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Hagemeister M, Hamilton L, Wandrey N, Hill M, Mounce E, Mosel N, Lytle K, Redinger M, Boley J, Fancher N, Haynes A, Fill I, Cole PA, Hill E, Moxley MA, Thomas AA. Evaluation of Rhodanine Indolinones as AANAT Inhibitors. ChemMedChem 2024; 19:e202300567. [PMID: 37984928 PMCID: PMC10843758 DOI: 10.1002/cmdc.202300567] [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: 10/19/2023] [Revised: 11/18/2023] [Accepted: 11/19/2023] [Indexed: 11/22/2023]
Abstract
Circadian rhythm (CR) dysregulation negatively impacts health and contributes to mental disorders. The role of melatonin, a hormone intricately linked to CR, is still a subject of active study. The enzyme arylalkylamine N-acetyltransferase (AANAT) is responsible for melatonin synthesis, and it is a potential target for disorders that involve abnormally high melatonin levels, such as seasonal affective disorder (SAD). Current AANAT inhibitors suffer from poor cell permeability, selectivity, and/or potency. To address the latter, we have employed an X-ray crystal-based model to guide the modification of a previously described AANAT inhibitor, containing a rhodanine-indolinone core. We made various structural modifications to the core structure, including testing the importance of a carboxylic acid group thought to bind in the CoA site, and we evaluated these changes using MD simulations in conjunction with enzymatic assay data. Additionally, we tested three AANAT inhibitors in a zebrafish locomotion model to determine their effects in vivo. Key discoveries were that potency could be modestly improved by replacing a 5-carbon alkyl chain with rings and that the central rhodanine ring could be replaced by other heterocycles and maintain potency.
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Affiliation(s)
- Mackenzie Hagemeister
- Department of Psychology, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Luke Hamilton
- Department of Biology, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Nicole Wandrey
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Mackinzi Hill
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Emery Mounce
- Department of Psychology, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Noah Mosel
- Department of Psychology, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Katie Lytle
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Makenna Redinger
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Jake Boley
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Nathan Fancher
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Alexis Haynes
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Ianna Fill
- Department of Psychology, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Philip A Cole
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Evan Hill
- Department of Psychology, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Michael A Moxley
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Allen A Thomas
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE, 69949, USA
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Lee K, Hwang OJ, Reiter RJ, Back K. Flavonoids inhibit both rice and sheep serotonin N-acetyltransferases and reduce melatonin levels in plants. J Pineal Res 2018; 65:e12512. [PMID: 29851162 DOI: 10.1111/jpi.12512] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 05/25/2018] [Indexed: 12/29/2022]
Abstract
The plant melatonin biosynthetic pathway has been well characterized, but inhibitors of melatonin synthesis have not been well studied. Here, we found that flavonoids potently inhibited plant melatonin synthesis. For example, flavonoids including morin and myricetin significantly inhibited purified, recombinant sheep serotonin N-acetyltransferase (SNAT). Flavonoids also dose-dependently and potently inhibited purified rice SNAT1 and SNAT2. Thus, myricetin (100 μmol/L) reduced rice SNAT1 and SNAT2 activity 7- and 10-fold, respectively, and also strongly inhibited the N-acetylserotonin methyltransferase activity of purified, recombinant rice caffeic acid O-methyltransferase. To explore the in vivo effects, rice leaves were treated with flavonoids and then cadmium. Flavonoid-treated leaves had lower melatonin levels than the untreated control. To explore the direct roles of flavonoids in melatonin biosynthesis, we first functionally characterized a putative rice flavonol synthase (FLS) in vitro and generated flavonoid-rich transgenic rice plants that overexpressed FLS. Such plants produced more flavonoids but less melatonin than the wild-type, which suggests that flavonoids indeed inhibit plant melatonin biosynthesis.
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Affiliation(s)
- Kyungjin Lee
- Department of Biotechnology, Bioenergy Research Center, Chonnam National University, Gwangju, Korea
| | - Ok Jin Hwang
- Department of Biotechnology, Bioenergy Research Center, Chonnam National University, Gwangju, Korea
| | - Russel J Reiter
- Department of Cellular and Structural Biology, The Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Kyoungwhan Back
- Department of Biotechnology, Bioenergy Research Center, Chonnam National University, Gwangju, Korea
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Rai N, Muthukumaran R, Amutha R. Identification of inhibitor against H. pylori HtrA protease using structure-based virtual screening and molecular dynamics simulations approaches. Microb Pathog 2018; 118:365-377. [PMID: 29555508 DOI: 10.1016/j.micpath.2018.03.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/21/2018] [Accepted: 03/15/2018] [Indexed: 12/17/2022]
Abstract
The HtrA protease of Helicobacter pylori, which efficiently colonizes at the gastric epithelial of host cells, disrupts the mucosal integrity of E-cadherin and spreads inflammatory diseases including gastric cancer by cleaving the cell-cell adhesion of the host. The lack of knowledge on the molecular diversity, structural and functional behavior of HpHtrA necessitated the present study to explore its inhibition mechanism. At first, the similarity of HpHtrA with other gastro-intestinal pathogenic HtrA bacteria and its remote relationship with the Human HtrA homologs were ensured by the phylogenetic analysis and hence was identified as a novel therapeutic target for further design of inhibitors. The three dimensional structure of HpHtrA was modeled and simulated to achieve its stable conformation and was used as a receptor to screen for the possible lead compound through virtual screening (using ∼ 1.3 million compounds). Molecular dynamics simulations followed by the binding energy analysis revealed the affinity of the compound 300040 in forming a stable complex with HpHtrA and thereby revealed its potent role in inhibiting HpHtrA. It is also worthy to mention that, structurally, the ligand binding at the catalytic site of HpHtrA is mainly facilitated by the significant dynamics of L2 loop. Based on the present study, the hydroxyl-piperidine with 4-aminopiperidine scaffold is proposed to be one of the best possible lead compounds for the inhibition of H. pylori.
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Affiliation(s)
- Nivedita Rai
- Centre for Bioinformatics, Pondicherry University, Pondicherry, 605014, India
| | - R Muthukumaran
- Centre for Bioinformatics, Pondicherry University, Pondicherry, 605014, India
| | - R Amutha
- Centre for Bioinformatics, Pondicherry University, Pondicherry, 605014, India.
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Kaminskyy D, Kryshchyshyn A, Lesyk R. 5-Ene-4-thiazolidinones - An efficient tool in medicinal chemistry. Eur J Med Chem 2017; 140:542-594. [PMID: 28987611 PMCID: PMC7111298 DOI: 10.1016/j.ejmech.2017.09.031] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 07/14/2017] [Accepted: 09/17/2017] [Indexed: 02/02/2023]
Abstract
The presented review is an attempt to summarize a huge volume of data on 5-ene-4-thiazolidinones being a widely studied class of small molecules used in modern organic and medicinal chemistry. The manuscript covers approaches to the synthesis of 5-ene-4-thiazolidinone derivatives: modification of the C5 position of the basic core; synthesis of the target compounds in the one-pot or multistage reactions or transformation of other related heterocycles. The most prominent pharmacological profiles of 5-ene derivatives of different 4-thiazolidinone subtypes belonging to hit-, lead-compounds, drug-candidates and drugs as well as the most studied targets have been discussed. Currently target compounds (especially 5-en-rhodanines) are assigned as frequent hitters or pan-assay interference compounds (PAINS) within high-throughput screening campaigns. Nevertheless, the crucial impact of the presence/nature of C5 substituent (namely 5-ene) on the pharmacological effects of 5-ene-4-thiazolidinones was confirmed by the numerous listed findings from the original articles. The main directions for active 5-ene-4-thiazolidinones optimization have been shown: i) complication of the fragment in the C5 position; ii) introduction of the substituents in the N3 position (especially fragments with carboxylic group or its derivatives); iii) annealing in complex heterocyclic systems; iv) combination with other pharmacologically attractive fragments within hybrid pharmacophore approach. Moreover, the utilization of 5-ene-4-thiazolidinones in the synthesis of complex compounds with potent pharmacological application is described. The chemical transformations cover mainly the reactions which involve the exocyclic double bond in C5 position of the main core and correspond to the abovementioned direction of the 5-ene-4-thiazolidinone modification.
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Affiliation(s)
- Danylo Kaminskyy
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, Lviv-10, 79010, Ukraine
| | - Anna Kryshchyshyn
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, Lviv-10, 79010, Ukraine
| | - Roman Lesyk
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, Lviv-10, 79010, Ukraine.
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Kaminskyy D, Kryshchyshyn A, Lesyk R. Recent developments with rhodanine as a scaffold for drug discovery. Expert Opin Drug Discov 2017; 12:1233-1252. [PMID: 29019278 DOI: 10.1080/17460441.2017.1388370] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Rhodanines, as one of the 4-thiazolidinones subtypes, are recognized as privileged heterocycles in medicinal chemistry. The main achievements include the development of drug-like molecules with numerous biological activities as well as approved drugs. Among rhodanines, 5-ene-rhodanines are of special interest, and are often claimed as pan assay interference compounds due to Michael acceptor functionality. Areas covered: Herein, the synthetic protocols for rhodanines and their transformation are reviewed. Biological activity is briefly discussed as well as biotargets, mode of actions and optimization directions. Furthermore, the utilization of 5-ene-rhodanines in Michael additions are discussed while both pro and contra arguments have been outlined within medicinal chemistry application. Expert opinion: Rhodanines remain privileged heterocycles in drug discovery. They are accessible building blocks for optimization and transformation into related heterocycles, simplified analogues and fused heterocycles with a thiazolidine framework. Michael acceptor functionality, as well as the thesis about low selectivity towards biotargets of rhodanines, must be confirmed experimentally and it cannot be based on just the presence of conjugated α,β-unsaturated carbonyl. Moreover, the positive aspects of Michael acceptors must be considered as well as their multitarget properties. New criteria for target affinity must be found. In conclusion, rhodanines are generally not problematic per se.
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Affiliation(s)
- Danylo Kaminskyy
- a Department of Pharmaceutical, Organic and Bioorganic Chemistry , Danylo Halytsky Lviv National Medical University , Lviv-10 , Ukraine
| | - Anna Kryshchyshyn
- a Department of Pharmaceutical, Organic and Bioorganic Chemistry , Danylo Halytsky Lviv National Medical University , Lviv-10 , Ukraine
| | - Roman Lesyk
- a Department of Pharmaceutical, Organic and Bioorganic Chemistry , Danylo Halytsky Lviv National Medical University , Lviv-10 , Ukraine
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6
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Andleeb H, Khan I, Bauzá A, Tahir MN, Simpson J, Hameed S, Frontera A. Synthesis and supramolecular self-assembly of thioxothiazolidinone derivatives driven by H-bonding and diverse π–hole interactions: A combined experimental and theoretical analysis. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.03.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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7
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Izmest’ev AN, Gazieva GA, Kulikov AS, Anikina LV, Kolotyrkina NG, Kravchenko AN. Synthesis and biological activity of oxindolylidene derivatives of imidazo[4,5-e]thiazolo[3,2-b]-1,2,4-triazin-7-ones and imidazo[4,5-e]thiazolo[2,3-с]-1,2,4-triazin-8-ones. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1070428017050177] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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A new method for the preparation of 5-acylidene and 5-imino substituted rhodanine derivatives and their antioxidant and antimicrobial activities. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.04.069] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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9
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Burall LS, Simpson AC, Chou L, Laksanalamai P, Datta AR. A novel gene, lstC, of Listeria monocytogenes is implicated in high salt tolerance. Food Microbiol 2015; 48:72-82. [PMID: 25790994 DOI: 10.1016/j.fm.2014.12.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 12/01/2014] [Accepted: 12/16/2014] [Indexed: 01/08/2023]
Abstract
Listeria monocytogenes, causative agent of human listeriosis, has been isolated from a wide variety of foods including deli meats, soft cheeses, cantaloupes, sprouts and canned mushrooms. Standard control measures for restricting microbial growth such as refrigeration and high salt are often inadequate as L. monocytogenes grows quite well in these environments. In an effort to better understand the genetic and physiological basis by which L. monocytogenes circumvents these controls, a transposon library of L. monocytogenes was screened for changes in their ability to grow in 7% NaCl and/ or at 5 °C. This work identified a transposon insertion upstream of an operon, here named lstABC, that led to a reduction in growth in 7% NaCl. In-frame deletion studies identified lstC which codes for a GNAT-acetyltransferase being responsible for the phenotype. Transcriptomic and RT-PCR analyses identified nine genes that were upregulated in the presence of high salt in the ΔlstC mutant. Further analysis of lstC and the genes affected by ΔlstC is needed to understand LstC's role in salt tolerance.
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Affiliation(s)
- Laurel S Burall
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Alexandra C Simpson
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Luoth Chou
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Pongpan Laksanalamai
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Atin R Datta
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA.
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10
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Ramesh V, Ananda Rao B, Sharma P, Swarna B, Thummuri D, Srinivas K, Naidu VGM, Jayathirtha Rao V. Synthesis and biological evaluation of new rhodanine analogues bearing 2-chloroquinoline and benzo[h]quinoline scaffolds as anticancer agents. Eur J Med Chem 2014; 83:569-80. [PMID: 24996143 DOI: 10.1016/j.ejmech.2014.06.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 05/31/2014] [Accepted: 06/08/2014] [Indexed: 10/25/2022]
Abstract
Several rhodanine derivatives (9-39) were synthesized for evaluation of their potential as anticancer agents. Villsmeier cyclization to synthesize aza-aromatic aldehydes, rhodanine derivatives preparation and Knoevenagel type of condensation between the rhodanines and aza-aromatic aldehydes are key steps used for the synthesis of 31 compounds. In vitro antiproliferative activity of the synthesized rhodanine derivatives (9-39) was studied on a panel of six human tumor cell lines viz. HGC, MNK-74, MCF-7, MDAMB-231, DU-145 and PC-3 cell lines. Some of the compounds were capable of inhibiting the proliferation of cancer cell lines at a micromolar concentration. Six compounds are found to be potent against HGC cell lines; compound 15 is found to be active against HGC - Gastric, MCF7 - Breast Cancer and DU145 - Prostate Cancer cell lines; compound 39 is potent against MNK-74; four compounds are found to be potent against MCF-7 cell lines; three compounds are active against MDAMB-231; nine compounds are found to be potent against DU-145; three compounds are active against PC-3 cell lines. These compounds constitute a promising starting point for the development of novel and more potent anticancer agents in future.
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Affiliation(s)
- Vadla Ramesh
- Crop Protection Chemicals Division, CSIR-Indian Institute of Chemical Technology, Uppal Road Tarnaka, Hyderabad 500007, India
| | - Boddu Ananda Rao
- Crop Protection Chemicals Division, CSIR-Indian Institute of Chemical Technology, Uppal Road Tarnaka, Hyderabad 500007, India
| | - Pankaj Sharma
- Crop Protection Chemicals Division, CSIR-Indian Institute of Chemical Technology, Uppal Road Tarnaka, Hyderabad 500007, India; Department of Medicinal Chemistry, National Institute of Pharmaceutical Education & Research, Balanagar, Hyderabad 500037, India
| | - B Swarna
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education & Research, Balanagar, Hyderabad 500037, India
| | - Dinesh Thummuri
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education & Research, Balanagar, Hyderabad 500037, India
| | - Kolupula Srinivas
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education & Research, Balanagar, Hyderabad 500037, India.
| | - V G M Naidu
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education & Research, Balanagar, Hyderabad 500037, India.
| | - Vaidya Jayathirtha Rao
- Crop Protection Chemicals Division, CSIR-Indian Institute of Chemical Technology, Uppal Road Tarnaka, Hyderabad 500007, India; AcSIR-IICT, CSIR-Indian Institute of Chemical Technology, Uppal Road Tarnaka, Hyderabad 500007, India; Department of Medicinal Chemistry, National Institute of Pharmaceutical Education & Research, Balanagar, Hyderabad 500037, India.
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11
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Zhang JL, Zheng QC, Li ZQ, Zhang HX. Theoretical evaluation and improvement on the potency of the rhodanine-based inhibitors for human serotoninN-acetyltransferase. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2013.854894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Shin JC, Jung HY, Harikishore A, Kwon OD, Yoon HS, Kim KT, Choi BH. The flavonoid myricetin reduces nocturnal melatonin levels in the blood through the inhibition of serotonin N-acetyltransferase. Biochem Biophys Res Commun 2013; 440:312-6. [PMID: 24076393 DOI: 10.1016/j.bbrc.2013.09.076] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 09/14/2013] [Indexed: 11/26/2022]
Abstract
Melatonin is secreted during the hours of darkness and is thought to influence the circadian and seasonal timing of a variety of physiological processes. AANAT, which is expressed in the pineal gland, retina, and various other tissues, catalyzes the conversion of serotonin to N-acetylserotonin and is the rate-limiting enzyme in the biosynthetic pathway of melatonin. The compounds that modulate the activity of AANAT can be used to treat patients with circadian rhythm disorders that are associated with specific circadian rhythm alterations, such as shift work disorder. In the present study, we screened modulators of AANAT activity from the water extracts of medicinal plants. Among the 267 tested medicinal plant extracts, Myricae Cortex (Myrica rubra), Perillae Herba (Perilla sikokiana), and Eriobotryae Folium (Eriobotrya japonica) showed potent inhibition of AANAT activity. Myricetin (5,7,3',4',5'-pentahydroxyflavonol), a main component of the Myricae Cortex, strongly inhibited the activity of AANAT and probably block the access to the substrate by docking to the catalytic residues that are important for AANAT activity. Myricetin significantly decreased the nocturnal serum melatonin levels in rats. In addition, the locomotor activity of rats treated with myricetin decreased during the nighttime and slightly increased throughout the day. These results suggest that myricetin could be used as a therapy to increase nighttime alertness by changing the circadian rhythm of serum melatonin and locomotor activity.
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Affiliation(s)
- Jae-Cheon Shin
- Pohang Center for Evaluation of Biomaterials, Pohang Technopark, Jigok-dong, Pohang, Gyeongbuk, South Korea; The College of Veterinary Medicine, Kyungpook National University, Sangyeok-dong, Daegu, South Korea
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Ray S, Mukhopadhyay C. Synthesis of molecular scaffolds assimilating both indolinone and thiazolidinone moieties under environmentally benevolent conditions. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.07.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Room temperature catalyst-free Knoevenagel condensation: facile access to isatinylidenerhodanines. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.01.069] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Finch KE, Knezevic CE, Nottbohm AC, Partlow KC, Hergenrother PJ. Selective small molecule inhibition of poly(ADP-ribose) glycohydrolase (PARG). ACS Chem Biol 2012; 7:563-70. [PMID: 22220926 DOI: 10.1021/cb200506t] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The poly(ADP-ribose) (PAR) post-translational modification is essential for diverse cellular functions, including regulation of transcription, response to DNA damage, and mitosis. Cellular PAR is predominantly synthesized by the enzyme poly(ADP-ribose) polymerase-1 (PARP-1). PARP-1 is a critical node in the DNA damage response pathway, and multiple potent PARP-1 inhibitors have been described, some of which show considerable promise in the clinic for the treatment of certain cancers. Cellular PAR is efficiently degraded by poly(ADP-ribose) glycohydrolase (PARG), an enzyme for which no potent, readily accessible, and specific inhibitors exist. Herein we report the discovery of small molecules that effectively inhibit PARG in vitro and in cellular lysates. These potent PARG inhibitors can be produced in two chemical steps from commercial starting materials and have complete specificity for PARG over the other known PAR glycohydrolase (ADP-ribosylhydrolase 3, ARH3) and over PARP-1 and thus will be useful tools for studying the biochemistry of PAR signaling.
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Affiliation(s)
- Kristin E. Finch
- Department of Chemistry, University of Illinois, 600 S. Mathews, Urbana, Illinois 61801, United
States
| | - Claire E. Knezevic
- Department of Chemistry, University of Illinois, 600 S. Mathews, Urbana, Illinois 61801, United
States
| | - Amanda C. Nottbohm
- Department of Chemistry, University of Illinois, 600 S. Mathews, Urbana, Illinois 61801, United
States
| | - Kathryn C. Partlow
- Department of Chemistry, University of Illinois, 600 S. Mathews, Urbana, Illinois 61801, United
States
| | - Paul J. Hergenrother
- Department of Chemistry, University of Illinois, 600 S. Mathews, Urbana, Illinois 61801, United
States
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16
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Furdas SD, Shekfeh S, Kannan S, Sippl W, Jung M. Rhodaninecarboxylic acids as novel inhibitors of histoneacetyltransferases. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md00211f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Virtual screening has identified rhodanine containing carboxylic acids as new inhibitors of histone acetyltransferases.
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Affiliation(s)
- Silviya D. Furdas
- Institute of Pharmaceutical Sciences
- Albert-Ludwigs-Unversity of Freiburg
- Freiburg
- Germany
| | - Suhaib Shekfeh
- Department of Pharmaceutical Chemistry
- Martin-Luther University of Halle-Wittenberg
- Germany
| | | | - Wolfgang Sippl
- Department of Pharmaceutical Chemistry
- Martin-Luther University of Halle-Wittenberg
- Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences
- Albert-Ludwigs-Unversity of Freiburg
- Freiburg
- Germany
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Pinson JA, Schmidt-Kittler O, Zhu J, Jennings IG, Kinzler KW, Vogelstein B, Chalmers DK, Thompson PE. Thiazolidinedione-based PI3Kα inhibitors: an analysis of biochemical and virtual screening methods. ChemMedChem 2011; 6:514-22. [PMID: 21360822 PMCID: PMC3187668 DOI: 10.1002/cmdc.201000467] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 11/29/2010] [Indexed: 12/27/2022]
Abstract
A series of synthesized and commercially available compounds were assessed against PI3Kα for in vitro inhibitory activity and the results compared to binding calculated in silico. Using published crystal structures of PI3Kγ and PI3Kδ co-crystallized with inhibitors as a template, docking was able to identify the majority of potent inhibitors from a decoy set of 1000 compounds. On the other hand, PI3Kα in the apo-form, modeled by induced fit docking, or built as a homology model gave only poor results. A PI3Kα homology model derived from a ligand-bound PI3Kδ crystal structure was developed that has a good ability to identify active compounds. The docking results identified binding poses for active compounds that differ from those identified to date and can contribute to our understanding of structure-activity relationships for PI3K inhibitors.
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Affiliation(s)
- Jo-Anne Pinson
- Medicinal Chemistry & Drug Action, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria 3052, Australia
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Bowers EM, Yan G, Mukherjee C, Orry A, Wang L, Holbert MA, Crump NT, Hazzalin CA, Liszczak G, Yuan H, Larocca C, Saldanha SA, Abagyan R, Sun Y, Meyers DJ, Marmorstein R, Mahadevan LC, Alani RM, Cole PA. Virtual ligand screening of the p300/CBP histone acetyltransferase: identification of a selective small molecule inhibitor. ACTA ACUST UNITED AC 2010; 17:471-82. [PMID: 20534345 DOI: 10.1016/j.chembiol.2010.03.006] [Citation(s) in RCA: 495] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 02/18/2010] [Accepted: 03/04/2010] [Indexed: 01/18/2023]
Abstract
The histone acetyltransferase (HAT) p300/CBP is a transcriptional coactivator implicated in many gene regulatory pathways and protein acetylation events. Although p300 inhibitors have been reported, a potent, selective, and readily available active-site-directed small molecule inhibitor is not yet known. Here we use a structure-based, in silico screening approach to identify a commercially available pyrazolone-containing small molecule p300 HAT inhibitor, C646. C646 is a competitive p300 inhibitor with a K(i) of 400 nM and is selective versus other acetyltransferases. Studies on site-directed p300 HAT mutants and synthetic modifications of C646 confirm the importance of predicted interactions in conferring potency. Inhibition of histone acetylation and cell growth by C646 in cells validate its utility as a pharmacologic probe and suggest that p300/CBP HAT is a worthy anticancer target.
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Affiliation(s)
- Erin M Bowers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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19
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Lepailleur A, Lemaître S, Feng X, Sopkova-de Oliveira Santos J, Delagrange P, Boutin J, Renard P, Bureau R, Rault S. Receptor- and Ligand-Based Study on Novel 2,2′-Bithienyl Derivatives as Non-Peptidic AANAT Inhibitors. J Chem Inf Model 2010; 50:446-60. [DOI: 10.1021/ci9004805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alban Lepailleur
- Centre d’Etudes et de Recherche sur le Médicament de Normandie, UPRES EA 4258, INC3M FR CNRS 3038, Université de Caen−Basse Normandie, UFR des Sciences Pharmaceutiques, Boulevard Becquerel, 14032 Caen Cedex, France, and Laboratoires Servier, 125, Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Stéphane Lemaître
- Centre d’Etudes et de Recherche sur le Médicament de Normandie, UPRES EA 4258, INC3M FR CNRS 3038, Université de Caen−Basse Normandie, UFR des Sciences Pharmaceutiques, Boulevard Becquerel, 14032 Caen Cedex, France, and Laboratoires Servier, 125, Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Xiao Feng
- Centre d’Etudes et de Recherche sur le Médicament de Normandie, UPRES EA 4258, INC3M FR CNRS 3038, Université de Caen−Basse Normandie, UFR des Sciences Pharmaceutiques, Boulevard Becquerel, 14032 Caen Cedex, France, and Laboratoires Servier, 125, Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Jana Sopkova-de Oliveira Santos
- Centre d’Etudes et de Recherche sur le Médicament de Normandie, UPRES EA 4258, INC3M FR CNRS 3038, Université de Caen−Basse Normandie, UFR des Sciences Pharmaceutiques, Boulevard Becquerel, 14032 Caen Cedex, France, and Laboratoires Servier, 125, Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Philippe Delagrange
- Centre d’Etudes et de Recherche sur le Médicament de Normandie, UPRES EA 4258, INC3M FR CNRS 3038, Université de Caen−Basse Normandie, UFR des Sciences Pharmaceutiques, Boulevard Becquerel, 14032 Caen Cedex, France, and Laboratoires Servier, 125, Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Jean Boutin
- Centre d’Etudes et de Recherche sur le Médicament de Normandie, UPRES EA 4258, INC3M FR CNRS 3038, Université de Caen−Basse Normandie, UFR des Sciences Pharmaceutiques, Boulevard Becquerel, 14032 Caen Cedex, France, and Laboratoires Servier, 125, Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Pierre Renard
- Centre d’Etudes et de Recherche sur le Médicament de Normandie, UPRES EA 4258, INC3M FR CNRS 3038, Université de Caen−Basse Normandie, UFR des Sciences Pharmaceutiques, Boulevard Becquerel, 14032 Caen Cedex, France, and Laboratoires Servier, 125, Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Ronan Bureau
- Centre d’Etudes et de Recherche sur le Médicament de Normandie, UPRES EA 4258, INC3M FR CNRS 3038, Université de Caen−Basse Normandie, UFR des Sciences Pharmaceutiques, Boulevard Becquerel, 14032 Caen Cedex, France, and Laboratoires Servier, 125, Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Sylvain Rault
- Centre d’Etudes et de Recherche sur le Médicament de Normandie, UPRES EA 4258, INC3M FR CNRS 3038, Université de Caen−Basse Normandie, UFR des Sciences Pharmaceutiques, Boulevard Becquerel, 14032 Caen Cedex, France, and Laboratoires Servier, 125, Chemin de Ronde, 78290 Croissy-sur-Seine, France
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Vovk MV, Pinchuk OM, Tolmachov AO, Gakh AA. Synthesis of 1-(4-trifluoromethoxyphenyl)-2,5-dimethyl-3-(2-R-thiazol-4-yl)-1H-pyrroles via chain heterocyclization. Molecules 2010; 15:997-1006. [PMID: 20335958 PMCID: PMC6263183 DOI: 10.3390/molecules15020997] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2009] [Revised: 02/22/2010] [Accepted: 02/22/2010] [Indexed: 11/17/2022] Open
Abstract
The title compounds, (4-trifluoromethoxyphenyl)-2,5-dimethyl-3-(2-R-thiazol-4-yl)-1H-pyrroles, were prepared in four steps starting from commercially available 4-trifluoromethoxyaniline. The pyrrole (second ring) was added in one step using the Paal-Knorr method. The thiazole (third ring) was added in three steps using chloroacylation with chloroacetonitrile followed by heterocyclization with thioamides/thioureas.
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Affiliation(s)
- Mykhaylo V. Vovk
- Institute of Organic Chemistry, NAS of Ukraine, Murmanska 5, 02094 Kyiv, Ukraine
- Authors to whom correspondence should be addressed; E-Mails: (M.V.V.); (A.A.G.)
| | - Oleksandr M. Pinchuk
- Institute of Organic Chemistry, NAS of Ukraine, Murmanska 5, 02094 Kyiv, Ukraine
| | | | - Andrei A. Gakh
- Oak Ridge National Laboratory, Oak Ridge, TN 37831-6242, USA
- Authors to whom correspondence should be addressed; E-Mails: (M.V.V.); (A.A.G.)
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Wu YW, Goody RS, Abagyan R, Alexandrov K. Structure of the disordered C terminus of Rab7 GTPase induced by binding to the Rab geranylgeranyl transferase catalytic complex reveals the mechanism of Rab prenylation. J Biol Chem 2009; 284:13185-92. [PMID: 19240028 DOI: 10.1074/jbc.m900579200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Protein prenylation is a widespread process that involves the transfer of either a farnesyl or a geranylgeranyl moiety to one or more C-terminal cysteines of the target protein. Rab geranylgeranyl transferase (RabGGTase) is responsible for the largest number of individual protein prenylation events in the cell. A decade-long effort to crystallize the catalytic ternary complex of RabGGTase has remained fruitless, prompting us to use a computational approach to predict the structure of this 200-kDa assembly. On the basis of high resolution structures of two sub-complexes, we have generated a composite model where the rigid parts of the protein are represented by precomputed grid potentials, whereas the mobile parts are described in atomic details using Internal Coordinate Mechanics. Selection of the best docking solution of the flexible parts on the grid is followed by explicit atomistic refinement of the lowest energy conformations enabling realistic modeling of complex structures. Using this approach we demonstrate that the flexible C terminus of Rab7 substrate forms a series of progressively weaker and less specific interactions that channel it into the active site of RabGGTase. We have validated the computational model through biochemical experiments and demonstrated that to be prenylated RabGTPase must possess at least nine amino acids between the prenylation motif and the hydrophobic sequence anchoring the beginning of the Rab C terminus on the enzyme. This sequence, known as the C-terminal interacting motif is shown to play a dual role in Rab prenylation by contributing a significant fraction of binding energy to the catalytic complex assembly and by orienting the C terminus of RabGTPase in the vicinity of the active site of RabGGTase. This mechanism is unique to RabGGTase when compared with other prenyltransferases, which encode the specificity for their cognate substrates directly at their active site.
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Affiliation(s)
- Yao-Wen Wu
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
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Lead Discovery Using Virtual Screening. TOPICS IN MEDICINAL CHEMISTRY 2009. [PMCID: PMC7176223 DOI: 10.1007/7355_2009_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The practice of virtual screening (VS) to identify chemical leads to known or novel targets is becoming a core function of the computational chemist within industry. By employing a range of techniques, when attempting to identify compounds with activity against a biological target, a small focused subset of a larger collection of compounds can be identified and tested, often with results much better than selecting a similar number of compounds at random. We will review the key methods available, their relative success, and provide practical insights into best practices and key gaps. We will also argue that the capability of VS methods has grown to a point where fuller integration with experimental methods, including HTS, could increase the effectiveness of both.
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