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Ribeiro IC, de Moraes JVB, Mariotini-Moura C, Polêto MD, da Rocha Torres Pavione N, de Castro RB, Miranda IL, Sartori SK, Alves KLS, Bressan GC, de Souza Vasconcellos R, Meyer-Fernandes JR, Diaz-Muñoz G, Fietto JLR. Synthesis of new non-natural L-glycosidic flavonoid derivatives and their evaluation as inhibitors of Trypanosoma cruzi ecto-nucleoside triphosphate diphosphohydrolase 1 (TcNTPDase1). Purinergic Signal 2024; 20:399-419. [PMID: 37975950 PMCID: PMC11303637 DOI: 10.1007/s11302-023-09974-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023] Open
Abstract
Trypanosoma cruzi is the pathogen of Chagas disease, a neglected tropical disease that affects more than 6 million people worldwide. There are no vaccines to prevent infection, and the therapeutic arsenal is very minimal and toxic. The unique E-NTPDase of T. cruzi (TcNTPDase1) plays essential roles in adhesion and infection and is a virulence factor. Quercetin is a flavonoid with antimicrobial, antiviral, and antitumor activities. Its potential as a partial inhibitor of NTPDases has also been demonstrated. In this work, we synthesized the non-natural L-glycoside derivatives of quercetin and evaluated them as inhibitors of recombinant TcNTPDase1 (rTcNTPDase1). These compounds, and quercetin and miquelianin, a natural quercetin derivative, were also tested. Compound 16 showed the most significant inhibitory effect (94%). Quercetin, miquelianin, and compound 14 showed inhibition close to 50%. We thoroughly investigated the inhibitory effect of 16. Our data suggested a competitive inhibition with a Ki of 8.39 μM (± 0.90). To better understand the interaction of compound 16 and rTcNTPDase1, we performed molecular dynamics simulations of the enzyme and docking analyses with the compounds. Our predictions show that compound 16 binds to the enzyme's catalytic site and interacts with important residues for NTPDase activity. As an inhibitor of a critical T. cruzi enzyme, (16) could be helpful as a starting point in the developing of a future treatment for Chagas disease. Furthermore, the discovery of (16) as an inhibitor of TcNTPDase1 may open new avenues in the study and development of new inhibitors of E-NTPDases.
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Affiliation(s)
- Isadora Cunha Ribeiro
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - Christiane Mariotini-Moura
- General Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Medicine and Nursing Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Marcelo Depolo Polêto
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - Raissa Barbosa de Castro
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Izabel Luzia Miranda
- Exact Science Institute, Chemistry Department, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Suélen Karine Sartori
- Exact Science Institute, Chemistry Department, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Kryssia Lohayne Santos Alves
- Exact Science Institute, Chemistry Department, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Gustavo Costa Bressan
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - José Roberto Meyer-Fernandes
- Laboratory of Cellular Biochemistry, Institute of Medical Biochemistry Leopoldo de Meis, Health Sciences Center, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gaspar Diaz-Muñoz
- Exact Science Institute, Chemistry Department, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
| | - Juliana Lopes Rangel Fietto
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
- General Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
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Bekker GJ, Fukunishi Y, Higo J, Kamiya N. Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations. ACS OMEGA 2024; 9:3412-3422. [PMID: 38284074 PMCID: PMC10809319 DOI: 10.1021/acsomega.3c06826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/16/2023] [Accepted: 12/28/2023] [Indexed: 01/30/2024]
Abstract
Flavin mononucleotide riboswitches are common among many pathogenic bacteria and are therefore considered to be an attractive target for antibiotics development. The riboswitch binds riboflavin (RBF, also known as vitamin B2), and although an experimental structure of their complex has been solved with the ligand bound deep inside the RNA molecule in a seemingly unreachable state, the binding mechanism between these molecules is not yet known. We have therefore used our Multicanonical Molecular Dynamics (McMD)-based dynamic docking protocol to analyze their binding mechanism by simulating the binding process between the riboswitch aptamer domain and the RBF, starting from the apo state of the riboswitch. Here, the refinement stage was crucial to identify the native binding configuration, as several other binding configurations were also found by McMD-based docking simulations. RBF initially binds the interface between P4 and P6 including U61 and G62, which forms a gateway where the ligand lingers until this gateway opens sufficiently to allow the ligand to pass through and slip into the hidden binding site including A48, A49, and A85.
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Affiliation(s)
- Gert-Jan Bekker
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshifumi Fukunishi
- Cellular
and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology
(AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Junichi Higo
- Graduate
School of Information Science, University
of Hyogo, 7-1-28 minatojima
Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Narutoshi Kamiya
- Graduate
School of Information Science, University
of Hyogo, 7-1-28 minatojima
Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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Mohebbinia Z, Firouzi R, Karimi-Jafari MH. Improving protein-ligand docking results using the Semiempirical quantum mechanics: testing on the PDBbind 2016 core set. J Biomol Struct Dyn 2024:1-11. [PMID: 38165642 DOI: 10.1080/07391102.2023.2299742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/20/2023] [Indexed: 01/04/2024]
Abstract
Molecular docking techniques are routinely employed for predicting ligand binding conformations and affinities in the in silico phase of the drug design and development process. In this study, a reliable semiempirical quantum mechanics (SQM) method, PM7, was employed for geometry optimization of top-ranked poses obtained from two widely used docking programs, AutoDock4 and AutoDock Vina. The PDBbind core set (version 2016), which contains high-quality crystal protein - ligand complexes with their corresponding experimental binding affinities, was used as an initial dataset in this research. It was shown that docking pose optimization improves the accuracy of pose predictions and is very useful for the refinement of docked complexes via removing clashes between ligands and proteins. It was also demonstrated that AutoDock Vina achieves a higher sampling power than AutoDock4 in generating accurate ligand poses (RMSD ≤ 2.0 Å), while AutoDock4 exhibits a better ranking power than AutoDock Vina. Finally, a new protocol based on a combination of the results obtained from the two docking programs was proposed for structure-based virtual screening studies, which benefits from the robust sampling abilities of AutoDock Vina and the reliable ranking performance of AutoDock4.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zainab Mohebbinia
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
| | - Rohoullah Firouzi
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
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Basu G, Sudo Y, Berliner L, Shaitan K, Hall D. Editors' Roundup: June 2023. Biophys Rev 2023; 15:307-311. [PMID: 37396446 PMCID: PMC10310647 DOI: 10.1007/s12551-023-01077-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2023] [Indexed: 07/04/2023] Open
Abstract
This commentary article represents the latest edition of the Biophysical Reviews 'Editors' Roundup' Series - a platform made available to the editorial board members of any journal with a genuine interest in promoting biophysical content. Each journal associated editor is able to submit a short description of up to five articles recently appearing in their journals with an explanation of why these articles are of interest. This edition (Vol. 15 Issue 3 June 2023) carries contributions from editorial members associated with Biophysics and Physicobiology (Biophysical Society of Japan), Biophysics (Russian Academy of Sciences), Cell Biochemistry and Biophysics (Springer), and Biophysical Reviews (IUPAB-International Union for Pure and Applied Biophysics).
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Affiliation(s)
- Gautam Basu
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12 C.I.T. Scheme VII-M, Kolkata, 700054 India
| | - Yuki Sudo
- Medicine, Dentistry and Pharmaceutical Sciences, Institute of Acadmic and Research, Okayama University, Kita-ku, Okayama, 700-8534 Japan
| | - Lawrence Berliner
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO USA
| | | | - Damien Hall
- WPI Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1164 Japan
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Bailly C, Vergoten G. Interaction of Camptothecin Anticancer Drugs with Ribosomal Proteins L15 and L11: A Molecular Docking Study. Molecules 2023; 28:molecules28041828. [PMID: 36838813 PMCID: PMC9967338 DOI: 10.3390/molecules28041828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 01/31/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
The antitumor drug topotecan (TPT) is a potent inhibitor of topoisomerase I, triggering DNA breaks lethal for proliferating cancer cells. The mechanism is common to camptothecins SN38 (the active metabolite of irinotecan) and belotecan (BLT). Recently, TPT was shown to bind the ribosomal protein L15, inducing an antitumor immune activation independent of topoisomerase I. We have modeled the interaction of four camptothecins with RPL15 derived from the 80S human ribosome. Two potential drug-binding sites were identified at Ile135 and Phe129. SN38 can form robust RPL15 complexes at both sites, whereas BLT essentially gave stable complexes with site Ile135. The empirical energy of interaction (ΔE) for SN38 binding to RPL15 is similar to that determined for TPT binding to the topoisomerase I-DNA complex. Molecular models with the ribosomal protein L11 sensitive to topoisomerase inhibitors show that SN38 can form a robust complex at a single site (Cys25), much more stable than those with TPT and BLT. The main camptothecin structural elements implicated in the ribosomal protein interaction are the lactone moiety, the aromatic system and the 10-hydroxyl group. The study provides guidance to the design of modulators of ribosomal proteins L11 and L15, both considered anticancer targets.
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Affiliation(s)
- Christian Bailly
- Institut de Chimie Pharmaceutique Albert Lespagnol (ICPAL), Faculté de Pharmacie, University of Lille, 3 rue du Professeur Laguesse, BP-83, F-59006 Lille, France
- CNRS, Inserm, CHU Lille, UMR9020-U1277—CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, University of Lille, F-59000 Lille, France
- OncoWitan, Consulting Scientific Office, Wasquehal, F-59290 Lille, France
- Correspondence:
| | - Gérard Vergoten
- Institut de Chimie Pharmaceutique Albert Lespagnol (ICPAL), Faculté de Pharmacie, University of Lille, 3 rue du Professeur Laguesse, BP-83, F-59006 Lille, France
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Hall D, Basu G, Ito N. Computational biophysics and structural biology of proteins-a Special Issue in honor of Prof. Haruki Nakamura's 70th birthday. Biophys Rev 2023; 14:1211-1222. [PMID: 36620377 PMCID: PMC9809522 DOI: 10.1007/s12551-022-01039-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 01/05/2023] Open
Abstract
Receiving his initial training jointly in theoretical and applied physics at the University of Tokyo, Professor Haruki Nakamura has had a long and eventful scientific career, along the way helping to shape the way that biophysics is carried out in Japan. Concentrating his research efforts on the simulation of protein structure and function, he has, over his career arc, acted as director of the Institute for Protein Research (Osaka, Japan), director of the Protein Data Bank of Japan (PDBj), president of the Biophysical Society of Japan (BSJ), president of the Protein Science Society of Japan (PSSJ), and group leader and professor of Bioinformatics and Computational Structural Biology at Osaka University. In 2022, Prof. Haruki Nakamura turned 70 years old, and to mark this occasion, his scientific colleagues from around the world have combined their efforts to produce this Festschrift Issue of the IUPAB Biophysical Reviews journal around the theme of the computational biophysics and structural biology of proteins.
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Affiliation(s)
- Damien Hall
- WPI Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1164 Japan
- Department of Applied Physics, Aalto University, 00076 Aalto, Finland
| | - Gautam Basu
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12 C.I.T. Scheme VII-M, Kolkata, 700054 India
| | - Nobutoshi Ito
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), Yushima, Bunkyo-Ku, Tokyo, 113-8510 Japan
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Nakamura H. Some reflections on a career in science and a note of thanks to the contributors of this Special Issue. Biophys Rev 2022; 14:1223-1226. [PMID: 36659991 PMCID: PMC9842830 DOI: 10.1007/s12551-022-01035-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Affiliation(s)
- Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 Japan
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