Araújo DAM, Rocha GB. Thermochemical and Quantum Descriptor Calculations for Gaining Insight into Ricin Toxin A (RTA) Inhibitors. ACS OMEGA 2021; 6:8764-8777. [PMID: 33842748 PMCID: PMC8027999 DOI: 10.1021/acsomega.0c02588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 12/30/2020] [Indexed: 05/03/2023]
Abstract
In this work, we performed a study to assess the interactions between the ricin toxin A (RTA) subunit of ricin and some of its inhibitors using modern semiempirical quantum chemistry and ONIOM quantum mechanics/molecular mechanics (QM/MM) methods. Two approaches were followed (calculation of binding enthalpies, ΔH bind, and reactivity quantum chemical descriptors) and compared with the respective half-maximal inhibitory concentration (IC50) experimental data, to gain insight into RTA inhibitors and verify which quantum chemical method would better describe RTA-ligand interactions. The geometries for all RTA-ligand complexes were obtained after running classical molecular dynamics simulations in aqueous media. We found that single-point energy calculations of ΔH bind with the PM6-DH+, PM6-D3H4, and PM7 semiempirical methods and ONIOM QM/MM presented a good correlation with the IC50 data. We also observed, however, that the correlation decreased significantly when we calculated ΔH bind after full-atom geometry optimization with all semiempirical methods. Based on the results from reactivity descriptors calculations for the cases studied, we noted that both types of interactions, molecular overlap and electrostatic interactions, play significant roles in the overall affinity of these ligands for the RTA binding pocket.
Collapse
Affiliation(s)
- Acassio Rocha-Santos
- Department
of Chemistry, Federal University of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | - Elton José
Ferreira Chaves
- Department
of Biotechnology, Federal University of
Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | - Igor Barden Grillo
- Department
of Chemistry, Federal University of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | - Amanara Souza de Freitas
- Department
of Chemical Engineering, Federal University
of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | | | - Gerd Bruno Rocha
- Department
of Chemistry, Federal University of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
- . Phone/Fax: +55-83-3216-7437
| |
Collapse
|
10
|
Chaves EJF, Gomes da Cruz LE, Padilha IQM, Silveira CH, Araujo DAM, Rocha GB. Discovery of RTA ricin subunit inhibitors: a computational study using PM7 quantum chemical method and steered molecular dynamics. J Biomol Struct Dyn 2021; 40:5427-5445. [PMID: 33526002 DOI: 10.1080/07391102.2021.1878058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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.
Collapse
Affiliation(s)
| | | | | | | | | | - Gerd Bruno Rocha
- Department of Chemistry, Federal University of Paraíba, João Pessoa, PB, Brazil
| |
Collapse
|
11
|
Ligand-Based Virtual Screening, Molecular Docking, Molecular Dynamics, and MM-PBSA Calculations towards the Identification of Potential Novel Ricin Inhibitors. Toxins (Basel) 2020; 12:toxins12120746. [PMID: 33256167 PMCID: PMC7761309 DOI: 10.3390/toxins12120746] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
Abstract
Ricin is a toxin found in the castor seeds and listed as a chemical weapon by the Chemical Weapons Convention (CWC) due to its high toxicity combined with the easiness of obtention and lack of available antidotes. The relatively frequent episodes of usage or attempting to use ricin in terrorist attacks reinforce the urge to develop an antidote for this toxin. In this sense, we selected in this work the current RTA (ricin catalytic subunit) inhibitor with the best experimental performance, as a reference molecule for virtual screening in the PubChem database. The selected molecules were then evaluated through docking studies, followed by drug-likeness investigation, molecular dynamics simulations and Molecular Mechanics Poisson–Boltzmann Surface Area (MM-PBSA) calculations. In every step, the selection of molecules was mainly based on their ability to occupy both the active and secondary sites of RTA, which are located right next to each other, but are not simultaneously occupied by the current RTA inhibitors. Results show that the three PubChem compounds 18309602, 18498053, and 136023163 presented better overall results than the reference molecule itself, showing up as new hits for the RTA inhibition, and encouraging further experimental evaluation.
Collapse
|
12
|
Fassio AV, Santos LH, Silveira SA, Ferreira RS, de Melo-Minardi RC. nAPOLI: A Graph-Based Strategy to Detect and Visualize Conserved Protein-Ligand Interactions in Large-Scale. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:1317-1328. [PMID: 30629512 DOI: 10.1109/tcbb.2019.2892099] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Essential roles in biological systems depend on protein-ligand recognition, which is mostly driven by specific non-covalent interactions. Consequently, investigating these interactions contributes to understanding how molecular recognition occurs. Nowadays, a large-scale data set of protein-ligand complexes is available in the Protein Data Bank, what led several tools to be proposed as an effort to elucidate protein-ligand interactions. Nonetheless, there is not an all-in-one tool that couples large-scale statistical, visual, and interactive analysis of conserved protein-ligand interactions. Therefore, we propose nAPOLI (Analysis of PrOtein-Ligand Interactions), a web server that combines large-scale analysis of conserved interactions in protein-ligand complexes at the atomic-level, interactive visual representations, and comprehensive reports of the interacting residues/atoms to detect and explore conserved non-covalent interactions. We demonstrate the potential of nAPOLI in detecting important conserved interacting residues through four case studies: two involving a human cyclin-dependent kinase 2 (CDK2), one related to ricin, and other to the human nuclear receptor subfamily 3 (hNR3). nAPOLI proved to be suitable to identify conserved interactions according to literature, as well as highlight additional interactions. Finally, we illustrate, with a virtual screening ligand selection, how nAPOLI can be widely applied in structural biology and drug design. nAPOLI is freely available at bioinfo.dcc.ufmg.br/napoli/.
Collapse
|
13
|
Bockman AR, Pruet JM. Exploring the scope of DBU-promoted amidations of 7-methoxycarbonylpterin. Beilstein J Org Chem 2020; 16:509-514. [PMID: 32273911 PMCID: PMC7113547 DOI: 10.3762/bjoc.16.46] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 03/19/2020] [Indexed: 11/23/2022] Open
Abstract
The synthetic utility of pterins is often hampered by the notorious insolubility of this heterocycle, slowing the development of medicinally relevant pteridine derivatives. Reactions which expedite the development of new pterins are thus of great importance. Through a dual role of diazabicycloundecene (DBU), 7-carboxymethylpterin is converted to the soluble DBU salt, with additional DBU promoting an ester-to-amide transformation. We have explored this reaction to assess its scope and identify structural features in the amines which significantly affect success, monitored the reaction kinetics using a pseudo-first order kinetics model, and further adapted the reaction conditions to allow for product formation in as little as 5 min, with yields often >80%.
Collapse
Affiliation(s)
- Anna R Bockman
- Department of Chemistry, Valparaiso University, 1710 Chapel Dr, Valparaiso, IN 46383, USA
| | - Jeffrey M Pruet
- Department of Chemistry, Valparaiso University, 1710 Chapel Dr, Valparaiso, IN 46383, USA
| |
Collapse
|
14
|
Chaves EJF, Padilha IQM, Araújo DAM, Rocha GB. Determining the Relative Binding Affinity of Ricin Toxin A Inhibitors by Using Molecular Docking and Nonequilibrium Work. J Chem Inf Model 2018; 58:1205-1213. [PMID: 29750861 DOI: 10.1021/acs.jcim.8b00036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ricin is a ribosome-inactivating protein (RIP type 2) consisting of two subunits, ricin toxin A (RTA) and ricin toxin B (RTB). Because of its cytotoxicity, ricin has worried world authorities for its potential use as a chemical weapon; therefore, its inhibition is of great biotechnological interest. RTA is the target for inhibitor synthesis, and pterin derivatives are promising candidates to inhibit it. In this study, we used a combination of the molecular docking approach and fast steered molecular dynamics (SMD) to assess the correlation between nonequilibrium work, ⟨ W⟩, and the IC50 for six RTA inhibitors. The results showed that molecular docking is a powerful tool to predict good bioactive poses of RTA inhibitors, and ⟨ W⟩ presented a strong correlation with IC50 ( R2 = 0.961). Such a profile ranked the RTA inhibitors better than the molecular docking approach. Therefore, the combination of docking and fast SMD simulation was shown to be a promising tool to distinguish RTA-active inhibitors from inactive ones and could be used as postdocking filtering approach.
Collapse
Affiliation(s)
- Elton J F Chaves
- Department of Biotechnology , Federal University of Paraíba , 58051-900 João Pessoa - PB , Brazil
| | - Itácio Q M Padilha
- Department of Biotechnology , Federal University of Paraíba , 58051-900 João Pessoa - PB , Brazil
| | - Demétrius A M Araújo
- Department of Biotechnology , Federal University of Paraíba , 58051-900 João Pessoa - PB , Brazil
| | - Gerd B Rocha
- Department of Chemistry , Federal University of Paraíba , 58051-900 João Pessoa - PB , Brazil
| |
Collapse
|
15
|
Pummerer rearrangement using bis(p-nitrophenyl) phosphorazidate as an azidation reagent: A novel synthesis of azidomethyl sulfides. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.08.065] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
|
16
|
Pterin-7-carboxamides as a new class of aldose reductase inhibitors. Bioorg Med Chem Lett 2016; 26:4870-4874. [DOI: 10.1016/j.bmcl.2016.09.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/06/2016] [Accepted: 09/14/2016] [Indexed: 11/21/2022]
|
17
|
Fabbro C, Armani S, Carloni LE, De Leo F, Wouters J, Bonifazi D. 2,5-Diamide-Substituted Five-Membered Heterocycles: Challenging Molecular Synthons. European J Org Chem 2014. [DOI: 10.1002/ejoc.201402654] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
18
|
Wiget PA, Manzano LA, Pruet JM, Gao G, Saito R, Monzingo AF, Jasheway KR, Robertus JD, Anslyn EV. Sulfur incorporation generally improves Ricin inhibition in pterin-appended glycine-phenylalanine dipeptide mimics. Bioorg Med Chem Lett 2013; 23:6799-804. [DOI: 10.1016/j.bmcl.2013.10.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
19
|
Saito R, Pruet JM, Manzano LA, Jasheway K, Monzingo AF, Wiget PA, Kamat I, Anslyn EV, Robertus JD. Peptide-conjugated pterins as inhibitors of ricin toxin A. J Med Chem 2012; 56:320-9. [PMID: 23214944 DOI: 10.1021/jm3016393] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Several 7-peptide-substituted pterins were synthesized and tested as competitive active-site inhibitors of ricin toxin A (RTA). Focus began on dipeptide conjugates, and these results further guided the construction of several tripeptide conjugates. The binding of these compounds to RTA was studied via a luminescence-based kinetic assay, as well as through X-ray crystallography. Despite the relatively polar, solvent exposed active site, several hydrophobic interactions, most commonly π-interactions not predicted by modeling programs, were identified in all of the best-performing inhibitors. Nearly all of these compounds provide IC₅₀ values in the low micromolar range.
Collapse
Affiliation(s)
- Ryota Saito
- Department of Chemistry, Toho University, 2-2-1 Miyama, Funabashi 274-8510, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|