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Scarano N, Brullo C, Musumeci F, Millo E, Bruzzone S, Schenone S, Cichero E. Recent Advances in the Discovery of SIRT1/2 Inhibitors via Computational Methods: A Perspective. Pharmaceuticals (Basel) 2024; 17:601. [PMID: 38794171 PMCID: PMC11123952 DOI: 10.3390/ph17050601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/03/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024] Open
Abstract
Sirtuins (SIRTs) are classified as class III histone deacetylases (HDACs), a family of enzymes that catalyze the removal of acetyl groups from the ε-N-acetyl lysine residues of histone proteins, thus counteracting the activity performed by histone acetyltransferares (HATs). Based on their involvement in different biological pathways, ranging from transcription to metabolism and genome stability, SIRT dysregulation was investigated in many diseases, such as cancer, neurodegenerative disorders, diabetes, and cardiovascular and autoimmune diseases. The elucidation of a consistent number of SIRT-ligand complexes helped to steer the identification of novel and more selective modulators. Due to the high diversity and quantity of the structural data thus far available, we reviewed some of the different ligands and structure-based methods that have recently been used to identify new promising SIRT1/2 modulators. The present review is structured into two sections: the first includes a comprehensive perspective of the successful computational approaches related to the discovery of SIRT1/2 inhibitors (SIRTIs); the second section deals with the most interesting SIRTIs that have recently appeared in the literature (from 2017). The data reported here are collected from different databases (SciFinder, Web of Science, Scopus, Google Scholar, and PubMed) using "SIRT", "sirtuin", and "sirtuin inhibitors" as keywords.
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Affiliation(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; (N.S.); (F.M.); (S.S.)
| | - Chiara Brullo
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (N.S.); (F.M.); (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; (N.S.); (F.M.); (S.S.)
| | - Enrico Millo
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (E.M.); (S.B.)
| | - Santina Bruzzone
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (E.M.); (S.B.)
- IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - 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; (N.S.); (F.M.); (S.S.)
| | - 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; (N.S.); (F.M.); (S.S.)
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Al-Ghamdi AR, Rahman S, Al-Wabli RI, Al-Mutairi MS, Rahman AFMM. Synthesis, Cytotoxicity, and Photophysical Investigations of 2-Amino-4,6-diphenylnicotinonitriles: An Experimental and Theoretical Study. Molecules 2024; 29:1808. [PMID: 38675628 PMCID: PMC11055175 DOI: 10.3390/molecules29081808] [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: 03/11/2024] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
In this study, we present a comprehensive investigation of 2-amino-4,6-diphenylnicotinonitriles (APNs, 1-6), including their synthesis, cytotoxicity against breast cancer cell lines, and photophysical properties. Compound 3 demonstrates exceptional cytotoxicity, surpassing the potency of Doxorubicin. The fluorescence spectra of the synthesized 1-6 in different solvents reveal solvent-dependent shifts in the emission maximum values, highlighting the influence of the solvent environment on their fluorescence properties. A quantum chemical TD-DFT analysis provides insights into the electronic structure and fluorescence behavior of 1-6, elucidating HOMO-LUMO energy gaps, electronegativity values, and dipole moments, contributing to a deeper understanding of their electronic properties and potential reactivity. These findings provide valuable knowledge for the development of APNs (1-6) as fluorescent sensors and potential anticancer agents.
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Affiliation(s)
- Alwah R. Al-Ghamdi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.R.A.-G.); (R.I.A.-W.); (M.S.A.-M.)
| | - Shofiur Rahman
- College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Reem I. Al-Wabli
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.R.A.-G.); (R.I.A.-W.); (M.S.A.-M.)
| | - Maha S. Al-Mutairi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.R.A.-G.); (R.I.A.-W.); (M.S.A.-M.)
| | - A. F. M. Motiur Rahman
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.R.A.-G.); (R.I.A.-W.); (M.S.A.-M.)
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Kondabanthini S, Akshinthala P, Katari NK, Srimannarayana M, Gundla R, Kapavarapu R, Pal M. A rapid synthesis of 5-substituted 7-amino-6-cyano-1,5-dihydro-1H-pyrano[2,3-d]pyrimidine-2,4(3H)-diones and their in silico / evaluation against SIRT1. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Synthesis, properties, and application of the new nanocatalyst of double layer hydroxides in the one-pot multicomponent synthesis of 2-amino-3-cyanopyridine derivatives. Sci Rep 2023; 13:1627. [PMID: 36709240 PMCID: PMC9884200 DOI: 10.1038/s41598-023-27940-6] [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: 11/20/2022] [Accepted: 01/10/2023] [Indexed: 01/30/2023] Open
Abstract
A new heterogeneous nanocatalyst LDH@3-chloropyltrimethoxysilane@1,3-benzenedisulfonyl amine@Cu (LDH@TRMS@BDSA@Cu) was synthesized and confirmed by analyzes such as Fourier transform infrared spectroscopy, Field Emission Scanning Electron Microscopy, energy scattered X-ray spectroscopy (EDX), elemental mapping, X-ray diffraction analysis, heat gravity/heat derivatization (TGA) and differential scanning calorimetry. The newly synthesized nanocatalyst effectively catalyzed the reaction between different aryl aldehydes, malononitrile, different acetophenones and ammonium acetate in solvent-free conditions and they were converted into 2-amino-3-cyanopyridine derivatives with high efficiency. The reaction showed advantages such as simplicity, high stability, environmental friendliness, excellent efficiency and short time. Also, this catalyst is recyclable and was recycled 4 times without losing significant catalytic power.
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Kondabanthini S, Katari NK, Srimannarayana M, Gundla R, Kapavarapu R, Pal M. Wang resin catalyzed sonochemical synthesis of dihydropyrano[2,3-c]pyrazole derivatives and their interactions with SIRT1. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Recent Advances in Multicomponent Reactions Catalysed under Operationally Heterogeneous Conditions. Catalysts 2022. [DOI: 10.3390/catal12070725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Multicomponent reactions (MCRs) have been gaining significance and attention over the past decade because of their ability to furnish complex products by using readily available and simple starting materials while simultaneously eliminating the need to separate and purify any intermediates. More so, most of these products have been found to exhibit diverse biological activities. Another paradigm shift which has occurred contemporarily is the switch to heterogeneous catalysis, which results in additional benefits such as the reduction of waste and an increase in the safety of the process. More importantly, it allows the user to recover and reuse the catalyst for multiple runs. In summary, both methodologies adhere to the principles of green chemistry, a philosophy which needs to become overarchingly enshrined. The plethora of reactions and catalysts which have been developed gives hope that chemists are slowly changing their ideology. As a result, this review attempts to discuss multicomponent reactions catalysed by operationally heterogeneous catalysts in the past 10 years. In this review, a further distinction is made between the MCRs which lead to the formation of heterocycles and those which do not.
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Ramarao S, Pothireddy M, Venkateshwarlu R, Moturu KMVR, Siddaiah V, Kapavarapu R, Dandela R, Pal M. Sonochemical Synthesis and In Silico Evaluation of Imidazo[1,2- a]Pyridine Derivatives as Potential Inhibitors of Sirtuins. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2077774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Sidda Ramarao
- Department of Organic Chemistry & FDW, Andhra University, Visakhapatnam, Andhra Pradesh, India
| | - Mohanreddy Pothireddy
- Department of Industrial and Engineering Chemistry, Institute of Chemical Technology, Indianoil Odisha Campus, Bhubaneswar, India
| | - Rapolu Venkateshwarlu
- Department of Organic Chemistry & FDW, Andhra University, Visakhapatnam, Andhra Pradesh, India
| | | | - Vidavalur Siddaiah
- Department of Organic Chemistry & FDW, Andhra University, Visakhapatnam, Andhra Pradesh, India
| | | | - Rambabu Dandela
- Department of Industrial and Engineering Chemistry, Institute of Chemical Technology, Indianoil Odisha Campus, Bhubaneswar, India
| | - Manojit Pal
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Hyderabad, India
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Challa CS, Katari NK, Nallanchakravarthula V, Nayakanti D, Kapavarapu R, Pal M. Wang-OSO3H catalyzed green synthesis of 2-arylamino-3-cyanopyridine derivatives under ultrasound: Their assessment as potential inhibitors of SIRT1. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132309] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Jalali-Mola S, Torabi M, Yarie M, Zolfigol MA. Acidic tributyl phosphonium-based ionic liquid: an efficient catalyst for preparation of diverse pyridine systems via a cooperative vinylogous anomeric-based oxidation. RSC Adv 2022; 12:34730-34739. [DOI: 10.1039/d2ra04631h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022] Open
Abstract
Experimental procedure for the synthesis of triaryl pyridines, indolyl pyridines and nicotinonitriles.
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Affiliation(s)
- Sepideh Jalali-Mola
- Department of Organic Chemistry, Faculty of Chemistry, Bu-Ali Sina University, Hamedan, Iran
| | - Morteza Torabi
- Department of Organic Chemistry, Faculty of Chemistry, Bu-Ali Sina University, Hamedan, Iran
| | - Meysam Yarie
- Department of Organic Chemistry, Faculty of Chemistry, Bu-Ali Sina University, Hamedan, Iran
| | - Mohammad Ali Zolfigol
- Department of Organic Chemistry, Faculty of Chemistry, Bu-Ali Sina University, Hamedan, Iran
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Abdjan MI, Aminah NS, Siswanto I, Kristanti AN, Takaya Y, Choudhary MI. Exploration of stilbenoid trimers as potential inhibitors of sirtuin1 enzyme using a molecular docking and molecular dynamics simulation approach. RSC Adv 2021; 11:19323-19332. [PMID: 35478645 PMCID: PMC9033617 DOI: 10.1039/d1ra02233d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 05/21/2021] [Indexed: 12/25/2022] Open
Abstract
A combination of molecular docking and molecular dynamics simulation (250 ns) has been carried out to study the interaction of stilbenoid trimer compounds with the SIRT1 enzyme as the target protein. SIRT1 expression regulates cellular stress responses that lead to the development of cancer. Redocking showed a good native ligand pose with an RMSD value of 1.40 Å at the receptor active site's coordinates. The molecular docking score uses a grid score functional (kcal mol−1), which shows results of 1NS: 79.56, TS1: −26.83, TS2: −87.77, and TS3: −83.67. The TS2 and TS3 candidates were chosen for further analysis because they had a lower grid score than the native ligand (1NS). Furthermore, prediction of binding free energy (kcal mol−1) using the Quantum Mechanics/generalized Born Surface Area (QM/MM-GBSA) method shows the results of 1NS: −31.52 ± 0.39, TS2: −58.99 ± 0.34, and TS3: −43.38 ± 0.35. These results indicate that the TS2 and TS3 compounds have good potential as inhibitors of the SIRT1 enzyme. Additionally, the amino acid residues were responsible for the inhibition mechanism through hydrogen bond interactions at the molecular level, including ASP22, PHE91, PRO11, ILE165, ASP166, and VAL230. The observations made in this study provide theoretical information for exploring the stilbenoid trimers as anticancer agents by targeting the SIRT1 enzyme. A combination of molecular docking and molecular dynamics simulation (250 ns) has been carried out to study the interaction of stilbenoid trimer compounds with the SIRT1 enzyme as the target protein.![]()
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Affiliation(s)
- Muhammad Ikhlas Abdjan
- Departement of Chemistry
- Faculty of Science and Technology
- Universitas Airlangga
- Surabaya 60115
- Indonesia
| | - Nanik Siti Aminah
- Departement of Chemistry
- Faculty of Science and Technology
- Universitas Airlangga
- Surabaya 60115
- Indonesia
| | - Imam Siswanto
- Departement of Chemistry
- Faculty of Science and Technology
- Universitas Airlangga
- Surabaya 60115
- Indonesia
| | - Alfinda Novi Kristanti
- Departement of Chemistry
- Faculty of Science and Technology
- Universitas Airlangga
- Surabaya 60115
- Indonesia
| | - Yoshiaki Takaya
- Faculty of Pharmacy
- Meijo University
- Nagoya
- Japan
- Adjunct Professor Department of Chemistry
| | - Muhammad Iqbal Choudhary
- H. E. J. Research Institute of Chemistry
- International Center for Chemical and Biological Sciences
- University of Karachi
- Karachi-75270
- Pakistan
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