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Alves Silva JC, Barden Grillo I, A Urquiza-Carvalho G, Bruno Rocha G. Exploring the electronic structure of knotted proteins: the case of two ornithine transcarbamylase family. J Mol Model 2024; 30:265. [PMID: 39008190 DOI: 10.1007/s00894-024-06009-9] [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: 01/31/2024] [Accepted: 06/06/2024] [Indexed: 07/16/2024]
Abstract
CONTEXT Geometrical knots are rare structural arrangements in proteins in which the polypeptide chain ties itself into a knot, which is very intriguing due to the uncertainty of their impact on the protein properties. Presently, classical molecular dynamics is the most employed technique in the few studies found on this topic, so any information on how the presence of knots affects the reactivity and electronic properties of proteins is even scarcer. Using the electronic structure methods and quantum chemical descriptors analysis, we found that the same amino-acid residues in the knot core have statistically larger values for the unknotted protein, for both hard-hard and soft-soft interaction descriptors. In addition, we present a computationally feasible protocol, where we show it is possible to separate the contribution of the geometrical knot to the reactivity and other electronic structure properties. METHODS In order to investigate these systems, we used PRIMoRDiA, a new software developed by our research group, to explore the electronic structure of biological macromolecules. We evaluated several local quantum chemical descriptors to unveil relevant patterns potentially originating from the presence of the geometrical knot in two proteins, belonging to the ornithine transcarbamylase family. We compared several sampled structures from these two enzymes that are highly similar in both tertiary structure and function, but one of them has a knot whereas the other does not. The sampling was carried out through molecular dynamics simulations using ff14SB force field along 50 ns, and the semiempirical convergence was performed with PM7 Hamiltonian.
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Affiliation(s)
- José Cícero Alves Silva
- Department of Chemistry, Federal University of Paraíba, Cid. Universitária, João Pessoa, 58051-900, Paraíba, Brazil
| | - Igor Barden Grillo
- Department of Chemistry, Federal University of Paraíba, Cid. Universitária, João Pessoa, 58051-900, Paraíba, Brazil
| | - Gabriel A Urquiza-Carvalho
- Department of Chemistry, Federal University of Pernambuco, Cid. Universitária, Recife, 50670-901, Pernambuco, Brazil
| | - Gerd Bruno Rocha
- Department of Chemistry, Federal University of Paraíba, Cid. Universitária, João Pessoa, 58051-900, Paraíba, Brazil.
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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.
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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
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Valencia J, Rubio V, Puerto G, Vasquez L, Bernal A, Mora JR, Cuesta SA, Paz JL, Insuasty B, Abonia R, Quiroga J, Insuasty A, Coneo A, Vidal O, Márquez E, Insuasty D. QSAR Studies, Molecular Docking, Molecular Dynamics, Synthesis, and Biological Evaluation of Novel Quinolinone-Based Thiosemicarbazones against Mycobacterium tuberculosis. Antibiotics (Basel) 2022; 12:antibiotics12010061. [PMID: 36671262 PMCID: PMC9854539 DOI: 10.3390/antibiotics12010061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
In this study, a series of novel quinolinone-based thiosemicarbazones were designed in silico and their activities tested in vitro against Mycobacterium tuberculosis (M. tuberculosis). Quantitative structure-activity relationship (QSAR) studies were performed using quinolinone and thiosemicarbazide as pharmacophoric nuclei; the best model showed statistical parameters of R2 = 0.83; F = 47.96; s = 0.31, and was validated by several different methods. The van der Waals volume, electron density, and electronegativity model results suggested a pivotal role in antituberculosis (anti-TB) activity. Subsequently, from this model a new series of quinolinone-thiosemicarbazone 11a-e was designed and docked against two tuberculosis protein targets: enoyl-acyl carrier protein reductase (InhA) and decaprenylphosphoryl-β-D-ribose-2'-oxidase (DprE1). Molecular dynamics simulation over 200 ns showed a binding energy of -71.3 to -12.7 Kcal/mol, suggesting likely inhibition. In vitro antimycobacterial activity of quinolinone-thiosemicarbazone for 11a-e was evaluated against M. bovis, M. tuberculosis H37Rv, and six different strains of drug-resistant M. tuberculosis. All compounds exhibited good to excellent activity against all the families of M. tuberculosis. Several of the here synthesized compounds were more effective than the standard drugs (isoniazid, oxafloxacin), 11d and 11e being the most active products. The results suggest that these compounds may contribute as lead compounds in the research of new potential antimycobacterial agents.
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Affiliation(s)
- Jhesua Valencia
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
| | - Vivian Rubio
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Gloria Puerto
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Luisa Vasquez
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Anthony Bernal
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
| | - José R. Mora
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170157, Ecuador
| | - Sebastian A. Cuesta
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170157, Ecuador
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - José Luis Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Cercado de Lima 15081, Peru
| | - Braulio Insuasty
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Rodrigo Abonia
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Jairo Quiroga
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Alberto Insuasty
- Grupo de Investigación en Materiales Funcionales Nanoestructurados, Universidad CESMAG, Pasto 520003, Colombia
| | - Andres Coneo
- Medicine Department, Division of Health Sciences, Universidad del Norte, Barranquilla 081007, Colombia
| | - Oscar Vidal
- Medicine Department, Division of Health Sciences, Universidad del Norte, Barranquilla 081007, Colombia
| | - Edgar Márquez
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
- Correspondence: (E.M.); (D.I.)
| | - Daniel Insuasty
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
- Correspondence: (E.M.); (D.I.)
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Nulek T, Klaysri R, Cedeno R, Nalaoh P, Bureekaew S, Promarak V, Flood AE. Separation of Etiracetam Enantiomers Using Enantiospecific Cocrystallization with 2-Chloromandelic Acid. ACS OMEGA 2022; 7:19465-19473. [PMID: 35721919 PMCID: PMC9202017 DOI: 10.1021/acsomega.2c01165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Chirality plays an important role in the pharmaceutical industry since the two enantiomers of a drug molecule usually display significantly different bioactivities, and hence, most products are produced as pure enantiomers. However, many drug precursors are synthesized as racemates, and hence, enantioseparation has become a significant process in the industry. Cocrystallization is one of the attractive crystallization approaches to obtain the desired enantiomer from racemic compounds. In this work, we propose a chiral resolution route for an antiepileptic drug, S-etiracetam (S-ETI), via enantiospecific cocrystallization with S-2-chloro-S-mandelic acid (CLMA) as a coformer. The experiments indicate that the system is highly enantiospecific; S-2CLMA cocrystallizes only with S-ETI but not with R-ETI or RS-ETI. Therefore, the chiral purification of S-ETI can be achieved efficiently with a 69.1% yield and close to 100% enantiopurity from the racemic solution. Additionally, structural simulations of the S-ETI:S-2CLMA cocrystal reveal that the cocrystal structure has higher thermodynamic stability than that of R-ETI:S-2CLMA by about 5.5 kcal/mol (per cocrystal formula unit), which helps to confirm the favorability of the enantiospecification in this system.
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Affiliation(s)
- Thitapond Nulek
- Department
of Chemical and Biomolecular Engineering, School of Energy Science
and Engineering, Vidyasirimedhi Institute
of Science and Technology, 555 Moo 1, Payupnai, Wang Chan, 21210 Rayong, Thailand
| | - Rachan Klaysri
- Department
of Chemical and Biomolecular Engineering, School of Energy Science
and Engineering, Vidyasirimedhi Institute
of Science and Technology, 555 Moo 1, Payupnai, Wang Chan, 21210 Rayong, Thailand
| | - Ruel Cedeno
- Department
of Chemical and Biomolecular Engineering, School of Energy Science
and Engineering, Vidyasirimedhi Institute
of Science and Technology, 555 Moo 1, Payupnai, Wang Chan, 21210 Rayong, Thailand
| | - Phattananawee Nalaoh
- Department
of Materials Science and Engineering, School of Molecular Science
and Engineering, Vidyasirimedhi Institute
of Science and Technology, 555 Moo 1, Payupnai, Wang Chan, 21210 Rayong, Thailand
| | - Sareeya Bureekaew
- Department
of Chemical and Biomolecular Engineering, School of Energy Science
and Engineering, Vidyasirimedhi Institute
of Science and Technology, 555 Moo 1, Payupnai, Wang Chan, 21210 Rayong, Thailand
| | - Vinich Promarak
- Department
of Materials Science and Engineering, School of Molecular Science
and Engineering, Vidyasirimedhi Institute
of Science and Technology, 555 Moo 1, Payupnai, Wang Chan, 21210 Rayong, Thailand
| | - Adrian E. Flood
- Department
of Chemical and Biomolecular Engineering, School of Energy Science
and Engineering, Vidyasirimedhi Institute
of Science and Technology, 555 Moo 1, Payupnai, Wang Chan, 21210 Rayong, Thailand
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