1
|
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.
Collapse
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.)
| |
Collapse
|
2
|
Scumaci D, Zheng Q. Epigenetic meets metabolism: novel vulnerabilities to fight cancer. Cell Commun Signal 2023; 21:249. [PMID: 37735413 PMCID: PMC10512595 DOI: 10.1186/s12964-023-01253-7] [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: 06/24/2023] [Accepted: 08/01/2023] [Indexed: 09/23/2023] Open
Abstract
Histones undergo a plethora of post-translational modifications (PTMs) that regulate nucleosome and chromatin dynamics and thus dictate cell fate. Several evidences suggest that the accumulation of epigenetic alterations is one of the key driving forces triggering aberrant cellular proliferation, invasion, metastasis and chemoresistance pathways. Recently a novel class of histone "non-enzymatic covalent modifications" (NECMs), correlating epigenome landscape and metabolic rewiring, have been described. These modifications are tightly related to cell metabolic fitness and are able to impair chromatin architecture. During metabolic reprogramming, the high metabolic flux induces the accumulation of metabolic intermediate and/or by-products able to react with histone tails altering epigenome homeostasis. The accumulation of histone NECMs is a damaging condition that cancer cells counteracts by overexpressing peculiar "eraser" enzymes capable of removing these modifications preserving histones architecture. In this review we explored the well-established NECMs, emphasizing the role of their corresponding eraser enzymes. Additionally, we provide a parterre of drugs aiming to target those eraser enzymes with the intent to propose novel routes of personalized medicine based on the identification of epi-biomarkers which might be selectively targeted for therapy. Video Abstract.
Collapse
Affiliation(s)
- Domenica Scumaci
- Research Center On Advanced Biochemistry and Molecular Biology, Magna Græcia University of Catanzaro, 88100, Catanzaro, Italy.
- Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, 88100, Catanzaro, Italy.
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
3
|
Elbatrawy OR, Hagras M, El Deeb MA, Agili F, Hegazy M, El-Husseiny AA, Mokhtar MM, Elkhawaga SY, Eissa IH, El-Kalyoubi S. Discovery of New Uracil and Thiouracil Derivatives as Potential HDAC Inhibitors. Pharmaceuticals (Basel) 2023; 16:966. [PMID: 37513878 PMCID: PMC10384246 DOI: 10.3390/ph16070966] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/25/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Background: Histone deacetylase inhibitors (HDACIs) are a relatively new class of potential drugs for treating cancer. Aim: Discovery of new anticancer agents targeting HDAC. Methods: New uracil and thiouracil derivatives panels were designed and synthesized as HDAC inhibitors. The synthesized compounds were tested against MCF-7, HepG2, and HCT-116. HDAC1 and HDAC4 inhibitory activities of these compounds were tested. The most active member was tested for its potential against cell cycle, apoptosis, caspase-3, and caspase-8. Docking studies were carried out against HDAC1. Results: Compounds 5a, 5b, 5f, 5i, 5k, and 5m exhibited promising cytotoxic activities. HDAC1 and HDAC4 inhibitory activities of these compounds were tested. Regarding the HDAC1 inhibitory activity, compound 5m was the most potent member (IC50 = 0.05 µg/mL) compared to trichostatin A (IC50 = 0.0349 µg/mL). For HDAC4, compound 5m showed superior activity (IC50 = 2.83 µg/mL) than trichostatin A (IC50 = 3.349 µg/mL). Compound 5m showed a high potential to arrest the HCT116 cell cycle at the G0-G1 phase. In addition, it showed an almost 17 times apoptotic effect (37.59%) compared to the control cells (2.17%). Furthermore, Compound 5m showed significant increases in the levels of caspase-3 and caspase-8. Finally, the uracil and thiouracil derivatives showed accepted binding mods against HDAC. Conclusions: Compound 5m has potential anticancer activity targeting HDAC with a significant apoptotic effect.
Collapse
Affiliation(s)
- Omnia R Elbatrawy
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo 11823, Egypt
| | - Mohamed Hagras
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Moshira A El Deeb
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo 11823, Egypt
| | - Fatimah Agili
- Chemistry Department, Faculty of Science (Female Section), Jazan University, Jazan 82621, Saudi Arabia
| | - Maghawry Hegazy
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Ahmed A El-Husseiny
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
- Department of Biochemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City 11829, Cairo, Egypt
| | - Mahmoud Mohamed Mokhtar
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Samy Y Elkhawaga
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Ibrahim H Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Samar El-Kalyoubi
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Port Said University, Port Said 42511, Egypt
| |
Collapse
|
4
|
Elbatrawy OR, El Deeb MA, Hagras M, Agili F, Hegazy M, El-Husseiny AA, Elkady MA, Eissa IH, El-Kalyoubi S. New thiouracil derivatives as histone deacetylase inhibitors and apoptosis inducers: design, synthesis and anticancer evaluation. Future Med Chem 2023; 15:1019-1035. [PMID: 37492951 DOI: 10.4155/fmc-2023-0106] [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] [Indexed: 07/27/2023] Open
Abstract
Background: Histone deacetylase (HDAC) inhibitors have good contributions in cancer management. Aim: To introduce new active HDAC inhibitors. Methods: Design and synthesis of 16 thiouracil derivatives with deep biological and computational investigation. Results: Compounds 7a, 7c, 7d, 7e, 8a and 8f showed the highest antiproliferative effects against MCF7, HepG2 and HCT116 cell lines. Compound 7e exhibited the highest activities against HDAC1 and HDAC4. Compound 7e arrested the cell cycle of HCT116 cells at G0-G1 with significant apoptotic effect. In addition, treatment with compound 7e was associated with a significant increase in the levels of caspase-3 and caspase-8. The docking studies gave good insight about the binding patterns of the synthesized compounds against HDAC1. Conclusion: Compound 7e has a promising anticancer activity targeting HDAC.
Collapse
Affiliation(s)
- Omnia R Elbatrawy
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, 11754, Egypt
| | - Moshira A El Deeb
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, 11754, Egypt
| | - Mohamed Hagras
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, 11884, Egypt
| | - Fatimah Agili
- Chemistry Department, Faculty of Science (Female Section), Jazan University, Jazan, 82621, Saudi Arabia
| | - Maghawry Hegazy
- Biochemistry & Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, 11884, Egypt
| | - Ahmed A El-Husseiny
- Biochemistry & Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, 11884, Egypt
- Department of Biochemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, 11829, Cairo, Egypt
| | - Mohamed A Elkady
- Biochemistry & Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, 11884, Egypt
| | - Ibrahim H Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, 11884, Egypt
| | - Samar El-Kalyoubi
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Port Said University, 42511, Port Said, Egypt
| |
Collapse
|
5
|
Mori M, Cazzaniga G, Meneghetti F, Villa S, Gelain A. Insights on the Modulation of SIRT5 Activity: A Challenging Balance. Molecules 2022; 27:4449. [PMID: 35889322 PMCID: PMC9316768 DOI: 10.3390/molecules27144449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 02/01/2023] Open
Abstract
SIRT5 is a member of the Sirtuin family, a class of deacetylating enzymes consisting of seven isoforms, involved in the regulation of several processes, including gene expression, metabolism, stress response, and aging. Considering that the anomalous activity of SIRT5 is linked to many pathological conditions, we present herein an overview of the most interesting modulators, with the aim of contributing to further development in this field.
Collapse
Affiliation(s)
| | | | | | - Stefania Villa
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.M.); (G.C.); (F.M.); (A.G.)
| | | |
Collapse
|
6
|
Recent Advances in the Biological Significance of Xanthine and its Derivatives: A Review. Pharm Chem J 2022. [DOI: 10.1007/s11094-022-02661-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
7
|
Zhao Q, Zhou J, Li F, Guo S, Zhang L, Li J, Qi Q, Shi Y. The Role and Therapeutic Perspectives of Sirtuin 3 in Cancer Metabolism Reprogramming, Metastasis, and Chemoresistance. Front Oncol 2022; 12:910963. [PMID: 35832551 PMCID: PMC9272524 DOI: 10.3389/fonc.2022.910963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/05/2022] [Indexed: 11/24/2022] Open
Abstract
Sirtuin 3 (SIRT3), the nicotinamide adenine dinucleotide (NAD+)-dependent deacetylase, acts as a metabolic modulator mainly located in mitochondria via regulating the process of the relevant biochemical processes by targeting crucial mediators. Recently, owing to its dual role in cancer, SIRT3 has attracted extensive attention. Cancer cells have different metabolic patterns from normal cells, and SIRT3-mediated metabolism reprogramming could be critical in the cancer context, which is closely related to the mechanism of metabolism reprogramming, metastasis, and chemoresistance in tumor cells. Therefore, it is crucial to elucidate the relevant pathological mechanisms and take appropriate countermeasures for the progression of clinical strategies to inhibit the development of cancer. In this review, existing available data on the regulation of cancer metabolism reprogramming, metastasis, and chemoresistance progression of SIRT3 are detailed, as well as the status quo of SIRT3 small molecule modulators is updated in the application of cancer therapy, aiming to highlight strategies directly targeting SIRT3-mediated tumor-suppressing and tumor-promoting, and provide new approaches for therapy application. Furthermore, we offer an effective evidence-based basis for the evolvement of potential personalized therapy management strategies for SIRT3 in cancer settings.
Collapse
Affiliation(s)
- QingYi Zhao
- Department of Acupuncture and Moxibustion, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jing Zhou
- Department of Acupuncture and Moxibustion, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Feng Li
- Department of Acupuncture and Moxibustion, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Sen Guo
- Department of Acupuncture and Moxibustion, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Liang Zhang
- Department of Acupuncture and Moxibustion, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jing Li
- Department of Acupuncture and Moxibustion, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qin Qi
- Department of Acupuncture and Moxibustion, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Outpatient Department, Shanghai Research Institute of Acupuncture and Meridian, Shanghai, China
- *Correspondence: Qin Qi, ; Yin Shi,
| | - Yin Shi
- Department of Acupuncture and Moxibustion, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Outpatient Department, Shanghai Research Institute of Acupuncture and Meridian, Shanghai, China
- *Correspondence: Qin Qi, ; Yin Shi,
| |
Collapse
|
8
|
Overview of SIRT5 as a potential therapeutic target: Structure, function and inhibitors. Eur J Med Chem 2022; 236:114363. [DOI: 10.1016/j.ejmech.2022.114363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/02/2022] [Accepted: 04/05/2022] [Indexed: 01/21/2023]
|
9
|
Loharch S, Chhabra S, Kumar A, Swarup S, Parkesh R. Discovery and characterization of small molecule SIRT3-specific inhibitors as revealed by mass spectrometry. Bioorg Chem 2021; 110:104768. [PMID: 33676042 DOI: 10.1016/j.bioorg.2021.104768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/03/2021] [Accepted: 02/20/2021] [Indexed: 01/01/2023]
Abstract
Sirtuins play a prominent role in several cellular processes and are implicated in various diseases. The understanding of biological roles of sirtuins is limited because of the non-availability of small molecule inhibitors, particularly the specific inhibitors directed against a particular SIRT. We performed a high-throughput screening of pharmacologically active compounds to discover novel, specific, and selective sirtuin inhibitor. Several unique in vitro sirtuin inhibitor pharmacophores were discovered. Here, we present the discovery of novel chemical scaffolds specific for SIRT3. We have demonstrated the in vitro activity of these compounds using label-free mass spectroscopy. We have further validated our results using biochemical, biophysical, and computational studies. Determination of kinetic parameters shows that the SIRT3 specific inhibitors have a moderately longer residence time, possibly implying high in vivo efficacy. The molecular docking results revealed the differential selectivity pattern of these inhibitors against sirtuins. The discovery of specific inhibitors will improve the understanding of ligand selectivity in sirtuins, and the binding mechanism as revealed by docking studies can be further exploited for discovering selective and potent ligands targeting sirtuins.
Collapse
Affiliation(s)
- Saurabh Loharch
- GNRPC, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Sonali Chhabra
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Abhinit Kumar
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Sapna Swarup
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Raman Parkesh
- GNRPC, CSIR-Institute of Microbial Technology, Chandigarh 160036, India; Academy of Scientific and Innovative Research, Ghaziabad 201002, India.
| |
Collapse
|