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Maccallini C, Budriesi R, De Filippis B, Amoroso R. Advancements in the Research of New Modulators of Nitric Oxide Synthases Activity. Int J Mol Sci 2024; 25:8486. [PMID: 39126054 PMCID: PMC11313090 DOI: 10.3390/ijms25158486] [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: 06/28/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
Nitric oxide (NO) has been defined as the "miracle molecule" due to its essential pleiotropic role in living systems. Besides its implications in physiologic functions, it is also involved in the development of several disease states, and understanding this ambivalence is crucial for medicinal chemists to develop therapeutic strategies that regulate NO production without compromising its beneficial functions in cell physiology. Although nitric oxide synthase (NOS), i.e., the enzyme deputed to the NO biosynthesis, is a well-recognized druggable target to regulate NO bioavailability, some issues have emerged during the past decades, limiting the progress of NOS modulators in clinical trials. In the present review, we discuss the most promising advancements in the research of small molecules that are able to regulate NOS activity with improved pharmacodynamic and pharmacokinetic profiles, providing an updated framework of this research field that could be useful for the design and development of new NOS modulators.
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Affiliation(s)
- Cristina Maccallini
- Department of Pharmacy, University “G. d’Annunzio” of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy; (B.D.F.); (R.A.)
| | - Roberta Budriesi
- Department of Pharmacy and Biotechnology, Food Chemistry and Nutraceutical Lab, Alma Mater Studiorum-University of Bologna, 40126 Bologna, Italy;
| | - Barbara De Filippis
- Department of Pharmacy, University “G. d’Annunzio” of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy; (B.D.F.); (R.A.)
| | - Rosa Amoroso
- Department of Pharmacy, University “G. d’Annunzio” of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy; (B.D.F.); (R.A.)
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2
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Maccallini C, Amoroso R. Neuronal Nitric Oxide Synthase and Post-Translational Modifications in the Development of Central Nervous System Diseases: Implications and Regulation. Molecules 2023; 28:6691. [PMID: 37764469 PMCID: PMC10538099 DOI: 10.3390/molecules28186691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
In the Central Nervous System (CNS), Nitric Oxide (NO) is mainly biosynthesized by neuronal Nitric Oxide Synthase (nNOS). The dysregulated activation of nNOS in neurons is critical in the development of different conditions affecting the CNS. The excessive production of NO by nNOS is responsible for a number of proteins' post-translational modifications (PTMs), which can lead to aberrant biochemical pathways, impairing CNS functions. In this review, we briefly revise the main implications of dysregulated nNOS in the progression of the most prevalent CNS neurodegenerative disorders, i.e., Alzheimer's disease (AD) and Parkinson's disease, as well as in the development of neuronal disorders. Moreover, a specific focus on compounds able to modulate nNOS activity as promising therapeutics to tackle different neuronal diseases is presented.
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Affiliation(s)
- Cristina Maccallini
- Department of Pharmacy, University “G. d’Annunzio” of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy;
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3
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Carrión MD, Rubio-Ruiz B, Franco-Montalban F, Amoia P, Zuccarini MC, De Simone C, Camacho ME, Amoroso R, Maccallini C. New amidine-benzenesulfonamides as iNOS inhibitors for the therapy of the triple negative breast cancer. Eur J Med Chem 2023; 248:115112. [PMID: 36641860 DOI: 10.1016/j.ejmech.2023.115112] [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: 11/21/2022] [Revised: 01/03/2023] [Accepted: 01/08/2023] [Indexed: 01/11/2023]
Abstract
Triple negative breast cancer (TNBC) is a specific breast cancer subtype, and poor prognosis is associated to this tumour when it is in the metastatic form. The overexpression of the inducible Nitric Oxide Synthase (iNOS) is considered a predictor of poor outcome in TNBC patients, and this enzyme is reported as a valuable molecular target to compromise TNBC progression. In this work, new amidines containing a benzenesulfonamide group were designed and synthesized as selective iNOS inhibitors. An in vitro biological evaluation was performed to assess compounds activity against both the inducible and constitutive NOSs. The most interesting compounds 1b and 2b were evaluated on MDA-MB-231 cells as antiproliferative agents, and 1b capability to counteract cell migration was also studied. Finally, an in-depth docking study was performed to shed light on the observed potency and selectivity of action of the most promising compounds.
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Affiliation(s)
- M Dora Carrión
- Department of Medicinal and Organic Chemistry, Faculty of Pharmacy, Campus Cartuja s/n, University of Granada, 18071, Granada, Spain
| | - Belén Rubio-Ruiz
- Department of Medicinal and Organic Chemistry, Faculty of Pharmacy, Campus Cartuja s/n, University of Granada, 18071, Granada, Spain; GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Avda. Ilustración 114, 18016, Granada, Spain
| | - Francisco Franco-Montalban
- Department of Medicinal and Organic Chemistry, Faculty of Pharmacy, Campus Cartuja s/n, University of Granada, 18071, Granada, Spain
| | - Pasquale Amoia
- Department of Pharmacy, University "G. d'Annunzio" of Chieti-Pescara, Via dei Vestini 31, 66100, Chieti, Italy
| | - Maria Chiara Zuccarini
- Department of Medical, Oral and Biotechnological Sciences, University "G. d'Annunzio" of Chieti-Pescara, Via dei Vestini 31, 66100, Chieti, Italy
| | - Chiara De Simone
- Department of Medical, Oral and Biotechnological Sciences, University "G. d'Annunzio" of Chieti-Pescara, Via dei Vestini 31, 66100, Chieti, Italy
| | - M Encarnación Camacho
- Department of Medicinal and Organic Chemistry, Faculty of Pharmacy, Campus Cartuja s/n, University of Granada, 18071, Granada, Spain.
| | - Rosa Amoroso
- Department of Pharmacy, University "G. d'Annunzio" of Chieti-Pescara, Via dei Vestini 31, 66100, Chieti, Italy.
| | - Cristina Maccallini
- Department of Pharmacy, University "G. d'Annunzio" of Chieti-Pescara, Via dei Vestini 31, 66100, Chieti, Italy
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4
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Mittal A, Kakkar R. Nitric Oxide Synthases and Their Inhibitors: A Review. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180816666190222154457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nitric Oxide (NO), an important biological mediator, is involved in the regulation of the cardiovascular, nervous and immune systems in mammals. Synthesis of NO is catalyzed by its biosynthetic enzyme, Nitric Oxide Synthase (NOS). There are three main isoforms of the enzyme, neuronal NOS, endothelial NOS and inducible NOS, which have very similar structures but differ in their expression and activities. NO is produced in the active site of the enzyme in two distinct cycles from oxidation of the substrate L-arg (L-arginine) in nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reaction. NOS has gained considerable attention of biochemists due to its complexity and unique catalytic mechanism. The review focuses on NOS structure, its function and catalytic reaction mechanism. In particular, the review is concluded with a discussion on the role of all three isoforms of NOS in physiological and pathological conditions and their inhibitors with a focus on the role of computational techniques in their development.
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Affiliation(s)
- Anshika Mittal
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Rita Kakkar
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India
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5
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Abstract
Introduction: The development of drug candidates with a defined selectivity profile and a unique molecular structure is of fundamental interest for drug discovery. In contrast to the costly screening of large substance libraries, the targeted de novo design of a drug by using structural information of either the biological target and/or structure-activity relationship data of active modulators offers an efficient and intellectually appealing alternative. Areas covered: This review provides an overview on the different techniques of de novo drug design (ligand-based drug design, structure-based drug design, and fragment-based drug design) and highlights successful examples of this targeted approach toward selective modulators of therapeutically relevant targets. Expert opinion: De novo drug design has established itself as a very efficient method for the development of potent and selective modulators for a variety of different biological target classes. The ever-growing wealth of structural data on therapeutic targets will certainly further enhance the importance of de novo design for the drug discovery process in the future. However, a consistent use of the terminology of de novo drug design in the scientific literature should be sought.
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Affiliation(s)
- Thomas Fischer
- a Center of Organic and Medicinal Chemistry, Institute of Chemistry and Biotechnology , Zurich University of Applied Sciences ZHAW , Wädenswil , Switzerland
| | - Silvia Gazzola
- b Dipartimento di Scienza e Alta Tecnologia , Università degli Studi dell'Insubria , Como , Italy
| | - Rainer Riedl
- a Center of Organic and Medicinal Chemistry, Institute of Chemistry and Biotechnology , Zurich University of Applied Sciences ZHAW , Wädenswil , Switzerland
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6
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Bignon E, Rizza S, Filomeni G, Papaleo E. Use of Computational Biochemistry for Elucidating Molecular Mechanisms of Nitric Oxide Synthase. Comput Struct Biotechnol J 2019; 17:415-429. [PMID: 30996821 PMCID: PMC6451115 DOI: 10.1016/j.csbj.2019.03.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/17/2019] [Accepted: 03/21/2019] [Indexed: 12/25/2022] Open
Abstract
Nitric oxide (NO) is an essential signaling molecule in the regulation of multiple cellular processes. It is endogenously synthesized by NO synthase (NOS) as the product of L-arginine oxidation to L-citrulline, requiring NADPH, molecular oxygen, and a pterin cofactor. Two NOS isoforms are constitutively present in cells, nNOS and eNOS, and a third is inducible (iNOS). Despite their biological relevance, the details of their complex structural features and reactivity mechanisms are still unclear. In this review, we summarized the contribution of computational biochemistry to research on NOS molecular mechanisms. We described in detail its use in studying aspects of structure, dynamics and reactivity. We also focus on the numerous outstanding questions in the field that could benefit from more extensive computational investigations.
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Affiliation(s)
- Emmanuelle Bignon
- Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Salvatore Rizza
- Redox Signaling and Oxidative Stress Group, Cell Stress and Survival Unit, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Giuseppe Filomeni
- Redox Signaling and Oxidative Stress Group, Cell Stress and Survival Unit, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark.,Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark.,Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark
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7
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Mittal A, Arora R, Kakkar R. Pharmacophore modeling, 3D-QSAR and molecular docking studies of quinazolines and aminopyridines as selective inhibitors of inducible nitric oxide synthase. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2019. [DOI: 10.1142/s0219633619500020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pharmacophore modeling and 3D-Quantitative Structure Activity Relationship (3D-QSAR) studies have been performed on a dataset of thirty-two quinazoline and aminopyridine derivatives to get an insight into the important structural features required for binding to inducible nitric oxide synthase (iNOS). A four-point CPH (Common Pharmacophore Hypothesis), AHPR.29, with a hydrogen bond acceptor, hydrophobic group, positively charged ionizable group and an aromatic ring, has been obtained as the best pharmacophore model. Satisfactory statistical parameters of correlation ([Formula: see text]) and cross-validated ([Formula: see text]) correlation coefficients, 0.9288 and 0.6353, respectively, show high robustness and good predictive ability of our selected model. The contour maps have been developed from this model and the analysis has provided an interpretable explanation of the effect that various features and substituents have on the potency and selectivity of inhibitors towards iNOS. Docking studies have also been performed in order to analyze the interactions between the enzyme and the inhibitors. Our proposed model can thus be further used for screening a large database of compounds and design new iNOS inhibitors.
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Affiliation(s)
- Anshika Mittal
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Ritu Arora
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Rita Kakkar
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India
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8
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Maccallini C, Di Matteo M, Gallorini M, Montagnani M, Graziani V, Ammazzalorso A, Amoia P, De Filippis B, Di Silvestre S, Fantacuzzi M, Giampietro L, Potenza MA, Re N, Pandolfi A, Cataldi A, Amoroso R. Discovery of N-{3-[(ethanimidoylamino)methyl]benzyl}-l-prolinamide dihydrochloride: A new potent and selective inhibitor of the inducible nitric oxide synthase as a promising agent for the therapy of malignant glioma. Eur J Med Chem 2018; 152:53-64. [PMID: 29689474 DOI: 10.1016/j.ejmech.2018.04.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 04/10/2018] [Accepted: 04/12/2018] [Indexed: 01/08/2023]
Abstract
In mammalian cells, aberrant iNOS induction may have detrimental consequences, and seems to be involved in the proliferation and progression of different tumors, such as malignant gliomas. Therefore, selective inhibition of iNOS could represent a feasible therapeutic strategy to treat these conditions. In this context, we have previously disclosed new acetamidines able to inhibit iNOS with a very high selectivity profile over eNOS or nNOS. Here we report the synthesis of a new series of compounds structurally related to the leading scaffold of N-[(3-aminomethyl)benzyl] acetamidine (1400 W), together with their in vitro activity and selectivity. Compound 39 emerged as the most promising molecule of this series, and it was ex vivo evaluated on isolated and perfused resistance arteries, confirming a high selectivity toward iNOS inhibition. Moreover, C6 rat glioma cell lines biological response to 39 was investigated, and preliminary MTT assay showed a significant decrease in cell metabolic activity of C6 rat glioma cells. Finally, results of a docking study shed light on the binding mode of 39 into NOS catalytic site.
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Affiliation(s)
| | - Mauro Di Matteo
- Department of Pharmacy - University of Chieti "G. d'Annunzio", Italy
| | | | - Monica Montagnani
- Department of Biomedical Sciences and Human Oncology, Medical School - University of Bari "Aldo Moro", Italy
| | | | | | - Pasquale Amoia
- Department of Pharmacy - University of Chieti "G. d'Annunzio", Italy
| | | | - Sara Di Silvestre
- Department of Medical, Oral and Biotechnological Sciences, Centro Scienze dell'Invecchiamento e Medicina Traslazionale (Ce.SI-MeT), University "G. d'Annunzio" Chieti-Pescara, Italy
| | | | | | - Maria A Potenza
- Department of Biomedical Sciences and Human Oncology, Medical School - University of Bari "Aldo Moro", Italy
| | - Nazzareno Re
- Department of Pharmacy - University of Chieti "G. d'Annunzio", Italy
| | - Assunta Pandolfi
- Department of Medical, Oral and Biotechnological Sciences, Centro Scienze dell'Invecchiamento e Medicina Traslazionale (Ce.SI-MeT), University "G. d'Annunzio" Chieti-Pescara, Italy
| | - Amelia Cataldi
- Department of Pharmacy - University of Chieti "G. d'Annunzio", Italy
| | - Rosa Amoroso
- Department of Pharmacy - University of Chieti "G. d'Annunzio", Italy
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9
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Marques SM, Daniel L, Buryska T, Prokop Z, Brezovsky J, Damborsky J. Enzyme Tunnels and Gates As Relevant Targets in Drug Design. Med Res Rev 2016; 37:1095-1139. [PMID: 27957758 DOI: 10.1002/med.21430] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/11/2016] [Accepted: 11/07/2016] [Indexed: 12/28/2022]
Abstract
Many enzymes contain tunnels and gates that are essential to their function. Gates reversibly switch between open and closed conformations and thereby control the traffic of small molecules-substrates, products, ions, and solvent molecules-into and out of the enzyme's structure via molecular tunnels. Many transient tunnels and gates undoubtedly remain to be identified, and their functional roles and utility as potential drug targets have received comparatively little attention. Here, we describe a set of general concepts relating to the structural properties, function, and classification of these interesting structural features. In addition, we highlight the potential of enzyme tunnels and gates as targets for the binding of small molecules. The different types of binding that are possible and the potential pharmacological benefits of such targeting are discussed. Twelve examples of ligands bound to the tunnels and/or gates of clinically relevant enzymes are used to illustrate the different binding modes and to explain some new strategies for drug design. Such strategies could potentially help to overcome some of the problems facing medicinal chemists and lead to the discovery of more effective drugs.
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Affiliation(s)
- Sergio M Marques
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Lukas Daniel
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Tomas Buryska
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
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10
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Maccallini C, Di Matteo M, Vullo D, Ammazzalorso A, Carradori S, De Filippis B, Fantacuzzi M, Giampietro L, Pandolfi A, Supuran CT, Amoroso R. Indazole, Pyrazole, and Oxazole Derivatives Targeting Nitric Oxide Synthases and Carbonic Anhydrases. ChemMedChem 2016; 11:1695-9. [PMID: 27377568 DOI: 10.1002/cmdc.201600204] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 05/30/2016] [Indexed: 01/26/2023]
Abstract
Nitric oxide (NO) is an essential endogenous mediator with a physiological role in the central nervous system as neurotransmitter and neuromodulator. A growing number of studies have demonstrated that abnormal nitrergic signaling is a crucial event in the development of neurodegeneration. In particular, the uncontrolled production of NO by neuronal nitric oxide synthase (nNOS) is observed in several neurodegenerative diseases. Moreover, it is well recognized that specific isoforms of human carbonic anhydrase (hCA) physiologically modulate crucial pathways of signal processing and that low expression of CA affects cognition, leading to mental retardation, Alzheimer's disease, and aging-related cognitive impairments. In light of this, dual agents that are able to target both NOS (inhibition) and CA (activation) could be useful drug candidates for the treatment of Alzheimer's disease, aging, and other neurodegenerative diseases. In the present work, we show the design, synthesis, and in vitro biological evaluation of new nitrogen-based heterocyclic compounds. Among the tested molecules, 2-amino-3-(4-hydroxyphenyl)-N-(1H-indazol-5-yl)propanamide hydrochloride (10 b) was revealed to be a potent dual agent, able to act as a selective nNOS inhibitor and activator of the hCA I isoform.
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Affiliation(s)
- Cristina Maccallini
- Department of Pharmacy, University of Chieti "G. d'Annunzio", 66100, Chieti, Italy.
| | - Mauro Di Matteo
- Department of Pharmacy, University of Chieti "G. d'Annunzio", 66100, Chieti, Italy
| | - Daniela Vullo
- Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Florence, Italy
| | | | - Simone Carradori
- Department of Pharmacy, University of Chieti "G. d'Annunzio", 66100, Chieti, Italy
| | - Barbara De Filippis
- Department of Pharmacy, University of Chieti "G. d'Annunzio", 66100, Chieti, Italy
| | | | - Letizia Giampietro
- Department of Pharmacy, University of Chieti "G. d'Annunzio", 66100, Chieti, Italy
| | - Assunta Pandolfi
- Department of Medical, Oral and Biotecnological Sciences, University "G. d'Annunzio", Aging Research Center, "G. d'Annunzio" University Foundation, 66100, Chieti, Italy
| | - Claudiu T Supuran
- Neurofarba Department, Section of Pharmaceutical and Nutriceutical Sciences, Università degli Studi di Firenze, Via U. Schiff 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Rosa Amoroso
- Department of Pharmacy, University of Chieti "G. d'Annunzio", 66100, Chieti, Italy.
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12
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Luna-Vázquez FJ, Ibarra-Alvarado C, Rojas-Molina A, Romo-Mancillas A, López-Vallejo FH, Solís-Gutiérrez M, Rojas-Molina JI, Rivero-Cruz F. Role of Nitric Oxide and Hydrogen Sulfide in the Vasodilator Effect of Ursolic Acid and Uvaol from Black Cherry Prunus serotina Fruits. Molecules 2016; 21:78. [PMID: 26771591 PMCID: PMC6273102 DOI: 10.3390/molecules21010078] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/05/2016] [Accepted: 01/06/2016] [Indexed: 12/27/2022] Open
Abstract
The present research aimed to isolate the non-polar secondary metabolites that produce the vasodilator effects induced by the dichloromethane extract of Prunus serotina (P. serotina) fruits and to determine whether the NO/cGMP and the H2S/KATP channel pathways are involved in their mechanism of action. A bioactivity-directed fractionation of the dichloromethane extract of P. serotina fruits led to the isolation of ursolic acid and uvaol as the main non-polar vasodilator compounds. These compounds showed significant relaxant effect on rat aortic rings in an endothelium- and concentration-dependent manner, which was inhibited by NG-nitro-L-arginine methyl ester (L-NAME), DL-propargylglycine (PAG) and glibenclamide (Gli). Additionally, both triterpenes increased NO and H2S production in aortic tissue. Molecular docking studies showed that ursolic acid and uvaol are able to bind to endothelial NOS and CSE with high affinity for residues that form the oligomeric interface of both enzymes. These results suggest that the vasodilator effect produced by ursolic acid and uvaol contained in P. serotina fruits, involves activation of the NO/cGMP and H2S/KATP channel pathways, possibly through direct activation of NOS and CSE.
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Affiliation(s)
- Francisco J Luna-Vázquez
- Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Centro Universitario, Querétaro 76010, Mexico.
| | - César Ibarra-Alvarado
- Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Centro Universitario, Querétaro 76010, Mexico.
| | - Alejandra Rojas-Molina
- Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Centro Universitario, Querétaro 76010, Mexico.
| | - Antonio Romo-Mancillas
- Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Centro Universitario, Querétaro 76010, Mexico.
| | - Fabián H López-Vallejo
- Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Centro Universitario, Querétaro 76010, Mexico.
| | - Mariana Solís-Gutiérrez
- Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Centro Universitario, Querétaro 76010, Mexico.
| | - Juana I Rojas-Molina
- Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Centro Universitario, Querétaro 76010, Mexico.
| | - Fausto Rivero-Cruz
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria s/n, México D.F. 04510, Mexico.
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13
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Maccallini C, Montagnani M, Paciotti R, Ammazzalorso A, De Filippis B, Di Matteo M, Di Silvestre S, Fantacuzzi M, Giampietro L, Potenza MA, Re N, Pandolfi A, Amoroso R. Selective Acetamidine-Based Nitric Oxide Synthase Inhibitors: Synthesis, Docking, and Biological Studies. ACS Med Chem Lett 2015; 6:635-40. [PMID: 26101565 DOI: 10.1021/acsmedchemlett.5b00149] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 04/28/2015] [Indexed: 12/19/2022] Open
Abstract
N-[(3-Aminomethyl)benzyl]acetamidine derivatives were synthesized and in vitro evaluated as inhibitors of the inducible isoform of nitric oxide synthase (iNOS). Because of the high potency of action and the excellent selectivity over the endothelial nitric oxide synthase (eNOS), compound 10 was ex vivo evaluated on isolated and perfused resistance arteries. The results confirm that compound 10 selectively inhibits the iNOS, without affecting the endothelial isoform. The outcome of the docking studies showed that the hydrophobic interaction is the driving force of the binding process, especially for iNOS, where the binding pocket is characterized by a significant lipophilic region.
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Affiliation(s)
- Cristina Maccallini
- Department
of Pharmacy, University of Chieti “G. d’Annunzio”, 66100 Chieti, Italy
| | - Monica Montagnani
- Department
of Biomedical Sciences and Human Oncology, Medical School, University of Bari “Aldo Moro”, 70121 Bari, Italy
| | - Roberto Paciotti
- Department
of Pharmacy, University of Chieti “G. d’Annunzio”, 66100 Chieti, Italy
| | | | - Barbara De Filippis
- Department
of Pharmacy, University of Chieti “G. d’Annunzio”, 66100 Chieti, Italy
| | - Mauro Di Matteo
- Department
of Pharmacy, University of Chieti “G. d’Annunzio”, 66100 Chieti, Italy
| | - Sara Di Silvestre
- Department
of Medical, Oral and Biotecnological Sciences, University “G.
d’Annunzio” Aging Research Center, “G. d’Annunzio” University Foundation, 66100 Chieti-Pescara, Italy
| | | | - Letizia Giampietro
- Department
of Pharmacy, University of Chieti “G. d’Annunzio”, 66100 Chieti, Italy
| | - Maria A. Potenza
- Department
of Biomedical Sciences and Human Oncology, Medical School, University of Bari “Aldo Moro”, 70121 Bari, Italy
| | - Nazzareno Re
- Department
of Pharmacy, University of Chieti “G. d’Annunzio”, 66100 Chieti, Italy
| | - Assunta Pandolfi
- Department
of Medical, Oral and Biotecnological Sciences, University “G.
d’Annunzio” Aging Research Center, “G. d’Annunzio” University Foundation, 66100 Chieti-Pescara, Italy
| | - Rosa Amoroso
- Department
of Pharmacy, University of Chieti “G. d’Annunzio”, 66100 Chieti, Italy
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14
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Madariaga-Mazón A, Hernández-Abreu O, Estrada-Soto S, Mata R. Insights on the vasorelaxant mode of action of malbrancheamide. J Pharm Pharmacol 2015; 67:551-8. [DOI: 10.1111/jphp.12346] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 10/05/2014] [Indexed: 01/25/2023]
Abstract
Abstract
Objectives
This study was conducted to evaluate the vasorelaxant effect of the fungal alkaloids malbrancheamides on pre-contracted rat aorta rings. Also, we explored the probable mode of action using experimental and theoretical docking studies.
Methods
The vasorelaxant effect was assessed on rat aorta rings pre-contracted with noradrenaline (0.1 μm). The mechanism of action was evaluated using different inhibitors of the pathways involved in the vasorelaxation process, such as l-NAME, indomethacin, tetraethylammonium and atropine. The docking analyses were carried out with AutoDock 4.2 software using the crystallized structure of the cyclooxygenase domain of eNOS.
Key findings
Malbrancheamides (1–3) induced a significant vasorelaxant activity in a concentration- and endothelium-intact model in rat aorta rings, and a lesser effect in an endothelium-denuded model. Malbrancheamide-induced vasorelaxation was significantly weakened by pretreatment of endothelium-intact aortic rings with L-NAME (10 μm), indicating a nitrergic relaxant mechanism. Docking analysis predicted that 1–3 could activate eNOS throughout an allosteric fashion at C1 and C2 pockets.
Conclusions
Experimental evidence revealed that malbrancheamides induced both endothelium-independent and endothelium-dependent relaxant effects. According to theoretical studies, it is feasible that the endothelium-independent relaxation exerted by malbrancheamide could be mediated by its calmodulin inhibitory properties throughout an interference with myosin light chain phosphorylation and a positive modulation of eNOS.
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Affiliation(s)
| | | | - Samuel Estrada-Soto
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
| | - Rachel Mata
- Facultad de Química, Universidad Nacional Autónoma de México, México, México
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15
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Abstract
Fragment hopping is a fragment-based approach to designing biologically active small molecules. The key of this approach is the determination of the minimal pharmacophoric elements in the three-dimensional space. Based on the derived minimal pharmacophoric elements, new fragments with different chemotypes can be generated and positioned to the active site of the target protein. Herein, we detail a protocol for performing fragment hopping. This approach can not only explore a wide chemical space to produce new ligands with novel scaffolds but also characterize and utilize the delicate differences in the active sites between isofunctional proteins to produce new ligands with high target selectivity/specificity.
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Affiliation(s)
- Kevin B Teuscher
- Department of Chemistry, Center for Cell and Genome Science, University of Utah, 315 South 1400 East, Salt Lake City, Utah, 84112-0850, USA
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16
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Mukherjee P, Cinelli MA, Kang S, Silverman RB. Development of nitric oxide synthase inhibitors for neurodegeneration and neuropathic pain. Chem Soc Rev 2014; 43:6814-38. [PMID: 24549364 PMCID: PMC4138306 DOI: 10.1039/c3cs60467e] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule in the human body, playing a crucial role in cell and neuronal communication, regulation of blood pressure, and in immune activation. However, overproduction of NO by the neuronal isoform of nitric oxide synthase (nNOS) is one of the fundamental causes underlying neurodegenerative disorders and neuropathic pain. Therefore, developing small molecules for selective inhibition of nNOS over related isoforms (eNOS and iNOS) is therapeutically desirable. The aims of this review focus on the regulation and dysregulation of NO signaling, the role of NO in neurodegeneration and pain, the structure and mechanism of nNOS, and the use of this information to design selective inhibitors of this enzyme. Structure-based drug design, the bioavailability and pharmacokinetics of these inhibitors, and extensive target validation through animal studies are addressed.
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Affiliation(s)
- Paramita Mukherjee
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA.
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17
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Cinelli MA, Li H, Chreifi G, Martásek P, Roman LJ, Poulos TL, Silverman RB. Simplified 2-aminoquinoline-based scaffold for potent and selective neuronal nitric oxide synthase inhibition. J Med Chem 2014; 57:1513-30. [PMID: 24472039 PMCID: PMC3954451 DOI: 10.1021/jm401838x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
![]()
Since high levels of nitric oxide
(NO) are implicated in neurodegenerative
disorders, inhibition of the neuronal isoform of nitric oxide synthase
(nNOS) and reduction of NO levels are therapeutically desirable. Nonetheless,
many nNOS inhibitors mimic l-arginine and are poorly bioavailable.
2-Aminoquinoline-based scaffolds were designed with the hope that
they could (a) mimic aminopyridines as potent, isoform-selective arginine
isosteres and (b) possess chemical properties more conducive to oral
bioavailability and CNS penetration. A series of these compounds was
synthesized and assayed against purified nNOS enzymes, endothelial
NOS (eNOS), and inducible NOS (iNOS). Several compounds built on a
7-substituted 2-aminoquinoline core are potent and isoform-selective;
X-ray crystallography indicates that aminoquinolines exert inhibitory
effects by mimicking substrate interactions with the conserved active
site glutamate residue. The most potent and selective compounds, 7 and 15, were tested in a Caco-2 assay and showed
good permeability and low efflux, suggesting high potential for oral
bioavailability.
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Affiliation(s)
- Maris A Cinelli
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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18
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Avila-Villarreal G, Hernández-Abreu O, Hidalgo-Figueroa S, Navarrete-Vázquez G, Escalante-Erosa F, Peña-Rodríguez LM, Villalobos-Molina R, Estrada-Soto S. Antihypertensive and vasorelaxant effects of dihydrospinochalcone-A isolated from Lonchocarpus xuul Lundell by NO production: computational and ex vivo approaches. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2013; 20:1241-1246. [PMID: 23880329 DOI: 10.1016/j.phymed.2013.06.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 05/11/2013] [Accepted: 06/20/2013] [Indexed: 06/02/2023]
Abstract
Current work was conducted to evaluate the vasorelaxant effect of dihydrospinochalcone-A (1) and isocordoin (2), compounds type chalcone isolated from Lonchocarpus xuul, an endemic tree of the Yucatan Peninsula, Mexico. Compounds 1 and 2 were found to induce significant relaxant effect in a concentration-dependent manner on aortic rat rings pre-contracted with noradrenaline (NA, 0.1 μM). Compound 1 was the most active and its effect was endothelium-dependent (Emax=79.67% and EC50=21.46 μM with endothelium and Emax=23.58% and EC50=91.8 μM without endothelium, respectively). The functional mechanism of action for 1 was elucidated. Pre-incubation with L-NAME (unspecific nitric oxide synthase inhibitor), indomethacin (unspecific COX inhibitor), ODQ (soluble guanylyl cyclase inhibitor), atropine (cholinergic receptor antagonist), TEA (unspecific potassium channel blocker) reduced relaxations induced by 1. Oral administration of 50 mg/kg of compound 1 exhibited significant decrease in diastolic and systolic blood pressure in SHR rats. The heart rate was not modified. Compound 1 was docked with a crystal structure of eNOS. Dihydrospinochalcone-A showed calculated affinity with eNOS in the C1 binding pockets, near the catalytic site; Trp449, Trp447 and His373 through aromatic and π-π interactions, also His463 and Arg367 are the residues that make hydrogen bonds with the carbonyl and hydroxyl groups. In conclusion, dihydrospinochalcone-A induces a significant antihypertensive effect due to its direct vasorelaxant action on rat aorta rings, through NO/sCG/PKG pathway and potassium channel opening.
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Affiliation(s)
- Gabriela Avila-Villarreal
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Colonia Chamilpa, 62209 Cuernavaca, Morelos, Mexico
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19
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Víteček J, Lojek A, Valacchi G, Kubala L. Arginine-based inhibitors of nitric oxide synthase: therapeutic potential and challenges. Mediators Inflamm 2012; 2012:318087. [PMID: 22988346 PMCID: PMC3441039 DOI: 10.1155/2012/318087] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 05/30/2012] [Indexed: 12/24/2022] Open
Abstract
In the past three decades, nitric oxide has been well established as an important bioactive molecule implicated in regulation of cardiovascular, nervous, and immune systems. Therefore, it is not surprising that much effort has been made to find specific inhibitors of nitric oxide synthases (NOS), the enzymes responsible for production of nitric oxide. Among the many NOS inhibitors developed to date, inhibitors based on derivatives and analogues of arginine are of special interest, as this category includes a relatively high number of compounds with good potential for experimental as well as clinical application. Though this group of inhibitors covers early nonspecific compounds, modern drug design strategies such as biochemical screening and computer-aided drug design have provided NOS-isoform-specific inhibitors. With an emphasis on major advances in this field, a comprehensive list of inhibitors based on their structural characteristics is discussed in this paper. We provide a summary of their biochemical properties as well as their observed effects both in vitro and in vivo. Furthermore, we focus in particular on their pharmacology and use in recent clinical studies. The potential of newly designed specific NOS inhibitors developed by means of modern drug development strategies is highlighted.
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Affiliation(s)
- Jan Víteček
- International Clinical Research Center-Center of Biomolecular and Cell Engineering, St. Anne's University Hospital Brno, 656 91 Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 65 Brno, Czech Republic
| | - Antonín Lojek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 65 Brno, Czech Republic
| | - Giuseppe Valacchi
- Department of Evolutionary Biology, University of Ferrara, 44100 Ferrara, Italy
- Department of Food and Nutrition, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Lukáš Kubala
- International Clinical Research Center-Center of Biomolecular and Cell Engineering, St. Anne's University Hospital Brno, 656 91 Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 65 Brno, Czech Republic
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20
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Rios MY, López-Martínez S, López-Vallejo F, Medina-Franco JL, Villalobos-Molina R, Ibarra-Barajas M, Navarrete-Vazquez G, Hidalgo-Figueroa S, Hernández-Abreu O, Estrada-Soto S. Vasorelaxant activity of some structurally related triterpenic acids from Phoradendron reichenbachianum (Viscaceae) mainly by NO production: Ex vivo and in silico studies. Fitoterapia 2012; 83:1023-9. [DOI: 10.1016/j.fitote.2012.05.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 05/21/2012] [Accepted: 05/21/2012] [Indexed: 11/26/2022]
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21
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Suaifan GA, Shehadehh M, Al-Ijel H, Taha MO. Extensive ligand-based modeling and in silico screening reveal nanomolar inducible nitric oxide synthase (iNOS) inhibitors. J Mol Graph Model 2012; 37:1-26. [PMID: 22609742 DOI: 10.1016/j.jmgm.2012.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Revised: 02/20/2012] [Accepted: 04/02/2012] [Indexed: 01/21/2023]
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22
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Ji H, Jing Q, Huang J, Silverman RB. Acid-Facilitated Debenzylation of N-Boc, N-Benzyl Double Protected 2-Aminopyridinomethylpyrrolidine Derivatives. Tetrahedron 2012; 68:1359-1366. [PMID: 22639474 PMCID: PMC3358821 DOI: 10.1016/j.tet.2011.12.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
2-Aminopyridinomethyl pyrrolidines represent a class of highly potent and selective neuronal nitric oxide synthase inhibitors. Conditions for a Mitsunobu reaction of a naphthol and a hindered secondary alcohol were optimized to give good to excellent yields. A key step in the synthesis of these inhibitors is the deprotection of the benzyl group from the N-Boc and N-Bn double protected 2-aminopyridine ring at a late stage of the synthesis, which has been proven difficult in our previous syntheses. Acetic acid was found to facilitate the N-Bn deprotection.
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Affiliation(s)
- Haitao Ji
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, and Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208-3113
| | - Qing Jing
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, and Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208-3113
| | - Jinwen Huang
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, and Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208-3113
| | - Richard B. Silverman
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, and Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208-3113
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23
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Floquet N, Hernandez JF, Boucher JL, Martinez J. L-arginine binding to human inducible nitric oxide synthase: an antisymmetric funnel route toward isoform-specific inhibitors? J Chem Inf Model 2011; 51:1325-35. [PMID: 21574590 DOI: 10.1021/ci100422v] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nitric oxide (NO) is an important signaling molecule produced by a family of enzymes called nitric oxide synthases (NOS). Because NO is involved in various pathological conditions, the development of potent and isoform-selective NOS inhibitors is an important challenge. In the present study, the dimer of oxygenase domain of human iNOS (iNOSoxy) complexed to its natural substrate L-arginine (L-Arg) and both heme and tetrahydro-L-biopterin (BH4) cofactors was studied through multiple molecular dynamics simulations. Starting from the X-ray structure available for that complex (PDB: 1NSI ), a 16 ns equilibration trajectory was first obtained. Twelve dynamics of slow extraction of L-Arg out from the iNOSoxy active site were then performed. The steered molecular dynamics (SMD) approach was used starting from three different points of the reference trajectory for a total simulation time of 35 ns. A probable unbinding/binding pathway of L-Arg was characterized. It was suggested that a driving force directed the substrate toward the heme pocket. Key intermediate steps/residues along the access route to the active site were identified along this "funnel shape" pathway and compared to existing data. A quasi-normal mode analysis performed on the SMD data suggested that large collective motions of the protein may be involved in L-Arg binding and that opening the route to the active site in one monomer promoted an inverse, closing motion in the second monomer. Finally, our findings might help to rationalize the design of human iNOS isoform competitive inhibitors.
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Affiliation(s)
- Nicolas Floquet
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 Université Montpellier 1, Université Montpellier 2, CNRS, Faculté de Pharmacie, Montpellier, France.
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24
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Malysiak-Mrozek B, Mrozek D. An Improved Method for Protein Similarity Searching by Alignment of Fuzzy Energy Signatures. INT J COMPUT INT SYS 2011. [DOI: 10.1080/18756891.2011.9727765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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25
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Ji H, Delker SL, Li H, Martásek P, Roman LJ, Poulos TL, Silverman RB. Exploration of the active site of neuronal nitric oxide synthase by the design and synthesis of pyrrolidinomethyl 2-aminopyridine derivatives. J Med Chem 2010; 53:7804-24. [PMID: 20958055 DOI: 10.1021/jm100947x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Neuronal nitric oxide synthase (nNOS) represents an important therapeutic target for the prevention of brain injury and the treatment of various neurodegenerative disorders. A series of trans-substituted amino pyrrolidinomethyl 2-aminopyridine derivatives (8-34) was designed and synthesized. A structure-activity relationship analysis led to the discovery of low nanomolar nNOS inhibitors ((±)-32 and (±)-34) with more than 1000-fold selectivity for nNOS over eNOS. Four enantiomerically pure isomers of 3'-[2''-(3'''-fluorophenethylamino)ethoxy]pyrrolidin-4'-yl}methyl}-4-methylpyridin-2-amine (4) also were synthesized. It was found that (3'R,4'R)-4 can induce enzyme elasticity to generate a new "hot spot" for ligand binding. The inhibitor adopts a unique binding mode, the same as that observed for (3'R,4'R)-3'-[2''-(3'''-fluorophenethylamino)ethylamino]pyrrolidin-4'-yl}methyl}-4-methylpyridin-2-amine ((3'R,4'R)-3) (J. Am. Chem. Soc. 2010, 132 (15), 5437 - 5442). On the basis of structure-activity relationships of 8-34 and different binding conformations of the cis and trans isomers of 3 and 4, critical structural requirements of the NOS active site for ligand binding are revealed.
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Affiliation(s)
- Haitao Ji
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, and Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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26
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Xue F, Li H, Fang J, Roman LJ, Martásek P, Poulos TL, Silverman RB. Peripheral but crucial: a hydrophobic pocket (Tyr(706), Leu(337), and Met(336)) for potent and selective inhibition of neuronal nitric oxide synthase. Bioorg Med Chem Lett 2010; 20:6258-61. [PMID: 20833542 PMCID: PMC2952696 DOI: 10.1016/j.bmcl.2010.08.096] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 08/17/2010] [Accepted: 08/18/2010] [Indexed: 10/19/2022]
Abstract
Selective inhibition of the neuronal isoform of nitric oxide synthase (nNOS) over endothelial nitric oxide synthase (eNOS) and inducible nitric oxide synthase (iNOS) has become a promising strategy for the discovery of new therapeutic agents for neurodegenerative diseases. However, because of the high sequence homology of different isozymes in the substrate binding pocket, developing inhibitors with both potency and excellent isoform selectivity remains a challenging problem. Herein, we report the evaluation of a recently discovered peripheral hydrophobic pocket (Tyr(706), Leu(337), and Met(336)) that opens up upon inhibitor binding and its potential in designing potent and selective nNOS inhibitors using three compounds, 2a, 2b, and 3. Crystal structure results show that inhibitors 2a and 3 adopted the same binding mode as lead compound 1. We also found that hydrophobic interactions between the 4-methyl group of the aminopyridine ring of these compounds with the side chain of Met(336), as well as the π-π stacking interaction between the pyridinyl motif and the side chain of Tyr(706) are important for the high potency and selectivity of these nNOS inhibitors.
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Affiliation(s)
- Fengtian Xue
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, Center for Molecular Innovation and Drug Discovery, and Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3113, , 847-491-5653
| | - Huiying Li
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Chemistry, and Chemistry, University of California, Irvine, California 92697-3900, , 949-824-7020
| | - Jianguo Fang
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, Center for Molecular Innovation and Drug Discovery, and Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3113, , 847-491-5653
| | - Linda J. Roman
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, Texas 78384-7760
| | - Pavel Martásek
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, Texas 78384-7760
| | - Thomas L. Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Chemistry, and Chemistry, University of California, Irvine, California 92697-3900, , 949-824-7020
| | - Richard B. Silverman
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, Center for Molecular Innovation and Drug Discovery, and Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3113, , 847-491-5653
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27
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Maccallini C, Patruno A, Lannutti F, Ammazzalorso A, De Filippis B, Fantacuzzi M, Franceschelli S, Giampietro L, Masella S, Felaco M, Re N, Amoroso R. N-Substituted acetamidines and 2-methylimidazole derivatives as selective inhibitors of neuronal nitric oxide synthase. Bioorg Med Chem Lett 2010; 20:6495-9. [DOI: 10.1016/j.bmcl.2010.09.059] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2010] [Revised: 09/03/2010] [Accepted: 09/10/2010] [Indexed: 12/18/2022]
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28
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Xue F, Huang J, Ji H, Fang J, Li H, Martásek P, Roman LJ, Poulos TL, Silverman RB. Structure-based design, synthesis, and biological evaluation of lipophilic-tailed monocationic inhibitors of neuronal nitric oxide synthase. Bioorg Med Chem 2010; 18:6526-37. [PMID: 20673724 PMCID: PMC2925225 DOI: 10.1016/j.bmc.2010.06.074] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Revised: 06/18/2010] [Accepted: 06/21/2010] [Indexed: 01/16/2023]
Abstract
Selective inhibitors of neuronal nitric oxide synthase (nNOS) have the potential to develop into new neurodegenerative therapeutics. Recently, we described the discovery of novel nNOS inhibitors (1a and 1b) based on a cis-pyrrolidine pharmacophore. These compounds and related ones were found to have poor blood-brain barrier permeability, presumably because of the basic nitrogens in the molecule. Here, a series of monocationic compounds was designed on the basis of docking experiments using the crystal structures of 1a,b bound to nNOS. These compounds were synthesized and evaluated for their ability to inhibit neuronal nitric oxide synthase. Despite the excellent overlap of these compounds with 1a,b bound to nNOS, they exhibited low potency. This is because they bound in the nNOS active site in the normal orientation rather than the expected flipped orientation used in the computer modeling. The biphenyl or phenoxyphenyl tail is disordered and does not form good protein-ligand interactions. These studies demonstrate the importance of the size and rigidity of the side chain tail and the second basic amino group for nNOS binding efficiency and the importance of the hydrophobic tail for conformational orientation in the active site of nNOS.
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Affiliation(s)
- Fengtian Xue
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, Center for Molecular Innovation and Drug Discovery, and Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3113
| | - Jinwen Huang
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, Center for Molecular Innovation and Drug Discovery, and Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3113
| | - Haitao Ji
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, Center for Molecular Innovation and Drug Discovery, and Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3113
| | - Jianguo Fang
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, Center for Molecular Innovation and Drug Discovery, and Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3113
| | - Huiying Li
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Chemistry, and Chemistry, University of California, Irvine, California 92697-3900
| | - Pavel Martásek
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas
- Department of Pediatrics and Center for Applied Genomics, 1 School of Medicine, Charles University, Prague, Czech Republic
| | - Linda J. Roman
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas
| | - Thomas L. Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Chemistry, and Chemistry, University of California, Irvine, California 92697-3900
| | - Richard B. Silverman
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, Center for Molecular Innovation and Drug Discovery, and Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3113
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Rocha JR, Freitas RF, Montanari CA. The GRID/CPCA approach in drug discovery. Expert Opin Drug Discov 2010; 5:333-46. [DOI: 10.1517/17460441003652959] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Fang J, Ji H, Lawton GR, Xue F, Roman LJ, Silverman RB. L337H mutant of rat neuronal nitric oxide synthase resembles human neuronal nitric oxide synthase toward inhibitors. J Med Chem 2009; 52:4533-7. [PMID: 19537690 DOI: 10.1021/jm900380j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A common dichotomy exists in inhibitor design: should the compounds be designed to block the enzymes of animals in the preclinical studies or to inhibit the human enzyme? We report that a single mutation of Leu-337 in rat neuronal nitric oxide synthase (nNOS) to His makes the enzyme resemble human nNOS more than rat nNOS. We expect that the approach used in this study can unite the dichotomy and speed up the process of inhibitor design and development.
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Affiliation(s)
- Jianguo Fang
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3113, USA
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Ji H, Tan S, Igarashi J, Li H, Derrick M, Martásek P, Roman LJ, Vásquez-Vivar J, Poulos TL, Silverman RB. Selective neuronal nitric oxide synthase inhibitors and the prevention of cerebral palsy. Ann Neurol 2009; 65:209-17. [PMID: 19235180 DOI: 10.1002/ana.21555] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE To design a new class of selective neuronal nitric oxide synthase (NOS) inhibitors, and demonstrate that administration in a rabbit model for cerebral palsy (CP) prevents hypoxia-ischemia-induced deaths and reduces the number of newborn kits exhibiting signs of CP. METHODS We used a novel computer-based drug design method called fragment hopping to identify new chemical entities, synthesized them, and conducted in vitro enzyme inhibition studies with the three isozymes of NOS and in vivo experiments to monitor cardiovascular effects on pregnant rabbit dams, NOS activity, and NO(x) (NO and NO(2)) concentration in fetal brain, and assess neurobehavioral effects on kits born to saline- and compound treated dams. RESULTS The computer-based design led to the development of powerful and highly selective compounds for inhibition of neuronal NOS over the other isozymes. After maternal administration in a rabbit model of CP, these compounds were found to distribute to fetal brain, to be nontoxic, without cardiovascular effects, inhibit fetal brain NOS activity in vivo, reduce NO concentration in fetal brain, and dramatically ameliorate deaths and number of newborn kits exhibiting signs of CP. INTERPRETATION This approach may lead to new preventive strategies for CP.
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Affiliation(s)
- Haitao Ji
- Department of Chemistry, Center for Drug Discovery and Chemical Biology, Northwestern University, Evanston, IL 60208-3113, USA
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Silverman RB. Design of selective neuronal nitric oxide synthase inhibitors for the prevention and treatment of neurodegenerative diseases. Acc Chem Res 2009; 42:439-51. [PMID: 19154146 DOI: 10.1021/ar800201v] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitric oxide (NO), which is produced from L-arginine by the nitric oxide synthase (NOS) family of enzymes, is an important second-messenger molecule that regulates several physiological functions. In endothelial cells, it relaxes smooth muscle, which decreases blood pressure. Macrophage cells produce NO as an immune defense system to destroy pathogens and microorganisms. In neuronal cells, NO controls the release of neurotransmitters and is involved in synaptogenesis, synaptic plasticity, memory function, and neuroendocrine secretion. NO is a free radical that is commonly thought to contribute to oxidative damage and molecule and tissue destruction, and thus it is somewhat surprising that it has so many significant beneficial physiological effects. However, the cell is generally protected from NO's toxic effects, except under certain pathological conditions in which excessive NO is produced. In that case, tissue damage and oxidative stress can result, leading to a wide variety of diseases, including rheumatoid arthritis, Alzheimer's disease, and Parkinson's disease, among others. In this Account, we describe research aimed at identifying small molecules that can selectively inhibit only the neuronal isozyme of NOS, nNOS. By targeting only nNOS, we attained the beneficial effects of lowering excess NO in the brain without the detrimental effects of inhibition of the two isozymes found elsewhere in the body (eNOS and iNOS). Initially, in pursuit of this goal, we sought to identify differences in the second sphere of amino acids in the active site of the isozymes. From this study, the first class of dual nNOS-selective inhibitors was identified. The moieties important for selectivity in the best lead compound were determined by structure modification. Enhancement provided highly potent, nNOS-selective dipeptide amides and peptidomimetics, which were active in a rabbit model for fetal neurodegeneration. Crystal structures of these compounds bound to NOS isozymes showed a one-amino-acid difference between nNOS and eNOS in the second sphere of amino acids; this was the difference that we were searching for from the beginning of this project. With the aid of these crystal structures, we developed a new fragment-based de novo design method called "fragment hopping", which allowed the design of a new class of nonpeptide nNOS-selective inhibitors. These compounds were modified to give low nanomolar, highly dual-selective nNOS inhibitors, which we recently showed are active in a rabbit model for the prevention of neurobehavioral symptoms of cerebral palsy. These compounds could also have general application in other neurodegenerative diseases for which excess NO is responsible.
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Affiliation(s)
- Richard B. Silverman
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, and the Center for Drug Discovery and Chemical Biology, Northwestern University, Evanston, Illinois 60208-3113
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Ji H, Li H, Martásek P, Roman LJ, Poulos TL, Silverman RB. Discovery of highly potent and selective inhibitors of neuronal nitric oxide synthase by fragment hopping. J Med Chem 2009; 52:779-97. [PMID: 19125620 DOI: 10.1021/jm801220a] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Selective inhibition of neuronal nitric oxide synthase (nNOS) has been shown to prevent brain injury and is important for the treatment of various neurodegenerative disorders. This study shows that not only greater inhibitory potency and isozyme selectivity but more druglike properties can be achieved by fragment hopping. On the basis of the structure of lead molecule 6, fragment hopping effectively extracted the minimal pharmacophoric elements in the active site of nNOS for ligand hydrophobic and steric interactions and generated appropriate lipophilic fragments for lead optimization. More potent and selective inhibitors with better druglike properties were obtained within the design of 20 derivatives (compounds 7-26). Our structure-based inhibitor design for nNOS and SAR analysis reveal the robustness and efficiency of fragment hopping in lead discovery and structural optimization, which implicates a broad application of this approach to many other therapeutic targets for which known druglike small-molecule modulators are still limited.
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Affiliation(s)
- Haitao Ji
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, USA
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Abstract
Analysis of the three-dimensional structures of protein ligand complexes provides valuable insight into both the common interaction patterns within a target family and the discriminating features between the different members of a target family. Knowledge of the common interaction patterns helps to design target family focused chemical libraries for hit finding, while the discriminating features can be exploited to optimize the selectivity profile of a lead compound against particular member of a target family. Herein, we review the computational tools which have been developed to analyze crystal structures of members of a target family.
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Affiliation(s)
- Bernard Pirard
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institute for Biomedical Research, Basel, Switzerland
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35
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Anchored plasticity opens doors for selective inhibitor design in nitric oxide synthase. Nat Chem Biol 2008; 4:700-7. [PMID: 18849972 PMCID: PMC2868503 DOI: 10.1038/nchembio.115] [Citation(s) in RCA: 184] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Accepted: 09/05/2008] [Indexed: 12/12/2022]
Abstract
Nitric oxide synthase (NOS) enzymes synthesize nitric oxide, a signal for vasodilatation and neurotransmission at low concentrations and a defensive cytotoxin at higher concentrations. The high active site conservation among all three NOS isozymes hinders the design of selective NOS inhibitors to treat inflammation, arthritis, stroke, septic shock and cancer. Our crystal structures and mutagenesis results identified an isozyme-specific induced-fit binding mode linking a cascade of conformational changes to a new specificity pocket. Plasticity of an isozyme-specific triad of distant second- and third-shell residues modulates conformational changes of invariant first-shell residues to determine inhibitor selectivity. To design potent and selective NOS inhibitors, we developed the anchored plasticity approach: anchor an inhibitor core in a conserved binding pocket, then extend rigid bulky substituents toward remote specificity pockets, which become accessible upon conformational changes of flexible residues. This approach exemplifies general principles for the design of selective enzyme inhibitors that overcome strong active site conservation.
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36
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Ji H, Stanton BZ, Igarashi J, Li H, Martásek P, Roman LJ, Poulos TL, Silverman RB. Minimal pharmacophoric elements and fragment hopping, an approach directed at molecular diversity and isozyme selectivity. Design of selective neuronal nitric oxide synthase inhibitors. J Am Chem Soc 2008; 130:3900-14. [PMID: 18321097 PMCID: PMC2929563 DOI: 10.1021/ja0772041] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fragment hopping, a new fragment-based approach for de novo inhibitor design focusing on ligand diversity and isozyme selectivity, is described. The core of this approach is the derivation of the minimal pharmacophoric element for each pharmacophore. Sites for both ligand binding and isozyme selectivity are considered in deriving the minimal pharmacophoric elements. Five general-purpose libraries are established: the basic fragment library, the bioisostere library, the rules for metabolic stability, the toxicophore library, and the side chain library. These libraries are employed to generate focused fragment libraries to match the minimal pharmacophoric elements for each pharmacophore and then to link the fragment to the desired molecule. This method was successfully applied to neuronal nitric oxide synthase (nNOS), which is implicated in stroke and neurodegenerative diseases. Starting with the nitroarginine-containing dipeptide inhibitors we developed previously, a small organic molecule with a totally different chemical structure was designed, which showed nanomolar nNOS inhibitory potency and more than 1000-fold nNOS selectivity. The crystallographic analysis confirms that the small organic molecule with a constrained conformation can exactly mimic the mode of action of the dipeptide nNOS inhibitors. Therefore, a new peptidomimetic strategy, referred to as fragment hopping, which creates small organic molecules that mimic the biological function of peptides by a pharmacophore-driven strategy for fragment-based de novo design, has been established as a new type of fragment-based inhibitor design. As an open system, the newly established approach efficiently incorporates the concept of early "ADME/Tox" considerations and provides a basic platform for medicinal chemistry-driven efforts.
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37
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Design of Benzene-1,2-diamines as selective inducible nitric oxide synthase inhibitors: a combined de novo design and docking analysis. J Mol Model 2008; 14:215-24. [DOI: 10.1007/s00894-007-0263-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2007] [Accepted: 12/04/2007] [Indexed: 10/22/2022]
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Erdal EP, Martásek P, Roman LJ, Silverman RB. Hydroxyethylene isosteres of selective neuronal nitric oxide synthase inhibitors. Bioorg Med Chem 2007; 15:6096-108. [PMID: 17614291 PMCID: PMC2001161 DOI: 10.1016/j.bmc.2007.06.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Revised: 06/13/2007] [Accepted: 06/15/2007] [Indexed: 10/23/2022]
Abstract
Nitric oxide (NO) is an important second messenger molecule for blood pressure homeostasis, as a neurotransmitter, and in the immune defense system. Excessive NO can lead to neurodegeneration and connective tissue damage. Three different isozymes of the enzyme nitric oxide synthase regulate NO production in endothelial (eNOS), neuronal (nNOS), and macrophage (iNOS) cells. Whereas creating a lower level of NO in some cells could be beneficial, it also could be detrimental to the protective effects that NO has on other cells. Therefore, it is essential that therapeutic NOS inhibitors be made that are subtype selective. Previously, we reported a series of nitroarginine-containing dipeptide amides as potent and selective nNOS inhibitors. Here we synthesize peptidomimetic hydroxyethylene isosteres of these dipeptide amides for potential increased bioavailability. None of the compounds is as potent or selective as the dipeptide amides, but they exhibit good inhibition and selectivity. When the terminal amino group was converted to a hydroxyl group, potency and selectivity greatly diminished, supporting the importance of the terminal amino group for binding.
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Affiliation(s)
- Erik P. Erdal
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, and the Center for Drug Discovery and Chemical Biology, Northwestern University, Evanston, Illinois 60208-3113
| | - Pavel Martásek
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78384-7760
| | - Linda J. Roman
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78384-7760
| | - Richard B. Silverman
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, and the Center for Drug Discovery and Chemical Biology, Northwestern University, Evanston, Illinois 60208-3113
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Aparna V, Desiraju GR, Gopalakrishnan B. Insights into ligand selectivity in nitric oxide synthase isoforms: A molecular dynamics study. J Mol Graph Model 2007; 26:457-70. [PMID: 17350298 DOI: 10.1016/j.jmgm.2007.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Revised: 02/12/2007] [Accepted: 02/12/2007] [Indexed: 11/20/2022]
Abstract
Molecular dynamics (MD) simulations were carried out for inducible nitric oxide synthase (iNOS) and endothelial nitric oxide synthase (eNOS) isoforms complexed with substrate (L-arginine) and the iNOS specific inhibitor GW 273629, 2 for a time period of 1.2ns. The simulations were compared both within and across the isoforms. iNOS specificity of inhibitor 2 is attributed to water mediated interactions and cooperative hydrogen bond networks. Juxtaposition of the carboxylic and ammonium groups in the substrate and inhibitor serve as a modulating key in binding to the isoforms. Based on these investigations, molecules 3 and 4 were rationally designed to attain specificity among the isoforms. The capability of the designed ligands was theoretically tested through MD simulations to envisage binding patterns with both isoforms. A detailed analysis of the molecular recognition pattern shows molecule 4 to be more selective to iNOS when compared to eNOS.
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Affiliation(s)
- V Aparna
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
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40
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Seo J, Igarashi J, Li H, Martásek P, Roman LJ, Poulos TL, Silverman RB. Structure-based design and synthesis of N(omega)-nitro-L-arginine-containing peptidomimetics as selective inhibitors of neuronal nitric oxide synthase. Displacement of the heme structural water. J Med Chem 2007; 50:2089-99. [PMID: 17425297 PMCID: PMC2562355 DOI: 10.1021/jm061305c] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The neuronal isoform of nitric oxide synthase (nNOS), the enzyme responsible for the production of nitric oxide in the central nervous system, represents an attractive target for the treatment of various neurodegenerative disorders. X-ray crystal structures of complexes of nNOS with two nNOS-selective inhibitors, (4S)-N-{4-amino-5-[(2-aminoethylamino]pentyl}-N'-nitroguanidine (1) and 4-N-(Nomega-nitro-l-argininyl)-trans-4-amino-l-proline amide (2), led to the discovery of a conserved structural water molecule that was hydrogen bonded between the two heme propionates and the inhibitors (Figure 2). On the basis of this observation, we hypothesized that by attaching a hydrogen bond donor group to the amide nitrogen of 2 or to the secondary amine nitrogen of 1, the inhibitor molecules could displace the structural water molecule and obtain a direct interaction with the heme cofactor. To test this hypothesis, peptidomimetic analogues 3-5, which have either an N-hydroxyl (3 and 5) or N-amino (4) donor group, were designed and synthesized. X-ray crystal structures of nNOS with inhibitors 3 and 5 bound verified that the N-hydroxyl group had, indeed, displaced the structural water molecule and provided a direct interaction with the heme propionate moiety (Figures 5 and 6). Surprisingly, in vitro activity assay results indicated that the addition of a hydroxyl group (3) only increased the potency slightly against the neuronal isoform over the parent compound (1). Rationalizations for the small increase in potency are consistent with other changes in the crystal structures.
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Affiliation(s)
- Jiwon Seo
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, and the Center for Drug Discovery and Chemical Biology, Northwestern University, Evanston, Illinois 60208-3113 USA
| | - Jotato Igarashi
- Departments of Molecular Biology and Biochemistry, Physiology and Biophysics, and Chemistry and Program in Macromolecular Structure, University of California, Irvine, California 92697-3900 USA
| | - Huiying Li
- Departments of Molecular Biology and Biochemistry, Physiology and Biophysics, and Chemistry and Program in Macromolecular Structure, University of California, Irvine, California 92697-3900 USA
| | - Pavel Martásek
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, Texas 78384-7760 USA
| | - Linda J. Roman
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, Texas 78384-7760 USA
| | - Thomas L. Poulos
- Departments of Molecular Biology and Biochemistry, Physiology and Biophysics, and Chemistry and Program in Macromolecular Structure, University of California, Irvine, California 92697-3900 USA
| | - Richard B. Silverman
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, and the Center for Drug Discovery and Chemical Biology, Northwestern University, Evanston, Illinois 60208-3113 USA
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41
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Seo J, Martásek P, Roman LJ, Silverman RB. Selective L-nitroargininylaminopyrrolidine and L-nitroargininylaminopiperidine neuronal nitric oxide synthase inhibitors. Bioorg Med Chem 2007; 15:1928-38. [PMID: 17239601 PMCID: PMC1853295 DOI: 10.1016/j.bmc.2007.01.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2006] [Accepted: 01/01/2007] [Indexed: 11/19/2022]
Abstract
Selective inhibition of the localized excess production of NO by neuronal nitric oxide synthase (nNOS) has been targeted as a potential means of treating various neurological disorders. Based on observations from the X-ray crystal structures of complexes of nNOS with two nNOS-selective inhibitors, (4S)-N-{4-amino-5-[(2-amino)ethylamino]pentyl}-N'-nitroguanidine (L-Arg(NO2)-L-Dbu-NH2 (1) and 4-N-(Nomega-nitro-L-argininyl)-trans-4-amino-L-proline amide (2), a series of descarboxamide analogues was designed and synthesized (3-7). The most potent compound was aminopyrrolidine analogue 3, which exhibited better potency and selectivity for nNOS than parent compound 2. In addition, 3 provided higher lipophilicity and a lower molecular weight than 2, therefore having better physicochemical properties. Nalpha-Methylated analogues (8-11) also were prepared for increased lipophilicity of the inhibitors, but they had 4- to 5-fold weaker binding affinity compared to their parent compounds.
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Affiliation(s)
- Jiwon Seo
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, and the Center for Drug Discovery and Chemical Biology, Northwestern University, Evanston, IL 60208-3113, USA
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42
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Ji H, Gómez-Vidal JA, Martásek P, Roman LJ, Silverman RB. Conformationally restricted dipeptide amides as potent and selective neuronal nitric oxide synthase inhibitors. J Med Chem 2006; 49:6254-63. [PMID: 17034131 PMCID: PMC2517862 DOI: 10.1021/jm0604124] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Four new conformationally restricted analogues of a potent and selective neuronal nitric oxide synthase inhibitor, l-nitroargininyl-l-2,4-diaminobutyramide (1), have been synthesized. N(alpha)-Methyl and N(alpha)-benzyl derivatives (3 and 4, respectively) of 4-N-(l-Arg(NO(2))-trans-4-amino-l-prolineamide (2) are also selective inhibitors, but the potency and selectivity of 3 are weak. Analogue 4 has only one-third the potency and one-half to one-third the selectivity of 2 against iNOS (inducible nitric oxide synthase) and eNOS (endothelial nitric oxide synthase), respectively. 3-N-(l-Arg(NO)(2))-trans-3-amino-l-prolineamide (6) is as potent an inhibitor of nNOS (neuronal nitric oxide synthase) as 2; selectivity for nNOS over iNOS is half of that for 2, but the selectivity for nNOS over eNOS is almost double that for 2. The corresponding cis-isomer (5) is a weak inhibitor of nNOS. These results are supported by computer modeling.
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Affiliation(s)
| | | | | | | | - Richard B. Silverman
- Address correspondence to this author at the Department of Chemistry Phone: 1−847−491−5653
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43
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Mestres J. Representativity of target families in the Protein Data Bank: impact for family-directed structure-based drug discovery. Drug Discov Today 2006; 10:1629-37. [PMID: 16376823 DOI: 10.1016/s1359-6446(05)03593-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Analysis of the population of enzyme structures in the Protein Data Bank across all levels of the functional classification based on enzyme commission (EC) numbers reveals that, in spite of the almost exponential growth in the number of structures deposited, progress in achieving complete occupancy at all EC levels is relatively slow. Moreover, inspection of the distribution of the population among the members of the different enzyme families uncovers a strong bias towards enzymes widely recognized as therapeutically relevant targets. The low representativity levels identified in some target families warn on the current scope and applicability of structure-based approaches to family-directed strategies in drug discovery.
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Affiliation(s)
- Jordi Mestres
- Chemogenomics Laboratory, Research Unit on Biomedical Informatics, Institut Municipal d'Investigació Mèdica and Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain.
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Dao KK, Teigen K, Kopperud R, Hodneland E, Schwede F, Christensen AE, Martinez A, Døskeland SO. Epac1 and cAMP-dependent protein kinase holoenzyme have similar cAMP affinity, but their cAMP domains have distinct structural features and cyclic nucleotide recognition. J Biol Chem 2006; 281:21500-21511. [PMID: 16728394 DOI: 10.1074/jbc.m603116200] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cAMP-dependent protein kinase (PKA I and II) and the cAMP-stimulated GDP exchange factors (Epac1 and -2) are major cAMP effectors. The cAMP affinity of the PKA holoenzyme has not been determined previously. We found that cAMP bound to PKA I with a K(d) value (2.9 microM) similar to that of Epac1. In contrast, the free regulatory subunit of PKA type I (RI) had K(d) values in the low nanomolar range. The cAMP sites of RI therefore appear engineered to respond to physiological cAMP concentrations only when in the holoenzyme form, whereas Epac can respond in its free form. Epac is phylogenetically younger than PKA, and its functional cAMP site has presumably evolved from site B of PKA. A striking feature is the replacement of a conserved Glu in PKA by Gln (Epac1) or Lys (Epac2). We found that such a switch (E326Q) in site B of human RIalpha led to a 280-fold decreased cAMP affinity. A similar single switch early in Epac evolution could therefore have decreased the high cAMP affinity of the free regulatory subunit sufficiently to allow Epac to respond to physiologically relevant cAMP levels. Molecular dynamics simulations and cAMP analog mapping indicated that the E326Q switch led to flipping of Tyr-373, which normally stacks with the adenine ring of cAMP. Combined molecular dynamics simulation, GRID analysis, and cAMP analog mapping of wild-type and mutated BI and Epac1 revealed additional differences, independent of the Glu/Gln switch, between the binding sites, regarding space (roominess), hydrophobicity/polarity, and side chain flexibility. This helped explain the specificity of current cAMP analogs and, more importantly, lays a foundation for the generation of even more discriminative analogs.
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Affiliation(s)
- Khanh Kim Dao
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Knut Teigen
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Reidun Kopperud
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Erlend Hodneland
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Frank Schwede
- BioLog Life Science Institute, Flughafendamm, D-28071 Bremen, Germany
| | - Anne E Christensen
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway; Haukeland University Hospital, 5009 Bergen, Norway
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
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Mbadugha BNA, Seo J, Ji H, Martásek P, Roman LJ, Shea TM, Li H, Poulos TL, Silverman RB. Hydroxyl-terminated peptidomimetic inhibitors of neuronal nitric oxide synthase. Bioorg Med Chem 2006; 14:3681-90. [PMID: 16480878 DOI: 10.1016/j.bmc.2006.01.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2005] [Revised: 01/11/2006] [Accepted: 01/12/2006] [Indexed: 10/25/2022]
Abstract
The X-ray structure of previously studied dipeptidomimetic inhibitors bound in the active site of neuronal nitric oxide synthase (nNOS) presented a possibility for optimizing the strength of enzyme-inhibitor interactions as well as for enhancing bioavailability. These desirable properties may be attainable by replacement of the terminal amino group of the parent compounds (1-6) with a hydroxyl group (11-13, and 18-20). The hypothesized effect would be twofold: first, a change from a positively charged amino group to a neutral hydroxyl group might afford more drug-like character and blood-brain barrier permeability to the inhibitors; second, as suggested by docking studies, the incorporated hydroxyl group might displace an active site water molecule with which the terminal amino group of the original compounds indirectly hydrogen bonds. In vitro activity assays of the hydroxyl-terminated analogs (11-13 and 18-20) showed greater than an order of magnitude increase in K(i) values (decreased potency) relative to the amino-terminated compounds. These experimental data support the importance to enzyme binding of a potential electrostatic interaction relative to a hydrogen bonding interaction.
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Affiliation(s)
- Bessie N A Mbadugha
- Department of Chemistry, Center for Drug Discovery and Chemical Biology, Northwestern University, Evanston, IL 60208-3113, USA
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Ultrasound energy improves myocardial perfusion in the presence of coronary occlusion. J Am Coll Cardiol 2004; 44:1454-8. [PMID: 15464327 DOI: 10.1016/j.jacc.2004.06.062] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2004] [Revised: 04/21/2004] [Accepted: 06/21/2004] [Indexed: 11/23/2022]
Abstract
OBJECTIVES We evaluated whether ultrasound improves myocardial tissue perfusion in 14 animals with coronary artery occlusion. BACKGROUND A recent study demonstrated that low-frequency ultrasound improves tissue perfusion in the rabbit ischemic limb, but there are no data on ultrasound enhancement of myocardial perfusion. METHODS Fourteen animals (9 dogs, 5 pigs) underwent thoracotomy and occlusion of a diagonal branch of the left anterior descending coronary artery. Myocardial tissue perfusion units (TPUs) and pH were measured before coronary occlusion, after occlusion, and after direct exposure of the ischemic myocardium in the presence of fixed occlusion to low-frequency ultrasound (27 kHz). RESULTS The TPU decreased from 100.9 +/- 13 at baseline to 71.1 +/- 13 (p < 0.01) after 60 min occlusion but rose by 19.7% to 85.1 +/- 8 (p < 0.01) after ultrasound exposure for 60 min. After 60-min coronary occlusion, myocardial pH fell from 7.43 +/- 14 to 7.05 +/- 0.15 (p < 0.01) but then improved to normal (7.46 +/- 0.32) after ultrasound for 60 min. Administration of L-Nomega-nitro-arginine methyl esther (L-NAME), an inhibitor of nitric oxide synthase, before ultrasound exposure, blocked improvement in myocardial tissue perfusion and pH by ultrasound. Quantitative histomorphology showed a significant increase in the capillary area of myocardium exposed to ultrasound versus non-exposed myocardium (16.2 +/- 7.9 vs. 8.2 +/- 2.1, p < 0.02). CONCLUSIONS Low-frequency, low-intensity ultrasound improves myocardial tissue perfusion and pH in the presence of a fixed coronary artery occlusion.
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Abstract
L-Arginine is the biological precursor of nitric oxide (NO), which serves as an important signal and effector molecule in animals. This review summarizes some structure-function aspects of the mammalian nitric oxide synthases, which are enzymes that catalyze the oxidation of L-arginine to NO and L-citrulline. These include aspects related to: 1) the chemical transformations of L-arginine during enzyme catalysis, 2) binding of L-arginine or its structural analogs to the nitric oxide synthases, and 3) how L-arginine levels may affect product formation by the nitric oxide synthases and how this can be modulated by structural analogs of L-arginine.
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Affiliation(s)
- Dennis J Stuehr
- Department of Immunology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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