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Tabana Y, Babu D, Fahlman R, Siraki AG, Barakat K. Target identification of small molecules: an overview of the current applications in drug discovery. BMC Biotechnol 2023; 23:44. [PMID: 37817108 PMCID: PMC10566111 DOI: 10.1186/s12896-023-00815-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023] Open
Abstract
Target identification is an essential part of the drug discovery and development process, and its efficacy plays a crucial role in the success of any given therapy. Although protein target identification research can be challenging, two main approaches can help researchers make significant discoveries: affinity-based pull-down and label-free methods. Affinity-based pull-down methods use small molecules conjugated with tags to selectively isolate target proteins, while label-free methods utilize small molecules in their natural state to identify targets. Target identification strategy selection is essential to the success of any drug discovery process and must be carefully considered when determining how to best pursue a specific project. This paper provides an overview of the current target identification approaches in drug discovery related to experimental biological assays, focusing primarily on affinity-based pull-down and label-free approaches, and discusses their main limitations and advantages.
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Affiliation(s)
- Yasser Tabana
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Dinesh Babu
- Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Richard Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Arno G Siraki
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada.
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Li H, Gao C, Liu C, Liu L, Zhuang J, Yang J, Zhou C, Feng F, Sun C, Wu J. A review of the biological activity and pharmacology of cryptotanshinone, an important active constituent in Danshen. Biomed Pharmacother 2021; 137:111332. [PMID: 33548911 DOI: 10.1016/j.biopha.2021.111332] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/13/2021] [Accepted: 01/25/2021] [Indexed: 02/07/2023] Open
Abstract
Cryptotanshinone (IUPAC name: (R)-1,2,6,7,8,9-hexahydro-1,6,6-trimethyl-phenanthro(1,2-b)furan-10,11-dione), a biologically active constituent extracted from the roots and rhizomes of the plant Salvia miltiorrhiza, has been studied in depth as a medicinally active compound and shown to have efficacy in the treatment of numerous diseases and disorders. In this review, we describe in detail the current status of cryptotanshinone research, including findings relating to the structure, pharmacokinetics, pharmacological activity, and derivatives of this compound. Cryptotanshinoneh as a diverse range of pharmacological effects, including anti-cancer, anti-inflammatory, immune regulatory, neuroprotective, and anti-fibrosis activities. Studies on the molecular mechanisms underlying the activities of cryptotanshinone have established that the JAK2/STAT3, PI3K/AKT, NF-κB, AMPK, and cell cycle pathways are involved in the inhibitory and pro-apoptotic effects of cryptotanshinone on different tumor cell lines, these molecular pathways interact in a coordinated manner to inhibit cell proliferation, migration and invasion,and induce transformation, autophagy, necrosis, and cellular immunity. The anti-inflammatory mechanisms of cryptotanshinone have been found to be associated with the TLR4-MyD88/PI3K/Nrf2 and TLR4-MyD88/NF-κB/MAPK pathways, whereasthe Hedgehog, NF-κB, and Nrf-2/HO-1 pathways are regulated by cryptotanshinone to reduce organ fibrosis, and its inhibitory effects on the PI3K/AKT-eNOS pathway have been linked to neuroprotective effects. Given the potential medicinal utility of cryptotanshinone, further research is needed to verify the efficacy and safety of this compound in clinical use, evaluate its pharmacological activity, and identify molecular targets.
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Affiliation(s)
- Huayao Li
- College of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, PR China.
| | - Chundi Gao
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, PR China.
| | - Cun Liu
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, PR China.
| | - Lijuan Liu
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang, 261041, Shandong, PR China; Department of Basic Medical Science, Qingdao University, Qingdao, 266071, PR China.
| | - Jing Zhuang
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang, 261041, Shandong, PR China; Qingdao Academy of Chinese Medical Sciences, Shandong University of Chinese Medicine, Qingdao, 266112, Shandong, PR China.
| | - Jing Yang
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang, 261041, Shandong, PR China.
| | - Chao Zhou
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, PR China; Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang, 261041, Shandong, PR China.
| | - Fubin Feng
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang, 261041, Shandong, PR China; Department of Basic Medical Science, Qingdao University, Qingdao, 266071, PR China.
| | - Changgang Sun
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang, 261041, Shandong, PR China; Chinese Medicine Innovation Institute, Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, PR China.
| | - Jibiao Wu
- College of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, PR China.
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Ha J, Park H, Park J, Park SB. Recent advances in identifying protein targets in drug discovery. Cell Chem Biol 2020; 28:394-423. [PMID: 33357463 DOI: 10.1016/j.chembiol.2020.12.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/11/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023]
Abstract
Phenotype-based screening has emerged as an alternative route for discovering new chemical entities toward first-in-class therapeutics. However, clarifying their mode of action has been a significant bottleneck for drug discovery. For target protein identification, conventionally bioactive small molecules are conjugated onto solid supports and then applied to isolate target proteins from whole proteome. This approach requires a high binding affinity between bioactive small molecules and their target proteins. Besides, the binding affinity can be significantly hampered after structural modifications of bioactive molecules with linkers. To overcome these limitations, two major strategies have recently been pursued: (1) the covalent conjugation between small molecules and target proteins using photoactivatable moieties or electrophiles, and (2) label-free target identification through monitoring target engagement by tracking the thermal, proteolytic, or chemical stability of target proteins. This review focuses on recent advancements in target identification from covalent capturing to label-free strategies.
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Affiliation(s)
- Jaeyoung Ha
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea
| | - Hankum Park
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jongmin Park
- Department of Chemistry, Kangwon National University, Chuncheon 24341, Korea.
| | - Seung Bum Park
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea; CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea.
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Ashrafizadeh M, Zarrabi A, Orouei S, Saberifar S, Salami S, Hushmandi K, Najafi M. Recent advances and future directions in anti-tumor activity of cryptotanshinone: A mechanistic review. Phytother Res 2020; 35:155-179. [PMID: 33507609 DOI: 10.1002/ptr.6815] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/29/2020] [Accepted: 07/02/2020] [Indexed: 12/13/2022]
Abstract
In respect to the enhanced incidence rate of cancer worldwide, studies have focused on cancer therapy using novel strategies. Chemotherapy is a common strategy in cancer therapy, but its adverse effects and chemoresistance have limited its efficacy. So, attempts have been directed towards minimally invasive cancer therapy using plant derived-natural compounds. Cryptotanshinone (CT) is a component of salvia miltiorrihiza Bunge, well-known as Danshen and has a variety of therapeutic and biological activities such as antioxidant, anti-inflammatory, anti-diabetic and neuroprotective. Recently, studies have focused on anti-tumor activity of CT against different cancers. Notably, this herbal compound is efficient in cancer therapy by targeting various molecular signaling pathways. In the present review, we mechanistically describe the anti-tumor activity of CT with an emphasis on molecular signaling pathways. Then, we evaluate the potential of CT in cancer immunotherapy and enhancing the efficacy of chemotherapy by sensitizing cancer cells into anti-tumor activity of chemotherapeutic agents, and elevating accumulation of anti-tumor drugs in cancer cells. Finally, we mention strategies to enhance the anti-tumor activity of CT, for instance, using nanoparticles to provide targeted drug delivery.
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Affiliation(s)
- Milad Ashrafizadeh
- Department of Basic Science, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Ali Zarrabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, 34956, Istanbul, Turkey.,Center of Excellence for Functional Surfaces and Interfaces (EFSUN), Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul, Turkey
| | - Sima Orouei
- MSc. Student, Department of Genetics, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Sedigheh Saberifar
- Department of Basic Sciences, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Saeed Salami
- DVM. Graduated, Kazerun Branch, Islamic Azad University, Kazeroon, Iran
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology & Zoonoses, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Masoud Najafi
- Radiology and Nuclear Medicine Department, School of Paramedical Sciences, Kermanshah University of Medical Sciences, Kermanshah, Iran
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γ-Propoxy-Sulfo-Lichenan Induces In Vitro Cell Differentiation of Human Keratinocytes. Molecules 2019; 24:molecules24030574. [PMID: 30764551 PMCID: PMC6384931 DOI: 10.3390/molecules24030574] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/29/2019] [Accepted: 02/05/2019] [Indexed: 11/17/2022] Open
Abstract
Background: As non-cellulosic β-d-glucans are known to exert wound-healing activity by triggering keratinocytes into cellular differentiation, the functionality of a semisynthetic lichenan-based polysaccharide on skin cell physiology was investigated. Methods: γ-Propoxy-sulfo-lichenan (γ-PSL, molecular weight 52 kDa, β-1,3/1,4-p-d-Glucose, degree of substitution 0.7) was prepared from lichenan. Differentiation of primary human keratinocytes was assayed by the protein analysis of differentiation specific markers and by gene expression analysis (qPCR). The gene array gave insight into the cell signaling induced by the polysaccharide. Results: γ-PSL (1 to 100 μg/mL) triggered keratinocytes, in a concentration-dependent manner, into the terminal differentiation, as shown by the increased protein expression of cytokeratin 1 (KRT1). Time-dependent gene expression analysis proved differentiation-inducing effects, indicating strong and fast KRT1 gene expression, while KRT10 expression showed a maximum after 12 to 24 h, followed by downregulation to the basal level. Involucrin gene expression was only changed to a minor extent, which was similar to loricrin and transglutaminase. Gene array indicated the influence of γ-PSL on MAP kinase and TGF-β mediated signaling towards keratinocyte differentiation. Conclusion: The propoxylated lichenan may improve wound healing by topical application to promote the terminal barrier formation of keratinocytes.
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