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Shahabipour S, Shamkhali AN, Razzaghi-Asl N. Cytotoxic monastrol derivatives as adjective inhibitors of drug-resistant Eg5: a molecular dynamics perspective. J Biomol Struct Dyn 2024:1-14. [PMID: 38450658 DOI: 10.1080/07391102.2024.2326195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
The mitotic kinesin Eg5 is a motor protein involved in the formation of bipolar spindle and cell division. Eg5 is overexpressed in various cancer cells and Eg5 targeting agents are promising candidates for cancer therapy. Subsequent to the discovery of monastrol as a small-molecule Eg5 modulator, numerous inhibitors/modulators have been reported from which a few entered clinical trials. Mutagenic investigations specified declined sensitivity of Eg5 allosteric site to monastrol due to the occurrence of drug-resistant mutations in some cell cultures. Accordingly, identification of tight binders to the mutant Eg5 allosteric site is an invaluable strategy to devise more efficient Eg5 modulators. We have previously synthesized a few dihydropyrimidinethione (DHPMT)-based 5-carboxamide monastrol derivatives (1-5) with higher cytotoxicities against AGS (IC50 9.90-98.48 µM) and MCF-7 (IC50 15.20-149.13 µM) cancer cell lines than monastrol. Within a current study, a structural insight was offered into the binding mechanism of intended derivatives inside the mutant Eg5 loop5/α2/α3 allosteric pocket. Molecular docking of the DHPMT R and S-enantiomers unraveled top-scored Eg5 complexes. Molecular dynamics (MD) simulations were carried out on 5 superior complexes as (R)-2/D130V-Eg5, (R)-4/D130V-Eg5, (R)-5/D130V-Eg5, (R)-5/L214I-Eg5, (R)-5/R119L-Eg5, and the control groups monastrol/D130V-Eg5, monastrol/L214I-Eg5, monastrol/R119L-Eg5. Free energy calculations were conducted through conformational sampling of MD-driven binding trajectories. Our results provided structural details on probable interaction mechanism of the cytotoxic DHPMTs that are difficult to address experimentally. The outputs of the current study propose new monastrol derivatives as probable resistance-overwhelming Eg5 modulators.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S Shahabipour
- Department of Applied Chemistry, Faculty of Science, University of Mohaghegh Ardabili, Ardabil, Iran
| | - A N Shamkhali
- Department of Applied Chemistry, Faculty of Science, University of Mohaghegh Ardabili, Ardabil, Iran
- Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - N Razzaghi-Asl
- Pharmaceutical Sciences Research Center, Ardabil University of Medical Sciences, Ardabil, Iran, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
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Abuasaker B, Garrido E, Vilaplana M, Gómez-Zepeda JD, Brun S, Garcia-Cajide M, Mauvezin C, Jaumot M, Pujol MD, Rubio-Martínez J, Agell N. α4-α5 Helices on Surface of KRAS Can Accommodate Small Compounds That Increase KRAS Signaling While Inducing CRC Cell Death. Int J Mol Sci 2023; 24:ijms24010748. [PMID: 36614192 PMCID: PMC9821572 DOI: 10.3390/ijms24010748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
KRAS is the most frequently mutated oncogene associated with the genesis and progress of pancreatic, lung and colorectal (CRC) tumors. KRAS has always been considered as a therapeutic target in cancer but until now only two compounds that inhibit one specific KRAS mutation have been approved for clinical use. In this work, by molecular dynamics and a docking process, we describe a new compound (P14B) that stably binds to a druggable pocket near the α4-α5 helices of the allosteric domain of KRAS. This region had previously been identified as the binding site for calmodulin (CaM). Using surface plasmon resonance and pulldown analyses, we prove that P14B binds directly to oncogenic KRAS thus competing with CaM. Interestingly, P14B favors oncogenic KRAS interaction with BRAF and phosphorylated C-RAF, and increases downstream Ras signaling in CRC cells expressing oncogenic KRAS. The viability of these cells, but not that of the normal cells, is impaired by P14B treatment. These data support the significance of the α4-α5 helices region of KRAS in the regulation of oncogenic KRAS signaling, and demonstrate that drugs interacting with this site may destine CRC cells to death by increasing oncogenic KRAS downstream signaling.
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Affiliation(s)
- Baraa Abuasaker
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, 08036 Barcelona, Spain
| | - Eduardo Garrido
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, 08036 Barcelona, Spain
- Departament de Ciència de Materials i Química Física, Facultat de Química, Universitat de Barcelona & Institut de Recerca en Química Teòrica i Computacional (IQTCUB), 08028 Barcelona, Spain
| | - Marta Vilaplana
- Departament de Farmacologia, Toxicologia i Química Terapèutica, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Jesús Daniel Gómez-Zepeda
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, 08036 Barcelona, Spain
| | - Sonia Brun
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, 08036 Barcelona, Spain
| | - Marta Garcia-Cajide
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, 08036 Barcelona, Spain
| | - Caroline Mauvezin
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, 08036 Barcelona, Spain
| | - Montserrat Jaumot
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, 08036 Barcelona, Spain
| | - Maria Dolors Pujol
- Departament de Farmacologia, Toxicologia i Química Terapèutica, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Jaime Rubio-Martínez
- Departament de Ciència de Materials i Química Física, Facultat de Química, Universitat de Barcelona & Institut de Recerca en Química Teòrica i Computacional (IQTCUB), 08028 Barcelona, Spain
- Correspondence: (J.R.-M.); (N.A.); Tel.: +34-934039263 (J.R.-M.); +34-934035267 (N.A.)
| | - Neus Agell
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, 08036 Barcelona, Spain
- Correspondence: (J.R.-M.); (N.A.); Tel.: +34-934039263 (J.R.-M.); +34-934035267 (N.A.)
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Sgrignani J, Cavalli A. Computational Identification of a Putative Allosteric Binding Pocket in TMPRSS2. Front Mol Biosci 2021; 8:666626. [PMID: 33996911 PMCID: PMC8119889 DOI: 10.3389/fmolb.2021.666626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/01/2021] [Indexed: 12/23/2022] Open
Abstract
Camostat, nafamostat, and bromhexine are inhibitors of the transmembrane serine protease TMPRSS2. The inhibition of TMPRSS2 has been shown to prevent the viral infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other viruses. However, while camostat and nafamostat inhibit TMPRSS2 by forming a covalent adduct, the mode of action of bromhexine remains unclear. TMPRSS2 is autocatalytically activated from its inactive form, zymogen, through a proteolytic cleavage that promotes the binding of Ile256 to a putative allosteric pocket (A-pocket). Computer simulations, reported here, indicate that Ile256 binding induces a conformational change in the catalytic site, thus providing the atomistic rationale to the activation process of the enzyme. Furthermore, computational docking and molecular dynamics simulations indicate that bromhexine competes with the N-terminal Ile256 for the same binding site, making it a potential allosteric inhibitor. Taken together, these findings provide the atomistic basis for the development of more selective and potent TMPRSS2 inhibitors.
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Affiliation(s)
- Jacopo Sgrignani
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Küçükgüzel I, Satılmış G, Gurukumar KR, Basu A, Tatar E, Nichols DB, Talele TT, Kaushik-Basu N. 2-Heteroarylimino-5-arylidene-4-thiazolidinones as a new class of non-nucleoside inhibitors of HCV NS5B polymerase. Eur J Med Chem 2013; 69:931-41. [PMID: 24161679 DOI: 10.1016/j.ejmech.2013.08.043] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 08/27/2013] [Accepted: 08/31/2013] [Indexed: 12/09/2022]
Abstract
Hepatitis C virus (HCV) NS5B polymerase is an important and attractive target for the development of anti-HCV drugs. Here we report on the design, synthesis and evaluation of twenty-four novel allosteric inhibitors bearing the 4-thiazolidinone scaffold as inhibitors of HCV NS5B polymerase. Eleven compounds tested were found to inhibit HCV NS5B with IC₅₀ values ranging between 19.8 and 64.9 μM. Compound 24 was the most active of this series with an IC₅₀ of 5.6 μM. A number of these derivatives further exhibited strong inhibition against HCV 1b and 2a genotypes in cell based antiviral assays. Molecular docking analysis predicted that the thiazolidinone derivatives bind to the NS5B thumb pocket-II (TP-II). Our results suggest that further optimization of the thiazolidinone scaffold may be possible to yield new derivatives with improved enzyme- and cell-based activity.
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Affiliation(s)
- Ilkay Küçükgüzel
- Marmara University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Haydarpaşa, 34668 İstanbul, Turkey.
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