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Teixeira R, Salaroglio IC, Oliveira NFB, Sequeira JGN, Fontrodona X, Romero I, Machuqueiro M, Tomaz AI, Garcia MH, Riganti C, Valente A. Fighting Multidrug Resistance with Ruthenium-Cyclopentadienyl Compounds: Unveiling the Mechanism of P-gp Inhibition. J Med Chem 2023; 66:14080-14094. [PMID: 37616241 PMCID: PMC10614197 DOI: 10.1021/acs.jmedchem.3c01120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Indexed: 08/26/2023]
Abstract
The search for more effective and selective drugs to overcome cancer multidrug resistance is urgent. As such, a new series of ruthenium-cyclopentadienyl ("RuCp") compounds with the general formula [Ru(η5-C5H4R)(4,4'-R'-2,2'-bipy)(PPh3)] were prepared and fully characterized. All compounds were evaluated toward non-small cell lung cancer cells with different degrees of cisplatin sensitivity (A549, NCI-H2228, Calu-3, and NCI-H1975), showing better cytotoxicity than the first-line chemotherapeutic drug cisplatin. Compounds 2 and 3 (R' = -OCH3; R = CHO (2) or CH2OH (3)) further inhibited the activity of P-gp and MRP1 efflux pumps by impairing their catalytic activity. Molecular docking calculations identified the R-site P-gp pocket as the preferred one, which was further validated using site-directed mutagenesis experiments in P-gp. Altogether, our results unveil the first direct evidence of the interaction between P-gp and "RuCp" compounds in the modulation of P-gp activity and establish them as valuable candidates to circumvent cancer MDR.
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Affiliation(s)
- Ricardo
G. Teixeira
- Centro
de Química Estrutural, Institute of Molecular Sciences and
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | | | - Nuno F. B. Oliveira
- BioISI:
Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - João G. N. Sequeira
- BioISI:
Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Xavier Fontrodona
- Departament
de Química and Serveis Tècnics de Recerca, Universitat de Girona, C/M. Aurèlia Campmany, 69, E-17003 Girona, Spain
| | - Isabel Romero
- Departament
de Química and Serveis Tècnics de Recerca, Universitat de Girona, C/M. Aurèlia Campmany, 69, E-17003 Girona, Spain
| | - Miguel Machuqueiro
- BioISI:
Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Ana Isabel Tomaz
- Centro
de Química Estrutural, Institute of Molecular Sciences and
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - M. Helena Garcia
- Centro
de Química Estrutural, Institute of Molecular Sciences and
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Chiara Riganti
- Department
of Oncology, University of Torino, 10126 Torino, Italy
- Molecular
Biotechnology Center “Guido Tarone”, University of Torino, 10126 Torino, Italy
| | - Andreia Valente
- Centro
de Química Estrutural, Institute of Molecular Sciences and
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
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Quintanilha DB, Santos HFD. Analysis of Pleurotin binding to human thioredoxin reductase using docking and molecular dynamics simulation. J Biomol Struct Dyn 2022:1-14. [PMID: 35758249 DOI: 10.1080/07391102.2022.2092553] [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: 10/17/2022]
Abstract
Thioredoxin reductase (TrxR) has been considered a potential target for cancer chemotherapy. It acts by controlling the redox homeostasis of human cells and, therefore, interfering in its function may trigger apoptosis, which is a crucial tumor suppression mechanism. Despite the great effort in the search for TrxR inhibitors, none was approved for human therapy. In the present study a virtual screening for natural organic compounds is discussed for a set of 72 compounds with known IC-50 for TrxR inhibition. The results suggest the Pleurotin, a naphthoquinone obtained from Hohenbuehelia grisea fungus, as a potential TrxR inhibitor, which acts by binding to the active site of the enzyme, between the N- and C-terminal domains. The presence of the ligand blocks the approximation of the C-terminal arm to the N-terminal, which is an essential step of the enzyme function. Besides, the two equivalent binding sites of TrxR were explored, by docking two ligands simultaneously. The results indicate that both sites have an allosteric correlation and, the presence of the ligand in one site may interfere, or even prevent, the binding of the second ligand at the other site. All these findings are quantitatively discussed based on the analysis of long molecular dynamics trajectories, which provides a full description of the ligand-receptor binding modes, average binding energies and conformational changes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Daniel B Quintanilha
- NEQC: Núcleo de Estudos em Química Computacional, Departamento de Química, Universidade Federal de Juiz de Fora, Juiz de Fora, MG, Brazil
| | - Hélio F Dos Santos
- NEQC: Núcleo de Estudos em Química Computacional, Departamento de Química, Universidade Federal de Juiz de Fora, Juiz de Fora, MG, Brazil
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Oliveira NF, Machuqueiro M. Novel US-CpHMD Protocol to Study the Protonation-Dependent Mechanism of the ATP/ADP Carrier. J Chem Inf Model 2022; 62:2550-2560. [PMID: 35442654 PMCID: PMC9775199 DOI: 10.1021/acs.jcim.2c00233] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We have designed a protocol combining constant-pH molecular dynamics (CpHMD) simulations with an umbrella sampling (US) scheme (US-CpHMD) to study the mechanism of ADP/ATP transport (import and export) by their inner mitochondrial membrane carrier protein [ADP/ATP carrier (AAC)]. The US scheme helped overcome the limitations of sampling the slow kinetics involved in these substrates' transport, while CpHMD simulations provided an unprecedented realism by correctly capturing the associated protonation changes. The import of anionic substrates along the mitochondrial membrane has a strong energetic disadvantage due to a smaller substrate concentration and an unfavorable membrane potential. These limitations may have created an evolutionary pressure on AAC to develop specific features benefiting the import of ADP. In our work, the potential of mean force profiles showed a clear selectivity in the import of ADP compared to ATP, while in the export, no selectivity was observed. We also observed that AAC sequestered both substrates at longer distances in the import compared to the export process. Furthermore, only in the import process do we observe transient protonation of both substrates when going through the AAC cavity, which is an important advantage to counteract the unfavorable mitochondrial membrane potential. Finally, we observed a substrate-induced disruption of the matrix salt-bridge network, which can promote the conformational transition (from the C- to M-state) required to complete the import process. This work unraveled several important structural features where the complex electrostatic interactions were pivotal to interpreting the protein function and illustrated the potential of applying the US-CpHMD protocol to other transport processes involving membrane proteins.
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Niu W, Du Z, Zhang C, Xu D, Li J, Sun M, Wu L, Yao H, Zhao L, Gao X. Broken electron transfer pathway in enzyme: Gold clusters inhibiting TrxR1/Trx via cell studies and theory simulations. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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pK a Calculations in Membrane Proteins from Molecular Dynamics Simulations. Methods Mol Biol 2021. [PMID: 34302677 DOI: 10.1007/978-1-0716-1468-6_11] [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: 08/01/2023]
Abstract
The conformational changes of membrane proteins are crucial to their function and usually lead to fluctuations in the electrostatic environment of the protein surface. A very effective way to quantify these changes is by calculating the pK a values of the protein's titratable residues, which can be regarded as electrostatic probes. To achieve this, we need to take advantage of the fast and reliable pK a calculators developed for globular proteins and adapt them to include the explicit effects of membranes. Here, we provide a detailed linear response approximation protocol that uses our own software (PypKa) to calculate reliable pK a values from short MD simulations of membrane proteins.
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Computational Analysis of the Interactions between the S100B Extracellular Chaperone and Its Amyloid β Peptide Client. Int J Mol Sci 2021; 22:ijms22073629. [PMID: 33807304 PMCID: PMC8037576 DOI: 10.3390/ijms22073629] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/24/2021] [Accepted: 03/27/2021] [Indexed: 02/01/2023] Open
Abstract
S100B is an astrocytic extracellular Ca2+-binding protein implicated in Alzheimer’s disease, whose role as a holdase-type chaperone delaying Aβ42 aggregation and toxicity was recently uncovered. Here, we employ computational biology approaches to dissect the structural details and dynamics of the interaction between S100B and Aβ42. Driven by previous structural data, we used the Aβ25–35 segment, which recapitulates key aspects of S100B activity, as a starting guide for the analysis. We used Haddock to establish a preferred binding mode, which was studied with the full length Aβ using long (1 μs) molecular dynamics (MD) simulations to investigate the structural dynamics and obtain representative interaction complexes. From the analysis, Aβ-Lys28 emerged as a key candidate for stabilizing interactions with the S100B binding cleft, in particular involving a triad composed of Met79, Thr82 and Glu86. Binding constant calculations concluded that coulombic interactions, presumably implicating the Lys28(Aβ)/Glu86(S100B) pair, are very relevant for the holdase-type chaperone activity. To confirm this experimentally, we examined the inhibitory effect of S100B over Aβ aggregation at high ionic strength. In agreement with the computational predictions, we observed that electrostatic perturbation of the Aβ-S100B interaction decreases anti-aggregation activity. Altogether, these findings unveil features relevant in the definition of selectivity of the S100B chaperone, with implications in Alzheimer’s disease.
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Sánchez Delgado GY, Arvellos JFA, Paschoal DFS, Dos Santos HF. Role of the Enzymatic Environment in the Reactivity of the Au III-C^N^C Anticancer Complexes. Inorg Chem 2021; 60:3181-3195. [PMID: 33600154 DOI: 10.1021/acs.inorgchem.0c03521] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The action mechanism of anticancer gold(III) complexes is a multi-step process and depends on their redox stability. First, the gold(III) complex undergoes a ligand exchange reaction in the presence of cellular thiols, such as those available in the active site of the enzyme TrxR, and then, the AuIII → AuI reduction occurs. Most experimental and theoretical studies describe these processes under chemical conditions without considering the enzyme structure effect. In the present study, molecular models are proposed for the [AuIII(C^N^C)(SHCys-R)]+ adduct, with the [AuIII(C^N^C)]+ moiety bonded to the Cys498 residue in the C-terminal arm of the TrxR. This one represents the product of the first ligand exchange reaction. Overall, our results suggest that the exchange of the auxiliary ligand (for instance, Cl- to S-R) plays a primary role in increasing the reduction potential, with the enzyme structure having a small effect. The parent compound [AuIII(C^N^C)Cl] has E° = -1.20 V, which enlarges to -0.72 V for [AuIII(C^N^C)CH3SH]+ and to -0.65 V for the largest model studied, Au-trx. In addition to the effect of the enzyme structure on the redox stability, we also analyze the Au transfer to the enzyme using a small peptide model (a tetramer). This reaction is dependent on the Cys497 protonation state. Thermodynamics and kinetic analysis suggests that the C^N^C ligand substitution by Cys497 is an exergonic process, with an energy barrier estimated at 20.2 kcal mol-1. The complete transfer of the Au ion to the enzyme's active site would lead to a total loss of enzyme activity, generating oxidative damage and, consequently, cancer cell death.
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Affiliation(s)
- Giset Y Sánchez Delgado
- NEQC: Núcleo de Estudos em Química Computacional, Department of Chemistry, Federal University of Juiz de Fora, Campus Universitário Martelos, 36.036-900 Juiz de Fora, Minas Gerais, Brazil
| | - Júlio F A Arvellos
- NEQC: Núcleo de Estudos em Química Computacional, Department of Chemistry, Federal University of Juiz de Fora, Campus Universitário Martelos, 36.036-900 Juiz de Fora, Minas Gerais, Brazil
| | - Diego F S Paschoal
- NQTCM: Núcleo de Química Teórica e Computacional de Macaé, Polo Ajuda, Universidade Federal do Rio de Janeiro, Campus UFRJ-Macaé, 27.971-525 Macaé, Rio de Janeiro, Brazil
| | - Hélio F Dos Santos
- NEQC: Núcleo de Estudos em Química Computacional, Department of Chemistry, Federal University of Juiz de Fora, Campus Universitário Martelos, 36.036-900 Juiz de Fora, Minas Gerais, Brazil
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Reis PBPS, Vila-Viçosa D, Rocchia W, Machuqueiro M. PypKa: A Flexible Python Module for Poisson–Boltzmann-Based pKa Calculations. J Chem Inf Model 2020; 60:4442-4448. [DOI: 10.1021/acs.jcim.0c00718] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Pedro B. P. S. Reis
- BioISI − Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- CONCEPT Lab, Istituto Italiano di Tecnologia (IIT), Via Melen-83, B Block, 16152 Genoa, Italy
| | - Diogo Vila-Viçosa
- BioISI − Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Walter Rocchia
- CONCEPT Lab, Istituto Italiano di Tecnologia (IIT), Via Melen-83, B Block, 16152 Genoa, Italy
| | - Miguel Machuqueiro
- BioISI − Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
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Bian M, Fan R, Zhao S, Liu W. Targeting the Thioredoxin System as a Strategy for Cancer Therapy. J Med Chem 2019; 62:7309-7321. [PMID: 30963763 DOI: 10.1021/acs.jmedchem.8b01595] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Thioredoxin reductase (TrxR) participates in the regulation of redox reactions in organisms. It works mainly via its substrate molecule, thioredoxin, to maintain the redox balance and regulate signal transduction, which controls cell proliferation, differentiation, death, and other important physiological processes. In recent years, increasing evidence has shown that the overactivation of TrxR is related to the development of tumors. The exploration of TrxR-targeted antitumor drugs has attracted wide attention and is expected to provide new therapies for cancer treatment. In this perspective, we highlight the specific relationship between TrxR and apoptotic signaling pathways. The cytoplasm and mitochondria both contain TrxR, resulting in the activation of apoptosis. TrxR activity influences reactive oxygen species (ROS) and further regulates the inflammatory signaling pathway. In addition, we discuss representative TrxR inhibitors with anticancer activity and analyze the challenges in developing TrxR inhibitors as anticancer drugs.
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Affiliation(s)
- Mianli Bian
- Institute of Chinese Medicine, School of Pharmacy , Nanjing University of Chinese Medicine , Nanjing 210023 , P. R. China
| | - Rong Fan
- Institute of Chinese Medicine, School of Pharmacy , Nanjing University of Chinese Medicine , Nanjing 210023 , P. R. China
| | - Sai Zhao
- Institute of Chinese Medicine, School of Pharmacy , Nanjing University of Chinese Medicine , Nanjing 210023 , P. R. China.,Institute of New Medicine Research , Nanjing Hicin Pharmaceutical Co. Ltd. , Nanjing 210046 , P. R. China
| | - Wukun Liu
- Institute of Chinese Medicine, School of Pharmacy , Nanjing University of Chinese Medicine , Nanjing 210023 , P. R. China.,State Key Laboratory of Natural Medicines , China Pharmaceutical University , Nanjing 210009 , P. R. China
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Bortoli M, Torsello M, Bickelhaupt FM, Orian L. Role of the Chalcogen (S, Se, Te) in the Oxidation Mechanism of the Glutathione Peroxidase Active Site. Chemphyschem 2017; 18:2990-2998. [DOI: 10.1002/cphc.201700743] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Marco Bortoli
- Dipartimento di Scienze Chimiche; Università degli Studi di Padova; Via Marzolo 1 35129 Padova Italy
| | | | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Institute for Molecules and Materials (IMM); Radboud University; Heyendaalseweg 135 6525 J Nijmegen The Netherlands
| | - Laura Orian
- Dipartimento di Scienze Chimiche; Università degli Studi di Padova; Via Marzolo 1 35129 Padova Italy
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