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Powis G, Meuillet EJ, Indarte M, Booher G, Kirkpatrick L. Pleckstrin Homology [PH] domain, structure, mechanism, and contribution to human disease. Biomed Pharmacother 2023; 165:115024. [PMID: 37399719 DOI: 10.1016/j.biopha.2023.115024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/14/2023] [Indexed: 07/05/2023] Open
Abstract
The pleckstrin homology [PH] domain is a structural fold found in more than 250 proteins making it the 11th most common domain in the human proteome. 25% of family members have more than one PH domain and some PH domains are split by one, or several other, protein domains although still folding to give functioning PH domains. We review mechanisms of PH domain activity, the role PH domain mutation plays in human disease including cancer, hyperproliferation, neurodegeneration, inflammation, and infection, and discuss pharmacotherapeutic approaches to regulate PH domain activity for the treatment of human disease. Almost half PH domain family members bind phosphatidylinositols [PIs] that attach the host protein to cell membranes where they interact with other membrane proteins to give signaling complexes or cytoskeleton scaffold platforms. A PH domain in its native state may fold over other protein domains thereby preventing substrate access to a catalytic site or binding with other proteins. The resulting autoinhibition can be released by PI binding to the PH domain, or by protein phosphorylation thus providing fine tuning of the cellular control of PH domain protein activity. For many years the PH domain was thought to be undruggable until high-resolution structures of human PH domains allowed structure-based design of novel inhibitors that selectively bind the PH domain. Allosteric inhibitors of the Akt1 PH domain have already been tested in cancer patients and for proteus syndrome, with several other PH domain inhibitors in preclinical development for treatment of other human diseases.
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Affiliation(s)
- Garth Powis
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA.
| | | | - Martin Indarte
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA
| | - Garrett Booher
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA
| | - Lynn Kirkpatrick
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA
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2
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Cossar PJ, Cardoso D, Mathwin D, Russell CC, Chiew B, Hamilton MP, Baker JR, Young KA, Chau N, Robinson PJ, McCluskey A. Wiskostatin and other carbazole scaffolds as off target inhibitors of dynamin I GTPase activity and endocytosis. Eur J Med Chem 2023; 247:115001. [PMID: 36577213 DOI: 10.1016/j.ejmech.2022.115001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022]
Abstract
Wiskostatin (1-(3,6-dibromo-9H-carbazol-9-yl)-3-(dimethylamino)propan-2-ol) (1) is a carbazole-based compound reported as a specific and relatively potent inhibitor of the N-WASP actin remodelling complex (S-isomer EC50 = 4.35 μM; R-isomer EC50 = 3.44 μM). An NMR solution structure showed that wiskostatin interacts with a cleft in the regulatory GTPase binding domain of N-WASP. However, numerous studies have reported wiskostatin's actions on membrane transport and cytokinesis that are independent of the N-WASP-Arp2/3 complex pathway, but offer limited alternative explanation. The large GTPase, dynamin has established functional roles in these pathways. This study reveals that wiskostatin and its analogues, as well as other carbazole-based compounds, are inhibitors of helical dynamin GTPase activity and endocytosis. We characterise the effects of wiskostatin on in vitro dynamin GTPase activity, in-cell endocytosis, and determine the importance of wiskostatin functional groups on these activities through design and synthesis of libraries of wiskostatin analogues. We also examine whether other carbazole-based scaffolds frequently used in research or the clinic also modulate dynamin and endocytosis. Understanding off-targets for compounds used as research tools is important to be able to confidently interpret their action on biological systems, particularly when the target and off-targets affect overlapping mechanisms (e.g. cytokinesis and endocytosis). Herein we demonstrate that wiskostatin is a dynamin inhibitor (IC50 20.7 ± 1.2 μM) and a potent inhibitor of clathrin mediated endocytosis (IC50 = 6.9 ± 0.3 μM). Synthesis of wiskostatin analogues gave rise to 1-(9H-carbazol-9-yl)-3-((4-methylbenzyl)amino)propan-2-ol (35) and 1-(9H-carbazol-9-yl)-3-((4-chlorobenzyl)amino)propan-2-ol (43) as potent dynamin inhibitors (IC50 = 1.0 ± 0.2 μM), and (S)-1-(3,6-dibromo-9H-carbazol-9-yl)-3-(dimethylamino)propan-2-ol (8a) and (R)-1-(3,6-dibromo-9H-carbazol-9-yl)-3-(dimethylamino)propan-2-ol (8b) that are amongst the most potent inhibitors of clathrin mediated endocytosis yet reported (IC50 = 2.3 ± 3.3 and 2.1 ± 1.7 μM, respectively).
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Affiliation(s)
- Peter J Cossar
- Chemistry, School of Environmental & Life Sciences, The University of Newcastle, University Drive, Callaghan NSW, 2308, Australia
| | - David Cardoso
- Cell Signalling Unit, Children's Medical Research Institute, The University of Sydney, Sydney, NSW, 2145, Australia
| | - Daniel Mathwin
- Chemistry, School of Environmental & Life Sciences, The University of Newcastle, University Drive, Callaghan NSW, 2308, Australia
| | - Cecilia C Russell
- Chemistry, School of Environmental & Life Sciences, The University of Newcastle, University Drive, Callaghan NSW, 2308, Australia
| | - Beatrice Chiew
- Chemistry, School of Environmental & Life Sciences, The University of Newcastle, University Drive, Callaghan NSW, 2308, Australia
| | - Michael P Hamilton
- Chemistry, School of Environmental & Life Sciences, The University of Newcastle, University Drive, Callaghan NSW, 2308, Australia
| | - Jennifer R Baker
- Chemistry, School of Environmental & Life Sciences, The University of Newcastle, University Drive, Callaghan NSW, 2308, Australia
| | - Kelly A Young
- Chemistry, School of Environmental & Life Sciences, The University of Newcastle, University Drive, Callaghan NSW, 2308, Australia
| | - Ngoc Chau
- Cell Signalling Unit, Children's Medical Research Institute, The University of Sydney, Sydney, NSW, 2145, Australia
| | - Phillip J Robinson
- Cell Signalling Unit, Children's Medical Research Institute, The University of Sydney, Sydney, NSW, 2145, Australia
| | - Adam McCluskey
- Chemistry, School of Environmental & Life Sciences, The University of Newcastle, University Drive, Callaghan NSW, 2308, Australia.
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3
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Odell LR, Robertson MJ, Young KA, McGeachie AB, Quan A, Robinson PJ, McCluskey A. Prodrugs of the Archetypal Dynamin Inhibitor Bis-T-22. ChemMedChem 2022; 17:e202200400. [PMID: 36351775 PMCID: PMC10947042 DOI: 10.1002/cmdc.202200400] [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: 07/21/2022] [Revised: 10/06/2022] [Indexed: 11/11/2022]
Abstract
The Bis-T series of compounds comprise some of the most potent inhibitors of dynamin GTPase activity yet reported, e. g., (2E,2'E)-N,N'-(propane-1,3-diyl)bis(2-cyano-3-(3,4-dihydroxyphenyl)acrylamide) (2), Bis-T-22. The catechol moieties are believed to limit cell permeability, rendering these compounds largely inactive in cells. To solve this problem, a prodrug strategy was envisaged and eight ester analogues were synthesised. The shortest and bulkiest esters (acetate and butyl/tert-butyl) were found to be insoluble under physiological conditions, whilst the remaining five were soluble and stable under these conditions. These five were analysed for plasma stability and half-lives ranged from ∼2.3 min (propionic ester 4), increasing with size and bulk, to greater than 24 hr (dimethyl carbamate 10). Similar profiles where observed with the rate of formation of Bis-T-22 with half-lives ranging from ∼25 mins (propionic ester 4). Propionic ester 4 was chosen to undergo further testing and was found to inhibit endocytosis in a dose-dependent manner with IC50 ∼8 μM, suggesting this compound is able to effectively cross the cell membrane where it is rapidly hydrolysed to the desired Bis-T-22 parent compound.
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Affiliation(s)
- Luke R. Odell
- The University of NewcastleUniversity DriveCallaghanNSW 2308Australia
- Present address: Department of Medicinal ChemistryUppsala UniversityBox 57475123UppsalaSweden
| | - Mark J Robertson
- The University of NewcastleUniversity DriveCallaghanNSW 2308Australia
- Present address: Chemistry, College of Science & EngineeringJames Cook UniversityTownsvilleQLD 4814Australia
| | - Kelly A Young
- The University of NewcastleUniversity DriveCallaghanNSW 2308Australia
| | - Andrew B. McGeachie
- Cell Signalling UnitChildren's Medical Research InstituteThe University of Sydney214 Hawkesbury RoadWestmeadNSW 2145Australia
| | - Annie Quan
- Cell Signalling UnitChildren's Medical Research InstituteThe University of Sydney214 Hawkesbury RoadWestmeadNSW 2145Australia
| | - Phillip J. Robinson
- Cell Signalling UnitChildren's Medical Research InstituteThe University of Sydney214 Hawkesbury RoadWestmeadNSW 2145Australia
| | - Adam McCluskey
- The University of NewcastleUniversity DriveCallaghanNSW 2308Australia
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4
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Jun J, Baek J, Kang D, Moon H, Kim H, Cho H, Hah JM. Novel 1,4,5,6-tetrahydrocyclopenta[d]imidazole-5-carboxamide-based JNK3 inhibitors: Design, synthesis, molecular docking, and therapeutic potential in neurodegenerative diseases. Eur J Med Chem 2022; 245:114917. [DOI: 10.1016/j.ejmech.2022.114917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/11/2022]
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Dhakal A, McKay C, Tanner JJ, Cheng J. Artificial intelligence in the prediction of protein-ligand interactions: recent advances and future directions. Brief Bioinform 2022; 23:bbab476. [PMID: 34849575 PMCID: PMC8690157 DOI: 10.1093/bib/bbab476] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/28/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022] Open
Abstract
New drug production, from target identification to marketing approval, takes over 12 years and can cost around $2.6 billion. Furthermore, the COVID-19 pandemic has unveiled the urgent need for more powerful computational methods for drug discovery. Here, we review the computational approaches to predicting protein-ligand interactions in the context of drug discovery, focusing on methods using artificial intelligence (AI). We begin with a brief introduction to proteins (targets), ligands (e.g. drugs) and their interactions for nonexperts. Next, we review databases that are commonly used in the domain of protein-ligand interactions. Finally, we survey and analyze the machine learning (ML) approaches implemented to predict protein-ligand binding sites, ligand-binding affinity and binding pose (conformation) including both classical ML algorithms and recent deep learning methods. After exploring the correlation between these three aspects of protein-ligand interaction, it has been proposed that they should be studied in unison. We anticipate that our review will aid exploration and development of more accurate ML-based prediction strategies for studying protein-ligand interactions.
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Affiliation(s)
- Ashwin Dhakal
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, 65211, USA
| | - Cole McKay
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Chemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, 65211, USA
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Xu Z, Chen H, Deng GJ, Huang H. Copper-catalyzed three-component formal [3 + 1 + 2] annulations for the synthesis of 2-aminopyrimidines from O-acyl ketoximes. Org Biomol Chem 2021; 19:8706-8710. [PMID: 34581386 DOI: 10.1039/d1ob01582f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A copper-based catalytic system has been developed to enable formal [3 + 1 + 2] annulations of ketoxime acetates, aldehydes, and cyanamides. This protocol offers a new strategy for the synthesis of highly substituted 2-aminopyrimidine compounds, and more importantly, pyrimidines have now been included in the N-heterocycle family constructed using O-acyl ketoximes as N-C-C synthons.
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Affiliation(s)
- Zhenhua Xu
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 411105, China.
| | - Hongbiao Chen
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 411105, China.
| | - Guo-Jun Deng
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 411105, China.
| | - Huawen Huang
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 411105, China.
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7
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Odell LR, Chau N, Russell CC, Young KA, Gilbert J, Robinson PJ, Sakoff JA, McCluskey A. Pyrimidyn-Based Dynamin Inhibitors as Novel Cytotoxic Agents. ChemMedChem 2021; 17:e202100560. [PMID: 34590434 DOI: 10.1002/cmdc.202100560] [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: 08/18/2021] [Revised: 09/28/2021] [Indexed: 11/06/2022]
Abstract
Five focused libraries of pyrimidine-based dynamin GTPase inhibitors, in total 69 compounds were synthesised, and their dynamin inhibition and broad-spectrum cytotoxicity examined. Dynamin plays a crucial role in mitosis, and as such inhibition of dynamin was expected to broadly correlate with the observed cytotoxicity. The pyrimidines synthesised ranged from mono-substituted to trisubstituted. The highest levels of dynamin inhibition were noted with di- and tri- substituted pyrimidines, especially those with pendent amino alkyl chains. Short chains and simple heterocyclic rings reduced dynamin activity. There were three levels of dynamin activity noted: 1-10, 10-25 and 25-60 μM. Screening of these compounds in a panel of cancer cell lines: SW480 (colon), HT29 (colon), SMA (spontaneous murine astrocytoma), MCF-7 (breast), BE2-C (glioblastoma), SJ-G2 (neuroblastoma), MIA (pancreas), A2780 (ovarian), A431 (skin), H460 (lung), U87 (glioblastoma) and DU145 (prostate) cell lines reveal a good correlation between the observed dynamin inhibition and the observed cytotoxicity. The most active analogues (31 a,b) developed returned average GI50 values of 1.0 and 0.78 μM across the twelve cell lines examined. These active analogues were: N2 -(3-dimethylaminopropyl)-N4 -dodecyl-6-methylpyrimidine-2,4-diamine (31 a) and N4 -(3-dimethylaminopropyl)-N2 -dodecyl-6-methylpyrimidine-2,4-diamine (31 b).
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Affiliation(s)
- Luke R Odell
- Chemistry, School of Environmental & Life Sciences, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Ngoc Chau
- Cell Signalling Unit Children's Medical Research Institute, The University of Sydney, Sydney, 2145 Hawkesbury Road, NSW 2145, Australia
| | - Cecilia C Russell
- Chemistry, School of Environmental & Life Sciences, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Kelly A Young
- Chemistry, School of Environmental & Life Sciences, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Jayne Gilbert
- Experimental Therapeutics Group, Department of Medical Oncology, Calvary Mater Newcastle Hospital, Edith Street, Waratah, NSW 2298, Australia
| | - Phillip J Robinson
- Cell Signalling Unit Children's Medical Research Institute, The University of Sydney, Sydney, 2145 Hawkesbury Road, NSW 2145, Australia
| | - Jennette A Sakoff
- Experimental Therapeutics Group, Department of Medical Oncology, Calvary Mater Newcastle Hospital, Edith Street, Waratah, NSW 2298, Australia
| | - Adam McCluskey
- Chemistry, School of Environmental & Life Sciences, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
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8
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Measuring Endocytosis During Proliferative Cell Quiescence. Methods Mol Biol 2020; 2233:19-42. [PMID: 33222125 DOI: 10.1007/978-1-0716-1044-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2023]
Abstract
Quiescence (also called "G0") is the state in which cells have exited the cell cycle but are capable to reenter as required. Though poorly understood, it represents one of the most prevalent cell states across all life. Many biologically important cell types reside in quiescence including mature hepatocytes, endothelial cells, and dormant adult stem cells. Furthermore, the quiescence program occurs in both short- and long-term varieties, depending on the physiological environments. A barrier slowing our understanding of quiescence has been a scarcity of available in vitro model systems to allow for the exploration of key regulatory pathways, such as endocytosis. Endocytosis, the internalization of extracellular material into the cell, is a fundamental and highly regulated process that impacts many cell biological functions. Accordingly, we have developed an in vitro model of deep quiescence in hTERT-immortalized RPE1 cells, combining both long-term contact inhibition and mitogen removal, to measure endocytosis. In addition, we present an analytical approach employing automated high-throughput microscopy and image analysis that yields high-content data allowing for meaningful and statistically robust interpretation. Importantly, the methods presented herein provide a suitable platform that can be easily adapted to investigate other regulatory processes across the cell cycle.
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9
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Tin(IV) compounds of tridentate thiosemicarbazone Schiff bases: Synthesis, characterization, in-silico analysis and in vitro cytotoxicity. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114729] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Oh Y, Jang M, Cho H, Yang S, Im D, Moon H, Hah JM. Discovery of 3-alkyl-5-aryl-1-pyrimidyl-1 H-pyrazole derivatives as a novel selective inhibitor scaffold of JNK3. J Enzyme Inhib Med Chem 2020; 35:372-376. [PMID: 31856610 PMCID: PMC6968587 DOI: 10.1080/14756366.2019.1705294] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
3-alkyl-5-aryl-1-pyrimidyl-1H-pyrazole derivatives were designed and synthesised as selective inhibitors of JNK3, a target for the treatment of neurodegenerative diseases. Following previous studies, we have designed JNK3 inhibitors to reduce the molecular weight and successfully identified a lead compound that exhibits equipotent activity towards JNK3. Kinase profiling results also showed high selectivity for JNK3 among 38 kinases. Among the derivatives, the IC50 value of 8a, (R)-2-(1-(2-((1-(cyclopropanecarbonyl)pyrrolidin-3-yl)amino)pyrimidin-4-yl)-5-(3,4-dichlorophenyl)-1H-pyrazol-3-yl)acetonitrile exhibited 227 nM, showing the highest inhibitory activity against JNK3.
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Affiliation(s)
- Youri Oh
- College of Pharmacy and Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan, Korea
| | - Miyoung Jang
- College of Pharmacy and Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan, Korea
| | - Hyunwook Cho
- College of Pharmacy and Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan, Korea
| | - Songyi Yang
- College of Pharmacy and Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan, Korea
| | - Daseul Im
- College of Pharmacy and Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan, Korea
| | - Hyungwoo Moon
- College of Pharmacy and Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan, Korea
| | - Jung-Mi Hah
- College of Pharmacy and Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan, Korea
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Abstract
This paper is the fortieth consecutive installment of the annual anthological review of research concerning the endogenous opioid system, summarizing articles published during 2017 that studied the behavioral effects of molecular, pharmacological and genetic manipulation of opioid peptides and receptors as well as effects of opioid/opiate agonists and antagonists. The review is subdivided into the following specific topics: molecular-biochemical effects and neurochemical localization studies of endogenous opioids and their receptors (1), the roles of these opioid peptides and receptors in pain and analgesia in animals (2) and humans (3), opioid-sensitive and opioid-insensitive effects of nonopioid analgesics (4), opioid peptide and receptor involvement in tolerance and dependence (5), stress and social status (6), learning and memory (7), eating and drinking (8), drug abuse and alcohol (9), sexual activity and hormones, pregnancy, development and endocrinology (10), mental illness and mood (11), seizures and neurologic disorders (12), electrical-related activity and neurophysiology (13), general activity and locomotion (14), gastrointestinal, renal and hepatic functions (15), cardiovascular responses (16), respiration and thermoregulation (17), and immunological responses (18).
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Affiliation(s)
- Richard J Bodnar
- Department of Psychology and Neuropsychology Doctoral Sub-Program, Queens College, City University of New York, CUNY, 65-30 Kissena Blvd., Flushing, NY, 11367, United States.
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12
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Nawrotek A, Benabdi S, Niyomchon S, Kryszke MH, Ginestier C, Cañeque T, Tepshi L, Mariani A, St Onge RP, Giaever G, Nislow C, Charafe-Jauffret E, Rodriguez R, Zeghouf M, Cherfils J. PH-domain-binding inhibitors of nucleotide exchange factor BRAG2 disrupt Arf GTPase signaling. Nat Chem Biol 2019; 15:358-366. [PMID: 30742123 DOI: 10.1038/s41589-019-0228-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 11/29/2018] [Indexed: 12/30/2022]
Abstract
Peripheral membrane proteins orchestrate many physiological and pathological processes, making regulation of their activities by small molecules highly desirable. However, they are often refractory to classical competitive inhibition. Here, we demonstrate that potent and selective inhibition of peripheral membrane proteins can be achieved by small molecules that target protein-membrane interactions by a noncompetitive mechanism. We show that the small molecule Bragsin inhibits BRAG2-mediated Arf GTPase activation in vitro in a manner that requires a membrane. In cells, Bragsin affects the trans-Golgi network in a BRAG2- and Arf-dependent manner. The crystal structure of the BRAG2-Bragsin complex and structure-activity relationship analysis reveal that Bragsin binds at the interface between the PH domain of BRAG2 and the lipid bilayer to render BRAG2 unable to activate lipidated Arf. Finally, Bragsin affects tumorsphere formation in breast cancer cell lines. Bragsin thus pioneers a novel class of drugs that function by altering protein-membrane interactions without disruption.
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Affiliation(s)
- Agata Nawrotek
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole normale supérieure Paris-Saclay, Cachan, France.,CNRS, Cachan, France
| | - Sarah Benabdi
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole normale supérieure Paris-Saclay, Cachan, France.,CNRS, Cachan, France
| | - Supaporn Niyomchon
- Institut Curie, PSL Research University, Chemical Cell Biology Group, Paris, France.,CNRS, Paris, France.,INSERM, Paris, France
| | - Marie-Hélène Kryszke
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole normale supérieure Paris-Saclay, Cachan, France.,CNRS, Cachan, France
| | - Christophe Ginestier
- Université Aix-Marseille, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Team, Marseille, France
| | - Tatiana Cañeque
- Institut Curie, PSL Research University, Chemical Cell Biology Group, Paris, France.,CNRS, Paris, France.,INSERM, Paris, France
| | - Livia Tepshi
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole normale supérieure Paris-Saclay, Cachan, France.,CNRS, Cachan, France
| | - Angelica Mariani
- Institut Curie, PSL Research University, Chemical Cell Biology Group, Paris, France.,CNRS, Paris, France.,INSERM, Paris, France
| | - Robert P St Onge
- Genome Technology Center, Stanford School of Medicine, Stanford, CA, USA
| | - Guri Giaever
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Emmanuelle Charafe-Jauffret
- Université Aix-Marseille, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Team, Marseille, France
| | - Raphaël Rodriguez
- Institut Curie, PSL Research University, Chemical Cell Biology Group, Paris, France.,CNRS, Paris, France.,INSERM, Paris, France
| | - Mahel Zeghouf
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole normale supérieure Paris-Saclay, Cachan, France. .,CNRS, Cachan, France.
| | - Jacqueline Cherfils
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole normale supérieure Paris-Saclay, Cachan, France. .,CNRS, Cachan, France.
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13
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Eschenburg S, Reubold TF. Modulation of dynamin function by small molecules. Biol Chem 2018; 399:1421-1432. [PMID: 30067507 DOI: 10.1515/hsz-2018-0257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/17/2018] [Indexed: 02/05/2023]
Abstract
Dynamins are essential as membrane remodelers in various cellular processes, like receptor-mediated endocytosis, synaptic vesicle recycling and spermatogenesis. Moreover, dynamin is involved in the internalization of numerous viruses and in the motility of several cancer cell lines. As tools for dissecting the underlying mechanisms of these important biological processes and as potential future therapeutics, small molecules have been developed in the last two decades that modulate the functions of dynamin. In this review we give an overview of the compound classes that are currently in use and describe how they affect dynamin function.
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Affiliation(s)
- Susanne Eschenburg
- Medizinische Hochschule Hannover, Institut für Biophysikalische Chemie, Carl-Neuberg-Str. 1, D-30625 Hannover, Germany
| | - Thomas F Reubold
- Medizinische Hochschule Hannover, Institut für Biophysikalische Chemie, Carl-Neuberg-Str. 1, D-30625 Hannover, Germany
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14
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Li D, Bheemanaboina RRY, Battini N, Tangadanchu VKR, Fang XF, Zhou CH. Novel organophosphorus aminopyrimidines as unique structural DNA-targeting membrane active inhibitors towards drug-resistant methicillin-resistant Staphylococcus aureus. MEDCHEMCOMM 2018; 9:1529-1537. [PMID: 30288226 DOI: 10.1039/c8md00301g] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 07/29/2018] [Indexed: 12/18/2022]
Abstract
A series of novel unique structural organophosphorus aminopyrimidines were developed as potential DNA-targeting membrane active inhibitors through an efficient one-pot procedure from aldehydes, phosphonate and aminopyrimidine. The biological assay revealed that some of the prepared compounds displayed antibacterial activities. In particular, imidazole derivative 2c exhibited more potent inhibitory activity against MRSA with an MIC value of 4 μg mL-1 in comparison with the clinical drugs chloromycin and norfloxacin. Experiments revealed that the active molecule 2c had the ability to rapidly kill the tested strains without obviously triggering the development of bacterial resistance, showed low toxicity to L929 cells and could disturb the cell membrane. The molecular docking study discovered that compound 2c could bind with DNA gyrase via hydrogen bonds and other weak interactions. Further exploration disclosed that the active molecule 2c could also effectively intercalate into MRSA DNA and form a steady 2c-DNA supramolecular complex, which might further block DNA replication to exert powerful antibacterial effects.
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Affiliation(s)
- Di Li
- Institute of Bioorganic & Medicinal Chemistry , Key Laboratory of Applied Chemistry of Chongqing Municipality , School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ; ; Tel: +86 23 68254967
| | - Rammohan R Yadav Bheemanaboina
- Institute of Bioorganic & Medicinal Chemistry , Key Laboratory of Applied Chemistry of Chongqing Municipality , School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ; ; Tel: +86 23 68254967
| | - Narsaiah Battini
- Institute of Bioorganic & Medicinal Chemistry , Key Laboratory of Applied Chemistry of Chongqing Municipality , School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ; ; Tel: +86 23 68254967
| | - Vijai Kumar Reddy Tangadanchu
- Institute of Bioorganic & Medicinal Chemistry , Key Laboratory of Applied Chemistry of Chongqing Municipality , School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ; ; Tel: +86 23 68254967
| | - Xian-Fu Fang
- Institute of Bioorganic & Medicinal Chemistry , Key Laboratory of Applied Chemistry of Chongqing Municipality , School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ; ; Tel: +86 23 68254967
| | - Cheng-He Zhou
- Institute of Bioorganic & Medicinal Chemistry , Key Laboratory of Applied Chemistry of Chongqing Municipality , School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ; ; Tel: +86 23 68254967
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15
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Li KJ, Qu RY, Liu YC, Yang JF, Devendar P, Chen Q, Niu CW, Xi Z, Yang GF. Design, Synthesis, and Herbicidal Activity of Pyrimidine-Biphenyl Hybrids as Novel Acetohydroxyacid Synthase Inhibitors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:3773-3782. [PMID: 29618205 DOI: 10.1021/acs.jafc.8b00665] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The issue of weed resistance to acetohydroxyacid synthase (EC 2.2.1.6, AHAS) inhibitors has become one of the largest obstacles for the application of this class of herbicides. In a continuing effort to discover novel AHAS inhibitors to overcome weed resistance, a series of pyrimidine-biphenyl hybrids (4aa-bb and 5aa-ah) were designed and synthesized via a scaffold hopping strategy. Among these derivatives, compounds 4aa ( Ki = 0.09 μM) and 4bb ( Ki = 0.02 μM) displayed higher inhibitory activities against Arabidopsis thaliana AHAS than those of the controls bispyribac ( Ki = 0.54 μM) and flumetsulam ( Ki = 0.38 μM). Remarkably, compounds 4aa, 4bb, 5ah, and 5ag exhibited excellent postemergence herbicidal activity and a broad spectrum of weed control at application rates of 37.5-150 g of active ingredient (ai)/ha. Furthermore, 4aa and 4bb showed higher herbicidal activity against AHAS inhibitor-resistant Descurainia sophia, Ammannia arenaria, and the corresponding sensitive weeds than that of bispyribac at 0.94-0.235 g ai/ha. Therefore, the pyrimidine-biphenyl motif and lead compounds 4aa and 4bb have great potential for the discovery of novel AHAS inhibitors to combat AHAS-inhibiting herbicide-resistant weeds.
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Affiliation(s)
- Ke-Jian Li
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry , Central China Normal University (CCNU) , Wuhan 430079 , P.R. China
| | - Ren-Yu Qu
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry , Central China Normal University (CCNU) , Wuhan 430079 , P.R. China
| | - Yu-Chao Liu
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry , Central China Normal University (CCNU) , Wuhan 430079 , P.R. China
| | - Jing-Fang Yang
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry , Central China Normal University (CCNU) , Wuhan 430079 , P.R. China
| | - Ponnam Devendar
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry , Central China Normal University (CCNU) , Wuhan 430079 , P.R. China
| | - Qiong Chen
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry , Central China Normal University (CCNU) , Wuhan 430079 , P.R. China
| | - Cong-Wei Niu
- State Key Laboratory of Elemento-Organic Chemistry , Nankai University (NKU) , Tianjin 300071 , P.R. China
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry , Nankai University (NKU) , Tianjin 300071 , P.R. China
- Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 30071 , P.R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry , Central China Normal University (CCNU) , Wuhan 430079 , P.R. China
- Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 30071 , P.R. China
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16
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Bezhentsev V, Ivanov S, Kumar S, Goel R, Poroikov V. Identification of potential drug targets for treatment of refractory epilepsy using network pharmacology. J Bioinform Comput Biol 2018; 16:1840002. [PMID: 29361895 DOI: 10.1142/s0219720018400024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Epilepsy is the fourth most common neurological disease after migraine, stroke, and Alzheimer's disease. Approximately one-third of all epilepsy cases are refractory to the existing anticonvulsants. Thus, there is an unmet need for newer antiepileptic drugs (AEDs) to manage refractory epilepsy (RE). Discovery of novel AEDs for the treatment of RE further retards for want of potential pharmacological targets, unavailable due to unclear etiology of this disease. In this regard, network pharmacology as an area of bioinformatics is gaining popularity. It combines the methods of network biology and polypharmacology, which makes it a promising approach for finding new molecular targets. This work is aimed at discovering new pharmacological targets for the treatment of RE using network pharmacology methods. In the framework of our study, the genes associated with the development of RE were selected based on analysis of available data. The methods of network pharmacology were used to select 83 potential pharmacological targets linked to the selected genes. Then, 10 most promising targets were chosen based on analysis of published data. All selected target proteins participate in biological processes, which are considered to play a key role in the development of RE. For 9 of 10 selected targets, the potential associations with different kinds of epilepsy have been recently mentioned in the literature published, which gives additional evidence that the approach applied is rather promising.
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Affiliation(s)
- Vladislav Bezhentsev
- * Department of Bioinformatics, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, Moscow 119121, Russia
| | - Sergey Ivanov
- * Department of Bioinformatics, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, Moscow 119121, Russia
| | - Sandeep Kumar
- † Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala 147002, Punjab, India
| | - Rajesh Goel
- † Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala 147002, Punjab, India
| | - Vladimir Poroikov
- * Department of Bioinformatics, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, Moscow 119121, Russia
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