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Mercurio I, D’Abrosca G, della Valle M, Malgieri G, Fattorusso R, Isernia C, Russo L, Di Gaetano S, Pedone EM, Pirone L, Del Gatto A, Zaccaro L, Alberga D, Saviano M, Mangiatordi GF. Molecular interactions between a diphenyl scaffold and PED/PEA15: Implications for type II diabetes therapeutics targeting PED/PEA15 - Phospholipase D1 interaction. Comput Struct Biotechnol J 2024; 23:2001-2010. [PMID: 38770160 PMCID: PMC11103223 DOI: 10.1016/j.csbj.2024.04.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 05/22/2024] Open
Abstract
In a recent study, we have identified BPH03 as a promising scaffold for the development of compounds aimed at modulating the interaction between PED/PEA15 (Phosphoprotein Enriched in Diabetes/Phosphoprotein Enriched in Astrocytes 15) and PLD1 (phospholipase D1), with potential applications in type II diabetes therapy. PED/PEA15 is known to be overexpressed in certain forms of diabetes, where it binds to PLD1, thereby reducing insulin-stimulated glucose transport. The inhibition of this interaction reestablishes basal glucose transport, indicating PED as a potential target of ligands capable to recover glucose tolerance and insulin sensitivity. In this study, we employ computational methods to provide a detailed description of BPH03 interaction with PED, evidencing the presence of a hidden druggable pocket within its PLD1 binding surface. We also elucidate the conformational changes that occur during PED interaction with BPH03. Moreover, we report new NMR data supporting the in-silico findings and indicating that BPH03 disrupts the PED/PLD1 interface displacing PLD1 from its interaction with PED. Our study represents a significant advancement toward the development of potential therapeutics for the treatment of type II diabetes.
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Affiliation(s)
- Ivan Mercurio
- Institute of Crystallography, CNR, Via Amendola 122/o, 70126 Bari, Italy
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Gianluca D’Abrosca
- Department of Clinical and Experimental Medicine, University of Foggia, Viale Pinto 1, 71122 Foggia, Italy
- Institute of Crystallography, CNR, Via Vivaldi 43, 81100, Caserta, Italy
| | - Maria della Valle
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Sonia Di Gaetano
- Institute of Biostructures and Bioimaging, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | - Emilia Maria Pedone
- Institute of Biostructures and Bioimaging, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | - Annarita Del Gatto
- Institute of Biostructures and Bioimaging, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | - Laura Zaccaro
- Institute of Biostructures and Bioimaging, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | - Domenico Alberga
- Institute of Crystallography, CNR, Via Amendola 122/o, 70126 Bari, Italy
| | - Michele Saviano
- Institute of Crystallography, CNR, Via Vivaldi 43, 81100, Caserta, Italy
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2
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Abdoli M, Bonardi A, Gratteri P, Supuran CT, Žalubovskis R. Synthesis, carbonic anhydrase inhibition studies and modelling investigations of phthalimide-hydantoin hybrids. J Enzyme Inhib Med Chem 2024; 39:2335927. [PMID: 38606915 PMCID: PMC11018007 DOI: 10.1080/14756366.2024.2335927] [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: 01/05/2024] [Accepted: 03/23/2024] [Indexed: 04/13/2024] Open
Abstract
A novel series of hydantoins incorporating phthalimides has been synthesised by condensation of activated phthalimides with 1-aminohydantoin and investigated for their inhibitory activity against a panel of human (h) carbonic anhydrase (CA, EC 4.2.1.1): the cytosolic isoforms hCA I, hCA II, and hCA VII, secreted isoform hCA VI, and the transmembrane hCA IX, by a stopped-flow CO2 hydrase assay. Although all newly developed compounds were totally inactive on hCA I and mainly ineffective towards hCA II, they generally exhibited moderate repressing effects on hCA VI, VII, and IX with KIs values in the submicromolar to micromolar ranges. The salts 3a and 3b, followed by derivative 5, displayed the best inhibitory activity of all the evaluated compounds and their binding mode was proposed in silico. These compounds can also be considered interesting starting points for the development of novel pharmacophores for this class of enzyme inhibitors.
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Affiliation(s)
- Morteza Abdoli
- Institute of Chemistry and Chemical Technology, Faculty of Natural Sciences and Technology, Riga Technical University, Riga, Latvia
| | - Alessandro Bonardi
- Department NEUROFARBA – Section of Pharmaceutical and Nutraceutical Sciences, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino (Florence), Italy
- Department of NEUROFARBA – Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Sesto Fiorentino (Florence), Italy
| | - Paola Gratteri
- Department NEUROFARBA – Section of Pharmaceutical and Nutraceutical Sciences, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino (Florence), Italy
| | - Claudiu T. Supuran
- Department of NEUROFARBA – Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Sesto Fiorentino (Florence), Italy
| | - Raivis Žalubovskis
- Institute of Chemistry and Chemical Technology, Faculty of Natural Sciences and Technology, Riga Technical University, Riga, Latvia
- Latvian Institute of Organic Synthesis, Riga, Latvia
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3
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Liu W, Hu X, Yan Y, Cai Y. Rational engineering of homospermidine synthase for enhanced catalytic efficiency toward spermidine synthesis. Synth Syst Biotechnol 2024; 9:549-557. [PMID: 38699566 PMCID: PMC11063116 DOI: 10.1016/j.synbio.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 05/05/2024] Open
Abstract
Spermidine is a naturally occurring polyamine widely utilized in the prevention and treatment of various diseases. Current spermidine biosynthetic methods have problems such as low efficiency and complex multi-enzyme catalysis. Based on sequence-structure-function relationships, we engineered the widely studied homospermidine synthase from Blastochloris viridis (BvHSS) and obtained mutants that could catalyze the production of spermidine from 1,3-diaminopropane and putrescine. The specific activities of BvHSS and the mutants D361E and E232D + D361E (E232D-D) were 8.72, 46.04 and 48.30 U/mg, respectively. The optimal pH for both mutants was 9.0, and the optimal temperature was 50 °C. Molecular docking and dynamics simulations revealed that mutating aspartic acid at position 361 to glutamic acid narrowed the substrate binding pocket, promoting stable spermidine production. Conversely, mutating glutamic acid at position 232 to aspartic acid enlarged the substrate channel entrance, facilitating substrate entry into the active pocket and enhancing spermidine generation. In whole-cell catalysis lasting 6 h, D361E and E232D-D synthesized 725.3 and 933.5 mg/L of spermidine, respectively. This study offers a practical approach for single-enzyme catalyzed spermidine synthesis and sheds light on the crucial residues influencing homospermidine synthase catalytic activity in spermidine production.
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Affiliation(s)
- Wenjing Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Xiaoxiang Hu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Yi Yan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
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4
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Di Petrillo A, Siguri C, Delogu GL, Fais A, Era B, Floris S, Pintus F, Kumar A, Fantini MC, Olla S. Exploring Asphodelus microcarpus as a source of xanthine oxidase inhibitors: Insights from in silico and in vitro studies. Chem Biol Interact 2024; 397:111087. [PMID: 38823536 DOI: 10.1016/j.cbi.2024.111087] [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: 03/05/2024] [Revised: 05/19/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024]
Abstract
Xanthine oxidase (XO) plays a critical role in purine catabolism, catalyzing the conversion of hypoxanthine to xanthine and xanthine to uric acid, contributing to superoxide anion production. This process is implicated in various human diseases, particularly gout. Traditional XO inhibitors, such as allopurinol and febuxostat, while effective, may present side effects. Our study focuses on Asphodelus microcarpus, a plant renowned for traditional anti-inflammatory uses. Recent investigations into its phenolic-rich flowers, notably abundant in luteolin derivatives, reveal its potential as a natural source of XO inhibitors. In the present research, XO inhibition by an ethanolic flowers extract from A. microcarpus is reported. In silico docking studies have highlighted luteolin derivatives as potential XO inhibitors, and molecular dynamics support that luteolin 7-O-glucoside has the highest binding stability compared to other compounds and controls. In vitro studies confirm that luteolin 7-O-glucoside inhibits XO more effectively than the standard inhibitor allopurinol, with an IC50 value of 4.8 μg/mL compared to 11.5 μg/mL, respectively. These findings underscore the potential therapeutic significance of A. microcarpus in managing conditions related to XO activity. The research contributes valuable insights into the health-promoting properties of A. microcarpus and its potential application in natural medicine, presenting a promising avenue for further exploration in disease management.
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Affiliation(s)
- Amalia Di Petrillo
- Department of Medical Sciences and Public Health, University of Cagliari, 09042, Monserrato, Italy.
| | - Chiara Siguri
- Institute for Genetic and Biomedical Research (IRGB), The National Research Council (CNR), 09042, Monserrato, Italy
| | - Giovanna L Delogu
- Department of Life and Environmental Sciences, University of Cagliari, 09042, Monserrato, Italy
| | - Antonella Fais
- Department of Life and Environmental Sciences, University of Cagliari, 09042, Monserrato, Italy
| | - Benedetta Era
- Department of Life and Environmental Sciences, University of Cagliari, 09042, Monserrato, Italy
| | - Sonia Floris
- Department of Life and Environmental Sciences, University of Cagliari, 09042, Monserrato, Italy
| | - Francesca Pintus
- Department of Life and Environmental Sciences, University of Cagliari, 09042, Monserrato, Italy
| | - Amit Kumar
- Department of Electrical and Electronic Engineering, University of Cagliari, Via Marengo 2, 09123, Cagliari, Italy
| | - Massimo Claudio Fantini
- Department of Medical Sciences and Public Health, University of Cagliari, 09042, Monserrato, Italy
| | - Stefania Olla
- Institute for Genetic and Biomedical Research (IRGB), The National Research Council (CNR), 09042, Monserrato, Italy
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5
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Asmare MM, Krishnaraj C, Radhakrishnan S, Kim BS, Yoon JS, Yun SI. In silico modelling of ciprofloxacin specific aptamer for the development of high-performance biosensor. J Mol Graph Model 2024; 130:108787. [PMID: 38749234 DOI: 10.1016/j.jmgm.2024.108787] [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: 02/08/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/31/2024]
Abstract
Ciprofloxacin (CFX), a widely used fluoroquinolone antibiotic, is critical in healthcare settings for treating patients. However, improper treatment of wastewater from these facilities can lead to environmental contamination with CFX. This underscores the need for an efficient, straightforward method for early detection. In this study, a DNA aptamer was selected through a hierarchical docking workflow, and the stability and interactions were assessed by Molecular Dynamics (MD) simulation. The aptamer-CFX complex that showed the most promise had a docking score of -8.596 kcal/mol and was further analyzed using MD simulation and MM/PBSA. Based on the overall results, the identified ssDNA sequence length of 60 nt (CAGCGCTAGGGCTTTTAGCGTAATGGGTAGGGTGGTGCGGTGCAGATATCGGAATTGGTG) was immobilized over a gold transducer surface through the self-assembled monolayer (SAM; Au-S-ssDNA) method. The ssDNA-modified surface has demonstrated a high affinity towards CFX, which is confirmed by cyclic voltammogram (CV) and electrochemical impedance spectroscopy measurements (EIS). The DNA-aptamer modified electrode demonstrated a good linear range (10 × 10-9 - 200 × 10-9 M), detection limit (1.0 × 10-9 M), selectivity, reproducibility, and stability. The optimized DNA-aptamer-based CFX sensor was further utilized for the accurate determination of CFX with good recoveries in real samples.
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Affiliation(s)
- Misgana Mengistu Asmare
- Department of Agricultural Convergence Technology, College of Agriculture and Life Science, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, 54896, Republic of Korea
| | - Chandran Krishnaraj
- Department of Agricultural Convergence Technology, College of Agriculture and Life Science, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, 54896, Republic of Korea; Department of Food Science and Technology, College of Agriculture and Life Sciences, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, 54896, Republic of Korea
| | - Sivaprakasam Radhakrishnan
- Department of Organic Materials & Fiber Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, 54896, Republic of Korea
| | - Byoung-Sukh Kim
- Department of Organic Materials & Fiber Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, 54896, Republic of Korea
| | - June-Sun Yoon
- Department of Agricultural Convergence Technology, College of Agriculture and Life Science, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, 54896, Republic of Korea.
| | - Soon-Il Yun
- Department of Agricultural Convergence Technology, College of Agriculture and Life Science, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, 54896, Republic of Korea; Department of Food Science and Technology, College of Agriculture and Life Sciences, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, 54896, Republic of Korea.
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6
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Bonardi A, Nocentini A, Giovannuzzi S, Paoletti N, Ammara A, Bua S, Abutaleb NS, Abdelsattar AS, Capasso C, Gratteri P, Flaherty DP, Seleem MN, Supuran CT. Development of Penicillin-Based Carbonic Anhydrase Inhibitors Targeting Multidrug-Resistant Neisseria gonorrhoeae. J Med Chem 2024; 67:9613-9627. [PMID: 38776401 DOI: 10.1021/acs.jmedchem.4c00740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
The development of antibacterial drugs with new mechanisms of action is crucial in combating the rise of antibiotic-resistant infections. Bacterial carbonic anhydrases (CAs, EC 4.2.1.1) have been validated as promising antibacterial targets against pathogens such as Helicobacter pylori, Neisseria gonorrhoeae, and vancomycin-resistant enterococci. A multitarget strategy is proposed to design penicillin-based CA inhibitor hybrids for tackling resistance by targeting multiple bacterial pathways, thereby resensitizing drug-resistant strains to clinical antibiotics. The sulfonamide derivatives potently inhibited the CAs from N. gonorrhoeae and Escherichia coli with KI values in the range of 7.1-617.2 nM. Computational simulations with the main penicillin-binding protein (PBP) of N. gonorrhoeae indicated that these hybrid derivatives maintained the mechanism of action of the lead β-lactams. A subset of derivatives showed potent PBP-related antigonococcal effects against multidrug-resistant N. gonorrhoeae strains, with several compounds significantly outperforming both the lead β-lactam and CA inhibitor drugs (MIC values in the range 0.25 to 0.5 μg/mL).
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Affiliation(s)
- Alessandro Bonardi
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
| | - Alessio Nocentini
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
| | - Simone Giovannuzzi
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
| | - Niccolò Paoletti
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
| | - Andrea Ammara
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
| | - Silvia Bua
- Research Institute of the University of Bucharest (ICUB), Bucharest 050663, Romania
| | - Nader S Abutaleb
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Abdallah S Abdelsattar
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | | | - Paola Gratteri
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
| | - Daniel P Flaherty
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Mohamed N Seleem
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
- Center for One Health Research, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Claudiu T Supuran
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
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7
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Shen Z, Xu L, Wu T, Wang H, Wang Q, Ge X, Kong F, Huang G, Pan X. Structural basis for urate recognition and apigenin inhibition of human GLUT9. Nat Commun 2024; 15:5039. [PMID: 38866775 DOI: 10.1038/s41467-024-49420-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024] Open
Abstract
Urate, the physiological form of uric acid and a potent antioxidant in serum, plays a pivotal role in scavenging reactive oxygen species. Yet excessive accumulation of urate, known as hyperuricemia, is the primary risk factor for the development of gout. The high-capacity urate transporter GLUT9 represents a promising target for gout treatment. Here, we present cryo-electron microscopy structures of human GLUT9 in complex with urate or its inhibitor apigenin at overall resolutions of 3.5 Å and 3.3 Å, respectively. In both structures, GLUT9 exhibits an inward open conformation, wherein the substrate binding pocket faces the intracellular side. These structures unveil the molecular basis for GLUT9's substrate preference of urate over glucose, and show that apigenin acts as a competitive inhibitor by occupying the substrate binding site. Our findings provide critical information for the development of specific inhibitors targeting GLUT9 as potential therapeutics for gout and hyperuricemia.
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Affiliation(s)
- Zilin Shen
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Li Xu
- Institute of Bio-Architecture and Bio-Interactions (IBABI), Shenzhen Medical Academy of Research and Translation (SMART), Shenzhen, 518107, Guangdong, China
| | - Tong Wu
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Huan Wang
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Qifan Wang
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Xiaofei Ge
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Fang Kong
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Gaoxingyu Huang
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, 310024, Zhejiang, China
| | - Xiaojing Pan
- Institute of Bio-Architecture and Bio-Interactions (IBABI), Shenzhen Medical Academy of Research and Translation (SMART), Shenzhen, 518107, Guangdong, China.
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8
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Schäfer JL, Keller BG. Implementation of Girsanov Reweighting in OpenMM and Deeptime. J Phys Chem B 2024. [PMID: 38865491 DOI: 10.1021/acs.jpcb.4c01702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Classical molecular dynamics (MD) simulations provide invaluable insights into complex molecular systems but face limitations in capturing phenomena occurring on time scales beyond their reach. To bridge this gap, various enhanced sampling techniques have been developed, which are complemented by reweighting techniques to recover the unbiased dynamics. Girsanov reweighting is a reweighting technique that reweights simulation paths, generated by a stochastic MD integrator, without evoking an effective model of the dynamics. Instead, it calculates the relative path probability density at the time resolution of the MD integrator. Efficient implementation of Girsanov reweighting requires that the reweighting factors are calculated on-the-fly during the simulations and thus needs to be implemented within the MD integrator. Here, we present a comprehensive guide for implementing Girsanov reweighting into MD simulations. We demonstrate the implementation in the MD simulation package OpenMM by extending the library openmmtools. Additionally, we implemented a reweighted Markov state model estimator within the time series analysis package Deeptime.
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Affiliation(s)
- Joana-Lysiane Schäfer
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin 14195, Germany
| | - Bettina G Keller
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin 14195, Germany
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9
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Laghezza A, Cerchia C, Genovese M, Montanari R, Capelli D, Wackerlig J, Simic S, Falbo E, Pecora L, Leuci R, Brunetti L, Piemontese L, Tortorella P, Biswas A, Singh RP, Tambe S, Sudeep CA, Pattnaik AK, Jayaprakash V, Paoli P, Lavecchia A, Loiodice F. A chemical modification of a peroxisome proliferator-activated receptor pan agonist produced a shift to a new dual alpha/gamma partial agonist endowed with mitochondrial pyruvate carrier inhibition and antidiabetic properties. Eur J Med Chem 2024; 275:116567. [PMID: 38865743 DOI: 10.1016/j.ejmech.2024.116567] [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: 04/12/2024] [Revised: 05/23/2024] [Accepted: 06/01/2024] [Indexed: 06/14/2024]
Abstract
New analogs of the PPAR pan agonist AL29-26 encompassed ligand (S)-7 showing potent activation of PPARα and -γ subtypes as a partial agonist. In vitro experiments and docking studies in the presence of PPAR antagonists were performed to help interpretation of biological data and investigate the main interactions at the binding sites. Further in vitro experiments showed that (S)-7 induced anti-steatotic effects and enhancement of the glucose uptake. This latter effect could be partially ascribed to a significant inhibition of the mitochondrial pyruvate carrier demonstrating that (S)-7 also acted through insulin-independent mechanisms. In vivo experiments showed that this compound reduced blood glucose and lipid levels in a diabetic mice model displaying no toxicity on bone, kidney, and liver. To our knowledge, this is the first example of dual PPARα/γ partial agonist showing these combined effects representing, therefore, the potential lead of new drugs for treatment of dyslipidemic type 2 diabetes.
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Affiliation(s)
- Antonio Laghezza
- Dipartimento Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", via Orabona 4, 70125, Bari, Italy
| | - Carmen Cerchia
- Dipartimento di Farmacia, "Drug Discovery" Laboratory, Università degli Studi di Napoli "Federico II", via D. Montesano 49, 80131, Napoli, Italy
| | - Massimo Genovese
- Dipartimento di Scienze Biomediche Sperimentali e Cliniche, Sezione di Scienze Biochimiche, Università degli Studi di Firenze, Viale Morgagni 50, 50134, Firenze, Italy
| | - Roberta Montanari
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Montelibretti, 00015 Monterotondo Stazione, Roma, Italy
| | - Davide Capelli
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Montelibretti, 00015 Monterotondo Stazione, Roma, Italy
| | - Judith Wackerlig
- Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, 1090, Vienna, Austria
| | - Stefan Simic
- Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, 1090, Vienna, Austria
| | - Emanuele Falbo
- Dipartimento di Farmacia, "Drug Discovery" Laboratory, Università degli Studi di Napoli "Federico II", via D. Montesano 49, 80131, Napoli, Italy
| | - Lucia Pecora
- Dipartimento di Scienze Biomediche Sperimentali e Cliniche, Sezione di Scienze Biochimiche, Università degli Studi di Firenze, Viale Morgagni 50, 50134, Firenze, Italy
| | - Rosalba Leuci
- Dipartimento Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", via Orabona 4, 70125, Bari, Italy
| | - Leonardo Brunetti
- Dipartimento Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", via Orabona 4, 70125, Bari, Italy
| | - Luca Piemontese
- Dipartimento Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", via Orabona 4, 70125, Bari, Italy
| | - Paolo Tortorella
- Dipartimento Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", via Orabona 4, 70125, Bari, Italy
| | - Abanish Biswas
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Ravi Pratap Singh
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Suhas Tambe
- Adgyl Lifescience Private Ltd., Bengaluru, 560058, India
| | - C A Sudeep
- Bioanalytical Section, Eurofins Advinus Biopharma Services India Pvt Ltd., Bengaluru, 560058, India
| | - Ashok Kumar Pattnaik
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Venkatesan Jayaprakash
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Paolo Paoli
- Dipartimento di Scienze Biomediche Sperimentali e Cliniche, Sezione di Scienze Biochimiche, Università degli Studi di Firenze, Viale Morgagni 50, 50134, Firenze, Italy
| | - Antonio Lavecchia
- Dipartimento di Farmacia, "Drug Discovery" Laboratory, Università degli Studi di Napoli "Federico II", via D. Montesano 49, 80131, Napoli, Italy.
| | - Fulvio Loiodice
- Dipartimento Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", via Orabona 4, 70125, Bari, Italy.
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10
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Sparkes E, Maloney CJ, Markham JW, Dane C, Boyd R, Gilchrist J, Moir M, Gordon R, Luo JL, Pike E, Walker KA, Kassiou M, McGregor IS, Kevin RC, Hibbs DE, Jorgensen WT, Banister SD, Cairns EA, Ametovski A. Structure-Activity Relationships, Deuteration, and Fluorination of Synthetic Cannabinoid Receptor Agonists Related to AKB48, 5F-AKB-48, and AFUBIATA. ACS Chem Neurosci 2024; 15:2160-2181. [PMID: 38766866 DOI: 10.1021/acschemneuro.3c00850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
Synthetic cannabinoid receptor agonists (SCRAs) are a growing class of new psychoactive substances (NPS) commonly derived from an N-alkylated indole, indazole, or 7-azaindole scaffold. Diversification of this core (at the 3-position) with amide-linked pendant amino acid groups and modular N-alkylation (of the indole/indazole/7-azaindole core) ensures that novel SCRAs continue to enter the illicit drug market rapidly. In response to the large number of SCRAs that have been detected, pharmacological evaluation of this NPS class has become increasingly common. Adamantane-derived SCRAs have consistently appeared throughout the market since 2011, and as such, a systematic set of these derivatives was synthesized and pharmacologically evaluated. Deuterated and fluorinated adamantane derivatives were prepared to evaluate typical hydrogen bioisosteres, as well as evaluation of the newly detected AFUBIATA.
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Affiliation(s)
- Eric Sparkes
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Chemistry, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Callan J Maloney
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Chemistry, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jack W Markham
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Chemistry, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Chianna Dane
- School of Chemistry, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Rochelle Boyd
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jayson Gilchrist
- School of Chemistry, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Michael Moir
- National Deuteration Facility, Australian Nuclear Science and Technology Organisation, Sydney, NSW 2234, Australia
| | - Rebecca Gordon
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jia Lin Luo
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Psychology, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward Pike
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Chemistry, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Chemistry, University of York, York YO10 5DD, U.K
| | - Katelyn A Walker
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Psychology, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Michael Kassiou
- School of Chemistry, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Iain S McGregor
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Psychology, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Richard C Kevin
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- Department of Clinical Pharmacology and Toxicology, St Vincent's Hospital Sydney, Sydney, NSW 2010, Australia
- School of Clinical Medicine, The University of New South Wales, Sydney, NSW 2052, Australia
| | - David E Hibbs
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - William T Jorgensen
- School of Chemistry, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Samuel D Banister
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Chemistry, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Elizabeth A Cairns
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Adam Ametovski
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Chemistry, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
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11
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Ben Mariem O, Palazzolo L, Torre B, Wei Y, Bianchi D, Guerrini U, Laurenzi T, Saporiti S, De Fabiani E, Pochini L, Indiveri C, Eberini I. Atomistic description of the OCTN1 recognition mechanism via in silico methods. PLoS One 2024; 19:e0304512. [PMID: 38829838 PMCID: PMC11146731 DOI: 10.1371/journal.pone.0304512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 05/14/2024] [Indexed: 06/05/2024] Open
Abstract
The Organic Cation Transporter Novel 1 (OCTN1), also known as SLC22A4, is widely expressed in various human tissues, and involved in numerous physiological and pathological processes remains. It facilitates the transport of organic cations, zwitterions, with selectivity for positively charged solutes. Ergothioneine, an antioxidant compound, and acetylcholine (Ach) are among its substrates. Given the lack of experimentally solved structures of this protein, this study aimed at generating a reliable 3D model of OCTN1 to shed light on its substrate-binding preferences and the role of sodium in substrate recognition and transport. A chimeric model was built by grafting the large extracellular loop 1 (EL1) from an AlphaFold-generated model onto a homology model. Molecular dynamics simulations revealed domain-specific mobility, with EL1 exhibiting the highest impact on overall stability. Molecular docking simulations identified cytarabine and verapamil as highest affinity ligands, consistent with their known inhibitory effects on OCTN1. Furthermore, MM/GBSA analysis allowed the categorization of substrates into weak, good, and strong binders, with molecular weight strongly correlating with binding affinity to the recognition site. Key recognition residues, including Tyr211, Glu381, and Arg469, were identified through interaction analysis. Ach demonstrated a low interaction energy, supporting the hypothesis of its one-directional transport towards to outside of the membrane. Regarding the role of sodium, our model suggested the involvement of Glu381 in sodium binding. Molecular dynamics simulations of systems at increasing levels of Na+ concentrations revealed increased sodium occupancy around Glu381, supporting experimental data associating Na+ concentration to molecule transport. In conclusion, this study provides valuable insights into the 3D structure of OCTN1, its substrate-binding preferences, and the role of sodium in the recognition. These findings contribute to the understanding of OCTN1 involvement in various physiological and pathological processes and may have implications for drug development and disease management.
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Affiliation(s)
- Omar Ben Mariem
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Luca Palazzolo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Beatrice Torre
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Yao Wei
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Davide Bianchi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Uliano Guerrini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Tommaso Laurenzi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Simona Saporiti
- Analytical Excellence and Program Management, Merck Serono S.p.A., Rome, Italy
| | - Emma De Fabiani
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Lorena Pochini
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata CS, Italy
| | - Cesare Indiveri
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata CS, Italy
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy
| | - Ivano Eberini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
- DSRC, Università degli Studi di Milano, Milan, Italy
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12
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Mishra S, Rout M, Singh MK, Dehury B, Pati S. Classical molecular dynamics simulation identifies catechingallate as a promising antiviral polyphenol against MPOX palmitoylated surface protein. Comput Biol Chem 2024; 110:108070. [PMID: 38678726 DOI: 10.1016/j.compbiolchem.2024.108070] [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: 01/24/2024] [Revised: 04/04/2024] [Accepted: 04/06/2024] [Indexed: 05/01/2024]
Abstract
Cumulative global prevalence of the emergent monkeypox (MPX) infection in the non-endemic countries has been professed as a global public health predicament. Lack of effective MPX-specific treatments sets the baseline for designing the current study. This research work uncovers the effective use of known antiviral polyphenols against MPX viral infection, and recognises their mode of interaction with the target F13 protein, that plays crucial role in formation of enveloped virions. Herein, we have employed state-of-the-art machine learning based AlphaFold2 to predict the three-dimensional structure of F13 followed by molecular docking and all-atoms molecular dynamics (MD) simulations to investigate the differential mode of F13-polyphenol interactions. Our extensive computational approach identifies six potent polyphenols Rutin, Epicatechingallate, Catechingallate, Quercitrin, Isoquecitrin and Hyperoside exhibiting higher binding affinity towards F13, buried inside a positively charged binding groove. Intermolecular contact analysis of the docked and MD simulated complexes divulges three important residues Asp134, Ser137 and Ser321 that are observed to be involved in ligand binding through hydrogen bonds. Our findings suggest that ligand binding induces minor conformational changes in F13 to affect the conformation of the binding site. Concomitantly, essential dynamics of the six-MD simulated complexes reveals Catechin gallate, a known antiviral agent as a promising polyphenol targeting F13 protein, dominated with a dense network of hydrophobic contacts. However, assessment of biological activities of these polyphenols need to be confirmed through in vitro and in vivo assays, which may pave the way for development of new novel antiviral drugs.
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Affiliation(s)
- Sarbani Mishra
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, Odisha 751023, India
| | - Madhusmita Rout
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, Odisha 751023, India
| | - Mahender Kumar Singh
- Data Science Laboratory, National Brain Research Centre, Gurgaon, Haryana 122052, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, Odisha 751023, India; Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India.
| | - Sanghamitra Pati
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, Odisha 751023, India.
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13
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Jiang T, Zhang Y, Yu S, Hu B. Discovering potential WRN inhibitors from natural product database through computational methods. J Mol Graph Model 2024; 129:108758. [PMID: 38507856 DOI: 10.1016/j.jmgm.2024.108758] [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: 11/15/2023] [Revised: 02/29/2024] [Accepted: 03/10/2024] [Indexed: 03/22/2024]
Abstract
Microsatellite instability (MSI) is a relatively common feature associated with multiple cancers, and Werner syndrome (WRN) ATP-dependent helicase has been recognized as a novel target for treating MSI cancers, such as colorectal cancer. A small-molecule inhibitor targeting WRN would be a promising strategy for treating colorectal cancer with high MSI expression. In this study, we employed a computer-assisted drug discovery strategy to screen over 30,000 natural product molecules. By using a combination of docking, ligand efficiency, Molecular Mechanics/Generalized Born Surface Area (MM/GBSA), and thermodynamic integration (TI) calculations, we identified MOL008980, MOL010740, MOL011832, T4743, TN1166, and TNP-002173 as potential WRN inhibitors. Subsequent molecular dynamics simulation revealed that these screened natural products possessed better binding dynamic characteristics than ATP substrate and were capable of inhibiting the dynamic process of WRN, making them potential strong ATP competitive inhibitors. In conclusion, our computational approach revealed potential WRN inhibitors from a natural product database, providing a theoretical basis for future research.
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Affiliation(s)
| | | | - Shuihong Yu
- College of Pharmacy, Anqing Medical College, Anqing, China
| | - Bingde Hu
- Navy Anqing Hospital, Anqing, China.
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14
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Lugtu-Pe JA, Zhang X, Mirzaie S, Chang HHR, AL-Mousawi N, Chen K, Li Y, Kane A, Bar-Shalom D, Wu XY. An emerging terpolymeric nanoparticle pore former as an internal recrystallization inhibitor of celecoxib in controlled release amorphous solid dispersion beads: Experimental studies and molecular dynamics analysis. Acta Pharm Sin B 2024; 14:2669-2684. [PMID: 38828156 PMCID: PMC11143779 DOI: 10.1016/j.apsb.2024.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/25/2024] [Accepted: 02/08/2024] [Indexed: 06/05/2024] Open
Abstract
Solid oral controlled release formulations feature numerous clinical advantages for drug candidates with adequate solubility and dissolution rate. However, most new chemical entities exhibit poor water solubility, and hence are exempt from such benefits. Although combining drug amorphization with controlled release formulation is promising to elevate drug solubility, like other supersaturating systems, the problem of drug recrystallization has yet to be resolved, particularly within the dosage form. Here, we explored the potential of an emerging, non-leachable terpolymer nanoparticle (TPN) pore former as an internal recrystallization inhibitor within controlled release amorphous solid dispersion (CRASD) beads comprising a poorly soluble drug (celecoxib) reservoir and insoluble polymer (ethylcellulose) membrane. Compared to conventional pore former, polyvinylpyrrolidone (PVP), TPN-containing membranes exhibited superior structural integrity, less crystal formation at the CRASD bead surface, and greater extent of celecoxib release. All-atom molecular dynamics analyses revealed that in the presence of TPN, intra-molecular bonding, crystal formation tendency, diffusion coefficient, and molecular flexibility of celecoxib were reduced, while intermolecular H-bonding was increased as compared to PVP. This work suggests that selection of a pore former that promotes prolonged molecular separation within a nanoporous controlled release membrane structure may serve as an effective strategy to enhance amorphicity preservation inside CRASD.
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Affiliation(s)
- Jamie Anne Lugtu-Pe
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
| | - Xuning Zhang
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
- Candoo Pharmatech Company Inc., Mississauga L5N 5M1, Canada
| | - Sako Mirzaie
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
| | - Hao Han R. Chang
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
| | - Nour AL-Mousawi
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
- Department of Pharmacy, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Kuan Chen
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
| | - Yongqiang Li
- Candoo Pharmatech Company Inc., Mississauga L5N 5M1, Canada
| | - Anil Kane
- Patheon by Thermo Fisher Scientific, Toronto Region Operations (TRO), Mississauga L5N 3X4, Canada
| | - Daniel Bar-Shalom
- Department of Pharmacy, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Xiao Yu Wu
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
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15
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Wu H, Handley TNG, Hoare BL, Hartono HA, Scott DJ, Chalmers DK, Bathgate RAD, Hossain MA. Developing insulin-like peptide 5-based antagonists for the G protein-coupled receptor, RXFP4. Biochem Pharmacol 2024; 224:116239. [PMID: 38679208 DOI: 10.1016/j.bcp.2024.116239] [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: 01/16/2024] [Revised: 04/05/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
Human insulin-like peptide 5 (INSL5) is a gut hormone produced by colonic L-cells, and its biological functions are mediated by Relaxin Family Peptide Receptor 4 (RXFP4). Our preliminary data indicated that RXFP4 agonists are potential drug leads for the treatment of constipation. More recently, we designed and developed a novel RXFP4 antagonist, A13-nR that was shown to block agonist-induced activity in cells and animal models. We showed that A13-nR was able to block agonist-induced increases in colon motility in mice of both genders that express the receptor, RXFP4. Our data also showed that colorectal propulsion induced by intracolonic administration of short-chain fatty acids was antagonized by A13-nR. Therefore, A13-nR is an important research tool and potential drug lead for the treatment of colon motility disorders, such as bacterial diarrhea. However, A13-nR acted as a partial agonist at high concentrations in vitro and demonstrated modest antagonist potency (∼35 nM). Consequently, the primary objective of this study is to pinpoint novel modifications to A13-nR that eliminate partial agonist effects while preserving or augmenting antagonist potency. In this work, we detail the creation of a series of A13-nR-modified analogues, among which analogues 3, 4, and 6 demonstrated significantly improved RXFP4 affinity (∼3 nM) with reduced partial agonist activity, enhanced antagonist potency (∼10 nM) and maximum agonist inhibition (∼80 %) when compared with A13-nR. These compounds have potential as candidates for further preclinical evaluations, marking a significant stride toward innovative therapeutics for colon motility disorders.
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Affiliation(s)
- Hongkang Wu
- The Florey, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Thomas N G Handley
- The Florey, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Bradley L Hoare
- The Florey, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Herodion A Hartono
- Faculty of Pharmacy and Pharmaceutical Sciences, Monash Institute of Pharmaceutical Sciences, Victoria 3052, Australia
| | - Daniel J Scott
- The Florey, The University of Melbourne, Parkville, Victoria 3052, Australia; Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - David K Chalmers
- Faculty of Pharmacy and Pharmaceutical Sciences, Monash Institute of Pharmaceutical Sciences, Victoria 3052, Australia
| | - Ross A D Bathgate
- The Florey, The University of Melbourne, Parkville, Victoria 3052, Australia; Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Mohammed Akhter Hossain
- The Florey, The University of Melbourne, Parkville, Victoria 3052, Australia; School of Chemistry, The University of Melbourne, Parkville, Victoria 3052, Australia.
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16
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Ranteh O, Tedasen A, Rahman MA, Ibrahim MA, Sama-Ae I. Bioactive compounds from Ocimum tenuiflorum and Poria cocos: A novel natural Compound for insomnia treatment based on A computational approach. Comput Biol Med 2024; 175:108491. [PMID: 38657467 DOI: 10.1016/j.compbiomed.2024.108491] [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: 09/05/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024]
Abstract
Insomnia, a widespread public health issue, is associated with substantial distress and daytime functionality impairments and can predispose to depression and cardiovascular disease. Cognitive Behavioral Anti-insomnia therapies including benzodiazepines often face limitations due to patient adherence or potential adverse effects. This study focused on identifying novel bioactive compounds from medicinal plants, aiming to discover and develop new therapeutic agents with low risk-to-benefit ratios using computational drug discovery methods. Through a systematic framework involving compound library preparation, evaluation of drug-likeness and pharmacokinetics, toxicity prediction, molecular docking, and molecular dynamic simulations, two natural compounds such as 2-(4-hydroxy-3-methoxyphenyl)-8-methoxy-6-prop-2-enyl-3,4-dihydro-2H-chromen-3-ol from Ocimum tenuiflorum and 7-(2-hydroxypropan-2-yl)-1,4a-dimethyl-9-oxo-3,4,10,10a-tetrahydro-2H-phenanthrene-1-carboxylic acid from Poria cocos exhibited high binding affinity with orexin receptor type 1 (OX1R) and type 2 (OX2R), surpassing commercial drugs used in insomnia treatment. Additionally, they showed interactions with critical amino acid residues within the receptors that play crucial roles in competitive inhibitor activity, like commercial drugs such as Suvorexant, Lemborexant, and Daridorexant. Further, molecular dynamics simulations of the protein-ligand complexes under conditions that mimic the in vivo environment revealed both compounds' sustained and robust interactions with the OX1R and OX2R, reinforcing their potential as effective therapeutic candidates. Furthermore, upon evaluating both compounds' drug-likeness, pharmacokinetics, and toxicity profiles, it was discerned that they displayed considerable drug-like properties and favorable pharmacokinetics, along with diminished toxicity. The research provides a solid foundation for further exploring and validating these compounds as potential anti-insomnia therapeutics.
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Affiliation(s)
- Onggan Ranteh
- Department of Community Public Health, School of Public Health, Walailak University, Tha Sala District, Nakhon Si Thammarat, 80160, Thailand; Excellent Centre of Dengue and Community Public Health (EC for DACH), Walailak University, Tha Sala District, Nakhon Si Thammarat, 80160, Thailand.
| | - Aman Tedasen
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Tha Sala District, Nakhon Si Thammarat, 80160, Thailand; Research Excellence Center for Innovation and Health Products, Walailak University, Tha Sala, Nakhon Si Thammarat, 80161, Thailand.
| | - Md Atiar Rahman
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Tha Sala District, Nakhon Si Thammarat, 80160, Thailand; Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong-4331, Bangladesh.
| | | | - Imran Sama-Ae
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Tha Sala District, Nakhon Si Thammarat, 80160, Thailand; Center of Excellence Research for Melioidosis and Microorganisms (CERMM), Walailak University, Tha Sala District, Nakhon Si Thammarat, 80160, Thailand.
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17
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Zeng H, Zhang S, Nie H, Li J, Yang J, Zhuang Y, Huang Y, Zeng M. Identification of FTY720 and COH29 as novel topoisomerase I catalytic inhibitors by experimental and computational studies. Bioorg Chem 2024; 147:107412. [PMID: 38696845 DOI: 10.1016/j.bioorg.2024.107412] [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: 03/16/2024] [Revised: 04/17/2024] [Accepted: 04/27/2024] [Indexed: 05/04/2024]
Abstract
The development of novel topoisomerase I (TOP1) inhibitors is crucial for overcoming the drawbacks and limitations of current TOP1 poisons. Here, we identified two potential TOP1 inhibitors, namely, FTY720 (a sphingosine 1-phosphate antagonist) and COH29 (a ribonucleotide reductase inhibitor), through experimental screening of known active compounds. Biological experiments verified that FTY720 and COH29 were nonintercalative TOP1 catalytic inhibitors that did not induce the formation of DNA-TOP1 covalent complexes. Molecular docking revealed that FTY720 and COH29 interacted favorably with TOP1. Molecular dynamics simulations revealed that FTY720 and COH29 could affect the catalytic domain of TOP1, thus resulting in altered DNA-binding cavity size. The alanine scanning and interaction entropy identified Arg536 as a hotspot residue. In addition, the bioinformatics analysis predicted that FTY720 and COH29 could be effective in treating malignant breast tumors. Biological experiments verified their antitumor activities using MCF-7 breast cancer cells. Their combinatory effects with TOP1 poisons were also investigated. Further, FTY720 and COH29 were found to cause less DNA damage compared with TOP1 poisons. The findings provide reliable lead compounds for the development of novel TOP1 catalytic inhibitors and offer new insights into the potential clinical applications of FTY720 and COH29 in targeting TOP1.
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Affiliation(s)
- Huang Zeng
- Institute of Hakka Medicinal Bio-resources, Medical College, Jiaying University, Meizhou 514031, China.
| | - Shengyuan Zhang
- Institute of Hakka Medicinal Bio-resources, Medical College, Jiaying University, Meizhou 514031, China
| | - Hua Nie
- Institute of Hakka Medicinal Bio-resources, Medical College, Jiaying University, Meizhou 514031, China
| | - Junhao Li
- Department of Physics and Astronomy, Uppsala University, Lägerhyddsvägen 1, SE-75121 Uppsala, Sweden
| | - Jiunlong Yang
- Institute of Hakka Medicinal Bio-resources, Medical College, Jiaying University, Meizhou 514031, China
| | - Yuanbei Zhuang
- Institute of Hakka Medicinal Bio-resources, Medical College, Jiaying University, Meizhou 514031, China
| | - Yingjie Huang
- Institute of Hakka Medicinal Bio-resources, Medical College, Jiaying University, Meizhou 514031, China
| | - Miao Zeng
- Institute of Hakka Medicinal Bio-resources, Medical College, Jiaying University, Meizhou 514031, China
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18
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Inan T, Flinko R, Lewis GK, MacKerell AD, Kurkcuoglu O. Identifying and Assessing Putative Allosteric Sites and Modulators for CXCR4 Predicted through Network Modeling and Site Identification by Ligand Competitive Saturation. J Phys Chem B 2024; 128:5157-5174. [PMID: 38647430 PMCID: PMC11139592 DOI: 10.1021/acs.jpcb.4c00925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
The chemokine receptor CXCR4 is a critical target for the treatment of several cancer types and HIV-1 infections. While orthosteric and allosteric modulators have been developed targeting its extracellular or transmembrane regions, the intramembrane region of CXCR4 may also include allosteric binding sites suitable for the development of allosteric drugs. To investigate this, we apply the Gaussian Network Model (GNM) to the monomeric and dimeric forms of CXCR4 to identify residues essential for its local and global motions located in the hinge regions of the protein. Residue interaction network (RIN) analysis suggests hub residues that participate in allosteric communication throughout the receptor. Mutual residues from the network models reside in regions with a high capacity to alter receptor dynamics upon ligand binding. We then investigate the druggability of these potential allosteric regions using the site identification by ligand competitive saturation (SILCS) approach, revealing two putative allosteric sites on the monomer and three on the homodimer. Two screening campaigns with Glide and SILCS-Monte Carlo docking using FDA-approved drugs suggest 20 putative hit compounds including antifungal drugs, anticancer agents, HIV protease inhibitors, and antimalarial drugs. In vitro assays considering mAB 12G5 and CXCL12 demonstrate both positive and negative allosteric activities of these compounds, supporting our computational approach. However, in vivo functional assays based on the recruitment of β-arrestin to CXCR4 do not show significant agonism and antagonism at a single compound concentration. The present computational pipeline brings a new perspective to computer-aided drug design by combining conformational dynamics based on network analysis and cosolvent analysis based on the SILCS technology to identify putative allosteric binding sites using CXCR4 as a showcase.
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Affiliation(s)
- Tugce Inan
- Department
of Chemical Engineering, Istanbul Technical
University, Istanbul 34469, Turkey
| | - Robin Flinko
- Institute
of Human Virology, University of Maryland
School of Medicine, Baltimore, Maryland 21201, United States
| | - George K. Lewis
- Institute
of Human Virology, University of Maryland
School of Medicine, Baltimore, Maryland 21201, United States
| | - Alexander D. MacKerell
- University
of Maryland Computer-Aided Drug Design Center, Department of Pharmaceutical
Sciences, School of Pharmacy, University
of Maryland, Baltimore, Maryland 21201, United States
| | - Ozge Kurkcuoglu
- Department
of Chemical Engineering, Istanbul Technical
University, Istanbul 34469, Turkey
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19
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Chen R, Wang Y, Shen Z, Ye C, Guo Y, Lu Y, Ding J, Dong X, Xu D, Zheng X. Discovery of potent CSK inhibitors through integrated virtual screening and molecular dynamic simulation. Arch Pharm (Weinheim) 2024:e2400066. [PMID: 38809025 DOI: 10.1002/ardp.202400066] [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: 01/24/2024] [Revised: 04/23/2024] [Accepted: 05/08/2024] [Indexed: 05/30/2024]
Abstract
Oncogenic overexpression or activation of C-terminal Src kinase (CSK) has been shown to play an important role in triple-negative breast cancer (TNBC) progression, including tumor initiation, growth, metastasis, drug resistance. This revelation has pivoted the focus toward CSK as a potential target for novel treatments. However, until now, there are few inhibitors designed to target the CSK protein. Responding to this, our research has implemented a comprehensive virtual screening protocol. By integrating energy-based screening methods with AI-driven scoring functions, such as Attentive FP, and employing rigorous rescoring methods like Glide docking and molecular mechanics generalized Born surface area (MM/GBSA), we have systematically sought out inhibitors of CSK. This approach led to the discovery of a compound with a potent CSK inhibitory activity, reflected by an IC50 value of 1.6 nM under a homogeneous time-resolved fluorescence (HTRF) bioassay. Subsequently, molecule 2 exhibits strong growth inhibition of MD anderson - metastatic breast (MDA-MB) -231, Hs578T, and SUM159 cells, showing a level of growth inhibition comparable to that observed with dasatinib. Treatment with molecule 2 also induced significant G1 phase accumulation and cell apoptosis. Furthermore, we have explored the explicit binding interactions of the compound with CSK using molecular dynamics simulations, providing valuable insights into its mechanism of action.
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Affiliation(s)
- Roufen Chen
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yuchen Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Zheyuan Shen
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Chenyi Ye
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Yu Guo
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yan Lu
- Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianjun Ding
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiaowu Dong
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Donghang Xu
- Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoli Zheng
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
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20
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Bachmann V, Schädel P, Westhoff J, Perić M, Schömberg F, Skaltsounis AL, Höppener S, Pantsar T, Fischer D, Vilotijević I, Werz O. Bromo-substituted indirubins for inhibition of protein kinase-mediated signalling involved in inflammatory mediator release in human monocytes. Bioorg Chem 2024; 149:107470. [PMID: 38838619 DOI: 10.1016/j.bioorg.2024.107470] [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: 03/28/2024] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 06/07/2024]
Abstract
Targeting protein kinases that regulate signalling pathways in inflammation is an effective pharmacological approach to alleviate uncontrolled inflammatory diseases. In this context, the natural product indirubin and its 6-bromo-substituted analogue 6-bromoindirubin-3 -glycerol-oxime ether (6BIGOE; 1) were identified as potent inhibitors of glycogen synthase kinase-3β (GSK-3β). These inhibitors suppress the release of pro-inflammatory cytokines and prostaglandins (PG) from human monocytes. However, indirubin derivatives target several protein kinases such as cyclin-dependent kinases (CDKs) which has been a major concern for their application in inflammation therapy. Here, we report on a library of 13 5-bromo-substituted indirubin derivatives that have been designed to improve potency and target selectivity. Side-by-side comparison of reference compound 1 (6BIGOE) with 5-bromo derivatives revealed its isomer 2 (5BIGOE), as the most potent derivative able to supress pro-inflammatory cytokine and PG release in lipopolysaccharide-stimulated human monocytes. Analysis of protein kinase inhibition in intact monocytes, supported by our in silico findings, proposed higher selectivity of 1 for GSK-3β inhibition with lesser potency against CDKs 8 and 9. In contrast, 2 supressed the activity of these CDKs with higher effectiveness than GSK-3β, representing additional targets of indirubins within the inflammatory response. Encapsulation of 1 and 2 into polymer-based nanoparticles (NP) improved their pharmacological potential. In conclusion, the 5- and 6-brominated indirubins 1 and 2 as dual GSK-3β and CDK8/9 inhibitors represent a novel concept for intervention with inflammatory disorders.
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Affiliation(s)
- Vivien Bachmann
- Department of Pharmaceutical/ Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, Philosophenweg 14, 07743 Jena, Germany
| | - Patrick Schädel
- Department of Pharmaceutical/ Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, Philosophenweg 14, 07743 Jena, Germany
| | - Jan Westhoff
- Division of Pharmaceutical Technology and Biopharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstraße 4, 91058 Erlangen, Germany
| | - Milica Perić
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743 Jena, Germany
| | - Fritz Schömberg
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743 Jena, Germany
| | - Alexios-Leandros Skaltsounis
- Department of Pharmacy, Division of Pharmacognosy and Natural Product Chemistry, University of Athens, Panepistimiopolis Zografou, GR-15771 Athens, Greece
| | - Stephanie Höppener
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743 Jena, Germany; Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany
| | - Tatu Pantsar
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonrinne 3, FI-70210 Kuopio, Finland
| | - Dagmar Fischer
- Division of Pharmaceutical Technology and Biopharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstraße 4, 91058 Erlangen, Germany; Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany; FAU NeW - Research Center for New Bioactive Compounds, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Ivan Vilotijević
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743 Jena, Germany.
| | - Oliver Werz
- Department of Pharmaceutical/ Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, Philosophenweg 14, 07743 Jena, Germany; Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany.
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21
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Merten EM, Sears JD, Leisner TM, Hardy PB, Ghoshal A, Hossain MA, Asressu KH, Brown PJ, Stashko MA, Herring L, Mordant AL, Webb TS, Mills CA, Barker NK, Streblow ZJ, Perveen S, Arrowsmith C, Arnold JJ, Cameron CE, Streblow DN, Moorman NJ, Heise M, Willson TM, Popov K, Pearce KH. Discovery of a cell-active chikungunya virus nsP2 protease inhibitor using a covalent fragment-based screening approach. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586341. [PMID: 38562906 PMCID: PMC10983941 DOI: 10.1101/2024.03.22.586341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that has been responsible for numerous large-scale outbreaks in the last twenty years. Currently, there are no FDA-approved therapeutics for any alphavirus infection. CHIKV non-structural protein 2 (nsP2), which contains a cysteine protease domain, is essential for viral replication, making it an attractive target for a drug discovery campaign. Here, we optimized a CHIKV nsP2 protease (nsP2pro) biochemical assay for the screening of a 6,120-compound cysteine-directed covalent fragment library. Using a 50% inhibition threshold, we identified 153 hits (2.5% hit rate). In dose-response follow up, RA-0002034, a covalent fragment that contains a vinyl sulfone warhead, inhibited CHIKV nsP2pro with an IC 50 of 58 ± 17 nM, and further analysis with time-dependent inhibition studies yielded a k inact /K I of 6.4 x 10 3 M -1 s -1 . LC-MS/MS analysis determined that RA-0002034 covalently modified the catalytic cysteine in a site-specific manner. Additionally, RA-0002034 showed no significant off-target reactivity against a panel of cysteine proteases. In addition to the potent biochemical inhibition of CHIKV nsP2pro activity and exceptional selectivity, RA-0002034 was tested in cellular models of alphavirus infection and effectively inhibited viral replication of both CHIKV and related alphaviruses. This study highlights the discovery and characterization of the chemical probe RA-0002034 as a promising hit compound from covalent fragment-based screening for development toward a CHIKV or pan-alphavirus therapeutic. Significance Statement Chikungunya virus is one of the most prominent and widespread alphaviruses and has caused explosive outbreaks of arthritic disease. Currently, there are no FDA-approved drugs to treat disease caused by chikungunya virus or any other alphavirus-caused infection. Here, we report the discovery of a covalent small molecule inhibitor of chikungunya virus nsP2 protease activity and viral replication of four diverse alphaviruses. This finding highlights the utility of covalent fragment screening for inhibitor discovery and represents a starting point towards the development of alphavirus therapeutics targeting nsP2 protease.
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22
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Peng BL, Ran T, Chen X, Ding JC, Wang ZR, Li WJ, Liu W. A CARM1 Inhibitor Potently Suppresses Breast Cancer Both In Vitro and In Vivo. J Med Chem 2024; 67:7921-7934. [PMID: 38713486 PMCID: PMC11129188 DOI: 10.1021/acs.jmedchem.3c02315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 03/22/2024] [Accepted: 04/25/2024] [Indexed: 05/08/2024]
Abstract
CARM1, belonging to the protein arginine methyltransferase (PRMT) family, is intricately associated with the progression of cancer and is viewed as a promising target for both cancer diagnosis and therapy. However, the number of specific and potent CARM1 inhibitors is limited. We herein discovered a CARM1 inhibitor, iCARM1, that showed better specificity and activity toward CARM1 compared to the known CARM1 inhibitors, EZM2302 and TP-064. Similar to CARM1 knockdown, iCARM1 suppressed the expression of oncogenic estrogen/ERα-target genes, whereas activated type I interferon (IFN) and IFN-induced genes (ISGs) in breast cancer cells. Consequently, iCARM1 potently suppressed breast cancer cell growth both in vitro and in vivo. The combination of iCARM1 with either endocrine therapy drugs or etoposide demonstrated synergistic effects in inhibiting the growth of breast tumors. In summary, targeting CARM1 by iCARM1 effectively suppresses breast tumor growth, offering a promising therapeutic approach for managing breast cancers in clinical settings.
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Affiliation(s)
- Bing-ling Peng
- Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- State
Key Laboratory of Cellular Stress Biology, School of Pharmaceutical
Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang
An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty
of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Ting Ran
- Bioland
Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong
Laboratory), KaiYuan
Road, Guangzhou, Guangdong 510530, China
| | - Xue Chen
- Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- State
Key Laboratory of Cellular Stress Biology, School of Pharmaceutical
Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang
An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty
of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Jian-cheng Ding
- Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- State
Key Laboratory of Cellular Stress Biology, School of Pharmaceutical
Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang
An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty
of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Zi-rui Wang
- Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- State
Key Laboratory of Cellular Stress Biology, School of Pharmaceutical
Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Wen-juan Li
- Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- State
Key Laboratory of Cellular Stress Biology, School of Pharmaceutical
Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang
An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty
of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Wen Liu
- Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- State
Key Laboratory of Cellular Stress Biology, School of Pharmaceutical
Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang
An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty
of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
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23
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Meqbil YJ, Aguilar J, Blaine AT, Chen L, Cassell RJ, Pradhan AA, van Rijn RM. Identification of 1,3,8-Triazaspiro[4.5]Decane-2,4-Dione Derivatives as a Novel δ Opioid Receptor-Selective Agonist Chemotype. J Pharmacol Exp Ther 2024; 389:301-309. [PMID: 38621994 PMCID: PMC11125782 DOI: 10.1124/jpet.123.001735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 03/25/2024] [Accepted: 04/08/2024] [Indexed: 04/17/2024] Open
Abstract
δ opioid receptors (DORs) hold potential as a target for neurologic and psychiatric disorders, yet no DOR agonist has proven efficacious in critical phase II clinical trials. The exact reasons for the failure to produce quality drug candidates for the DOR are unclear. However, it is known that certain DOR agonists can induce seizures and exhibit tachyphylaxis. Several studies have suggested that those adverse effects are more prevalent in delta agonists that share the (+)-4-[(αR)-α-((2S,5R)-4-allyl-2,5-dimethyl-1-piperazinyl)-3-methoxybenzyl]-N,N-diethylbenzamide (SNC80)/4-[(αR*)-α-((2S*,5R*)-4-allyl-2,5-dimethyl-1-piperazinyl)-3-hydroxybenzyl]-N,N-diethylbenzamide chemotype. There is a need to find novel lead candidates for drug development that have improved pharmacological properties to differentiate them from the current failed delta agonists. Our objective in this study was to identify novel DOR agonists. We used a β-arrestin assay to screen a small G-protein coupled receptors (GPCR)-focused chemical library. We identified a novel chemotype of DOR agonists that appears to bind to the orthosteric site based of docking and molecular dynamic simulation. The most potent agonist hit compound is selective for the DOR over a panel of 167 other GPCRs, is slightly biased toward G-protein signaling and has anti-allodynic efficacy in a complete Freund's adjuvant model of inflammatory pain in C57BL/6 male and female mice. The newly discovered chemotype contrasts with molecules like SNC80 that are highly efficacious β-arrestin recruiters and may suggest this novel class of DOR agonists could be expanded on to develop a clinical candidate drug. SIGNIFICANCE STATEMENT: δ opioid receptors are a clinical target for various neurological disorders, including migraine and chronic pain. Many of the clinically tested delta opioid agonists share a single chemotype, which carries risks during drug development. Through a small-scale high-throughput screening assay, this study identified a novel δ opioid receptor agonist chemotype, which may serve as alternative for the current analgesic clinical candidates.
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Affiliation(s)
- Yazan J Meqbil
- Borch Department of Medicinal Chemistry and Molecular Pharmacology (Y.J.M., A.T.B., R.J.C., R.M.v.R.), Computational Interdisciplinary Graduate Programs, Computational Life Sciences (Y.J.M.), and Interdisciplinary Life Science-PULSe (A.T.B.), Purdue University, West Lafayette, Indiana; Purdue Institute for Integrative Neuroscience, West Lafayette, Indiana (R.M.v.R.); Purdue Institute for Drug Discovery, West Lafayette, Indiana (L.C., R.M.v.R.); Septerna Inc., South San Francisco, California (R.M.v.R.); and Center for Clinical Pharmacology, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri (J.A., A.A.P.)
| | - Jhoan Aguilar
- Borch Department of Medicinal Chemistry and Molecular Pharmacology (Y.J.M., A.T.B., R.J.C., R.M.v.R.), Computational Interdisciplinary Graduate Programs, Computational Life Sciences (Y.J.M.), and Interdisciplinary Life Science-PULSe (A.T.B.), Purdue University, West Lafayette, Indiana; Purdue Institute for Integrative Neuroscience, West Lafayette, Indiana (R.M.v.R.); Purdue Institute for Drug Discovery, West Lafayette, Indiana (L.C., R.M.v.R.); Septerna Inc., South San Francisco, California (R.M.v.R.); and Center for Clinical Pharmacology, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri (J.A., A.A.P.)
| | - Arryn T Blaine
- Borch Department of Medicinal Chemistry and Molecular Pharmacology (Y.J.M., A.T.B., R.J.C., R.M.v.R.), Computational Interdisciplinary Graduate Programs, Computational Life Sciences (Y.J.M.), and Interdisciplinary Life Science-PULSe (A.T.B.), Purdue University, West Lafayette, Indiana; Purdue Institute for Integrative Neuroscience, West Lafayette, Indiana (R.M.v.R.); Purdue Institute for Drug Discovery, West Lafayette, Indiana (L.C., R.M.v.R.); Septerna Inc., South San Francisco, California (R.M.v.R.); and Center for Clinical Pharmacology, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri (J.A., A.A.P.)
| | - Lan Chen
- Borch Department of Medicinal Chemistry and Molecular Pharmacology (Y.J.M., A.T.B., R.J.C., R.M.v.R.), Computational Interdisciplinary Graduate Programs, Computational Life Sciences (Y.J.M.), and Interdisciplinary Life Science-PULSe (A.T.B.), Purdue University, West Lafayette, Indiana; Purdue Institute for Integrative Neuroscience, West Lafayette, Indiana (R.M.v.R.); Purdue Institute for Drug Discovery, West Lafayette, Indiana (L.C., R.M.v.R.); Septerna Inc., South San Francisco, California (R.M.v.R.); and Center for Clinical Pharmacology, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri (J.A., A.A.P.)
| | - Robert J Cassell
- Borch Department of Medicinal Chemistry and Molecular Pharmacology (Y.J.M., A.T.B., R.J.C., R.M.v.R.), Computational Interdisciplinary Graduate Programs, Computational Life Sciences (Y.J.M.), and Interdisciplinary Life Science-PULSe (A.T.B.), Purdue University, West Lafayette, Indiana; Purdue Institute for Integrative Neuroscience, West Lafayette, Indiana (R.M.v.R.); Purdue Institute for Drug Discovery, West Lafayette, Indiana (L.C., R.M.v.R.); Septerna Inc., South San Francisco, California (R.M.v.R.); and Center for Clinical Pharmacology, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri (J.A., A.A.P.)
| | - Amynah A Pradhan
- Borch Department of Medicinal Chemistry and Molecular Pharmacology (Y.J.M., A.T.B., R.J.C., R.M.v.R.), Computational Interdisciplinary Graduate Programs, Computational Life Sciences (Y.J.M.), and Interdisciplinary Life Science-PULSe (A.T.B.), Purdue University, West Lafayette, Indiana; Purdue Institute for Integrative Neuroscience, West Lafayette, Indiana (R.M.v.R.); Purdue Institute for Drug Discovery, West Lafayette, Indiana (L.C., R.M.v.R.); Septerna Inc., South San Francisco, California (R.M.v.R.); and Center for Clinical Pharmacology, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri (J.A., A.A.P.)
| | - Richard M van Rijn
- Borch Department of Medicinal Chemistry and Molecular Pharmacology (Y.J.M., A.T.B., R.J.C., R.M.v.R.), Computational Interdisciplinary Graduate Programs, Computational Life Sciences (Y.J.M.), and Interdisciplinary Life Science-PULSe (A.T.B.), Purdue University, West Lafayette, Indiana; Purdue Institute for Integrative Neuroscience, West Lafayette, Indiana (R.M.v.R.); Purdue Institute for Drug Discovery, West Lafayette, Indiana (L.C., R.M.v.R.); Septerna Inc., South San Francisco, California (R.M.v.R.); and Center for Clinical Pharmacology, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri (J.A., A.A.P.)
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24
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Smith OB, Frkic RL, Rahman MG, Jackson CJ, Kaczmarski JA. Identification and Characterization of a Bacterial Periplasmic Solute Binding Protein That Binds l-Amino Acid Amides. Biochemistry 2024; 63:1322-1334. [PMID: 38696389 DOI: 10.1021/acs.biochem.4c00096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
Periplasmic solute-binding proteins (SBPs) are key ligand recognition components of bacterial ATP-binding cassette (ABC) transporters that allow bacteria to import nutrients and metabolic precursors from the environment. Periplasmic SBPs comprise a large and diverse family of proteins, of which only a small number have been empirically characterized. In this work, we identify a set of 610 unique uncharacterized proteins within the SBP_bac_5 family that are found in conserved operons comprising genes encoding (i) ABC transport systems and (ii) putative amidases from the FmdA_AmdA family. From these uncharacterized SBP_bac_5 proteins, we characterize a representative periplasmic SBP from Mesorhizobium sp. A09 (MeAmi_SBP) and show that MeAmi_SBP binds l-amino acid amides but not the corresponding l-amino acids. An X-ray crystal structure of MeAmi_SBP bound to l-serinamide highlights the residues that impart distinct specificity for l-amino acid amides and reveals a structural Ca2+ binding site within one of the lobes of the protein. We show that the residues involved in ligand and Ca2+ binding are conserved among the 610 SBPs from experimentally uncharacterized FmdA_AmdA amidase-associated ABC transporter systems, suggesting these homologous systems are also likely to be involved in the sensing, uptake, and metabolism of l-amino acid amides across many Gram-negative nitrogen-fixing soil bacteria. We propose that MeAmi_SBP is involved in the uptake of such solutes to supplement pathways such as the citric acid cycle and the glutamine synthetase-glutamate synthase pathway. This work expands our currently limited understanding of microbial interactions with l-amino acid amides and bacterial nitrogen utilization.
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Affiliation(s)
- Oliver B Smith
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Rebecca L Frkic
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Marina G Rahman
- ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Joe A Kaczmarski
- ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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25
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La Spada G, Miniero DV, Rullo M, Cipolloni M, Delre P, Colliva C, Colella M, Leonetti F, Liuzzi GM, Mangiatordi GF, Giacchè N, Pisani L. Structure-based design of multitargeting ChEs-MAO B inhibitors based on phenyl ring bioisosteres: AChE/BChE selectivity switch and drug-like characterization. Eur J Med Chem 2024; 274:116511. [PMID: 38820854 DOI: 10.1016/j.ejmech.2024.116511] [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: 03/27/2024] [Revised: 05/06/2024] [Accepted: 05/17/2024] [Indexed: 06/02/2024]
Abstract
A structure-based drug design approach was focused on incorporating phenyl ring heterocyclic bioisosteres into coumarin derivative 1, previously reported as potent dual AChE-MAO B inhibitor, with the aim of improving drug-like features. Structure-activity relationships highlighted that bioisosteric rings were tolerated by hMAO B enzymatic cleft more than hAChE. Interestingly, linker homologation at the basic nitrogen enabled selectivity to switch from hAChE to hBChE. In the present work, we identified thiophene-based isosteres 7 and 15 as dual AChE-MAO B (IC50 = 261 and 15 nM, respectively) and BChE-MAO B (IC50 = 375 and 20 nM, respectively) inhibitors, respectively. Both 7 and 15 were moderately water-soluble and membrane-permeant agents by passive diffusion (PAMPA-HDM). Moreover, they were able to counteract oxidative damage induced by both H2O2 and 6-OHDA in SH-SY5Y cells and predicted to penetrate into CNS in a cell-based model mimicking blood-brain barrier. Molecular dynamics (MD) simulations shed light on key differences in AChE and BChE recognition processes promoted by the basic chain homologation from 7 to 15.
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Affiliation(s)
- Gabriella La Spada
- Dept. of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125, Bari, Italy
| | - Daniela Valeria Miniero
- Dept. of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, Via E. Orabona 4, 70125, Bari, Italy
| | - Mariagrazia Rullo
- Dept. of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125, Bari, Italy
| | - Marco Cipolloni
- Tes Pharma s.r.l., via Palmiro Togliatti 20, 06073, Corciano, PG, Italy
| | - Pietro Delre
- CNR, Institute of Crystallography, 70126, Bari, Italy
| | - Carolina Colliva
- Tes Pharma s.r.l., via Palmiro Togliatti 20, 06073, Corciano, PG, Italy
| | - Marco Colella
- Dept. of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125, Bari, Italy
| | - Francesco Leonetti
- Dept. of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125, Bari, Italy
| | - Grazia Maria Liuzzi
- Dept. of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, Via E. Orabona 4, 70125, Bari, Italy
| | | | - Nicola Giacchè
- Tes Pharma s.r.l., via Palmiro Togliatti 20, 06073, Corciano, PG, Italy
| | - Leonardo Pisani
- Dept. of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125, Bari, Italy.
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26
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Garcia-Maldonado E, Huber AD, Chai SC, Nithianantham S, Li Y, Wu J, Poudel S, Miller DJ, Seetharaman J, Chen T. Chemical manipulation of an activation/inhibition switch in the nuclear receptor PXR. Nat Commun 2024; 15:4054. [PMID: 38744881 PMCID: PMC11094003 DOI: 10.1038/s41467-024-48472-1] [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: 09/19/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
Nuclear receptors are ligand-activated transcription factors that can often be useful drug targets. Unfortunately, ligand promiscuity leads to two-thirds of receptors remaining clinically untargeted. PXR is a nuclear receptor that can be activated by diverse compounds to elevate metabolism, negatively impacting drug efficacy and safety. This presents a barrier to drug development because compounds designed to target other proteins must avoid PXR activation while retaining potency for the desired target. This problem could be avoided by using PXR antagonists, but these compounds are rare, and their molecular mechanisms remain unknown. Here, we report structurally related PXR-selective agonists and antagonists and their corresponding co-crystal structures to describe mechanisms of antagonism and selectivity. Structural and computational approaches show that antagonists induce PXR conformational changes incompatible with transcriptional coactivator recruitment. These results guide the design of compounds with predictable agonist/antagonist activities and bolster efforts to generate antagonists to prevent PXR activation interfering with other drugs.
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Affiliation(s)
- Efren Garcia-Maldonado
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Andrew D Huber
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Sergio C Chai
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Stanley Nithianantham
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yongtao Li
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jing Wu
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shyaron Poudel
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jayaraman Seetharaman
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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27
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Bodenbender JP, Marino V, Philipp J, Tropitzsch A, Kernstock C, Stingl K, Kempf M, Haack TB, Zuleger T, Mazzola P, Kohl S, Weisschuh N, Dell'Orco D, Kühlewein L. Comprehensive analysis of two hotspot codons in the TUBB4B gene and associated phenotypes. Sci Rep 2024; 14:10551. [PMID: 38719929 PMCID: PMC11078972 DOI: 10.1038/s41598-024-61019-0] [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] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
Our purpose was to elucidate the genotype and ophthalmological and audiological phenotype in TUBB4B-associated inherited retinal dystrophy (IRD) and sensorineural hearing loss (SNHL), and to model the effects of all possible amino acid substitutions at the hotspot codons Arg390 and Arg391. Six patients from five families with heterozygous missense variants in TUBB4B were included in this observational study. Ophthalmological testing included best-corrected visual acuity, fundus examination, optical coherence tomography, fundus autofluorescence imaging, and full-field electroretinography (ERG). Audiological examination included pure-tone and speech audiometry in adult patients and auditory brainstem response testing in a child. Genetic testing was performed by disease gene panel analysis based on genome sequencing. The molecular consequences of the substitutions of residues 390 and 391 on TUBB4B and its interaction with α-tubulin were predicted in silico on its three-dimensional structure obtained by homology modelling. Two independent patients had amino acid exchanges at position 391 (p.(Arg391His) or p.(Arg391Cys)) of the TUBB4B protein. Both had a distinct IRD phenotype with peripheral round yellowish lesions with pigmented spots and mild or moderate SNHL, respectively. Yet the phenotype was milder with a sectorial pattern of bone spicules in one patient, likely due to a genetically confirmed mosaicism for p.(Arg391His). Three patients were heterozygous for an amino acid exchange at position 390 (p.(Arg390Gln) or p.(Arg390Trp)) and presented with another distinct retinal phenotype with well demarcated pericentral retinitis pigmentosa. All showed SNHL ranging from mild to severe. One additional patient showed a variant distinct from codon 390 or 391 (p.(Tyr310His)), and presented with congenital profound hearing loss and reduced responses in ERG. Variants at codon positions 390 and 391 were predicted to decrease the structural stability of TUBB4B and its complex with α-tubulin, as well as the complex affinity. In conclusion, the twofold larger reduction in heterodimer affinity exhibited by Arg391 substitutions suggested an association with the more severe retinal phenotype, compared to the substitution at Arg390.
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Affiliation(s)
- Jan-Philipp Bodenbender
- University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Valerio Marino
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Verona, Italy
| | - Julia Philipp
- Department of Otolaryngology-Head & Neck Surgery, Hearing Research Center, University of Tübingen Medical Center, Tübingen, Germany
| | - Anke Tropitzsch
- Department of Otolaryngology-Head & Neck Surgery, Hearing Research Center, University of Tübingen Medical Center, Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Christoph Kernstock
- University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Katarina Stingl
- University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Melanie Kempf
- University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Theresia Zuleger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Pascale Mazzola
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Susanne Kohl
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Nicole Weisschuh
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Daniele Dell'Orco
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Verona, Italy
| | - Laura Kühlewein
- University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany.
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany.
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28
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De-la-Torre P, Martínez-García C, Gratias P, Mun M, Santana P, Akyuz N, González W, Indzhykulian AA, Ramírez D. Identification of Druggable Binding Sites and Small Molecules as Modulators of TMC1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.05.583611. [PMID: 38826329 PMCID: PMC11142246 DOI: 10.1101/2024.03.05.583611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Our ability to hear and maintain balance relies on the proper functioning of inner ear sensory hair cells, which translate mechanical stimuli into electrical signals via mechano-electrical transducer (MET) channels, composed of TMC1/2 proteins. However, the therapeutic use of ototoxic drugs, such as aminoglycosides and cisplatin, which can enter hair cells through MET channels, often leads to profound auditory and vestibular dysfunction. Despite extensive research on otoprotective compounds targeting MET channels, our understanding of how small molecule modulators interact with these channels remains limited, hampering the discovery of novel compounds. Here, we propose a structure-based screening approach, integrating 3D-pharmacophore modeling, molecular simulations, and experimental validation. Our pipeline successfully identified several novel compounds and FDA-approved drugs that reduced dye uptake in cultured cochlear explants, indicating MET modulation activity. Molecular docking and free-energy estimations for binding allowed us to identify three potential drug binding sites within the channel pore, phospholipids, and key amino acids involved in modulator interactions. We also identified shared ligand-binding features between TMC and structurally related TMEM16 protein families, providing novel insights into their distinct inhibition, while potentially guiding the rational design of MET-channel-specific modulators. Our pipeline offers a broad application to discover small molecule modulators for a wide spectrum of mechanosensitive ion channels.
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Affiliation(s)
- Pedro De-la-Torre
- Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School and Mass Eye and Ear, Boston, MA, USA
| | | | - Paul Gratias
- Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School and Mass Eye and Ear, Boston, MA, USA
| | - Matthew Mun
- Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School and Mass Eye and Ear, Boston, MA, USA
| | - Paula Santana
- Facultad de Ingeniería, Instituto de Ciencias Químicas Aplicadas, Universidad Autónoma de Chile, Santiago, Chile
| | - Nurunisa Akyuz
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Wendy González
- Center for Bioinformatics and Molecular Simulations (CBSM), University of Talca, Talca 3460000, Chile
| | - Artur A. Indzhykulian
- Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School and Mass Eye and Ear, Boston, MA, USA
| | - David Ramírez
- Department of Pharmacology, Faculty of Biological Sciences, University of Concepción, Chile
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29
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Gamal MA, Fahim SH, Giovannuzzi S, Fouad MA, Bonardi A, Gratteri P, Supuran CT, Hassan GS. Probing benzenesulfonamide-thiazolidinone hybrids as multitarget directed ligands for efficient control of type 2 diabetes mellitus through targeting the enzymes: α-glucosidase and carbonic anhydrase II. Eur J Med Chem 2024; 271:116434. [PMID: 38653067 DOI: 10.1016/j.ejmech.2024.116434] [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: 01/21/2024] [Revised: 04/07/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024]
Abstract
Diabetes mellitus is a chronic metabolic disorder characterized by improper expression/function of a number of key enzymes that can be regarded as targets for anti-diabetic drug design. Herein, we report the design, synthesis, and biological assessment of two series of thiazolidinone-based sulfonamides 4a-l and 5a-c as multitarget directed ligands (MTDLs) with potential anti-diabetic activity through targeting the enzymes: α-glucosidase and human carbonic anhydrase (hCA) II. The synthesized sulfonamides were evaluated for their inhibitory activity against α-glucosidase where most of the compounds showed good to potent activities. Compounds 4d and 4e showed potent inhibitory activities (IC50 = 0.440 and 0.3456 μM), comparable with that of the positive control (acarbose; IC50 = 0.420 μM). All the synthesized derivatives were also tested for their inhibitory activities against hCA I, II, IX, and XII. They exhibited different levels of inhibition against these isoforms. Compound 4d outstood as the most potent one against hCA II with Ki equals to 7.0 nM, more potent than the reference standard (acetazolamide; Ki = 12.0 nM). In silico studies for the most active compounds within the active sites of α-glucosidase and hCA II revealed good binding modes that can explain their biological activities. MM-GBSA refinements and molecular dynamic simulations were performed on the top-ranking docking pose of the most potent compound 4d to confirm the formation of stable complex with both targets. Compound 4d was screened for its in vivo antihyperglycemic efficacy by using the oral glucose tolerance test. Compound 4d decreased blood glucose level to 217 mg/dl, better than the standard acarbose (234 mg/dl). Hence, this revealed its synergistic mode of action on post prandial hyperglycemia and hepatic gluconeogenesis. Thus, these benzenesulfonamide thiazolidinone hybrids could be considered as promising multi-target candidates for the treatment of type II diabetes mellitus.
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Affiliation(s)
- Mona A Gamal
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St, Cairo, 11562, Egypt
| | - Samar H Fahim
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St, Cairo, 11562, Egypt.
| | - Simone Giovannuzzi
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Marwa A Fouad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St, Cairo, 11562, Egypt; Pharmaceutical Chemistry Department, School of Pharmacy, Newgiza University, New Giza, km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
| | - Alessandro Bonardi
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Paola Gratteri
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Claudiu T Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Ghaneya S Hassan
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St, Cairo, 11562, Egypt; Pharmaceutical Chemistry Department, School of Pharmacy, Badr University in Cairo (BUC), Badr City, Egypt
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30
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Stadler KA, Ortiz-Joya LJ, Singh Sahrawat A, Buhlheller C, Gruber K, Pavkov-Keller T, O'Hagan TB, Guarné A, Pulido S, Marín-Villa M, Zangger K, Gubensäk N. Structural investigation of Trypanosoma cruzi Akt-like kinase as drug target against Chagas disease. Sci Rep 2024; 14:10039. [PMID: 38693166 PMCID: PMC11063076 DOI: 10.1038/s41598-024-59654-8] [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: 01/19/2024] [Accepted: 04/12/2024] [Indexed: 05/03/2024] Open
Abstract
According to the World Health Organization, Chagas disease (CD) is the most prevalent poverty-promoting neglected tropical disease. Alarmingly, climate change is accelerating the geographical spreading of CD causative parasite, Trypanosoma cruzi, which additionally increases infection rates. Still, CD treatment remains challenging due to a lack of safe and efficient drugs. In this work, we analyze the viability of T. cruzi Akt-like kinase (TcAkt) as drug target against CD including primary structural and functional information about a parasitic Akt protein. Nuclear Magnetic Resonance derived information in combination with Molecular Dynamics simulations offer detailed insights into structural properties of the pleckstrin homology (PH) domain of TcAkt and its binding to phosphatidylinositol phosphate ligands (PIP). Experimental data combined with Alpha Fold proposes a model for the mechanism of action of TcAkt involving a PIP-induced disruption of the intramolecular interface between the kinase and the PH domain resulting in an open conformation enabling TcAkt kinase activity. Further docking experiments reveal that TcAkt is recognized by human inhibitors PIT-1 and capivasertib, and TcAkt inhibition by UBMC-4 and UBMC-6 is achieved via binding to TcAkt kinase domain. Our in-depth structural analysis of TcAkt reveals potential sites for drug development against CD, located at activity essential regions.
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Affiliation(s)
- Karina A Stadler
- Institute of Chemistry/Organic and Bioorganic Chemistry, University of Graz, Graz, Austria
| | - Lesly J Ortiz-Joya
- Institute of Chemistry/Organic and Bioorganic Chemistry, University of Graz, Graz, Austria
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
- Department of Biochemistry, McGill University, Montreal, Canada
| | - Amit Singh Sahrawat
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Innophore GmbH, Graz, Austria
| | | | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Innophore GmbH, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | | | - Alba Guarné
- Department of Biochemistry, McGill University, Montreal, Canada
| | - Sergio Pulido
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
- LifeFactors ZF SAS, Rionegro, Colombia
| | - Marcel Marín-Villa
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Klaus Zangger
- Institute of Chemistry/Organic and Bioorganic Chemistry, University of Graz, Graz, Austria.
- Field of Excellence BioHealth, University of Graz, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
| | - Nina Gubensäk
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.
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31
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Gizzio J, Thakur A, Haldane A, Post CB, Levy RM. Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.584161. [PMID: 38559238 PMCID: PMC10979876 DOI: 10.1101/2024.03.08.584161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Protein kinases are molecular machines with rich sequence variation that distinguishes the two main evolutionary branches - tyrosine kinases (TKs) from serine/threonine kinases (STKs). Using a sequence co-variation Potts statistical energy model we previously concluded that TK catalytic domains are more likely than STKs to adopt an inactive conformation with the activation loop in an autoinhibitory "folded" conformation, due to intrinsic sequence effects. Here we investigated the structural basis for this phenomenon by integrating the sequence-based model with structure-based molecular dynamics (MD) to determine the effects of mutations on the free energy difference between active and inactive conformations, using a novel thermodynamic cycle involving many (n=108) protein-mutation free energy perturbation (FEP) simulations in the active and inactive conformations. The sequence and structure-based results are consistent and support the hypothesis that the inactive conformation "DFG-out Activation Loop Folded", is a functional regulatory state that has been stabilized in TKs relative to STKs over the course of their evolution via the accumulation of residue substitutions in the activation loop and catalytic loop that facilitate distinct substrate binding modes in trans and additional modes of regulation in cis for TKs.
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Affiliation(s)
- Joan Gizzio
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Abhishek Thakur
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Allan Haldane
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122
| | - Carol Beth Post
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907
| | - Ronald M. Levy
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
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32
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Huettemann P, Mahadevan P, Lempart J, Tse E, Dehury B, Edwards BFP, Southworth DR, Sahoo BR, Jakob U. Amyloid Accelerator Polyphosphate Implicated as the Mystery Density in α-Synuclein Fibrils. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592011. [PMID: 38746133 PMCID: PMC11092616 DOI: 10.1101/2024.05.01.592011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Aberrant aggregation of α-Synuclein is the pathological hallmark of a set of neurodegenerative diseases termed synucleinopathies. Recent advances in cryo-electron microscopy have led to the structural determination of the first synucleinopathy-derived α-Synuclein fibrils, which contain a non-proteinaceous, "mystery density" at the core of the protofilaments, hypothesized to be highly negatively charged. Guided by previous studies that demonstrated that polyphosphate (polyP), a universally conserved polyanion, significantly accelerates α-Synuclein fibril formation, we conducted blind docking and molecular dynamics simulation experiments to model the polyP binding site in α-Synuclein fibrils. Here we demonstrate that our models uniformly place polyP into the lysine-rich pocket, which coordinates the mystery density in patient-derived fibrils. Subsequent in vitro studies and experiments in cells revealed that substitution of the two critical lysine residues K43 and K45 leads to a loss of all previously reported effects of polyP binding on α-Synuclein, including stimulation of fibril formation, change in filament conformation and stability as well as alleviation of cytotoxicity. In summary, our study demonstrates that polyP fits the unknown electron density present in in vivo α-Synuclein fibrils and suggests that polyP exerts its functions by neutralizing charge repulsion between neighboring lysine residues.
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33
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Wang T, Tong J, Zhang X, Wang Z, Xu L, Pan P, Hou T. Structure-based virtual screening of novel USP5 inhibitors targeting the zinc finger ubiquitin-binding domain. Comput Biol Med 2024; 174:108397. [PMID: 38603896 DOI: 10.1016/j.compbiomed.2024.108397] [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: 01/23/2024] [Revised: 03/21/2024] [Accepted: 04/01/2024] [Indexed: 04/13/2024]
Abstract
The equilibrium of cellular protein levels is pivotal for maintaining normal physiological functions. USP5 belongs to the deubiquitination enzyme (DUBs) family, controlling protein degradation and preserving cellular protein homeostasis. Aberrant expression of USP5 is implicated in a variety of diseases, including cancer, neurodegenerative diseases, and inflammatory diseases. In this paper, a multi-level virtual screening (VS) approach was employed to target the zinc finger ubiquitin-binding domain (ZnF-UBD) of USP5, leading to the identification of a highly promising candidate compound 0456-0049. Molecular dynamics (MD) simulations were then employed to assess the stability of complex binding and predict hotspot residues in interactions. The results indicated that the candidate stably binds to the ZnF-UBD of USP5 through crucial interactions with residues ARG221, TRP209, GLY220, ASN207, TYR261, TYR259, and MET266. Binding free energy calculations, along with umbrella sampling (US) simulations, underscored a superior binding affinity of the candidate relative to known inhibitors. Moreover, US simulations revealed conformational changes of USP5 during ligand dissociation. These insights provide a valuable foundation for the development of novel inhibitors targeting USP5.
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Affiliation(s)
- Tianhao Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, PR China; College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, PR China
| | - Jianbo Tong
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, PR China.
| | - Xing Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, PR China; College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, PR China
| | - Zhe Wang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, 310058, Zhejiang, PR China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, PR China
| | - Peichen Pan
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, PR China.
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, PR China.
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Alimi D, Hraoui M, Hajri A, Taamalli W, Selmi S, Sebai H. Bioactivity and molecular docking studies of selected plant compounds. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:4391-4399. [PMID: 38323805 DOI: 10.1002/jsfa.13327] [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: 11/15/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/08/2024]
Abstract
BACKGROUND The shortcomings of synthetic pesticides are becoming increasingly evident. In the pursuit of looking for alternative, environmentally friendly pesticides, the potential use of two naturally occurring sesquiterpenes, α-bisabolol and bisabolol oxide A, as bactericides or acaricides, was investigated against three gram-positive and three gram-negative bacteria, and the eggs and larvae of the cattle tick Hyalomma scupense, respectively. The primary targeted site of synthetic insecticides is acetylcholinesterase (AChE), so the inhibitory activity of both sesquiterpenes was evaluated. Then, molecular docking and molecular mechanics generalized Born surface area (MM-GBSA) studies were performed to gain insight into their binding mode in the AChE active site. RESULTS Bisabolol oxide A showed good activity against Staphylococcus aureus, Escherichia coli, and Salmonella enteritidis with inhibition zones ranging from 16 to 34 mm and minimal inhibitory concentration (CIM) of 3.125 mg mL-1. Ovicidal and larvicidal assays revealed promising activity of α-bisabolol and bisabolol oxide A against H. scupense, with bisabolol oxide A being more effective against larval ticks with lethal concentration (LC50) value of 0.78%. Both compounds also displayed potent anti-AChE activity with inhibition concentration (IC50) values of 37.09 and 28.14 μg mL-1, respectively. Furthermore, α-bisabolol and bisabolol oxide A exhibited good and comparable docking scores (-7.289 and -7.139 Kcal mol-1, respectively) and were found to accommodate in the active-site gorge of AChE via hydrogen bonding and hydrophobic interactions. CONCLUSION Bisabolol oxide A and, to a lesser degree, α-bisabolol are active against bacteria and ectoparasites and may represent an economical and sustainable alternative to toxic synthetic pesticides to control pathogens. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Dhouha Alimi
- Laboratory of Functional Physiology and Valorization of Bio-resources (LR23ES08), Higher Institute of Biotechnology of Beja, Beja, Tunisia
- University of Jendouba, Jendouba, Tunisia
| | - Manel Hraoui
- Laboratory of Functional Physiology and Valorization of Bio-resources (LR23ES08), Higher Institute of Biotechnology of Beja, Beja, Tunisia
- University of Jendouba, Jendouba, Tunisia
| | - Azhar Hajri
- Laboratory of Functional Physiology and Valorization of Bio-resources (LR23ES08), Higher Institute of Biotechnology of Beja, Beja, Tunisia
- University of Jendouba, Jendouba, Tunisia
| | - Wael Taamalli
- Laboratory of Olive Biotechnology, Center of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Slimen Selmi
- Laboratory of Functional Physiology and Valorization of Bio-resources (LR23ES08), Higher Institute of Biotechnology of Beja, Beja, Tunisia
- University of Jendouba, Jendouba, Tunisia
| | - Hichem Sebai
- Laboratory of Functional Physiology and Valorization of Bio-resources (LR23ES08), Higher Institute of Biotechnology of Beja, Beja, Tunisia
- University of Jendouba, Jendouba, Tunisia
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Salvadori L, Paiella M, Castiglioni B, Belladonna ML, Manenti T, Ercolani C, Cornioli L, Clemente N, Scircoli A, Sardella R, Tensi L, Astolfi A, Barreca ML, Chiappalupi S, Gentili G, Bosetti M, Sorci G, Filigheddu N, Riuzzi F. Equisetum arvense standardized dried extract hinders age-related osteosarcopenia. Biomed Pharmacother 2024; 174:116517. [PMID: 38574619 DOI: 10.1016/j.biopha.2024.116517] [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: 01/18/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 04/06/2024] Open
Abstract
Age-associated osteosarcopenia is an unresolved syndrome characterized by the concomitant loss of bone (osteopenia) and skeletal muscle (sarcopenia) tissues increasing falls, immobility, morbidity, and mortality. Unbalanced resorption of bone in the remodeling process and excessive protein breakdown, especially fast type II myosin heavy chain (MyHC-II) isoform and myofiber metabolic shift, are the leading causes of bone and muscle deterioration in the elderly, respectively. Equisetum arvense (EQ) is a plant traditionally recommended for many pathological conditions due to its anti-inflammatory properties. Thus, considering that a chronic low-grade inflammatory state predisposes to both osteoporosis and sarcopenia, we tested a standardized hydroalcoholic extract of EQ in in vitro models of muscle atrophy [C2C12 myotubes treated with proinflammatory cytokines (TNFα/IFNγ), excess glucocorticoids (dexamethasone), or the osteokine, receptor activator of nuclear factor kappa-B ligand (RANKL)] and osteoclastogenesis (RAW 264.7 cells treated with RANKL). We found that EQ counteracted myotube atrophy, blunting the activity of several pathways depending on the applied stimulus, and reduced osteoclast formation and activity. By in silico target fishing, IKKB-dependent nuclear factor kappa-B (NF-κB) inhibition emerges as a potential common mechanism underlying EQ's anti-atrophic effects. Consumption of EQ (500 mg/kg/day) by pre-geriatric C57BL/6 mice for 3 months translated into: i) maintenance of muscle mass and performance; ii) restrained myofiber oxidative shift; iii) slowed down age-related modifications in osteoporotic bone, significantly preserving trabecular connectivity density; iv) reduced muscle- and spleen-related inflammation. EQ can preserve muscle functionality and bone remodeling during aging, potentially valuable as a natural treatment for osteosarcopenia.
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Affiliation(s)
- Laura Salvadori
- Department of Translational Medicine, University of Piemonte Orientale, Novara 28100, Italy; Interuniversity Institute of Myology (IIM), Perugia 06132, Italy
| | - Martina Paiella
- Department of Translational Medicine, University of Piemonte Orientale, Novara 28100, Italy; Interuniversity Institute of Myology (IIM), Perugia 06132, Italy
| | - Beatrice Castiglioni
- Department Pharmaceutical Sciences, University of Piemonte Orientale, Novara, Italy
| | | | | | | | - Luca Cornioli
- Laboratori Biokyma srl, Anghiari, Arezzo 52031, Italy
| | - Nausicaa Clemente
- Department of Health Sciences and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale, Novara 28100, Italy
| | - Andrea Scircoli
- Department of Translational Medicine, University of Piemonte Orientale, Novara 28100, Italy; Interuniversity Institute of Myology (IIM), Perugia 06132, Italy
| | - Roccaldo Sardella
- Department of Pharmaceutical Sciences, University of Perugia, Perugia 06123, Italy
| | - Leonardo Tensi
- Department of Pharmaceutical Sciences, University of Perugia, Perugia 06123, Italy
| | - Andrea Astolfi
- Department of Pharmaceutical Sciences, University of Perugia, Perugia 06123, Italy
| | | | - Sara Chiappalupi
- Interuniversity Institute of Myology (IIM), Perugia 06132, Italy; Department of Medicine and Surgery, University of Perugia, Perugia 06132, Italy
| | - Giulia Gentili
- Interuniversity Institute of Myology (IIM), Perugia 06132, Italy; Department of Medicine and Surgery, University of Perugia, Perugia 06132, Italy
| | - Michela Bosetti
- Department Pharmaceutical Sciences, University of Piemonte Orientale, Novara, Italy
| | - Guglielmo Sorci
- Interuniversity Institute of Myology (IIM), Perugia 06132, Italy; Department of Medicine and Surgery, University of Perugia, Perugia 06132, Italy
| | - Nicoletta Filigheddu
- Department of Translational Medicine, University of Piemonte Orientale, Novara 28100, Italy; Interuniversity Institute of Myology (IIM), Perugia 06132, Italy
| | - Francesca Riuzzi
- Interuniversity Institute of Myology (IIM), Perugia 06132, Italy; Department of Medicine and Surgery, University of Perugia, Perugia 06132, Italy.
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Akkaya D, Seyhan G, Sari S, Barut B. In vitro and in silico investigation of FDA-approved drugs to be repurposed against Alzheimer's disease. Drug Dev Res 2024; 85:e22184. [PMID: 38634273 DOI: 10.1002/ddr.22184] [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: 02/06/2024] [Revised: 03/06/2024] [Accepted: 04/01/2024] [Indexed: 04/19/2024]
Abstract
Alzheimer's disease (AD), one of the main causes of dementia, is a neurodegenerative disorder. Cholinesterase inhibitors are used in the treatment of AD, but prolonged use of these drugs can lead to serious side effects. Drug repurposing is an approach that aims to reveal the effectiveness of drugs in different diseases beyond their clinical uses. In this work, we investigated in vitro and in silico inhibitory effects of 11 different drugs on cholinesterases. The results showed that trimebutine, theophylline, and levamisole had the highest acetylcholinesterase inhibitory actions among the tested drugs, and these drugs inhibited by 68.70 ± 0.46, 53.25 ± 3.40, and 44.03 ± 1.20%, respectively at 1000 µM. In addition, these drugs are bound to acetylcholinesterase via competitive manner. Molecular modeling predicted good fitness in acetylcholinesterase active site for these drugs and possible central nervous system action for trimebutine. All of these results demonstrated that trimebutine was determined to be the drug with the highest potential for use in AD.
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Affiliation(s)
- Didem Akkaya
- Faculty of Pharmacy, Department of Biochemistry, Karadeniz Technical University, Trabzon, Turkey
| | - Gökçe Seyhan
- Faculty of Pharmacy, Department of Biochemistry, Karadeniz Technical University, Trabzon, Turkey
| | - Suat Sari
- Faculty of Pharmacy, Pharmaceutical Chemistry Department, Hacettepe University, Ankara, Turkey
| | - Burak Barut
- Faculty of Pharmacy, Department of Biochemistry, Karadeniz Technical University, Trabzon, Turkey
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37
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Son NT, Gianibbi B, Panti A, Spiga O, Bastos JK, Fusi F. Vasorelaxant Activity of (2S)-Sakuranetin and Other Flavonoids Isolated from the Green Propolis of the Caatinga Mimosa tenuiflora. PLANTA MEDICA 2024; 90:454-468. [PMID: 38599606 DOI: 10.1055/a-2294-7042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Some in vitro and in vivo evidence is consistent with the cardiovascular beneficial activity of propolis. As the single actors responsible for this effect have never been identified, an in-depth investigation of flavonoids isolated from the green propolis of the Caatinga Mimosa tenuiflora was performed and their mechanism of action was described. A comprehensive electrophysiology, functional, and molecular docking approach was applied. Most flavanones and flavones were effective CaV1.2 channel blockers with a potency order of (2S)-sakuranetin > eriodictyol-7,3'-methyl ether > quercetin 3-methyl ether > 5,4'-dihydroxy-6,7-dimethoxyflavanone > santin > axillarin > penduletin > kumatakenin, ermanin and viscosine being weak or modest stimulators. Except for eriodictyol 5-O-methyl ether, all the flavonoids were also effective spasmolytic agents of vascular rings, kumatakenin and viscosine also showing an endothelium-dependent activity. (2S)-Sakuranetin also stimulated KCa1.1 channels both in single myocytes and vascular rings. In silico analysis provided interesting insights into the mode of action of (2S)-sakuranetin within both CaV1.2 and KCa1.1 channels. The green propolis of the Caatinga Mimosa tenuiflora is a valuable source of multi-target vasoactive flavonoids: this evidence reinforces its nutraceutical value in the cardiovascular disease prevention arena.
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Affiliation(s)
- Ninh The Son
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
- Department of Chemistry, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Caugiay, Hanoi, Vietnam
| | - Beatrice Gianibbi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Siena, Italy
| | - Alice Panti
- Dipartimento di Scienze della Vita, Università di Siena, Siena, Italy
| | - Ottavia Spiga
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Siena, Italy
| | - Jairo Kenupp Bastos
- School of Pharmaceutical Sciences of Ribeirão Preto, Ribeirão Preto, University of São Paulo, Ribeirão Preto-SP, Brazil
| | - Fabio Fusi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Siena, Italy
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38
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Schmitz B, Frieg B, Homeyer N, Jessen G, Gohlke H. Extracting binding energies and binding modes from biomolecular simulations of fragment binding to endothiapepsin. Arch Pharm (Weinheim) 2024; 357:e2300612. [PMID: 38319801 DOI: 10.1002/ardp.202300612] [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: 10/20/2023] [Revised: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 02/08/2024]
Abstract
Fragment-based drug discovery (FBDD) aims to discover a set of small binding fragments that may be subsequently linked together. Therefore, in-depth knowledge of the individual fragments' structural and energetic binding properties is essential. In addition to experimental techniques, the direct simulation of fragment binding by molecular dynamics (MD) simulations became popular to characterize fragment binding. However, former studies showed that long simulation times and high computational demands per fragment are needed, which limits applicability in FBDD. Here, we performed short, unbiased MD simulations of direct fragment binding to endothiapepsin, a well-characterized model system of pepsin-like aspartic proteases. To evaluate the strengths and limitations of short MD simulations for the structural and energetic characterization of fragment binding, we predicted the fragments' absolute free energies and binding poses based on the direct simulations of fragment binding and compared the predictions to experimental data. The predicted absolute free energies are in fair agreement with the experiment. Combining the MD data with binding mode predictions from molecular docking approaches helped to correctly identify the most promising fragments for further chemical optimization. Importantly, all computations and predictions were done within 5 days, suggesting that MD simulations may become a viable tool in FBDD projects.
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Affiliation(s)
- Birte Schmitz
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Benedikt Frieg
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Nadine Homeyer
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Gisela Jessen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, Jülich, Germany
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Sparkes E, Timmerman A, Markham JW, Boyd R, Gordon R, Walker KA, Kevin RC, Hibbs DE, Banister SD, Cairns EA, Stove C, Ametovski A. Synthesis and Functional Evaluation of Synthetic Cannabinoid Receptor Agonists Related to ADB-HEXINACA. ACS Chem Neurosci 2024; 15:1787-1812. [PMID: 38597712 DOI: 10.1021/acschemneuro.3c00818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024] Open
Abstract
ADB-HEXINACA has been recently reported as a synthetic cannabinoid receptor agonist (SCRA), one of the largest classes of new psychoactive substances (NPSs). This compound marks the entry of the n-hexyl tail group into the SCRA landscape, which has continued in the market with recent, newly detected SCRAs. As such, a proactive characterization campaign was undertaken, including the synthesis, characterization, and pharmacological evaluation of ADB-HEXINACA and a library of 41 closely related analogues. Two in vitro functional assays were employed to assess activity at CB1 and CB2 cannabinoid receptors, measuring Gβγ-coupled agonism through a fluorescence-based membrane potential assay (MPA) and β-arrestin 2 (βarr2) recruitment via a live cell-based nanoluciferase complementation reporter assay. ADB-HEXINACA was a potent and efficacious CB1 agonist (CB1 MPA pEC50 = 7.87 ± 0.12 M; Emax = 124 ± 5%; βarr2 pEC50 = 8.27 ± 0.14 M; Emax = 793 ± 42.5), as were most compounds assessed. Isolation of the heterocyclic core and alkyl tails allowed for the comprehensive characterization of structure-activity relationships in this compound class, which were rationalized in silico via induced fit docking experiments. Overall, most compounds assessed are possibly emerging NPSs.
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Affiliation(s)
- Eric Sparkes
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, New South Wales 2050, Australia
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2050, Australia
| | - Axelle Timmerman
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Jack W Markham
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, New South Wales 2050, Australia
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2050, Australia
- Sydney Pharmacy School, The University of Sydney, Sydney, New South Wales 2050, Australia
| | - Rochelle Boyd
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, New South Wales 2050, Australia
- Sydney Pharmacy School, The University of Sydney, Sydney, New South Wales 2050, Australia
| | - Rebecca Gordon
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, New South Wales 2050, Australia
- Sydney Pharmacy School, The University of Sydney, Sydney, New South Wales 2050, Australia
| | - Katelyn A Walker
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, New South Wales 2050, Australia
- School of Psychology, The University of Sydney, Sydney, New South Wales 2050, Australia
| | - Richard C Kevin
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, New South Wales 2050, Australia
- Department of Clinical Pharmacology and Toxicology, St Vincent's Hospital Sydney, Sydney, New South Wales 2010, Australia
- School of Clinical Medicine, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - David E Hibbs
- Sydney Pharmacy School, The University of Sydney, Sydney, New South Wales 2050, Australia
| | - Samuel D Banister
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, New South Wales 2050, Australia
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2050, Australia
| | - Elizabeth A Cairns
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, New South Wales 2050, Australia
- Sydney Pharmacy School, The University of Sydney, Sydney, New South Wales 2050, Australia
| | - Christophe Stove
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Adam Ametovski
- Lambert Initiative for Cannabinoid Therapeutics, Brain and Mind Centre, The University of Sydney, Sydney, New South Wales 2050, Australia
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2050, Australia
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40
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Baltasar-Marchueta M, Llona L, M-Alicante S, Barbolla I, Ibarluzea MG, Ramis R, Salomon AM, Fundora B, Araujo A, Muguruza-Montero A, Nuñez E, Pérez-Olea S, Villanueva C, Leonardo A, Arrasate S, Sotomayor N, Villarroel A, Bergara A, Lete E, González-Díaz H. Identification of Riluzole derivatives as novel calmodulin inhibitors with neuroprotective activity by a joint synthesis, biosensor, and computational guided strategy. Biomed Pharmacother 2024; 174:116602. [PMID: 38636396 DOI: 10.1016/j.biopha.2024.116602] [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: 01/19/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/20/2024] Open
Abstract
The development of new molecules for the treatment of calmodulin related cardiovascular or neurodegenerative diseases is an interesting goal. In this work, we introduce a novel strategy with four main steps: (1) chemical synthesis of target molecules, (2) Förster Resonance Energy Transfer (FRET) biosensor development and in vitro biological assay of new derivatives, (3) Cheminformatics models development and in vivo activity prediction, and (4) Docking studies. This strategy is illustrated with a case study. Firstly, a series of 4-substituted Riluzole derivatives 1-3 were synthetized through a strategy that involves the construction of the 4-bromoriluzole framework and its further functionalization via palladium catalysis or organolithium chemistry. Next, a FRET biosensor for monitoring Ca2+-dependent CaM-ligands interactions has been developed and used for the in vitro assay of Riluzole derivatives. In particular, the best inhibition (80%) was observed for 4-methoxyphenylriluzole 2b. Besides, we trained and validated a new Networks Invariant, Information Fusion, Perturbation Theory, and Machine Learning (NIFPTML) model for predicting probability profiles of in vivo biological activity parameters in different regions of the brain. Next, we used this model to predict the in vivo activity of the compounds experimentally studied in vitro. Last, docking study conducted on Riluzole and its derivatives has provided valuable insights into their binding conformations with the target protein, involving calmodulin and the SK4 channel. This new combined strategy may be useful to reduce assay costs (animals, materials, time, and human resources) in the drug discovery process of calmodulin inhibitors.
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Affiliation(s)
- Maider Baltasar-Marchueta
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Leire Llona
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | | | - Iratxe Barbolla
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Markel Garcia Ibarluzea
- Donostia International Physics Center, Donostia, Spain; Departament of Physics, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Rafael Ramis
- Donostia International Physics Center, Donostia, Spain; Departament of Physics, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Ane Miren Salomon
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Brenda Fundora
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Ariane Araujo
- Biofisika Institute, CSIC-UPV/EHU, Leioa 48940, Spain
| | | | - Eider Nuñez
- Biofisika Institute, CSIC-UPV/EHU, Leioa 48940, Spain
| | - Scarlett Pérez-Olea
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Christian Villanueva
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Aritz Leonardo
- Donostia International Physics Center, Donostia, Spain; Departament of Physics, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Sonia Arrasate
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Nuria Sotomayor
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | | | - Aitor Bergara
- Donostia International Physics Center, Donostia, Spain; Departament of Physics, University of the Basque Country, UPV/EHU, Leioa, Spain.
| | - Esther Lete
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain.
| | - Humberto González-Díaz
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain; Biofisika Institute, CSIC-UPV/EHU, Leioa 48940, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao 48011, Spain.
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41
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Rout M, Dey S, Mishra S, Panda S, Singh MK, Sinha R, Dehury B, Pati S. Machine learning and classical MD simulation to identify inhibitors against the P37 envelope protein of monkeypox virus. J Biomol Struct Dyn 2024; 42:3935-3948. [PMID: 37221882 DOI: 10.1080/07391102.2023.2216290] [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: 03/22/2023] [Accepted: 05/16/2023] [Indexed: 05/25/2023]
Abstract
Monkeypox virus (MPXV) outbreak is a serious public health concern that requires international attention. P37 of MPXV plays a pivotal role in DNA replication and acts as one of the promising targets for antiviral drug design. In this study, we intent to screen potential analogs of existing FDA approved drugs of MPXV against P37 using state-of-the-art machine learning and computational biophysical techniques. AlphaFold2 guided all-atoms molecular dynamics simulations optimized P37 structure is used for molecular docking and binding free energy calculations. Similar to members of Phospholipase-D family , the predicted P37 structure also adopts a β-α-β-α-β sandwich fold, harbouring strongly conserved HxKxxxxD motif. The binding pocket comprises of Tyr48, Lys86, His115, Lys117, Ser130, Asn132, Trp280, Asn240, His325, Lys327 and Tyr346 forming strong hydrogen bonds and dense hydrophobic contacts with the screened analogs and is surrounded by positively charged patches. Loops connecting the two domains and C-terminal region exhibit high degree of flexibility. In some structural ensembles, the partial disorderness in the C-terminal region is presumed to be due to its low confidence score, acquired during structure prediction. Transition from loop to β-strands (244-254 aa) in P37-Cidofovir and its analog complexes advocates the need for further investigations. MD simulations support the accuracy of the molecular docking results, indicating the potential of analogs as potent binders of P37. Taken together, our results provide preferable understanding of molecular recognition and dynamics of ligand-bound states of P37, offering opportunities for development of new antivirals against MPXV. However, the need of in vitro and in vivo assays for confirmation of these results still persists.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Madhusmita Rout
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
| | - Suchanda Dey
- Biomics and Biodiversity Lab, Siksha 'O' Anusandhan (deemed to be) University, Bhubaneswar, Odisha, India
| | - Sarbani Mishra
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
| | - Sunita Panda
- Mycology Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
| | - Mahender Kumar Singh
- Data Science Laboratory, National Brain Research Centre, Gurgaon, Haryana, India
| | - Rohan Sinha
- Computer Science, National Institute of Technology Patna, Patna, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
| | - Sanghamitra Pati
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
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Yan J, Bhadane R, Ran M, Ma X, Li Y, Zheng D, Salo-Ahen OMH, Zhang H. Development of Aptamer-DNAzyme based metal-nucleic acid frameworks for gastric cancer therapy. Nat Commun 2024; 15:3684. [PMID: 38693181 PMCID: PMC11063048 DOI: 10.1038/s41467-024-48149-9] [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: 08/22/2023] [Accepted: 04/23/2024] [Indexed: 05/03/2024] Open
Abstract
The metal-nucleic acid nanocomposites, first termed metal-nucleic acid frameworks (MNFs) in this work, show extraordinary potential as functional nanomaterials. However, thus far, realized MNFs face limitations including harsh synthesis conditions, instability, and non-targeting. Herein, we discover that longer oligonucleotides can enhance the synthesis efficiency and stability of MNFs by increasing oligonucleotide folding and entanglement probabilities during the reaction. Besides, longer oligonucleotides provide upgraded metal ions binding conditions, facilitating MNFs to load macromolecular protein drugs at room temperature. Furthermore, longer oligonucleotides facilitate functional expansion of nucleotide sequences, enabling disease-targeted MNFs. As a proof-of-concept, we build an interferon regulatory factor-1(IRF-1) loaded Ca2+/(aptamer-deoxyribozyme) MNF to target regulate glucose transporter (GLUT-1) expression in human epidermal growth factor receptor-2 (HER-2) positive gastric cancer cells. This MNF nanodevice disrupts GSH/ROS homeostasis, suppresses DNA repair, and augments ROS-mediated DNA damage therapy, with tumor inhibition rate up to 90%. Our work signifies a significant advancement towards an era of universal MNF application.
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Affiliation(s)
- Jiaqi Yan
- Department of Orthopaedics Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases Shanghai Institute of Traumatology and Orthopaedics Ruijin Hospital Shanghai Jiao Tong University School of Medicine 197 Ruijin 2nd Road, Shanghai, 200025, PR China
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Rajendra Bhadane
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
- Structural Bioinformatics Laboratory, Biochemistry, Åbo Akademi University, 20520, Turku, Finland
| | - Meixin Ran
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Xiaodong Ma
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Yuanqiang Li
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Dongdong Zheng
- Department of Ultrasound, Fudan University Shanghai Cancer Center, Shanghai, 200032, PR China
| | - Outi M H Salo-Ahen
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- Structural Bioinformatics Laboratory, Biochemistry, Åbo Akademi University, 20520, Turku, Finland
| | - Hongbo Zhang
- Department of Orthopaedics Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases Shanghai Institute of Traumatology and Orthopaedics Ruijin Hospital Shanghai Jiao Tong University School of Medicine 197 Ruijin 2nd Road, Shanghai, 200025, PR China.
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland.
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
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43
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Wan K, He J, Shi X. Construction of High Accuracy Machine Learning Interatomic Potential for Surface/Interface of Nanomaterials-A Review. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2305758. [PMID: 37640376 DOI: 10.1002/adma.202305758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/24/2023] [Indexed: 08/31/2023]
Abstract
The inherent discontinuity and unique dimensional attributes of nanomaterial surfaces and interfaces bestow them with various exceptional properties. These properties, however, also introduce difficulties for both experimental and computational studies. The advent of machine learning interatomic potential (MLIP) addresses some of the limitations associated with empirical force fields, presenting a valuable avenue for accurate simulations of these surfaces/interfaces of nanomaterials. Central to this approach is the idea of capturing the relationship between system configuration and potential energy, leveraging the proficiency of machine learning (ML) to precisely approximate high-dimensional functions. This review offers an in-depth examination of MLIP principles and their execution and elaborates on their applications in the realm of nanomaterial surface and interface systems. The prevailing challenges faced by this potent methodology are also discussed.
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Affiliation(s)
- Kaiwei Wan
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Jianxin He
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Xinghua Shi
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
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Dinh Thanh N, Son Hai D, Ngoc Toan V, Thi Kim Van H, Thi Kim Giang N, Minh Tri N. Sulfonyl thioureas with a benzo[d]thiazole ring as dual acetylcholinesterase/butyrylcholinesterase and human monoamine oxidase A and B inhibitors: An in vitro and in silico study. Arch Pharm (Weinheim) 2024; 357:e2300557. [PMID: 38321839 DOI: 10.1002/ardp.202300557] [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: 10/01/2023] [Revised: 12/30/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024]
Abstract
A series of sulfonyl thioureas 6a-q containing a benzo[d]thiazole ring with an ester functional group was synthesized from corresponding substituted 2-aminobenzo[d]thiazoles 3a-q and p-toluenesulfonyl isothiocyanate. They had remarkable inhibitory activity against acetylcholinesterase (AChE), butyrylcholinesterase (BChE), monoamine oxidase (MAO)-A, and MAO-B. Among thioureas, several compounds had notable activity in the order of 6k > 6 h > 6c (AChE), 6j > 6g > 6k (BChE), 6k > 6g > 6f (MAO-A), and 6i > 6k > 6h (MAO-B). Compound 6k was an inhibitor of interest due to its potent or good activity against all studied enzymes, with IC50 values of 0.027 ± 0.008 μM (AChE), 0.043 ± 0.004 μM (BChE), 0.353 ± 0.01 μM (MAO-A), and 0.716 ± 0.02 μM (MAO-B). This inhibitory capacity was comparable to that of the reference drugs for each enzyme. Kinetic studies of two compounds with potential activity, 6k (against AChE) and 6j (against BChE), had shown that both 6k and 6j followed competitive-type enzyme inhibition, with Ki constants of 24.49 and 12.16 nM, respectively. Induced fit docking studies for enzymes 4EY7, 7BO4, 2BXR, and 2BYB showed active interactions between sulfonyl thioureas of benzo[d]thiazoles and the residues in the active pocket with ligands 6k, 6i, and 6j, respectively. The stability of the ligand-protein complexes while each ligand entered the active site of each enzyme (4EY7, 7BO4, 2BXR, or 2BYB) was confirmed by molecular dynamics simulations.
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Affiliation(s)
- Nguyen Dinh Thanh
- Department of Organic Chemistry, Faculty of Chemistry, University of Science (Vietnam National University, Ha Noi), Ha Noi, Hoan Kiem, Viet Nam
| | - Do Son Hai
- Department of Organic Chemistry, Faculty of Chemistry, University of Science (Vietnam National University, Ha Noi), Ha Noi, Hoan Kiem, Viet Nam
- Institute of Science and Technology, Ministry of Public Security of Vietnam, Ha Noi, Cau Giay, Viet Nam
| | - Vu Ngoc Toan
- Department of Organic Chemistry, Faculty of Chemistry, University of Science (Vietnam National University, Ha Noi), Ha Noi, Hoan Kiem, Viet Nam
- Institute of New Technology, Military Institute of Science and Technology, Ha Noi, Cau Giay, Viet Nam
| | - Hoang Thi Kim Van
- Department of Organic Chemistry, Faculty of Chemistry, University of Science (Vietnam National University, Ha Noi), Ha Noi, Hoan Kiem, Viet Nam
- Faculty of Chemical Technology, Viet Tri University of Industry, Tien Kien, Lam Thao, Phu Tho, Viet Nam
| | - Nguyen Thi Kim Giang
- Department of Organic Chemistry, Faculty of Chemistry, University of Science (Vietnam National University, Ha Noi), Ha Noi, Hoan Kiem, Viet Nam
- Institute of Science and Technology, Ministry of Public Security of Vietnam, Ha Noi, Cau Giay, Viet Nam
| | - Nguyen Minh Tri
- Department of Organic Chemistry, Faculty of Chemistry, University of Science (Vietnam National University, Ha Noi), Ha Noi, Hoan Kiem, Viet Nam
- Institute of New Technology, Military Institute of Science and Technology, Ha Noi, Cau Giay, Viet Nam
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Qin Y, Li G, Wang L, Yin G, Zhang X, Wang H, Zheng P, Hua W, Cheng Y, Zhao Y, Zhang J. Modular preparation of biphenyl triazoles via click chemistry as non-competitive hyaluronidase inhibitors. Bioorg Chem 2024; 146:107291. [PMID: 38521011 DOI: 10.1016/j.bioorg.2024.107291] [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: 01/13/2024] [Revised: 03/06/2024] [Accepted: 03/15/2024] [Indexed: 03/25/2024]
Abstract
Hyaluronidase is a promising target in drug discovery, given its overexpression in a range of physiological and pathological processes, including tumor migration, skin aging, sagging, and wrinkling, as well as inflammation and bacterial infections. In this study, to identify novel hyaluronidase inhibitors, we applied click chemistry for the modular synthesis of 370 triazoles in 96-well plates, starting with biphenyl azide. Utilizing an optimized turbidimetric screening assay in microplates, we identified Fmoc-containing triazoles 5 and 6, as well as quinoline-containing triazoles 15 and 16, as highly effective hyaluronidase inhibitors. Subsequent research indicated that these triazoles potentially interact with a novel binding site of hyaluronidase. Notably, these inhibitors displayed minimal cytotoxicity and showed promising anti-inflammatory effects in LPS-stimulated macrophages. Remarkably, compound 6 significantly reduced NO release by 74 % at a concentration of 20 μM.
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Affiliation(s)
- Yiman Qin
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei 230032, PR China
| | - Guanyi Li
- School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Ling Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei 230032, PR China
| | - Guangyuan Yin
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei 230032, PR China
| | - Xiang Zhang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei 230032, PR China
| | - Hongxiang Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei 230032, PR China
| | - Pengfei Zheng
- First School of Clinical Medicine, Anhui Medical University, Hefei 230032, PR China
| | - Wentao Hua
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei 230032, PR China
| | - Yan Cheng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei 230032, PR China
| | - Yaxue Zhao
- School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, PR China.
| | - Jiong Zhang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei 230032, PR China.
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46
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Chinnamadhu A, Ramakrishnan J, Suresh S, Poomani K. Binding properties of selective inhibitors of P323L mutated RdRp of SARS-CoV-2: a combined molecular screening, docking and dynamics simulation study. J Biomol Struct Dyn 2024; 42:4283-4296. [PMID: 37301607 DOI: 10.1080/07391102.2023.2219762] [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: 03/03/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023]
Abstract
Since 2019 the SARS-CoV-2 and its variants caused COVID-19, such incidents brought the world in pandemic situation. This happened due to furious mutations in SARS-CoV-2, in which some variants had high transmissibility and infective, this led the virus emerged as virulent and worsened the COVID-19 situation. Among the variants, P323L is one of the important mutants of RdRp in SARS-CoV-2. To inhibit the erroneous function of this mutated RdRp, we have screened 943 molecules against the P323L mutated RdRp with the criteria that the molecules with 90% similar to the structure of remdesivir (control drug) resulted nine molecules. Further, these molecules were evaluated by induced fit docking (IFD) identified two molecules (M2 & M4) which are forming strong intermolecular interactions with the key residues of mutated RdRp and has high binding affinity. Docking score of the M2 and M4 molecules with mutated RdRp are -9.24 and -11.87 kcal/mol, respectively. Further, to understand the intermolecular interactions, conformational stability, the molecular dynamics simulation and binding free energy calculations were performed. The binding free energy values of M2 and M4 molecules with the P323L mutated RdRp complexes are -81.60 and -83.07 kcal/mol, respectively. The results of this in silico study confirm that M4 is a potential molecule; hence, it may be considered as the potential inhibitor of P323L mutated RdRp to treat COVID-19 after clinical investigation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Archana Chinnamadhu
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Jaganathan Ramakrishnan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Suganya Suresh
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Kumaradhas Poomani
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
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47
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Shaimardanov AR, Shulga DA, Palyulin VA. Do electrostatic interactions make a difference in physics-based AutoDock4 scoring function? J Comput Chem 2024. [PMID: 38661234 DOI: 10.1002/jcc.27373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024]
Abstract
Physics-based scoring function AutoDock4 is one of the most successfully applied tools in the area of structure-based drug design. However, current scoring functions are still far from being perfect. In a recent work highlighting the strengths and deficiencies of current scoring functions, we discovered that the residual error of ΔGbind predictions made by AutoDock4 is highly correlated to the presence of formally charged fragments in a ligand. In this work, we study how the use of the high-quality atomic charges, applied for contemporary force fields calculation, affects the quality of the experimental ΔGbind prediction by means of AutoDock4. We initially expected that the previously found discrepancy could be attributed to the Gasteiger charges used within AutoDock4. We show that AutoDock4 is, surprisingly, not sensitive to the charges used, and the use of QC-derived atomic charges does not lead to any statistical improvements. We also briefly discuss the role of the explicit empirical hydrogen bond term along with the electrostatic term.
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Affiliation(s)
- Arslan R Shaimardanov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Dmitry A Shulga
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Vladimir A Palyulin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
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48
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Chen Z, Yu J, Wang H, Xu P, Fan L, Sun F, Huang S, Zhang P, Huang H, Gu S, Zhang B, Zhou Y, Wan X, Pei G, Xu HE, Cheng J, Wang S. Flexible scaffold-based cheminformatics approach for polypharmacological drug design. Cell 2024; 187:2194-2208.e22. [PMID: 38552625 DOI: 10.1016/j.cell.2024.02.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 02/04/2024] [Accepted: 02/27/2024] [Indexed: 04/28/2024]
Abstract
Effective treatments for complex central nervous system (CNS) disorders require drugs with polypharmacology and multifunctionality, yet designing such drugs remains a challenge. Here, we present a flexible scaffold-based cheminformatics approach (FSCA) for the rational design of polypharmacological drugs. FSCA involves fitting a flexible scaffold to different receptors using different binding poses, as exemplified by IHCH-7179, which adopted a "bending-down" binding pose at 5-HT2AR to act as an antagonist and a "stretching-up" binding pose at 5-HT1AR to function as an agonist. IHCH-7179 demonstrated promising results in alleviating cognitive deficits and psychoactive symptoms in mice by blocking 5-HT2AR for psychoactive symptoms and activating 5-HT1AR to alleviate cognitive deficits. By analyzing aminergic receptor structures, we identified two featured motifs, the "agonist filter" and "conformation shaper," which determine ligand binding pose and predict activity at aminergic receptors. With these motifs, FSCA can be applied to the design of polypharmacological ligands at other receptors.
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Affiliation(s)
- Zhangcheng Chen
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jing Yu
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Huan Wang
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Peiyu Xu
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Luyu Fan
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Fengxiu Sun
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Sijie Huang
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Pei Zhang
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | | | - Shuo Gu
- ComMedX, Beijing 100094, China
| | | | - Yue Zhou
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | | | - Gang Pei
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - H Eric Xu
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Jianjun Cheng
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| | - Sheng Wang
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
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49
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Sampson JM, Cannon DA, Duan J, Epstein JCK, Sergeeva AP, Katsamba PS, Mannepalli SM, Bahna FA, Adihou H, Guéret SM, Gopalakrishnan R, Geschwindner S, Rees DG, Sigurdardottir A, Wilkinson T, Dodd RB, De Maria L, Mobarec JC, Shapiro L, Honig B, Buchanan A, Friesner RA, Wang L. Robust prediction of relative binding energies for protein-protein complex mutations using free energy perturbation calculations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590325. [PMID: 38712280 PMCID: PMC11071377 DOI: 10.1101/2024.04.22.590325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Computational free energy-based methods have the potential to significantly improve throughput and decrease costs of protein design efforts. Such methods must reach a high level of reliability, accuracy, and automation to be effectively deployed in practical industrial settings in a way that impacts protein design projects. Here, we present a benchmark study for the calculation of relative changes in protein-protein binding affinity for single point mutations across a variety of systems from the literature, using free energy perturbation (FEP+) calculations. We describe a method for robust treatment of alternate protonation states for titratable amino acids, which yields improved correlation with and reduced error compared to experimental binding free energies. Following careful analysis of the largest outlier cases in our dataset, we assess limitations of the default FEP+ protocols and introduce an automated script which identifies probable outlier cases that may require additional scrutiny and calculates an empirical correction for a subset of charge-related outliers. Through a series of three additional case study systems, we discuss how protein FEP+ can be applied to real-world protein design projects, and suggest areas of further study.
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Affiliation(s)
| | | | - Jianxin Duan
- Schrödinger, GmbH, Life Sciences Software, Mannheim, Germany
| | | | - Alina P. Sergeeva
- Columbia University, Department of Systems Biology, New York, NY, USA
| | | | - Seetha M. Mannepalli
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, NY, USA, 10027
| | - Fabiana A. Bahna
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, NY, USA, 10027
| | - Hélène Adihou
- AstraZeneca, Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, Gothenburg, Sweden
- Max Planck Institute of Molecular Physiology, AstraZeneca-MPI Satellite Unit, Dortmund, Germany
| | - Stéphanie M. Guéret
- AstraZeneca, Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, Gothenburg, Sweden
- Max Planck Institute of Molecular Physiology, AstraZeneca-MPI Satellite Unit, Dortmund, Germany
| | - Ranganath Gopalakrishnan
- AstraZeneca, Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, Gothenburg, Sweden
- Max Planck Institute of Molecular Physiology, AstraZeneca-MPI Satellite Unit, Dortmund, Germany
| | - Stefan Geschwindner
- AstraZeneca, Mechanistic and Structural Biology, Discovery Sciences, R&D, Cambridge, UK
| | | | | | | | - Roger B. Dodd
- AstraZeneca, Biologics Engineering, R&D, Cambridge, UK
| | - Leonardo De Maria
- AstraZeneca, Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, Gothenburg, Sweden
| | - Juan Carlos Mobarec
- AstraZeneca, Mechanistic and Structural Biology, Discovery Sciences, R&D, Cambridge, UK
| | - Lawrence Shapiro
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, NY, USA, 10027
- Columbia University, Department of Biochemistry and Molecular Biophysics, New York, NY, USA
| | - Barry Honig
- Columbia University, Department of Systems Biology, New York, NY, USA
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, NY, USA, 10027
- Columbia University, Department of Biochemistry and Molecular Biophysics, New York, NY, USA
- Columbia University, Department of Medicine, New York, NY, USA
| | | | | | - Lingle Wang
- Schrödinger, Inc., Life Sciences Software, New York, NY, USA
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50
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Albani M, Fassi EMA, Moretti RM, Garofalo M, Montagnani Marelli M, Roda G, Sgrignani J, Cavalli A, Grazioso G. Computational Design of Novel Cyclic Peptides Endowed with Autophagy-Inhibiting Activity on Cancer Cell Lines. Int J Mol Sci 2024; 25:4622. [PMID: 38731842 PMCID: PMC11083565 DOI: 10.3390/ijms25094622] [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: 03/26/2024] [Revised: 04/17/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024] Open
Abstract
(1) Autophagy plays a significant role in development and cell proliferation. This process is mainly accomplished by the LC3 protein, which, after maturation, builds the nascent autophagosomes. The inhibition of LC3 maturation results in the interference of autophagy activation. (2) In this study, starting from the structure of a known LC3B binder (LIR2-RavZ peptide), we identified new LC3B ligands by applying an in silico drug design strategy. The most promising peptides were synthesized, biophysically assayed, and biologically evaluated to ascertain their potential antiproliferative activity on five humans cell lines. (3) A cyclic peptide (named Pep6), endowed with high conformational stability (due to the presence of a disulfide bridge), displayed a Kd value on LC3B in the nanomolar range. Assays accomplished on PC3, MCF-7, and A549 cancer cell lines proved that Pep6 exhibited cytotoxic effects comparable to those of the peptide LIR2-RavZ, a reference LC3B ligand. Furthermore, it was ineffective on both normal prostatic epithelium PNT2 and autophagy-defective prostate cancer DU145 cells. (4) Pep6 can be considered a new autophagy inhibitor that can be employed as a pharmacological tool or even as a template for the rational design of new small molecules endowed with autophagy inhibitory activity.
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Affiliation(s)
- Marco Albani
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.A.); (G.R.)
| | - Enrico Mario Alessandro Fassi
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.A.); (G.R.)
| | - Roberta Manuela Moretti
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy; (R.M.M.); (M.M.M.)
| | - Mariangela Garofalo
- Department of Pharmaceutical and Pharmacological Sciences, Università di Padova, Via F. Marzolo 5, 35131 Padova, Italy;
| | - Marina Montagnani Marelli
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy; (R.M.M.); (M.M.M.)
| | - Gabriella Roda
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.A.); (G.R.)
| | - Jacopo Sgrignani
- Institute for Research in Biomedicine (IRB), Via Chiesa 5, 6500 Bellinzona, Switzerland; (J.S.); (A.C.)
| | - Andrea Cavalli
- Institute for Research in Biomedicine (IRB), Via Chiesa 5, 6500 Bellinzona, Switzerland; (J.S.); (A.C.)
- Swiss Institute of Bioinformatics (SIB), University of Lausanne, Quartier UNIL-Sorge, Bâtiment Amphipôle, 1015 Lausanne, Switzerland
| | - Giovanni Grazioso
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.A.); (G.R.)
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