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Ren H, Mao K, Yuan X, Mu Y, Zhao S, Fan X, Zhu L, Ye Z, Lan J. AN698/40746067 suppresses bone marrow adiposity to ameliorate hyperlipidemia-induced osteoporosis through targeted inhibition of ENTR1. Biomed Pharmacother 2024; 176:116843. [PMID: 38810405 DOI: 10.1016/j.biopha.2024.116843] [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: 03/15/2024] [Revised: 05/22/2024] [Accepted: 05/26/2024] [Indexed: 05/31/2024] Open
Abstract
Hyperlipidemia-induced osteoporosis is marked by increased bone marrow adiposity, and treatment with statins for hyperlipidemia often leads to new-onset osteoporosis. Endosome-associated trafficking regulator 1 (ENTR1) has been found to interact with different proteins in pathophysiology, but its exact role in adipogenesis is not yet understood. This research aimed to explore the role of ENTR1 in adipogenesis and to discover a new small molecule that targets ENTR1 for evaluating its effectiveness in treating hyperlipidemia-induced osteoporosis. We found that ENTR1 expression increased during the adipogenesis of bone marrow mesenchymal cells (BMSCs). ENTR1 gain- and loss-of-function assays significantly enhanced lipid droplets formation. Mechanistically, ENTR1 binds peroxisome proliferator-activated receptor γ (PPARγ) and enhances its expression, thereby elevating adipogenic markers including C/EBPα and LDLR. Therapeutically, AN698/40746067 attenuated adipogenesis by targeting ENTR1 to suppress PPARγ. In vivo, AN698/40746067 reduced bone marrow adiposity and bone loss, as well as prevented lipogenesis-related obesity, inflammation, steatohepatitis, and abnormal serum lipid levels during hyperlipidemia. Together, these findings suggest that ENTR1 facilitates adipogenesis by PPARγ involved in BMSCs' differentiation, and targeted inhibition of ENTR1 by AN698/40746067 may offer a promising therapy for addressing lipogenesis-related challenges and alleviating osteoporosis following hyperlipidemia.
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Affiliation(s)
- Huiping Ren
- Department of Prosthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Research Center of Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan 250012, China
| | - Kai Mao
- Department of Prosthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Research Center of Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan 250012, China
| | - Xin Yuan
- Department of Prosthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Research Center of Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan 250012, China
| | - Yuqing Mu
- Department of Prosthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Research Center of Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan 250012, China
| | - Shuaiqi Zhao
- Department of Prosthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Research Center of Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan 250012, China
| | - Xin Fan
- Department of Stomatology, Affiliated Hospital of Weifang Medical University, 261053 China
| | - Lina Zhu
- Department of Pediatric Dentistry, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, Shandong Key Laboratory of Oral Tissue Regeneration, Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan 250012, China
| | - Zhou Ye
- Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, The University of Hong Kong, 999077, Hong Kong Special Administrative Region of China
| | - Jing Lan
- Department of Prosthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Research Center of Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan 250012, China.
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2
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Song J, Liu Y, Guo Y, Yuan M, Zhong W, Tang J, Guo Y, Guo L. Therapeutic effects of tetrandrine in inflammatory diseases: a comprehensive review. Inflammopharmacology 2024; 32:1743-1757. [PMID: 38568399 DOI: 10.1007/s10787-024-01452-9] [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: 09/18/2023] [Accepted: 02/20/2024] [Indexed: 05/30/2024]
Abstract
Inflammation can be triggered by any factor. The primary pathological manifestations can be summarized as the deterioration, exudation, and proliferation of local tissues, which can cause systemic damage in severe cases. Inflammatory lesions are primarily localized but may interact with body systems to cause provocative storms, parenchymal organ lesions, vascular and central nervous system necrosis, and other pathologic responses. Tetrandrine (TET) is a bisbenzylquinoline alkaloid extracted from the traditional Chinese herbal medicine Stephania tetrandra, which has been shown to have significant efficacy in inflammatory conditions such as rheumatoid arthritis, hepatitis, nephritis, etc., through NF-κB, MAPK, ERK, and STAT3 signaling pathways. TET can regulate the body's imbalanced metabolic pathways, reverse the inflammatory process, reduce other pathological damage caused by inflammation, and prevent the vicious cycle. More importantly, TET does not disrupt body's normal immune function while clearing the body's inflammatory state. Therefore, it is necessary to pay attention to its dosage and duration during treatment to avoid unexpected side effects caused by a long half-life. In summary, TET has a promising future in treating inflammatory diseases. The author reviews current therapeutic studies of TET in inflammatory conditions to provide some ideas for subsequent anti-inflammatory studies of TET.
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Affiliation(s)
- Jiawen Song
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- School of Pharmacy/School of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yushi Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- School of Pharmacy/School of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yurou Guo
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- School of Pharmacy/School of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Minghao Yuan
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- School of Pharmacy/School of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Wenxiao Zhong
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- School of Pharmacy/School of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Jiamei Tang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- School of Pharmacy/School of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yiping Guo
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- School of Pharmacy/School of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Li Guo
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- School of Pharmacy/School of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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3
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Darwish DG, El-Sherief HAM, Abdel-Aziz SA, Abuo-Rahma GEDA. A decade's overview of 2-aminothiophenes and their fused analogs as promising anticancer agents. Arch Pharm (Weinheim) 2024; 357:e2300758. [PMID: 38442316 DOI: 10.1002/ardp.202300758] [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: 12/24/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 03/07/2024]
Abstract
Over the past decades, cancer has been a challenging domain for medicinal chemists as it is an international health concern. In association, small molecules such as 2-aminothiophenes and their derivatives showed significant antitumor activity through variable modes of action. Therefore, this article aims to review the advances regarding these core scaffolds over the past 10 years, where 2-aminothiophenes and their fused analogs are classified and discussed according to their biological activity and mode of action, in the interest of boosting new design pathways for medicinal chemists to develop targeted antitumor candidates.
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Affiliation(s)
- Donia G Darwish
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, New Minia, Minia, Egypt
| | - Hany A M El-Sherief
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, New Minia, Minia, Egypt
| | - Salah A Abdel-Aziz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, New Minia, Minia, Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut, Egypt
| | - Gamal El-Din A Abuo-Rahma
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, New Minia, Minia, Egypt
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia, Egypt
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4
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Khan MS, Mohammad HA, Shahwan M, Yadav DK, Anwar S, Shamsi A. Identifying Phosphodiesterase-5 Inhibitors with Drug Repurposing Approach: Implications in Vasodysfunctional Disorders. ChemistryOpen 2024; 13:e202300196. [PMID: 38060834 PMCID: PMC11095156 DOI: 10.1002/open.202300196] [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: 09/20/2023] [Revised: 10/12/2023] [Indexed: 05/16/2024] Open
Abstract
Phosphodiesterase type 5 (PDE5) is a multidomain protein that plays a crucial role in regulating cellular cyclic guanosine monophosphate (cGMP), a key signaling molecule involved in various physiological processes. Dysregulation of PDE5 and cGMP signaling is associated with a range of vasodysfunctional disorders, necessitating the development of effective therapeutic interventions. This study adopts comprehensive approach, combining virtual screening and molecular dynamics (MD) simulations, to repurpose FDA-approved drugs as potential PDE5 inhibitors. The initial focus involves selecting compounds based on their binding affinity. Shortlisted compounds undergo a meticulous analysis for their drug profiling and biological significance, followed by the activity evaluation and interaction analysis. Notably, based on binding potential and drug profiling, two molecules, Dutasteride and Spironolactone, demonstrate strong potential as PDE5 inhibitors. Furthermore, all atom MD simulations were employed (500 ns) to explore dynamic behavior of Dutasteride and Spironolactone in complexes with PDE5. Principal components analysis (PCA) and free energy landscape (FEL) analyses are further leveraged to decipher that the binding of Dutasteride and Spironolactone stabilizes the structure of PDE5 with minimal conformational changes. In summary, Dutasteride and Spironolactone exhibit remarkable affinity for PDE5 and possess characteristics that suggest their potential as therapeutic agents for conditions associated with PDE5 dysfunction.
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Affiliation(s)
| | | | - Moyad Shahwan
- Center for Medical and Bio-Allied Health Sciences ResearchAjman University (UAE)
| | - Dharmendra Kumar Yadav
- Gachon Institute of Pharmaceutical Science and Department of PharmacyCollege of PharmacyGachon UniversityIncheon (Republic ofKorea
| | - Saleha Anwar
- Centre for Interdisciplinary Research in Basic SciencesJamia Millia Islamia, Jamia NagarNew Delhi110025India
| | - Anas Shamsi
- Center for Medical and Bio-Allied Health Sciences ResearchAjman University (UAE)
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5
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Almoyad MA, Wahab S, Mohanto S, Khan NJ. Repurposing Drugs to Modulate Sortilin: Structure-Guided Strategies Against Atherogenesis, Coronary Artery Disease, and Neurological Disorders. ACS OMEGA 2024; 9:18438-18448. [PMID: 38680294 PMCID: PMC11044209 DOI: 10.1021/acsomega.4c00470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/10/2024] [Accepted: 03/26/2024] [Indexed: 05/01/2024]
Abstract
Sortilin (SORT1) is a multifunctional protein intricately involved in atherogenesis, coronary artery disease (CAD), and various neurological disorders. It has materialized as a potential pharmacological target for therapeutic development due to its diverse biological roles in pathological processes. Despite its central role under these conditions, effective therapeutic strategies targeting SORT1 remain challenging. In this study, we introduce a drug repurposing strategy guided by structural insights to identify potent SORT1 inhibitors with broad therapeutic potential. Our approach combines molecular docking, virtual screening, and molecular dynamics (MD) simulations, enabling the systematic evaluation of 3648 FDA-approved drugs for their potential to modulate SORT1. The investigation reveals a subset of repurposed drugs exhibiting highly favorable binding profiles and stable interactions within the binding site of SORT1. Notably, two hits, ergotamine and digitoxin, were carefully chosen based on their drug profiles and subjected to analyze their interactions with SORT1 and stability assessment via all-atom MD simulations spanning 300 ns (ns). The structural analyses uncover the complex binding interactions between these identified compounds and SORT1, offering essential mechanistic insights. Additionally, we explore the clinical implications of repurposing these compounds as potential therapeutic agents, emphasizing their significance in addressing atherogenesis, CAD, and neurological disorders. Overall, this study highlights the efficacy of structure-guided drug repurposing and provides a solid foundation for future research endeavors aimed at the development of effective therapies targeting SORT1 under diverse pathological conditions.
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Affiliation(s)
- Mohammad
Ali Abdullah Almoyad
- Department
of Basic Medical Sciences, College of Applied Medical Sciences, King Khalid University, Khamis Mushyt, PO Box. 4536, Abha 61412, Saudi Arabia
| | - Shadma Wahab
- Department
of Pharmacognosy, College of Pharmacy, King
Khalid University, Abha 61421, Saudi Arabia
| | - Sourav Mohanto
- Department
of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka 575018, India
| | - Nida Jamil Khan
- Department
of Biosciences, Jamia Millia Islamia University, New Delhi 110025, India
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6
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Bardhan A, Brown W, Albright S, Tsang M, Davidson LA, Deiters A. Direct Activation of Nucleobases with Small Molecules for the Conditional Control of Antisense Function. Angew Chem Int Ed Engl 2024; 63:e202318773. [PMID: 38411401 DOI: 10.1002/anie.202318773] [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: 12/06/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 02/28/2024]
Abstract
Conditionally controlled antisense oligonucleotides provide precise interrogation of gene function at different developmental stages in animal models. Only one example of small molecule-induced activation of antisense function exist. This has been restricted to cyclic caged morpholinos that, based on sequence, can have significant background activity in the absence of the trigger. Here, we provide a new approach using azido-caged nucleobases that are site-specifically introduced into antisense morpholinos. The caging group design is a simple azidomethylene (Azm) group that, despite its very small size, efficiently blocks Watson-Crick base pairing in a programmable fashion. Furthermore, it undergoes facile decaging via Staudinger reduction when exposed to a small molecule phosphine, generating the native antisense oligonucleotide under conditions compatible with biological environments. We demonstrated small molecule-induced gene knockdown in mammalian cells, zebrafish embryos, and frog embryos. We validated the general applicability of this approach by targeting three different genes.
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Affiliation(s)
- Anirban Bardhan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Wes Brown
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Savannah Albright
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Michael Tsang
- Department of Cell Biology, Center for Integrative Organ Systems., University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Lance A Davidson
- Department of Bioengineering, Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
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7
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Zhu X, Li Y, Dong Q, Tian C, Gong J, Bai X, Ruan J, Gao J. Small Molecules Promote the Rapid Generation of Dental Epithelial Cells from Human-Induced Pluripotent Stem Cells. Int J Mol Sci 2024; 25:4138. [PMID: 38673725 PMCID: PMC11049943 DOI: 10.3390/ijms25084138] [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: 02/22/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Human-induced pluripotent stem cells (hiPSCs) offer a promising source for generating dental epithelial (DE) cells. Whereas the existing differentiation protocols were time-consuming and relied heavily on growth factors, herein, we developed a three-step protocol to convert hiPSCs into DE cells in 8 days. In the first phase, hiPSCs were differentiated into non-neural ectoderm using SU5402 (an FGF signaling inhibitor). The second phase involved differentiating non-neural ectoderm into pan-placodal ectoderm and simultaneously inducing the formation of oral ectoderm (OE) using LDN193189 (a BMP signaling inhibitor) and purmorphamine (a SHH signaling activator). In the final phase, OE cells were differentiated into DE through the application of Purmorphamine, XAV939 (a WNT signaling inhibitor), and BMP4. qRT-PCR and immunostaining were performed to examine the expression of lineage-specific markers. ARS staining was performed to evaluate the formation of the mineralization nodule. The expression of PITX2, SP6, and AMBN, the emergence of mineralization nodules, and the enhanced expression of AMBN and AMELX in spheroid culture implied the generation of DE cells. This study delineates the developmental signaling pathways and uses small molecules to streamline the induction of hiPSCs into DE cells. Our findings present a simplified and quicker method for generating DE cells, contributing valuable insights for dental regeneration and dental disease research.
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Affiliation(s)
- Ximei Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (X.Z.); (Y.L.); (Q.D.)
- Center of Oral Public Health, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China;
| | - Yue Li
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (X.Z.); (Y.L.); (Q.D.)
- Center of Oral Public Health, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China;
| | - Qiannan Dong
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (X.Z.); (Y.L.); (Q.D.)
- Center of Oral Public Health, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China;
| | - Chunli Tian
- Center of Oral Public Health, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China;
| | - Jing Gong
- Department of Pediatric Dentistry, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (J.G.); (X.B.)
| | - Xiaofan Bai
- Department of Pediatric Dentistry, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (J.G.); (X.B.)
| | - Jianping Ruan
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (X.Z.); (Y.L.); (Q.D.)
- Center of Oral Public Health, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China;
| | - Jianghong Gao
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (X.Z.); (Y.L.); (Q.D.)
- Center of Oral Public Health, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China;
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8
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Dutta N, Gerke JA, Odron SF, Morris JD, Hruby A, Kim J, Torres TC, Shemtov SJ, Clarke JG, Chang MC, Shaghasi H, Ray MN, Averbukh M, Hoang S, Oorloff M, Alcala A, Vega M, Mehta HH, Thorwald MA, Crews P, Vermulst M, Garcia G, Johnson TA, Higuchi-Sanabria R. Investigating impacts of the mycothiazole chemotype as a chemical probe for the study of mitochondrial function and aging. GeroScience 2024:10.1007/s11357-024-01144-w. [PMID: 38570396 DOI: 10.1007/s11357-024-01144-w] [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: 11/15/2023] [Accepted: 03/16/2024] [Indexed: 04/05/2024] Open
Abstract
Small molecule inhibitors of the mitochondrial electron transport chain (ETC) hold significant promise to provide valuable insights to the field of mitochondrial research and aging biology. In this study, we investigated two molecules: mycothiazole (MTZ) - from the marine sponge C. mycofijiensis and its more stable semisynthetic analog 8-O-acetylmycothiazole (8-OAc) as potent and selective chemical probes based on their high efficiency to inhibit ETC complex I function. Similar to rotenone (Rote), MTZ, a newly employed ETC complex I inhibitor, exhibited higher cytotoxicity against cancer cell lines compared to certain non-cancer cell lines. Interestingly, 8-OAc demonstrated greater selectivity for cancer cells when compared to both MTZ and Rote, which has promising potential for anticancer therapeutic development. Furthermore, in vivo experiments with these small molecules utilizing a C. elegans model demonstrate their unexplored potential to investigate aging studies. We observed that both molecules have the ability to induce a mitochondria-specific unfolded protein response (UPRMT) pathway, that extends lifespan of worms when applied in their adult stage. We also found that these two molecules employ different pathways to extend lifespan in worms. Whereas MTZ utilizes the transcription factors ATFS-1 and HSF1, which are involved in the UPRMT and heat shock response (HSR) pathways respectively, 8-OAc only required HSF1 and not ATFS-1 to mediate its effects. This observation underscores the value of applying stable, potent, and selective next generation chemical probes to elucidate an important insight into the functional roles of various protein subunits of ETC complexes and their regulatory mechanisms associated with aging.
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Affiliation(s)
- Naibedya Dutta
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Joe A Gerke
- Department of Natural Sciences & Mathematics, Dominican University of California, San Rafael, CA, 94901, USA
| | - Sofia F Odron
- Department of Natural Sciences & Mathematics, Dominican University of California, San Rafael, CA, 94901, USA
| | - Joseph D Morris
- Department of Natural Sciences & Mathematics, Dominican University of California, San Rafael, CA, 94901, USA
| | - Adam Hruby
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Juri Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Toni Castro Torres
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Sarah J Shemtov
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jacqueline G Clarke
- Department of Natural Sciences & Mathematics, Dominican University of California, San Rafael, CA, 94901, USA
| | - Michelle C Chang
- Department of Natural Sciences & Mathematics, Dominican University of California, San Rafael, CA, 94901, USA
| | - Hooriya Shaghasi
- Department of Natural Sciences & Mathematics, Dominican University of California, San Rafael, CA, 94901, USA
| | - Marissa N Ray
- Department of Natural Sciences & Mathematics, Dominican University of California, San Rafael, CA, 94901, USA
| | - Maxim Averbukh
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Sally Hoang
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Maria Oorloff
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Athena Alcala
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Matthew Vega
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Hemal H Mehta
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Max A Thorwald
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Phillip Crews
- Department of Chemistry & Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Marc Vermulst
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Gilberto Garcia
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Tyler A Johnson
- Department of Natural Sciences & Mathematics, Dominican University of California, San Rafael, CA, 94901, USA.
| | - Ryo Higuchi-Sanabria
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA.
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9
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Laurindo LF, Sosin AF, Lamas CB, de Alvares Goulart R, Dos Santos Haber JF, Detregiachi CRP, Barbalho SM. Exploring the logic and conducting a comprehensive evaluation of AdipoRon-based adiponectin replacement therapy against hormone-related cancers-a systematic review. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:2067-2082. [PMID: 37864589 DOI: 10.1007/s00210-023-02792-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 10/13/2023] [Indexed: 10/23/2023]
Abstract
The potential benefits of adiponectin replacement therapy extend to numerous human diseases, with current research showing particular interest in its effectiveness against specific cancer forms, especially hormone-related. However, limitations in the pharmacological use of the intact protein have led to a focus on alternative options. AdipoRon is an extensively studied non-peptidic drug candidate for adiponectin replacement therapy. While researchers have explored the efficacy and therapeutic applications of AdipoRon in various disease conditions, their effects against cancer models advanced more, with no review regarding AdipoRon's efficacy against hormone-related cancers being published. The present systematic review aims to fill this gap. Preclinical evidence was compiled from PubMed, EMBASE, COCHRANE, and Google Scholar following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, and the manuscript's quality assessment was conducted using the Joanna Briggs Institute (JBI) Checklist Critical Appraisal Tool for Systematic Reviews' Quality. The included nine studies incorporated various cell and animal models of the pancreas, gynaecological system, and osteosarcoma cancers. AdipoRon demonstrated effectiveness against pancreatic cancer by activating p44/42 MAPK, mitochondrial dysfunction, and AMPK-mediated inhibition of ACC1. In gynaecological cancers, it exhibited promising anticancer effects through the activation of AMPK, potential inhibition of mTOR, and modulation of the SET1B/BOD1/AdipoR1 signaling cascade. Against osteosarcoma, AdipoRon worked by perturbing ERK1/2 signaling and reducing p70S6K phosphorylation. AdipoRon shows promise in preclinical studies, but human trials are crucial for clinical safety and effectiveness. Caution is needed due to potential off-target effects, especially in cancer therapy with multi-target approaches. Structural biology and computational methods can help predict these effects.
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Affiliation(s)
- Lucas Fornari Laurindo
- Department of Biochemistry and Pharmacology, School of Medicine, Faculdade de Medicina de Marília (FAMEMA), Marília, São Paulo, 17519-030, Brazil.
- Department of Biochemistry and Pharmacology, School of Medicine, Universidade de Marília (UNIMAR), Marília, São Paulo, 17525-902, Brazil.
| | - Andreline Franchi Sosin
- Department of Biochemistry and Pharmacology, School of Medicine, Faculdade de Medicina de Marília (FAMEMA), Marília, São Paulo, 17519-030, Brazil
| | - Caroline Barbalho Lamas
- Department of Gerontology, School of Gerontology, Universidade Federal de São Carlos (UFSCar), São Carlos, São Paulo, 13565-905, Brazil
| | - Ricardo de Alvares Goulart
- Department of Biochemistry and Pharmacology, School of Medicine, Universidade de Marília (UNIMAR), Marília, São Paulo, 17525-902, Brazil
- Postgraduate Program in Structural and Functional Interactions in Rehabilitation, School of Medicine, Universidade de Marília (UNIMAR), Marília, São Paulo, 17525-902, Brazil
| | | | - Claudia Rucco Penteado Detregiachi
- Department of Biochemistry and Pharmacology, School of Medicine, Universidade de Marília (UNIMAR), Marília, São Paulo, 17525-902, Brazil
- Postgraduate Program in Structural and Functional Interactions in Rehabilitation, School of Medicine, Universidade de Marília (UNIMAR), Marília, São Paulo, 17525-902, Brazil
| | - Sandra Maria Barbalho
- Department of Biochemistry and Pharmacology, School of Medicine, Universidade de Marília (UNIMAR), Marília, São Paulo, 17525-902, Brazil
- Postgraduate Program in Structural and Functional Interactions in Rehabilitation, School of Medicine, Universidade de Marília (UNIMAR), Marília, São Paulo, 17525-902, Brazil
- Department of Biochemistry and Nutrition, School of Food and Technology of Marília (FATEC), Marília, São Paulo, 17500-000, Brazil
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10
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Werz O, Stettler H, Theurer C, Seibel J. The 125th Anniversary of Aspirin-The Story Continues. Pharmaceuticals (Basel) 2024; 17:437. [PMID: 38675399 PMCID: PMC11054228 DOI: 10.3390/ph17040437] [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: 02/27/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
The year 2024 marks the 125th anniversary of aspirin, still one of the most frequently used drugs worldwide. Despite its veritable age, it is still relevant in pharmacotherapy and its use has spread to new areas over time. Due to aspirin's multiple pharmacological actions unified in one single molecule (i.e., analgesic, antipyretic, anti-inflammatory, antithrombotic, and antiviral effects), it continues to attract considerable attention in the scientific community and is subject to intense basic and clinical research. In fact, recent results confirmed aspirin's potential role as an antiviral drug and as an agent that can block harmful platelet functions in inflammatory/immunological processes. These features may open up new horizons for this ancient drug. The future of aspirin looks, therefore, bright and promising. Aspirin is not yet ready for retirement; on the contrary, its success story continues. This 125th anniversary paper will concisely review the various therapeutic uses of aspirin with a particular emphasis on the latest research results and their implications (e.g., use as an antiviral agent). In addition, the reader is provided with future perspectives for this remarkable drug.
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Affiliation(s)
- Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Hans Stettler
- Bayer Consumer Care AG, Peter Merian-Strasse 84, 4002 Basel, Switzerland;
| | - Christoph Theurer
- Bayer Vital GmbH, Kaiser-Wilhelm-Allee 70, 51373 Leverkusen, Germany;
| | - Jens Seibel
- Bayer Vital GmbH, Kaiser-Wilhelm-Allee 70, 51373 Leverkusen, Germany;
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11
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Vaccarin C, Mapanao AK, Deberle LM, Becker AE, Borgna F, Marzaro G, Schibli R, Müller C. Design and Preclinical Evaluation of a Novel Prostate-Specific Membrane Antigen Radioligand Modified with a Transthyretin Binder. Cancers (Basel) 2024; 16:1262. [PMID: 38610940 PMCID: PMC11011029 DOI: 10.3390/cancers16071262] [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: 02/16/2024] [Revised: 03/19/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Transthyretin binders have previously been used to improve the pharmacokinetic properties of small-molecule drug conjugates and could, thus, be utilized for radiopharmaceuticals as an alternative to the widely explored "albumin binder concept". In this study, a novel PSMA ligand modified with a transthyretin-binding entity (TB-01) was synthesized and labeled with lutetium-177 to obtain [177Lu]Lu-PSMA-TB-01. A high and specific uptake of [177Lu]Lu-PSMA-TB-01 was found in PSMA-positive PC-3 PIP cells (69 ± 3% after 4 h incubation), while uptake in PSMA-negative PC-3 flu cells was negligible (<1%). In vitro binding studies showed a 174-fold stronger affinity of [177Lu]Lu-PSMA-TB-01 to transthyretin than to human serum albumin. Biodistribution studies in PC-3 PIP/flu tumor-bearing mice confirmed the enhanced blood retention of [177Lu]Lu-PSMA-TB-01 (16 ± 1% IA/g at 1 h p.i.), which translated to a high tumor uptake (69 ± 13% IA/g at 4 h p.i.) with only slow wash-out over time (31 ± 8% IA/g at 96 h p.i.), while accumulation in the PC-3 flu tumor and non-targeted normal tissue was reasonably low. Further optimization of the radioligand design would be necessary to fine-tune the biodistribution and enable its use for therapeutic purposes. This study was the first of this kind and could motivate the use of the "transthyretin binder concept" for the development of future radiopharmaceuticals.
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Affiliation(s)
- Christian Vaccarin
- Center for Radiopharmaceutical Sciences ETH-PSI, Paul Scherrer Institute, 5232 Villigen-PSI, Switzerland; (C.V.); (A.K.M.); (L.M.D.); (A.E.B.); (F.B.); (R.S.)
| | - Ana Katrina Mapanao
- Center for Radiopharmaceutical Sciences ETH-PSI, Paul Scherrer Institute, 5232 Villigen-PSI, Switzerland; (C.V.); (A.K.M.); (L.M.D.); (A.E.B.); (F.B.); (R.S.)
| | - Luisa M. Deberle
- Center for Radiopharmaceutical Sciences ETH-PSI, Paul Scherrer Institute, 5232 Villigen-PSI, Switzerland; (C.V.); (A.K.M.); (L.M.D.); (A.E.B.); (F.B.); (R.S.)
| | - Anna E. Becker
- Center for Radiopharmaceutical Sciences ETH-PSI, Paul Scherrer Institute, 5232 Villigen-PSI, Switzerland; (C.V.); (A.K.M.); (L.M.D.); (A.E.B.); (F.B.); (R.S.)
| | - Francesca Borgna
- Center for Radiopharmaceutical Sciences ETH-PSI, Paul Scherrer Institute, 5232 Villigen-PSI, Switzerland; (C.V.); (A.K.M.); (L.M.D.); (A.E.B.); (F.B.); (R.S.)
| | - Giovanni Marzaro
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, I-35131 Padua, Italy;
| | - Roger Schibli
- Center for Radiopharmaceutical Sciences ETH-PSI, Paul Scherrer Institute, 5232 Villigen-PSI, Switzerland; (C.V.); (A.K.M.); (L.M.D.); (A.E.B.); (F.B.); (R.S.)
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Cristina Müller
- Center for Radiopharmaceutical Sciences ETH-PSI, Paul Scherrer Institute, 5232 Villigen-PSI, Switzerland; (C.V.); (A.K.M.); (L.M.D.); (A.E.B.); (F.B.); (R.S.)
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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12
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Catalani E, Brunetti K, Del Quondam S, Bongiorni S, Picchietti S, Fausto AM, Lupidi G, Marcantoni E, Perrotta C, Achille G, Buonanno F, Ortenzi C, Cervia D. Exposure to the Natural Compound Climacostol Induces Cell Damage and Oxidative Stress in the Fruit Fly Drosophila melanogaster. TOXICS 2024; 12:102. [PMID: 38393197 PMCID: PMC10891975 DOI: 10.3390/toxics12020102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024]
Abstract
The ciliate Climacostomum virens produces the metabolite climacostol that displays antimicrobial activity and cytotoxicity on human and rodent tumor cells. Given its potential as a backbone in pharmacological studies, we used the fruit fly Drosophila melanogaster to evaluate how the xenobiotic climacostol affects biological systems in vivo at the organismal level. Food administration with climacostol demonstrated its harmful role during larvae developmental stages but not pupation. The midgut of eclosed larvae showed apoptosis and increased generation of reactive oxygen species (ROS), thus demonstrating gastrointestinal toxicity. Climacostol did not affect enteroendocrine cell proliferation, suggesting moderate damage that does not initiate the repairing program. The fact that climacostol increased brain ROS and inhibited the proliferation of neural cells revealed a systemic (neurotoxic) role of this harmful substance. In this line, we found lower expression of relevant antioxidant enzymes in the larvae and impaired mitochondrial activity. Adult offsprings presented no major alterations in survival and mobility, as well the absence of abnormal phenotypes. However, mitochondrial activity and oviposition behavior was somewhat affected, indicating the chronic toxicity of climacostol, which continues moderately until adult stages. These results revealed for the first time the detrimental role of ingested climacostol in a non-target multicellular organism.
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Affiliation(s)
- Elisabetta Catalani
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), Università degli Studi della Tuscia, 01100 Viterbo, Italy; (E.C.); (K.B.); (S.D.Q.); (S.P.); (A.M.F.)
| | - Kashi Brunetti
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), Università degli Studi della Tuscia, 01100 Viterbo, Italy; (E.C.); (K.B.); (S.D.Q.); (S.P.); (A.M.F.)
| | - Simona Del Quondam
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), Università degli Studi della Tuscia, 01100 Viterbo, Italy; (E.C.); (K.B.); (S.D.Q.); (S.P.); (A.M.F.)
| | - Silvia Bongiorni
- Department of Ecological and Biological Sciences (DEB), Università degli Studi della Tuscia, 01100 Viterbo, Italy;
| | - Simona Picchietti
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), Università degli Studi della Tuscia, 01100 Viterbo, Italy; (E.C.); (K.B.); (S.D.Q.); (S.P.); (A.M.F.)
| | - Anna Maria Fausto
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), Università degli Studi della Tuscia, 01100 Viterbo, Italy; (E.C.); (K.B.); (S.D.Q.); (S.P.); (A.M.F.)
| | - Gabriele Lupidi
- School of Science and Technology, Section of Chemistry, Università degli Studi di Camerino, 62032 Camerino, Italy; (G.L.); (E.M.)
| | - Enrico Marcantoni
- School of Science and Technology, Section of Chemistry, Università degli Studi di Camerino, 62032 Camerino, Italy; (G.L.); (E.M.)
| | - Cristiana Perrotta
- Department of Biomedical and Clinical Sciences (DIBIC), Università degli Studi di Milano, 20157 Milano, Italy;
| | - Gabriele Achille
- Laboratory of Protistology and Biology Education, Department of Education, Cultural Heritage, and Tourism (ECHT), Università degli Studi di Macerata, 62100 Macerata, Italy; (G.A.); (F.B.); (C.O.)
| | - Federico Buonanno
- Laboratory of Protistology and Biology Education, Department of Education, Cultural Heritage, and Tourism (ECHT), Università degli Studi di Macerata, 62100 Macerata, Italy; (G.A.); (F.B.); (C.O.)
| | - Claudio Ortenzi
- Laboratory of Protistology and Biology Education, Department of Education, Cultural Heritage, and Tourism (ECHT), Università degli Studi di Macerata, 62100 Macerata, Italy; (G.A.); (F.B.); (C.O.)
| | - Davide Cervia
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), Università degli Studi della Tuscia, 01100 Viterbo, Italy; (E.C.); (K.B.); (S.D.Q.); (S.P.); (A.M.F.)
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13
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Yang Y, Liu P, Zhou M, Yin L, Wang M, Liu T, Jiang X, Gao H. Small-molecule drugs of colorectal cancer: Current status and future directions. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166880. [PMID: 37696461 DOI: 10.1016/j.bbadis.2023.166880] [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: 07/26/2023] [Revised: 08/24/2023] [Accepted: 09/04/2023] [Indexed: 09/13/2023]
Abstract
Colorectal cancer (CRC) is the third most commonly diagnosed cancer and the world's fourth most deadly cancer. CRC, as a genetic susceptible disease, faces significant challenges in optimizing prognosis through optimal drug treatment modalities. In recent decades, the development of innovative small-molecule drugs is expected to provide targeted interventions that accurately address the different molecular characteristics of CRC. Although the clinical application of single-target drugs is limited by the heterogeneity and high metastasis of CRC, novel small-molecule drug treatment strategies such as dual/multiple-target drugs, drug repurposing, and combination therapies can help overcome these challenges and provide new insights for improving CRC treatment. In this review, we focus on the current status of a range of small molecule drugs that are being considered for CRC therapy, including single-target drugs, dual/multiple-target drugs, drug repurposing and combination strategies, which will pave the way for targeting CRC vulnerabilities with small-molecule drugs in future personalized treatment.
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Affiliation(s)
- Yiren Yang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Pengyu Liu
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Mingyang Zhou
- University of Pennsylvania, Philadelphia, PA 19104-6323, United States
| | - Linzhou Yin
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Miao Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Ting Liu
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Xiaowen Jiang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China.
| | - Huiyuan Gao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China.
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14
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Hasselbeck S, Cheng X. Molecular Marvels: Small Molecules Paving the Way for Enhanced Gene Therapy. Pharmaceuticals (Basel) 2023; 17:41. [PMID: 38256875 PMCID: PMC10818943 DOI: 10.3390/ph17010041] [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: 12/09/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
In the rapidly evolving landscape of genetic engineering, the advent of CRISPR-Cas technologies has catalyzed a paradigm shift, empowering scientists to manipulate the genetic code with unprecedented accuracy and efficiency. Despite the remarkable capabilities inherent to CRISPR-Cas systems, recent advancements have witnessed the integration of small molecules to augment their functionality, introducing new dimensions to the precision and versatility of gene editing applications. This review delves into the synergy between CRISPR-Cas technologies based specifically on Cas9 and small-molecule drugs, elucidating the pivotal role of chemicals in optimizing target specificity and editing efficiency. By examining a diverse array of applications, ranging from therapeutic interventions to agricultural advancements, we explore how the judicious use of chemicals enhances the precision of CRISPR-Cas9-mediated genetic modifications. In this review, we emphasize the significance of small-molecule drugs in fine-tuning the CRISPR-Cas9 machinery, which allows researchers to exert meticulous control over the editing process. We delve into the mechanisms through which these chemicals bolster target specificity, mitigate off-target effects, and contribute to the overall refinement of gene editing outcomes. Additionally, we discuss the potential of chemical integration in expanding the scope of CRISPR-Cas9 technologies, enabling tailored solutions for diverse genetic manipulation challenges. As CRISPR-Cas9 technologies continue to evolve, the integration of small-molecule drugs emerges as a crucial avenue for advancing the precision and applicability of gene editing techniques. This review not only synthesizes current knowledge but also highlights future prospects, paving the way for a deeper understanding of the synergistic interplay between CRISPR-Cas9 systems and chemical modulators in the pursuit of more controlled and efficient genetic modifications.
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Affiliation(s)
- Sebastian Hasselbeck
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany;
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Xinlai Cheng
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany;
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany
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15
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Song X, Wang L, Tang W, Yuan L, Liu Q, Li J, Fan D. Selumetinib overcomes gefitinib primary and acquired resistance by regulating MIG6/STAT3 in NSCLC. Arch Pharm Res 2023; 46:924-938. [PMID: 38032449 DOI: 10.1007/s12272-023-01471-0] [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: 05/28/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023]
Abstract
Gefitinib, as the first-generation epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI), has achieved great advances in the treatment of non-small cell lung cancer (NSCLC), but drug resistance will inevitably occur. Therefore, exploring the resistance mechanism of gefitinib and developing new combination treatment strategies are of great importance. In our study, the results showed that selumetinib (AZD6244) synergistically inhibited the proliferation of NSCLC with gefitinib. Selumetinib also enhanced gefitinib-induced apoptosis and migration inhibition ability in gefitinib-resistant lung cancer cell lines. Subsequently, the negative regulation between MIG6 and STAT3 was observed and verified through the STRING database and western blotting assays. Sustained activation of STAT3 was significantly downregulated when co-treatment with selumetinib in gefitinib-resistant cells. However, the downregulation of p-STAT3, resulting from the combination of selumetinib and gefitinib was counteracted by the deletion of MIG6, suggesting that selumetinib enhanced gefitinib sensitivity by regulating MIG6/STAT3 in NSCLC. In contrast, p-STAT3 was further inhibited after treatment with gefitinib and selumetinib when MIG6 was overexpressed. Furthermore, the combined administration of selumetinib and gefitinib effectively promoted the sensitivity of lung cancer xenografts to gefitinib in vivo, and the tumor inhibition rate reached 81.49%, while the tumor inhibition rate of the gefitinib monotherapy group was only 31.95%. Overall, MIG6/STAT3 negative regulation plays an important role in the sustained activation of STAT3 and the resistance to EGFR-TKIs. Our study also suggests that EGFR-TKIs combined with MEK1/2 inhibitors, such as selumetinib, may be beneficial to those NSCLC patients who develop a primary or acquired resistance to EGFR-TKIs, providing theoretical support for combining TKIs and selumetinib in clinical cancer treatment.
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Affiliation(s)
- Xiaoping Song
- Department of Pharmaceutical Engineering, School of Chemical Engineering, Northwest University, 229 Taibai North Road, Xi'an, 710069, China
- Biotech. and Biomed. Research Institute, Northwest University, 229 Taibai North Road, Xi'an, 710069, China
| | - Lina Wang
- Department of Pharmaceutical Engineering, School of Chemical Engineering, Northwest University, 229 Taibai North Road, Xi'an, 710069, China
- Biotech. and Biomed. Research Institute, Northwest University, 229 Taibai North Road, Xi'an, 710069, China
| | - Wei Tang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266100, China
| | - Luyao Yuan
- Department of Pharmaceutical Engineering, School of Chemical Engineering, Northwest University, 229 Taibai North Road, Xi'an, 710069, China
| | - Qingchao Liu
- Department of Pharmaceutical Engineering, School of Chemical Engineering, Northwest University, 229 Taibai North Road, Xi'an, 710069, China
- Biotech. and Biomed. Research Institute, Northwest University, 229 Taibai North Road, Xi'an, 710069, China
| | - Jing Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266100, China.
| | - Daidi Fan
- Department of Pharmaceutical Engineering, School of Chemical Engineering, Northwest University, 229 Taibai North Road, Xi'an, 710069, China.
- Biotech. and Biomed. Research Institute, Northwest University, 229 Taibai North Road, Xi'an, 710069, China.
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16
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Barbalho SM, Méndez-Sánchez N, Fornari Laurindo L. AdipoRon and ADP355, adiponectin receptor agonists, in Metabolic-associated Fatty Liver Disease (MAFLD) and Nonalcoholic Steatohepatitis (NASH): A systematic review. Biochem Pharmacol 2023; 218:115871. [PMID: 37866803 DOI: 10.1016/j.bcp.2023.115871] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 10/24/2023]
Abstract
Adiponectin replacement therapy holds the potential to benefit numerous human diseases, and ongoing research applies particular interest in how adiponectin acts against Metabolic-associated Fatty Liver Disease (MAFLD) and Nonalcoholic Steatohepatitis (NASH). However, the pharmacological limitations of the intact protein have prompted a focus on alternative options, specifically peptidic and small molecule agonists targeting the adiponectin receptor. AdipoRon is an extensively researched non-peptidic drug candidate in adiponectin replacement therapy. In turn, ADP355 is an adiponectin-based active short peptide. They have garnered significant attention due to their potential as substitutes for adiponectin. Researchers have studied AdipoRon's and ADP355's efficacy and therapeutic applications in various disease conditions. However, the effects of AdipoRon and ADP355 against NAFLD and NASH models advanced more, and no systematic review explored this area before. This systematic review was conceived to address the deficiency mentioned above and consider the lack of clinical evidence. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were utilized. To assess the risk of bias in systematic review, The Joanna Briggs Institute (JBI) Critical Appraisal Checklist was employed. Results from pre-clinical evidence show that AdipoRon and ADP355 represent promising effects in NAFLD and NASH-related models, including reducing hepatic steatosis, modulating inflammation, improving insulin sensitivity, enhancing mitochondrial function, and protecting against liver fibrosis. While AdipoRon and ADP355 exhibit promise in pre-clinical studies and experimental models, additional clinical trials are necessary to assess their effectiveness, safety, and potential translational therapeutic potential uses in NAFLD and NASH human cases.
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Affiliation(s)
- Sandra Maria Barbalho
- Department of Biochemistry and Pharmacology, School of Medicine, University of Marília (UNIMAR), São Paulo, Brazil; Postgraduate Program in Structural and Functional Interactions in Rehabilitation, University of Marília (UNIMAR), São Paulo, Brazil.
| | - Nahum Méndez-Sánchez
- Liver Research Unit, Medica Sur Clinic & Foundation, Mexico City, Mexico; Faculty of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
| | - Lucas Fornari Laurindo
- Department of Biochemistry and Pharmacology, School of Medicine, University of Marília (UNIMAR), São Paulo, Brazil; Department of Biochemistry and Pharmacology, School of Medicine, Faculdade de Medicina de Marília (FAMEMA), Marília, São Paulo, Brazil
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17
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Dutta N, Gerke JA, Odron SF, Morris JD, Hruby A, Castro Torres T, Shemtov SJ, Clarke JG, Chang MC, Shaghasi H, Ray MN, Averbukh M, Hoang S, Oorloff M, Alcala A, Vega M, Mehta HH, Thorwald MA, Crews P, Vermulst M, Garcia G, Johnson TA, Higuchi-Sanabria R. Investigating impacts of marine sponge derived mycothiazole and its acetylated derivative on mitochondrial function and aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.27.568896. [PMID: 38077060 PMCID: PMC10705228 DOI: 10.1101/2023.11.27.568896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Small molecule inhibitors of the mitochondrial electron transport chain (ETC) hold significant promise to provide valuable insights to the field of mitochondrial research and aging biology. In this study, we investigated two molecules: mycothiazole (MTZ) - from the marine sponge C. mycofijiensis and its more stable semisynthetic analog 8-O-acetylmycothiazole (8-OAc) as potent and selective chemical probes based on their high efficiency to inhibit ETC complex I function. Similar to rotenone (Rote), a widely used ETC complex I inhibitor, these two molecules showed cytotoxicity to cancer cells but strikingly demonstrate a lack of toxicity to non-cancer cells, a highly beneficial feature in the development of anti-cancer therapeutics. Furthermore, in vivo experiments with these small molecules utilizing C.elegans model demonstrate their unexplored potential to investigate aging studies. We observed that both molecules have the ability to induce a mitochondria-specific unfolded protein response (UPRMT) pathway, that extends lifespan of worms when applied in their adult stage. Interestingly, we also found that these two molecules employ different pathways to extend lifespan in worms. Whereas MTZ utilize the transcription factors ATFS-1 and HSF-1, which are involved in the UPRMT and heat shock response (HSR) pathways respectively, 8-OAc only required HSF-1 and not ATFS-1 to mediate its effects. This observation underscores the value of applying stable, potent, and selective next generation chemical probes to elucidate an important insight into the functional roles of various protein subunits of ETC complexes and their regulatory mechanisms associated with aging.
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Affiliation(s)
- Naibedya Dutta
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, United States
| | - Joe A Gerke
- Department of Natural Sciences & Mathematics, Dominican University of California, San Rafael, CA 94901, United States
| | - Sofia F Odron
- Department of Natural Sciences & Mathematics, Dominican University of California, San Rafael, CA 94901, United States
| | - Joseph D Morris
- Department of Natural Sciences & Mathematics, Dominican University of California, San Rafael, CA 94901, United States
| | - Adam Hruby
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, United States
| | - Toni Castro Torres
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, United States
| | - Sarah J Shemtov
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, United States
| | - Jacqueline G Clarke
- Department of Natural Sciences & Mathematics, Dominican University of California, San Rafael, CA 94901, United States
| | - Michelle C Chang
- Department of Natural Sciences & Mathematics, Dominican University of California, San Rafael, CA 94901, United States
| | - Hooriya Shaghasi
- Department of Natural Sciences & Mathematics, Dominican University of California, San Rafael, CA 94901, United States
| | - Marissa N. Ray
- Department of Natural Sciences & Mathematics, Dominican University of California, San Rafael, CA 94901, United States
| | - Maxim Averbukh
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, United States
| | - Sally Hoang
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, United States
| | - Maria Oorloff
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, United States
| | - Athena Alcala
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, United States
| | - Matthew Vega
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, United States
| | - Hemal H Mehta
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, United States
| | - Max A Thorwald
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, United States
| | - Phillip Crews
- Department of Chemistry & Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, 95064, United States
| | - Marc Vermulst
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, United States
| | - Gilberto Garcia
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, United States
| | - Tyler A Johnson
- Department of Natural Sciences & Mathematics, Dominican University of California, San Rafael, CA 94901, United States
| | - Ryo Higuchi-Sanabria
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, United States
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18
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Mehta M, Bui TA, Yang X, Aksoy Y, Goldys EM, Deng W. Lipid-Based Nanoparticles for Drug/Gene Delivery: An Overview of the Production Techniques and Difficulties Encountered in Their Industrial Development. ACS MATERIALS AU 2023; 3:600-619. [PMID: 38089666 PMCID: PMC10636777 DOI: 10.1021/acsmaterialsau.3c00032] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 02/13/2024]
Abstract
Over the past decade, the therapeutic potential of nanomaterials as novel drug delivery systems complementing conventional pharmacology has been widely acknowledged. Among these nanomaterials, lipid-based nanoparticles (LNPs) have shown remarkable pharmacological performance and promising therapeutic outcomes, thus gaining substantial interest in preclinical and clinical research. In this review, we introduce the main types of LNPs used in drug formulations such as liposomes, nanoemulsions, solid lipid nanoparticles, nanostructured lipid carriers, and lipid polymer hybrid nanoparticles, focusing on their main physicochemical properties and therapeutic potential. We discuss computational studies and modeling techniques to enhance the understanding of how LNPs interact with therapeutic cargo and to predict the potential effectiveness of such interactions in therapeutic applications. We also analyze the benefits and drawbacks of various LNP production techniques such as nanoprecipitation, emulsification, evaporation, thin film hydration, microfluidic-based methods, and an impingement jet mixer. Additionally, we discuss the major challenges associated with industrial development, including stability and sterilization, storage, regulatory compliance, reproducibility, and quality control. Overcoming these challenges and facilitating regulatory compliance represent the key steps toward LNP's successful commercialization and translation into clinical settings.
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Affiliation(s)
- Meenu Mehta
- School
of Biomedical Engineering, Faculty of Engineering and Information
Technology, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Thuy Anh Bui
- School
of Biomedical Engineering, Faculty of Engineering and Information
Technology, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Xinpu Yang
- School
of Biomedical Engineering, Faculty of Engineering and Information
Technology, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Yagiz Aksoy
- Cancer
Diagnosis and Pathology Group, Kolling Institute of Medical Research,
Royal North Shore Hospital, St Leonards NSW 2065 Australia - Sydney
Medical School, University of Sydney, Sydney NSW 2006 Australia
| | - Ewa M. Goldys
- Graduate
School of Biomedical Engineering, ARC Centre of Excellence in Nanoscale
Biophotonics, Faculty of Engineering, UNSW Sydney, NSW 2052, Australia
| | - Wei Deng
- School
of Biomedical Engineering, Faculty of Engineering and Information
Technology, University of Technology Sydney, Ultimo, NSW 2007, Australia
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19
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Wu K, Karapetyan E, Schloss J, Vadgama J, Wu Y. Advancements in small molecule drug design: A structural perspective. Drug Discov Today 2023; 28:103730. [PMID: 37536390 PMCID: PMC10543554 DOI: 10.1016/j.drudis.2023.103730] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/05/2023]
Abstract
In this review, we outline recent advancements in small molecule drug design from a structural perspective. We compare protein structure prediction methods and explore the role of the ligand binding pocket in structure-based drug design. We examine various structural features used to optimize drug candidates, including functional groups, stereochemistry, and molecular weight. Computational tools such as molecular docking and virtual screening are discussed for predicting and optimizing drug candidate structures. We present examples of drug candidates designed based on their molecular structure and discuss future directions in the field. By effectively integrating structural information with other valuable data sources, we can improve the drug discovery process, leading to the identification of novel therapeutics with improved efficacy, specificity, and safety profiles.
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Affiliation(s)
- Ke Wu
- Division of Cancer Research and Training, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90095, USA
| | - Eduard Karapetyan
- Division of Cancer Research and Training, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90095, USA
| | - John Schloss
- Division of Cancer Research and Training, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90095, USA; School of Pharmacy, American University of Health Sciences, Signal Hill, CA 90755, USA
| | - Jaydutt Vadgama
- Division of Cancer Research and Training, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90095, USA; School of Pharmacy, American University of Health Sciences, Signal Hill, CA 90755, USA.
| | - Yong Wu
- Division of Cancer Research and Training, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90095, USA.
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20
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Sun J, Si S, Ru J, Wang X. DeepdlncUD: Predicting regulation types of small molecule inhibitors on modulating lncRNA expression by deep learning. Comput Biol Med 2023; 163:107226. [PMID: 37450966 DOI: 10.1016/j.compbiomed.2023.107226] [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: 03/17/2023] [Revised: 05/31/2023] [Accepted: 07/01/2023] [Indexed: 07/18/2023]
Abstract
Targeting lncRNAs by small molecules (SM-lncR) to alter their expression levels has emerged as an important therapeutic modality for disease treatment. To date, no computational tools have been dedicated to predicting small molecule-mediated upregulation or downregulation of lncRNA expression. Here, we introduce DeepdlncUD, which integrates predictions of nine deep learning algorithms together, to infer the regulation types of small molecules on modulating lncRNA expression. Through systematic optimization on a training set of 771 upregulation and 739 downregulation SM-lncR pairs, each encoding 1369 sequence, representational, and physiochemical features, this method outperforms a recently released program, DeepsmirUD, by achieving 0.674 in AUC (area under the receiver operating characteristic curve), 0.722 in AUCPR (area under the precision-recall curve), 0.681 in F1-score, and 0.516 in Jaccard Index on a test set of 222 SM-lncR pairs. By extracting 125 upregulation and 46 downregulation SM-lncR pairs that involve disease-associated lncRNAs, DeepdlncUD is shown to gain an accuracy of 0.700 in the pathological context. Using connectivity scores, around half of the small molecules are correctly estimated as drugs to treat lncRNA-regulated diseases. This tool can be run at a fast speed to assist the discovery of potential small molecule drugs of lncRNA targets on a large scale. DeepdlncUD is publicly available at https://github.com/2003100127/deepdlncud.
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Affiliation(s)
- Jianfeng Sun
- Botnar Research Centre, University of Oxford, Headington, Oxford, OX3 7LD, UK.
| | - Shuyue Si
- School of Mathematics and Physics, Xi'an Jiaotong-liverpool University, Renai, Suzhou, 215028, China
| | - Jinlong Ru
- Chair of Prevention of Microbial Diseases, School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Xia Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
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21
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Jefremow A, Neurath MF. Novel Small Molecules in IBD: Current State and Future Perspectives. Cells 2023; 12:1730. [PMID: 37443765 PMCID: PMC10341073 DOI: 10.3390/cells12131730] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Biologicals have dominated the therapeutic scenery in inflammatory bowel diseases (IBDs), namely ulcerative colitis (UC) and Crohn's disease (CD), for the past 20 years. The development of tofacitinib was the starting point for an era of small molecules after the era of biologicals. These new agents may challenge the use of biological agents in the future. They share properties that appeal to both patients and physicians. Low production costs, a lack of immunogenicity, and ease of use are only some of their benefits. On the other hand, patients and their physicians must manage the potential side effects of small molecules such as JAK inhibitors or S1P1R modulators. Here, we present agents that have already entered the clinical routine and those that are still being investigated in clinical trials.
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Affiliation(s)
- André Jefremow
- Department of Medicine 1, University Erlangen-Nürnberg, 91054 Erlangen, Germany;
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany
| | - Markus F. Neurath
- Department of Medicine 1, University Erlangen-Nürnberg, 91054 Erlangen, Germany;
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany
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22
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Abstract
Although fragment-based drug discovery (FBDD) has been successfully implemented and well-explored for protein targets, its feasibility for RNA targets is emerging. Despite the challenges associated with the selective targeting of RNA, efforts to integrate known methods of RNA binder discovery with fragment-based approaches have been fruitful, as a few bioactive ligands have been identified. Here, we review various fragment-based approaches implemented for RNA targets and provide insights into experimental design and outcomes to guide future work in the area. Indeed, investigations surrounding the molecular recognition of RNA by fragments address rather important questions such as the limits of molecular weight that confer selective binding and the physicochemical properties favorable for RNA binding and bioactivity.
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Affiliation(s)
- Blessy M. Suresh
- UF Scripps Biomedical Research & The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Amirhossein Taghavi
- UF Scripps Biomedical Research & The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L. Childs-Disney
- UF Scripps Biomedical Research & The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D. Disney
- UF Scripps Biomedical Research & The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
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23
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Shin YH, Kim DE, Yu KL, Park CM, Kim HG, Kim KC, Bae S, Yoon CH. A Novel Time-Resolved Fluorescence Resonance Energy Transfer Assay for the Discovery of Small-Molecule Inhibitors of HIV-1 Tat-Regulated Transcription. Int J Mol Sci 2023; 24:ijms24119139. [PMID: 37298089 DOI: 10.3390/ijms24119139] [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: 05/02/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) transactivator (Tat)-mediated transcription is essential for HIV-1 replication. It is determined by the interaction between Tat and transactivation response (TAR) RNA, a highly conserved process representing a prominent therapeutic target against HIV-1 replication. However, owing to the limitations of current high-throughput screening (HTS) assays, no drug that disrupts the Tat-TAR RNA interaction has been uncovered yet. We designed a homogenous (mix-and-read) time-resolved fluorescence resonance energy transfer (TR-FRET) assay using europium cryptate as a fluorescence donor. It was optimized by evaluating different probing systems for Tat-derived peptides or TAR RNA. The specificity of the optimal assay was validated by mutants of the Tat-derived peptides and TAR RNA fragment, individually and by competitive inhibition with known TAR RNA-binding peptides. The assay generated a constant Tat-TAR RNA interaction signal, discriminating the compounds that disrupted the interaction. Combined with a functional assay, the TR-FRET assay identified two small molecules (460-G06 and 463-H08) capable of inhibiting Tat activity and HIV-1 infection from a large-scale compound library. The simplicity, ease of operation, and rapidity of our assay render it suitable for HTS to identify Tat-TAR RNA interaction inhibitors. The identified compounds may also act as potent molecular scaffolds for developing a new HIV-1 drug class.
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Affiliation(s)
- Young Hyun Shin
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
| | - Dong-Eun Kim
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
| | - Kyung Lee Yu
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
| | - Chul Min Park
- Department for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Daejeon 34114, Republic of Korea
| | - Hong Gi Kim
- Department for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Daejeon 34114, Republic of Korea
| | - Kyung-Chang Kim
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
| | - Songmee Bae
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
| | - Cheol-Hee Yoon
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
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24
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Thereza Fiori-Duarte A, Bitencourt de Souza Ferreira L, Sanches Ascencio A, Fábio Kawano D. Modulation of Pseudomonas aeruginosa quorum sensing by ajoene through direct competition with small RNAs for binding at the proximal site of Hfq - a structure-based perspective. Gene 2023:147506. [PMID: 37224934 DOI: 10.1016/j.gene.2023.147506] [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: 03/14/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 05/26/2023]
Abstract
Bacteria can communicate to each other via quorum sensing, a cell density-dependent gene regulation system that stimulates the expression of virulence factors in the neighboring cells. Although the interaction of the natural product ajoene with the Hfq protein has been associated with the disruption of the quorum sensing system in Pseudomonas aeruginosa, there is no information concerning the corresponding ligand-target interaction process. Herein we observed a strong correlation (p < 0.00001) between the estimated affinities for the binding of 23 ajoene analogues at the proximal site of the Hfq protein of P. aeruginosa and their corresponding IC50 values, which reflect the reduction in the transcription of a virulence factor after quorum sensing inhibition. In this concern, our analyses reinforces previous propositions suggesting that ajoene could target the Hfq protein and affects its interaction with RNAs. Based on docking simulations, we tried to elucidate the binding mode of ajoene into the proximal Hfq site and the also to established the minimum set of groups that would be necessary for a good interaction at this site, which includes a single hydrogen bond acceptor feature surrounded by groups that interact via π-sulfur (i.e., disulfide sulfurs) and/or π-alkyl/π-π stacking interactions (e.g., vinyl or small aryl/heteroaryl/heterocyclic groups). Because of the widespread role of Hfq as a matchmaker between messenger and small regulatory RNAs in Gram-negatives, we believe the discussion here provided for P. aeruginosa could be extrapolated for Gram-negatives in general, while the interaction of ajoene over the Hfq protein of Gram-positives would still remain more controversial.
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Affiliation(s)
- Ana Thereza Fiori-Duarte
- Group on the Research & Development of Bioactive Compounds (GR&DBC), Faculty of Pharmaceutical Sciences, University of Campinas - UNICAMP, Rua Cândido Portinari 200, 13083-871 Campinas-SP, Brazil
| | - Luciana Bitencourt de Souza Ferreira
- Group on the Research & Development of Bioactive Compounds (GR&DBC), Faculty of Pharmaceutical Sciences, University of Campinas - UNICAMP, Rua Cândido Portinari 200, 13083-871 Campinas-SP, Brazil
| | - Amanda Sanches Ascencio
- Group on the Research & Development of Bioactive Compounds (GR&DBC), Faculty of Pharmaceutical Sciences, University of Campinas - UNICAMP, Rua Cândido Portinari 200, 13083-871 Campinas-SP, Brazil
| | - Daniel Fábio Kawano
- Group on the Research & Development of Bioactive Compounds (GR&DBC), Faculty of Pharmaceutical Sciences, University of Campinas - UNICAMP, Rua Cândido Portinari 200, 13083-871 Campinas-SP, Brazil.
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25
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Sun J, Xu M, Ru J, James-Bott A, Xiong D, Wang X, Cribbs AP. Small molecule-mediated targeting of microRNAs for drug discovery: Experiments, computational techniques, and disease implications. Eur J Med Chem 2023; 257:115500. [PMID: 37262996 DOI: 10.1016/j.ejmech.2023.115500] [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: 03/28/2023] [Revised: 05/05/2023] [Accepted: 05/15/2023] [Indexed: 06/03/2023]
Abstract
Small molecules have been providing medical breakthroughs for human diseases for more than a century. Recently, identifying small molecule inhibitors that target microRNAs (miRNAs) has gained importance, despite the challenges posed by labour-intensive screening experiments and the significant efforts required for medicinal chemistry optimization. Numerous experimentally-verified cases have demonstrated the potential of miRNA-targeted small molecule inhibitors for disease treatment. This new approach is grounded in their posttranscriptional regulation of the expression of disease-associated genes. Reversing dysregulated gene expression using this mechanism may help control dysfunctional pathways. Furthermore, the ongoing improvement of algorithms has allowed for the integration of computational strategies built on top of laboratory-based data, facilitating a more precise and rational design and discovery of lead compounds. To complement the use of extensive pharmacogenomics data in prioritising potential drugs, our previous work introduced a computational approach based on only molecular sequences. Moreover, various computational tools for predicting molecular interactions in biological networks using similarity-based inference techniques have been accumulated in established studies. However, there are a limited number of comprehensive reviews covering both computational and experimental drug discovery processes. In this review, we outline a cohesive overview of both biological and computational applications in miRNA-targeted drug discovery, along with their disease implications and clinical significance. Finally, utilizing drug-target interaction (DTIs) data from DrugBank, we showcase the effectiveness of deep learning for obtaining the physicochemical characterization of DTIs.
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Affiliation(s)
- Jianfeng Sun
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD, UK.
| | - Miaoer Xu
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - Jinlong Ru
- Chair of Prevention of Microbial Diseases, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, 85354, Germany
| | - Anna James-Bott
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD, UK
| | - Dapeng Xiong
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Xia Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
| | - Adam P Cribbs
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD, UK.
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26
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Docherty JH, Lister TM, Mcarthur G, Findlay MT, Domingo-Legarda P, Kenyon J, Choudhary S, Larrosa I. Transition-Metal-Catalyzed C-H Bond Activation for the Formation of C-C Bonds in Complex Molecules. Chem Rev 2023. [PMID: 37163671 DOI: 10.1021/acs.chemrev.2c00888] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Site-predictable and chemoselective C-H bond functionalization reactions offer synthetically powerful strategies for the step-economic diversification of both feedstock and fine chemicals. Many transition-metal-catalyzed methods have emerged for the selective activation and functionalization of C-H bonds. However, challenges of regio- and chemoselectivity have emerged with application to highly complex molecules bearing significant functional group density and diversity. As molecular complexity increases within molecular structures the risks of catalyst intolerance and limited applicability grow with the number of functional groups and potentially Lewis basic heteroatoms. Given the abundance of C-H bonds within highly complex and already diversified molecules such as pharmaceuticals, natural products, and materials, design and selection of reaction conditions and tolerant catalysts has proved critical for successful direct functionalization. As such, innovations within transition-metal-catalyzed C-H bond functionalization for the direct formation of carbon-carbon bonds have been discovered and developed to overcome these challenges and limitations. This review highlights progress made for the direct metal-catalyzed C-C bond forming reactions including alkylation, methylation, arylation, and olefination of C-H bonds within complex targets.
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Affiliation(s)
- Jamie H Docherty
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Thomas M Lister
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Gillian Mcarthur
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Michael T Findlay
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Pablo Domingo-Legarda
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Jacob Kenyon
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Shweta Choudhary
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Igor Larrosa
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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27
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Chen Z, Wang X, Chen X, Huang J, Wang C, Wang J, Wang Z. Accelerating therapeutic protein design with computational approaches toward the clinical stage. Comput Struct Biotechnol J 2023; 21:2909-2926. [PMID: 38213894 PMCID: PMC10781723 DOI: 10.1016/j.csbj.2023.04.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/11/2023] [Accepted: 04/27/2023] [Indexed: 01/13/2024] Open
Abstract
Therapeutic protein, represented by antibodies, is of increasing interest in human medicine. However, clinical translation of therapeutic protein is still largely hindered by different aspects of developability, including affinity and selectivity, stability and aggregation prevention, solubility and viscosity reduction, and deimmunization. Conventional optimization of the developability with widely used methods, like display technologies and library screening approaches, is a time and cost-intensive endeavor, and the efficiency in finding suitable solutions is still not enough to meet clinical needs. In recent years, the accelerated advancement of computational methodologies has ushered in a transformative era in the field of therapeutic protein design. Owing to their remarkable capabilities in feature extraction and modeling, the integration of cutting-edge computational strategies with conventional techniques presents a promising avenue to accelerate the progression of therapeutic protein design and optimization toward clinical implementation. Here, we compared the differences between therapeutic protein and small molecules in developability and provided an overview of the computational approaches applicable to the design or optimization of therapeutic protein in several developability issues.
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Affiliation(s)
- Zhidong Chen
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Xinpei Wang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Xu Chen
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Juyang Huang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Chenglin Wang
- Shenzhen Qiyu Biotechnology Co., Ltd, Shenzhen 518107, China
| | - Junqing Wang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Zhe Wang
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
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28
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Tran BN, Tran KL, Nguyen TT, Bui LPT, Nguyen CN. A Novel Alginate Film Based on Nanocoating Approach for Enteric-Release Tablets. AAPS PharmSciTech 2023; 24:99. [PMID: 37024646 DOI: 10.1208/s12249-023-02557-0] [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: 12/20/2022] [Accepted: 03/13/2023] [Indexed: 04/08/2023] Open
Abstract
The objective of this study was to propose a new coating film for biodegradable polymers and environmentally friendly processing. Here, a novel implementation of solid lipid nanoparticles (SLN) into a biodegradable alginate (ALG) film composition created a new gastric-resistant film for an enteric-release tablet. Experiments were performed on a water-soluble substance (thiamine nitrate) to characterize the effects of SLN upon the addition of the ALG coating formulation. The coated tablets or cast films were characterized based on delayed-release properties, surface morphology, moisture resistance, and chemical interactions. The SLN-ALG film displayed gastric-resistant properties (< 10% drug substance dissolved at pH 1.2) and rapid disintegration in the intestinal medium (pH 6.8). Morphological analysis using a microscope and scanning electron microscope confirmed the uniformity and smoothness of the SLN-ALG film, which improved the mechanical properties of the film. Fourier transform infrared spectroscopy and differential scanning calorimetry indicated that SLN contributed to the formation of the film, which maintained free carboxylic groups, making the SLN-ALG film a higher acid resistance, but soluble in pH 6.8 buffer. These promising results suggest a novel nanotechnology-based coating formulation for various enteric-release dosage forms. Because of their biodegradability, the proposed ingredients and processes are safe and environment-friendly.
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Affiliation(s)
- Bao Ngoc Tran
- Department of Pharmaceutical Industry, Hanoi University of Pharmacy, Hanoi, Vietnam
| | - Khanh-Ly Tran
- Department of Pharmaceutical Industry, Hanoi University of Pharmacy, Hanoi, Vietnam
| | - Thach-Tung Nguyen
- Department of Pharmaceutics, Hanoi University of Pharmacy, Hanoi, Vietnam
| | - Lan-Phuong T Bui
- National Institute of Pharmaceutical Technology, Hanoi University of Pharmacy, Hanoi, Vietnam
| | - Chien Ngoc Nguyen
- Department of Pharmaceutical Industry, Hanoi University of Pharmacy, Hanoi, Vietnam.
- National Institute of Pharmaceutical Technology, Hanoi University of Pharmacy, Hanoi, Vietnam.
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29
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Jaume-Santero F, Bornet A, Valery A, Naderi N, Vicente Alvarez D, Proios D, Yazdani A, Bournez C, Fessard T, Teodoro D. Transformer Performance for Chemical Reactions: Analysis of Different Predictive and Evaluation Scenarios. J Chem Inf Model 2023; 63:1914-1924. [PMID: 36952584 PMCID: PMC10091402 DOI: 10.1021/acs.jcim.2c01407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The prediction of chemical reaction pathways has been accelerated by the development of novel machine learning architectures based on the deep learning paradigm. In this context, deep neural networks initially designed for language translation have been used to accurately predict a wide range of chemical reactions. Among models suited for the task of language translation, the recently introduced molecular transformer reached impressive performance in terms of forward-synthesis and retrosynthesis predictions. In this study, we first present an analysis of the performance of transformer models for product, reactant, and reagent prediction tasks under different scenarios of data availability and data augmentation. We find that the impact of data augmentation depends on the prediction task and on the metric used to evaluate the model performance. Second, we probe the contribution of different combinations of input formats, tokenization schemes, and embedding strategies to model performance. We find that less stable input settings generally lead to better performance. Lastly, we validate the superiority of round-trip accuracy over simpler evaluation metrics, such as top-k accuracy, using a committee of human experts and show a strong agreement for predictions that pass the round-trip test. This demonstrates the usefulness of more elaborate metrics in complex predictive scenarios and highlights the limitations of direct comparisons to a predefined database, which may include a limited number of chemical reaction pathways.
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Affiliation(s)
- Fernando Jaume-Santero
- Department of Radiology and Medical Informatics, University of Geneva, 1205 Geneva, Switzerland
- Geneva School of Business Administration, HES-SO University of Applied Sciences and Arts of Western Switzerland, 1227 Geneva, Switzerland
| | - Alban Bornet
- Department of Radiology and Medical Informatics, University of Geneva, 1205 Geneva, Switzerland
- Geneva School of Business Administration, HES-SO University of Applied Sciences and Arts of Western Switzerland, 1227 Geneva, Switzerland
| | | | - Nona Naderi
- Geneva School of Business Administration, HES-SO University of Applied Sciences and Arts of Western Switzerland, 1227 Geneva, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - David Vicente Alvarez
- Department of Radiology and Medical Informatics, University of Geneva, 1205 Geneva, Switzerland
- Geneva School of Business Administration, HES-SO University of Applied Sciences and Arts of Western Switzerland, 1227 Geneva, Switzerland
| | - Dimitrios Proios
- Department of Radiology and Medical Informatics, University of Geneva, 1205 Geneva, Switzerland
| | - Anthony Yazdani
- Department of Radiology and Medical Informatics, University of Geneva, 1205 Geneva, Switzerland
| | | | | | - Douglas Teodoro
- Department of Radiology and Medical Informatics, University of Geneva, 1205 Geneva, Switzerland
- Geneva School of Business Administration, HES-SO University of Applied Sciences and Arts of Western Switzerland, 1227 Geneva, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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Hocine S, Duchamp E, Mishra A, Fourquez JM, Hanessian S. Synthesis of Aza-Bridged Perhydroazulene Chimeras of Tropanes and Hederacine A. J Org Chem 2023; 88:4675-4686. [PMID: 36940388 DOI: 10.1021/acs.joc.3c00169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2023]
Abstract
We report the synthesis of two novel azaperhydroazulene tropane-hederacine chimeras A and B, which contain an 8-azabicyclo[3.2.1]octane ring and a 7-azabicyclo[4.1.1]octane ring, respectively. The synthesis of both chimeras was achieved by epoxide ring opening and was governed by the stereochemistry of the hydroxy-epoxide unit. Finally, a density functional theory study was conducted to explain the regioselectivity of the cyclization and the importance of the stereochemistry of the hydroxyl group.
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Affiliation(s)
- Sofiane Hocine
- Department of Chemistry, Université de Montréal, Station Centre-Ville, C.P. 6128, Montreal, Quebec H3C 3J7, Canada
| | - Edouard Duchamp
- Department of Chemistry, Université de Montréal, Station Centre-Ville, C.P. 6128, Montreal, Quebec H3C 3J7, Canada
| | - Akash Mishra
- Department of Chemistry, Université de Montréal, Station Centre-Ville, C.P. 6128, Montreal, Quebec H3C 3J7, Canada
| | | | - Stephen Hanessian
- Department of Chemistry, Université de Montréal, Station Centre-Ville, C.P. 6128, Montreal, Quebec H3C 3J7, Canada
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Kuzu E, Kuzu B. Tandem Synthesis of Novel thiazole-substituted pyrrolo[1,2-d][1,2,4]triazin-4(3H)-one Derivatives and their Theoretical Pharmacokinetic Profiles. Chem Heterocycl Compd (N Y) 2023. [DOI: 10.1007/s10593-023-03165-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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32
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Current Status of Oligonucleotide-Based Protein Degraders. Pharmaceutics 2023; 15:pharmaceutics15030765. [PMID: 36986626 PMCID: PMC10055846 DOI: 10.3390/pharmaceutics15030765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Transcription factors (TFs) and RNA-binding proteins (RBPs) have long been considered undruggable, mainly because they lack ligand-binding sites and are equipped with flat and narrow protein surfaces. Protein-specific oligonucleotides have been harnessed to target these proteins with some satisfactory preclinical results. The emerging proteolysis-targeting chimera (PROTAC) technology is no exception, utilizing protein-specific oligonucleotides as warheads to target TFs and RBPs. In addition, proteolysis by proteases is another type of protein degradation. In this review article, we discuss the current status of oligonucleotide-based protein degraders that are dependent either on the ubiquitin–proteasome system or a protease, providing a reference for the future development of degraders.
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Sakyi PO, Kwofie SK, Tuekpe JK, Gwira TM, Broni E, Miller WA, Wilson MD, Amewu RK. Inhibiting Leishmania donovani Sterol Methyltransferase to Identify Lead Compounds Using Molecular Modelling. Pharmaceuticals (Basel) 2023; 16:ph16030330. [PMID: 36986430 PMCID: PMC10054574 DOI: 10.3390/ph16030330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/25/2023] Open
Abstract
The recent outlook of leishmaniasis as a global public health concern coupled with the reportage of resistance and lack of efficacy of most antileishmanial drugs calls for a concerted effort to find new leads. The study combined In silico and in vitro approaches to identify novel potential synthetic small-molecule inhibitors targeting the Leishmania donovani sterol methyltransferase (LdSMT). The LdSMT enzyme in the ergosterol biosynthetic pathway is required for the parasite’s membrane fluidity, distribution of membrane proteins, and control of the cell cycle. The lack of LdSMT homologue in the human host and its conserved nature among all Leishmania parasites makes it a viable target for future antileishmanial drugs. Initially, six known inhibitors of LdSMT with IC50 < 10 μM were used to generate a pharmacophore model with a score of 0.9144 using LigandScout. The validated model was used to screen a synthetic library of 95,630 compounds obtained from InterBioScreen limited. Twenty compounds with pharmacophore fit scores above 50 were docked against the modelled three-dimensional structure of LdSMT using AutoDock Vina. Consequently, nine compounds with binding energies ranging from −7.5 to −8.7 kcal/mol were identified as potential hit molecules. Three compounds comprising STOCK6S-06707, STOCK6S-84928, and STOCK6S-65920 with respective binding energies of −8.7, −8.2, and −8.0 kcal/mol, lower than 22,26-azasterol (−7.6 kcal/mol), a known LdSMT inhibitor, were selected as plausible lead molecules. Molecular dynamics simulation studies and molecular mechanics Poisson–Boltzmann surface area calculations showed that the residues Asp25 and Trp208 were critical for ligand binding. The compounds were also predicted to have antileishmanial activity with reasonable pharmacological and toxicity profiles. When the antileishmanial activity of the three hits was evaluated in vitro against the promastigotes of L. donovani, mean half-maximal inhibitory concentrations (IC50) of 21.9 ± 1.5 μM (STOCK6S-06707), 23.5 ± 1.1 μM (STOCK6S-84928), and 118.3 ± 5.8 μM (STOCK6S-65920) were obtained. Furthermore, STOCK6S-84928 and STOCK6S-65920 inhibited the growth of Trypanosoma brucei, with IC50 of 14.3 ± 2.0 μM and 18.1 ± 1.4 μM, respectively. The identified compounds could be optimised to develop potent antileishmanial therapeutic agents.
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Affiliation(s)
- Patrick O. Sakyi
- Department of Chemistry, School of Physical and Mathematical Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 56, Ghana
- Department of Chemical Sciences, School of Sciences, University of Energy and Natural Resources, Sunyani P.O. Box 214, Ghana
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 77, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra P.O. Box LG 54, Ghana
- Correspondence: (S.K.K.); (R.K.A.); Tel.: +233-203797922 (S.K.K.); +233-543823483 (R.K.A.)
| | - Julius K. Tuekpe
- Department of Biochemistry, Cell, and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - Theresa M. Gwira
- Department of Biochemistry, Cell, and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - Emmanuel Broni
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 77, Ghana
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra P.O. Box LG 581, Ghana
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA
- Department of Molecular Pharmacology and Neuroscience, Loyola University Medical Center, Maywood, IL 60153, USA
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael D. Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra P.O. Box LG 581, Ghana
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA
| | - Richard K. Amewu
- Department of Chemistry, School of Physical and Mathematical Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 56, Ghana
- Correspondence: (S.K.K.); (R.K.A.); Tel.: +233-203797922 (S.K.K.); +233-543823483 (R.K.A.)
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Mondal A, Barik GK, Sarkar S, Mondal D, Ahmad M, Vijayakanth T, Mondal J, Santra MK, Talukdar P. Nontoxic Artificial Chloride Channel Formation in Epithelial Cells by Isophthalic Acid-Based Small Molecules. Chemistry 2023; 29:e202202887. [PMID: 36399427 DOI: 10.1002/chem.202202887] [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: 09/15/2022] [Revised: 11/18/2022] [Accepted: 11/18/2022] [Indexed: 11/19/2022]
Abstract
Artificial channels capable of facilitating the transport of Cl- ions across cell membranes while being nontoxic to the cells are rare. Such synthetic ion channels can mimic the functions of membrane transport proteins and, therefore, have the potential to treat channelopathies by replacing defective ion channels. Here we report isophthalic acid-based structurally simple molecules 1 a and 2 a, which self-assemble to render supramolecular nanochannels that allow selective transport of Cl- ions. As evident from the single-crystal X-ray diffraction analysis, the self-assembly is governed by intermolecular hydrogen bonding and π-π stacking interactions. The MD simulation studies for both 1 a and 2 a confirmed the formation of stable Cl- channel assembly in the lipid membrane and Cl- transport through them. The MQAE assay showed the efficacy of the compounds in delivering Cl- ions into cells, and the MTT assays proved that the compounds are nontoxic to cells even at a concentration of 100 μM.
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Affiliation(s)
- Abhishek Mondal
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India
| | | | - Susmita Sarkar
- Center for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, 500046, Telangana, India
| | - Debashis Mondal
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India
| | - Manzoor Ahmad
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India
| | - Thangavel Vijayakanth
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Jagannath Mondal
- Center for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, 500046, Telangana, India
| | | | - Pinaki Talukdar
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India
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35
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Ngo C, Ekanayake A, Zhang C. Identification of Covalent Ligands – from Single Targets to Whole Proteome. Isr J Chem 2023. [DOI: 10.1002/ijch.202200105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Chau Ngo
- Department of Chemistry Loker Hydrocarbon Research Institute University of Southern California 90089 Los Angeles California USA
| | - Arunika Ekanayake
- Department of Chemistry Loker Hydrocarbon Research Institute University of Southern California 90089 Los Angeles California USA
- Current address: Department of Chemistry University of Alberta T6G 2G2 Edmonton AB Canada
| | - Chao Zhang
- Department of Chemistry Loker Hydrocarbon Research Institute University of Southern California 90089 Los Angeles California USA
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36
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Synthesis and cytotoxic/antimicrobial screening of 2-alkenylimidazo[1,2-a]pyrimidines. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02997-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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37
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Zhang Y, Ranaei Pirmardan E, Barakat A, Naseri M, Hafezi-Moghadam A. Nanoarchitectonics for Photo-Controlled Intracellular Drug Release in Immune Modulation. ACS APPLIED MATERIALS & INTERFACES 2022; 14:42976-42987. [PMID: 36103264 DOI: 10.1021/acsami.2c12440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Local stimuli differentiate monocytes into M2-like macrophages that mechanistically drive the pathologies in cancer and age-related macular degeneration (AMD). A photo-controlled nanodrug that halts macrophage polarization through Rho-associated kinase (ROCK) inhibition was developed. A small-molecule ROCK inhibitor, fasudil, was conjugated to a photo-responsive group and a short poly(ethylene glycol) (PEG) chain. This resulted in the novel amphiphilic prodrug, PEG-2-(4'-(di(prop-2-yn-1-yl)amino)-4-nitro-[1,1'-biphenyl]-yl)propan-1-ol (PANBP)-Fasudil, that spontaneously formed micelles. Ultraviolet (UV) irradiation of PEG-PANBP-Fasudil nanoparticles rapidly released fasudil. For visualization of linker degradation, a reporter nanoprobe was synthesized, in which 2-Me-4-OMe TokyoGreen (TG), a fluorophore that does not fluoresce in conjugation, was incorporated. Irradiation of nanoprobe-laden monocytes activated the reporter fluorophore. Cytokine stimulation differentiated monocytes into macrophages, while UV irradiation prevented polarization of PEG-PANBP-Fasudil nanoparticle-laden monocytes. Nanoarchitectonics-based design opens new possibilities for intracellular drug delivery and precise spatiotemporal immune cell modulation toward the development of new therapies.
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Affiliation(s)
- Yuanlin Zhang
- Molecular Biomarkers Nano-Imaging Laboratory, Brigham and Women's Hospital, and Department of Radiology, Harvard Medical School, 75 Francis St., Thorn Research Building, Boston, Massachusetts 02115, United States
| | - Ehsan Ranaei Pirmardan
- Molecular Biomarkers Nano-Imaging Laboratory, Brigham and Women's Hospital, and Department of Radiology, Harvard Medical School, 75 Francis St., Thorn Research Building, Boston, Massachusetts 02115, United States
| | - Aliaa Barakat
- Molecular Biomarkers Nano-Imaging Laboratory, Brigham and Women's Hospital, and Department of Radiology, Harvard Medical School, 75 Francis St., Thorn Research Building, Boston, Massachusetts 02115, United States
| | - Marzieh Naseri
- Molecular Biomarkers Nano-Imaging Laboratory, Brigham and Women's Hospital, and Department of Radiology, Harvard Medical School, 75 Francis St., Thorn Research Building, Boston, Massachusetts 02115, United States
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111, United States
| | - Ali Hafezi-Moghadam
- Molecular Biomarkers Nano-Imaging Laboratory, Brigham and Women's Hospital, and Department of Radiology, Harvard Medical School, 75 Francis St., Thorn Research Building, Boston, Massachusetts 02115, United States
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38
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Fernandes ES, Ferro ES, Simão G, Alves de Góis G, Arbiser J, Pereira Costa SK. Editorial: Current challenges in inflammation and pain biology: The role of natural and synthetic compounds. Front Physiol 2022; 13:1008538. [PMID: 36160841 PMCID: PMC9491223 DOI: 10.3389/fphys.2022.1008538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 08/12/2022] [Indexed: 12/04/2022] Open
Affiliation(s)
- Elizabeth Soares Fernandes
- Programa de Pós-graduação em Biotecnologia Aplicada à Saúde da Criança e do Adolescente, Faculdades Pequeno Príncipe, Curitiba, Brazil
- Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Brazil
- *Correspondence: Elizabeth Soares Fernandes,
| | | | - Gisele Simão
- Programa de Pós-graduação em Biotecnologia Aplicada à Saúde da Criança e do Adolescente, Faculdades Pequeno Príncipe, Curitiba, Brazil
- Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Brazil
| | | | - Jack Arbiser
- Veterans Administration Medical Center, School of Medicine, Emory University, Atlanta, NY, United States
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Qin L, Dai H, Wang J. Key Considerations in Targeted Protein Degradation Drug Discovery and Development. Front Chem 2022; 10:934337. [PMID: 35978859 PMCID: PMC9376879 DOI: 10.3389/fchem.2022.934337] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Targeting proteins’ enzymatic functions with small molecule inhibitors, as well as functions of receptor proteins with small-molecule agonists and antagonists, were the major forms of small-molecule drug development. These small-molecule modulators are based on a conventional occupancy-driven pharmacological approach. For proteome space traditionally considered undruggable by small-molecule modulators, such as enzymes with scaffolding functions, transcription factors, and proteins that lack well-defined binding pockets for small molecules, targeted protein degraders offer the opportunity to drug the proteome with an event-driven pharmacological approach. A degrader molecule, either PROTAC or molecular glue, brings the protein of interest (POI) and E3 ubiquitin ligase in close proximity and engages the ubiquitin-proteasome system (UPS), the cellular waste disposal system for the degradation of the POI. For the development of targeted protein degraders to meet therapeutic needs, several aspects will be considered, namely, the selective degradation of disease-causing proteins, the oral bioavailability of degraders beyond Lipinski’s rule of five (bRo5) scope, demands of new E3 ubiquitin ligases and molecular glue degraders, and drug resistance of the new drug modality. This review will illustrate several under-discussed key considerations in targeted protein degradation drug discovery and development: 1) the contributing factors for the selectivity of PROTAC molecules and the design of PROTACs to selectively degrade synergistic pathological proteins; 2) assay development in combination with a multi-omics approach for the identification of new E3 ligases and their corresponding ligands, as well as molecular glue degraders; 3) a molecular design to improve the oral bioavailability of bRo5 PROTACs, and 4) drug resistance of degraders.
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Affiliation(s)
- Liena Qin
- Insilico Medicine Ltd., Shanghai, China
- *Correspondence: Liena Qin, ; Han Dai, ; Junfeng Wang,
| | - Han Dai
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- *Correspondence: Liena Qin, ; Han Dai, ; Junfeng Wang,
| | - Junfeng Wang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- International Magnetobiology Frontier Research Center, Hefei, China
- Institute of Physical Science and Information Technology, Anhui University, Hefei, China
- *Correspondence: Liena Qin, ; Han Dai, ; Junfeng Wang,
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40
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Zeng K, Han L, Chen Y. Endogenous Proteins Modulation in Live Cells with Small Molecules and Light. Chembiochem 2022; 23:e202200244. [PMID: 35822393 DOI: 10.1002/cbic.202200244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/23/2022] [Indexed: 11/05/2022]
Abstract
The protein modulation by light illumination enables the biological role investigation in high spatiotemporal precision. Compared to genetic methods, the small molecules approach is uniquely suited for modulating endogenous proteins. The endogenous protein modulation in live cells with small molecules and light has recently advanced on three distinctive frontiers: i) the infrared-light-induced or localized decaging of small molecules by photolysis, ii) the visible-light-induced photocatalytic releasing of small molecules, and iii) the small-molecule-ligand-directed caging for photo-modulation of proteins. Together, these methods provide powerful chemical biology tool kits for spatiotemporal modulation of endogenous proteins with potential therapeutic applications. This Concept aims to inspire organic chemists and chemical biologists to delve into this burgeoning endogenous protein modulation field for new biological discoveries.
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Affiliation(s)
- Kaixing Zeng
- Shanghai Institute Of Organic Chemistry State Key Laboratory of Bioorganic Chemistry, BNPC, CHINA
| | - Lili Han
- Shanghai Institute Of Organic Chemistry State Key Laboratory of Bioorganic Chemistry, BNPC, CHINA
| | - Yiyun Chen
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, BNPC, 345 Lingling Road, 200032, Shanghai, CHINA
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41
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Standing D, Dandawate P, Anant S. Prolactin receptor signaling: A novel target for cancer treatment - Exploring anti-PRLR signaling strategies. Front Endocrinol (Lausanne) 2022; 13:1112987. [PMID: 36714582 PMCID: PMC9880166 DOI: 10.3389/fendo.2022.1112987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/22/2022] [Indexed: 01/15/2023] Open
Abstract
Prolactin (PRL) is a peptide hormone mainly secreted from the anterior pituitary gland. PRL is reported to play a role in pregnancy, mammary gland development, immune modulation, reproduction, and differentiation of islet cells. PRL binds to its receptor PRLR, which belongs to a superfamily of the class I cytokine receptor that has no intrinsic kinase activity. In canonical signaling, PRL binding to PRLR induces downstream signaling including JAK-STAT, AKT and MAPK pathways. This leads to increased cell proliferation, stemness, migration, apoptosis inhibition, and resistance to chemotherapy. PRL-signaling is upregulated in numerous hormone-dependent cancers including breast, prostate, ovarian, and endometrial cancer. However, more recently, the pathway has been reported to play a tumor-promoting role in other cancer types such as colon, pancreas, and hepatocellular cancers. Hence, the signaling pathway is an attractive target for drug development with blockade of the receptor being a potential therapeutic approach. Different strategies have been developed to target this receptor including modification of PRL peptides (Del1-9-G129R-hPRL, G129R-Prl), growth hormone receptor/prolactin receptor bispecific antibody antagonist, neutralizing antibody LFA102, an antibody-drug conjugate (ABBV-176) of the humanized antibody h16f (PR-1594804) and pyrrolobenzodiazepine dimer, a bispecific antibody targeting both PRLR and CD3, an in vivo half-life extended fusion protein containing PRLR antagonist PrlRA and albumin binding domain. There have also been attempts to discover and develop small molecular inhibitors targeting PRLR. Recently, using structure-based virtual screening, we identified a few antipsychotic drugs including penfluridol as a molecule that inhibits PRL-signaling to inhibit PDAC tumor progression. In this review, we will summarize the recent advances in the biology of this receptor in cancer and give an account of PRLR antagonist development for the treatment of cancer.
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