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Grossi G, Scarano N, Musumeci F, Tonelli M, Kanov E, Carbone A, Fossa P, Gainetdinov RR, Cichero E, Schenone S. Discovery of a Novel Chemo-Type for TAAR1 Agonism via Molecular Modeling. Molecules 2024; 29:1739. [PMID: 38675561 PMCID: PMC11052455 DOI: 10.3390/molecules29081739] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/27/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
The search for novel effective TAAR1 ligands continues to draw great attention due to the wide range of pharmacological applications related to TAAR1 targeting. Herein, molecular docking studies of known TAAR1 ligands, characterized by an oxazoline core, have been performed in order to identify novel promising chemo-types for the discovery of more active TAAR1 agonists. In particular, the oxazoline-based compound S18616 has been taken as a reference compound for the computational study, leading to the development of quite flat and conformationally locked ligands. The choice of a "Y-shape" conformation was suggested for the design of TAAR1 ligands, interacting with the protein cavity delimited by ASP103 and aromatic residues such as PHE186, PHE195, PHE268, and PHE267. The obtained results allowed us to preliminary in silico screen an in-house series of pyrimidinone-benzimidazoles (1a-10a) as a novel scaffold to target TAAR1. Combined ligand-based (LBCM) and structure based (SBCM) computational methods suggested the biological evaluation of compounds 1a-10a, leading to the identification of derivatives 1a-3a (hTAAR1 EC50 = 526.3-657.4 nM) as promising novel TAAR1 agonists.
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Affiliation(s)
- Giancarlo Grossi
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (G.G.); (N.S.); (F.M.); (M.T.); (A.C.); (P.F.); (S.S.)
| | - Naomi Scarano
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (G.G.); (N.S.); (F.M.); (M.T.); (A.C.); (P.F.); (S.S.)
| | - Francesca Musumeci
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (G.G.); (N.S.); (F.M.); (M.T.); (A.C.); (P.F.); (S.S.)
| | - Michele Tonelli
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (G.G.); (N.S.); (F.M.); (M.T.); (A.C.); (P.F.); (S.S.)
| | - Evgeny Kanov
- Institute of Translational Biomedicine, St. Petersburg State University, 199034 St. Petersburg, Russia (R.R.G.)
- St. Petersburg University Hospital, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anna Carbone
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (G.G.); (N.S.); (F.M.); (M.T.); (A.C.); (P.F.); (S.S.)
| | - Paola Fossa
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (G.G.); (N.S.); (F.M.); (M.T.); (A.C.); (P.F.); (S.S.)
| | - Raul R. Gainetdinov
- Institute of Translational Biomedicine, St. Petersburg State University, 199034 St. Petersburg, Russia (R.R.G.)
- St. Petersburg University Hospital, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Elena Cichero
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (G.G.); (N.S.); (F.M.); (M.T.); (A.C.); (P.F.); (S.S.)
| | - Silvia Schenone
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (G.G.); (N.S.); (F.M.); (M.T.); (A.C.); (P.F.); (S.S.)
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Elseginy SA. Identifying and characterising promising small molecule inhibitors of kinesin spindle protein using ligand-based virtual screening, molecular docking, molecular dynamics and MM‑GBSA calculations. J Comput Aided Mol Des 2024; 38:16. [PMID: 38556596 PMCID: PMC10982093 DOI: 10.1007/s10822-024-00553-5] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 02/22/2024] [Indexed: 04/02/2024]
Abstract
The kinesin spindle protein (Eg5) is a mitotic protein that plays an essential role in the formation of the bipolar spindles during the mitotic phase. Eg5 protein controls the segregation of the chromosomes in mitosis which renders it a vital target for cancer treatment. In this study our approach to identifying novel scaffold for Eg5 inhibitors is based on targeting the novel allosteric pocket (α4/α6/L11). Extensive computational techniques were applied using ligand-based virtual screening and molecular docking by two approaches, MOE and AutoDock, to screen a library of commercial compounds. We identified compound 8-(3-(1H-imidazol-1-ylpropylamino)-3-methyl-7-((naphthalen-3-yl)methyl)-1H-purine-2, 6 (3H,7H)-dione (compound 5) as a novel scaffold for Eg5 inhibitors. This compound inhibited cancer cell Eg5 ATPase at 2.37 ± 0.15 µM. The molecular dynamics simulations revealed that the identified compound formed stable interactions in the allosteric pocket (α4/α6/L11) of the receptor, indicating its potential as a novel Eg5 inhibitor.
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Affiliation(s)
- Samia A Elseginy
- Chemical Industries Research Division, Green Chemistry Department, National Research Centre, Cairo, 12622, Egypt.
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Onisuru O, Achilonu I. Describing the ligandin properties of Plasmodium falciparum and vivax glutathione transferase towards bromosulfophthalein from empirical and computational modelling viewpoints. J Biomol Struct Dyn 2024:1-16. [PMID: 38506165 DOI: 10.1080/07391102.2024.2329291] [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: 12/14/2023] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Abstract
Research has spotlighted glutathione transferase (GST) as a promising target for antimalarial drug development due to its pivotal role in cellular processes, including metabolizing toxins and managing oxidative stress. This interest arises from GST's potential to combat multidrug resistance in existing antimalarial drugs. Plasmodium falciparum GST (PfGST) and Plasmodium vivax GST (PvGST) are key targets; inhibiting them not only disrupt detoxification but also reduce their antioxidant capacity, a critical feature for potent antimalarials. Bromosulfophthalein (BSP), a clinical liver function dye, emerged as a potent cytosolic GST inhibitor. This study explored BSP's inhibitory properties on PfGST and PvGST, showcasing its binding capabilities through empirical and computational analyses. The study revealed BSP's ability to significantly inhibit GST activity, altering the proteins' structures and stability. Specifically, BSP binding induced spectral changes and impacted the proteins' thermal stability, reducing their melting temperatures. Computational simulations highlighted BSP's strong binding to PfGST and PvGST at their dimer interface, stabilized by various interactions, including hydrogen bonds and van der Waals forces. Notably, BSP's binding altered the proteins' compactness and conformational dynamics, suggesting a potential non-competitive, allosteric inhibition mechanism. This study provided novel insights into BSP's candidacy as an antimalarial drug by targeting PfGST and PvGST. Its ability to disrupt crucial functions of these enzymes' positions BSP as a promising candidate for further drug development in combating malariaCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Olalekan Onisuru
- Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg, South Africa
| | - Ikechukwu Achilonu
- Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg, South Africa
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Podolak M, Holota S, Deyak Y, Dziduch K, Dudchak R, Wujec M, Bielawski K, Lesyk R, Bielawska A. Tubulin inhibitors. Selected scaffolds and main trends in the design of novel anticancer and antiparasitic agents. Bioorg Chem 2024; 143:107076. [PMID: 38163424 DOI: 10.1016/j.bioorg.2023.107076] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/02/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
Design of tubulin inhibitors as anticancer drugs dynamically developed over the past 20 years. The modern arsenal of potential tubulin-targeting anticancer agents is represented by small molecules, monoclonal antibodies, and antibody-drug conjugates. Moreover, targeting tubulin has been a successful strategy in the development of antiparasitic drugs. In the present review, an overall picture of the research and development of potential tubulin-targeting agents using small molecules between 2018 and 2023 is provided. The data about some most often used and prospective chemotypes of small molecules (privileged heterocycles, moieties of natural molecules) and synthetic methodologies (analogue-based, fragment-based drug design, molecular hybridization) applied for the design of novel agents with an impact on the tubulin system are summarized. The design and prospects of multi-target agents with an impact on the tubulin system were also highlighted. Reported in the review data contribute to the "structure-activity" profile of tubulin-targeting small molecules as anticancer and antiparasitic agents and will be useful for the application by medicinal chemists in further exploration, design, improvement, and optimization of this class of molecules.
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Affiliation(s)
- Magdalena Podolak
- Department of Biotechnology, Medical University of Bialystok, Kilinskiego 1, 15-089 Bialystok, Poland
| | - Serhii Holota
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, 79010 Lviv, Ukraine
| | - Yaroslava Deyak
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, 79010 Lviv, Ukraine; Department of Pharmaceutical Disciplines, Uzhhorod National University, Narodna Square 3, 88000 Uzhhorod, Ukraine
| | - Katarzyna Dziduch
- Doctoral School, Medical University of Lublin, Chodzki 7, 20-093 Lublin, Poland
| | - Rostyslav Dudchak
- Department of Biotechnology, Medical University of Bialystok, Kilinskiego 1, 15-089 Bialystok, Poland
| | - Monika Wujec
- Department of Organic Chemistry, Medical University of Lublin, Chodzki 4a, 20-093 Lublin, Poland
| | - Krzysztof Bielawski
- Department of Synthesis and Technology of Drugs, Medical University of Bialystok, Kilinskiego 1, 15-089 Bialystok, Poland
| | - Roman Lesyk
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, 79010 Lviv, Ukraine.
| | - Anna Bielawska
- Department of Biotechnology, Medical University of Bialystok, Kilinskiego 1, 15-089 Bialystok, Poland
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Liao Y, Yuan C, Huang M, Si W, Li D, Wu W, Zhang S, Wu R, Quan Y, Yu X, Liao S. AZD7762 induces CRBN dependent BAG3 degradation through ubiquitin-proteasome pathway. Anticancer Drugs 2024; 35:46-54. [PMID: 37449977 PMCID: PMC10720835 DOI: 10.1097/cad.0000000000001532] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 06/16/2023] [Indexed: 07/18/2023]
Abstract
Protein degraders are currently under rapid development as a promising modality for drug discovery. They are compounds that orchestrate interactions between a target protein and an E3 ubiquitin ligase, prompting intracellular protein degradation through proteasomal pathway. More protein degraders identification will greatly promote the development of this field. BAG3 is widely recognized as an excellent therapeutic target in cancer treatments. Exploring protein degraders that target BAG3 degradation has profound implications. Herein, molecular docking was applied to assess binding energy between 81 clinical phase I kinase inhibitors and BAG3. BAG3 protein and mRNA level were detected by western blot and quantitative real-time PCR. CCK8 assay and colony formation assay were applied to detect the cell viability and proliferation rate. Cell death was accessed using flow cytometry combined with PI and Annexin V double staining. AZD7762, a Chk1 kinase inhibitor, was identified to induce BAG3 degradation in a ubiquitin-proteasome pathway. AZD7762-induced BAG3 degradation was not dependent on Chk1 expression or activity. CRBN, an E3 ligase, was identified to bind to BAG3 and mediated BAG3 ubiquitination in the presence of AZD7762. By targeting Chk1 and BAG3, two ideal therapeutic targets in cancer treatment, AZD7762 would be a powerful chemotherapy agent in the future.
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Affiliation(s)
- Yanli Liao
- Department of Scientific Research and Experiment Center, Zhaoqing Medical College
| | - Chao Yuan
- Department of Scientific Research and Experiment Center, Zhaoqing Medical College
| | - Mi Huang
- Department of Scientific Research and Experiment Center, Zhaoqing Medical College
| | - WenXia Si
- Department of Scientific Research and Experiment Center, Zhaoqing Medical College
| | - Duanzhuo Li
- Department of Scientific Research and Experiment Center, Zhaoqing Medical College
| | - Weibin Wu
- Department of Scientific Research and Experiment Center, Zhaoqing Medical College
| | - Shifa Zhang
- Department of Scientific Research and Experiment Center, Zhaoqing Medical College
| | - Runkun Wu
- Department of Oncology, Zhaoqing First People’s Hospital Affiliated to Zhaoqing Medical College, Zhaoqing, Guangdong, China
| | - Yi Quan
- Department of Oncology, Zhaoqing First People’s Hospital Affiliated to Zhaoqing Medical College, Zhaoqing, Guangdong, China
| | - Xin Yu
- Department of Scientific Research and Experiment Center, Zhaoqing Medical College
| | - Shengjie Liao
- Department of Scientific Research and Experiment Center, Zhaoqing Medical College
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Sarkari A, Lou E. Electrical properties of cancer cells: A next generation biophysical therapeutic target: Comment on "The distinguishing electrical properties of cancer cells" by Di Gregorio, Israel, Staelens, Tankel, Shankar, and Tuszyński. Phys Life Rev 2023; 47:110-112. [PMID: 37832176 DOI: 10.1016/j.plrev.2023.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 10/15/2023]
Affiliation(s)
- Akshat Sarkari
- Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, United States of America
| | - Emil Lou
- Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, United States of America; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America; Graduate Faculty, Integrative Biology and Physiology Department, University of Minnesota, Minneapolis, MN, United States of America.
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Abbotto E, Casini B, Piacente F, Scarano N, Cerri E, Tonelli M, Astigiano C, Millo E, Sturla L, Bruzzone S, Cichero E. Novel Thiazole-Based SIRT2 Inhibitors Discovered via Molecular Modelling Studies and Enzymatic Assays. Pharmaceuticals (Basel) 2023; 16:1316. [PMID: 37765125 PMCID: PMC10535842 DOI: 10.3390/ph16091316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/09/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Recently, the development of sirtuin small molecule inhibitors (SIRTIs) has been gaining attention for the treatment of different cancer types, but also to contrast neurodegenerative disease, diabetes, and autoimmune syndromes. In the search for SIRT2 modulators, the availability of several X-crystallographic data regarding SIRT2-ligand complexes has allowed for setting up a structure-based study, which is herein presented. A set of 116 SIRT2 inhibitors featuring different chemical structures has been collected from the literature and used for molecular docking studies involving 4RMG and 5MAT PDB codes. The information found highlights key contacts with the SIRT2 binding pocket such as Van der Waals and π-π stacking with Tyr104, Phe119, Phe234, and Phe235 in order to achieve high inhibitory ability values. Following the preliminary virtual screening studies, a small in-house library of compounds (1a-7a), previously investigated as putative HSP70 inhibitors, was described to guide the search for dual-acting HSP70/SIRT2 inhibitors. Biological and enzymatic assays validated the whole procedure. Compounds 2a and 7a were found to be the most promising derivatives herein proposed.
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Affiliation(s)
- Elena Abbotto
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (E.A.); (F.P.); (E.C.); (C.A.); (E.M.); (L.S.)
| | - Beatrice Casini
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (B.C.); (N.S.); (M.T.)
| | - Francesco Piacente
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (E.A.); (F.P.); (E.C.); (C.A.); (E.M.); (L.S.)
| | - Naomi Scarano
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (B.C.); (N.S.); (M.T.)
| | - Elena Cerri
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (E.A.); (F.P.); (E.C.); (C.A.); (E.M.); (L.S.)
| | - Michele Tonelli
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (B.C.); (N.S.); (M.T.)
| | - Cecilia Astigiano
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (E.A.); (F.P.); (E.C.); (C.A.); (E.M.); (L.S.)
| | - Enrico Millo
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (E.A.); (F.P.); (E.C.); (C.A.); (E.M.); (L.S.)
| | - Laura Sturla
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (E.A.); (F.P.); (E.C.); (C.A.); (E.M.); (L.S.)
| | - Santina Bruzzone
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (E.A.); (F.P.); (E.C.); (C.A.); (E.M.); (L.S.)
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy
| | - Elena Cichero
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (B.C.); (N.S.); (M.T.)
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