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Chilaka SK, Chellu RK, Soda AK, Kurva S, Nanubolu JB, Madabhushi S. Base‐Catalyzed Domino Reaction Between Aldoxime and <i>N</i>‐Chlorosuccinimide in Alcohol: One‐Pot Synthesis of Alkyl 3‐(3‐Aryl‐1,2,4‐oxadiazol‐5‐yl)propanoates. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202200265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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2
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Cañizares-Carmenate Y, Mena-Ulecia K, MacLeod Carey D, Perera-Sardiña Y, Hernández-Rodríguez EW, Marrero-Ponce Y, Torrens F, Castillo-Garit JA. Machine learning approach to discovery of small molecules with potential inhibitory action against vasoactive metalloproteases. Mol Divers 2021; 26:1383-1397. [PMID: 34216326 DOI: 10.1007/s11030-021-10260-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/17/2021] [Indexed: 11/26/2022]
Abstract
With the advancement of combinatorial chemistry and big data, drug repositioning has boomed. In this sense, machine learning and artificial intelligence techniques offer a priori information to identify the most promising candidates. In this study, we combine QSAR and docking methodologies to identify compounds with potential inhibitory activity of vasoactive metalloproteases for the treatment of cardiovascular diseases. To develop this study, we used a database of 191 thermolysin inhibitor compounds, which is the largest as far as we know. First, we use Dragon's molecular descriptors (0-3D) to develop classification models using Bayesian networks (Naive Bayes) and artificial neural networks (Multilayer Perceptron). The obtained models are used for virtual screening of small molecules in the international DrugBank database. Second, docking experiments are carried out for all three enzymes using the Autodock Vina program, to identify possible interactions with the active site of human metalloproteases. As a result, high-performance artificial intelligence QSAR models are obtained for training and prediction sets. These allowed the identification of 18 compounds with potential inhibitory activity and an adequate oral bioavailability profile, which were evaluated using docking. Four of them showed high binding energies for the three enzymes, and we propose them as potential dual ACE/NEP inhibitors for the control of blood pressure. In summary, the in silico strategies used here constitute an important tool for the early identification of new antihypertensive drug candidates, with substantial savings in time and money.
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Affiliation(s)
- Yudith Cañizares-Carmenate
- Unit of Computer-Aided Molecular ''Biosilico" Discovery and Bioinformatic Research (CAMD-BIR Unit), Facultad de Química-Farmacia, Universidad Central ''Marta Abreu" de Las Villas, 54830, Santa Clara, Villa Clara, Cuba
| | - Karel Mena-Ulecia
- Departamento de Ciencias Biológicas Y Químicas, Facultad de Recursos Naturales, Universidad Católica de Temuco, Ave. Rudecindo Ortega, 02950, Temuco, Chile
- Núcleo de Investigación en Bioproductos Y Materiales Avanzados (BIOMA), Facultad de Ingeniería, Universidad Católica de Temuco, Ave. Rudecindo Ortega, 02950, Temuco, Chile
| | - Desmond MacLeod Carey
- Facultad de Ingeniería, Inorganic Chemistry and Molecular Materials Center, Instituto de Ciencias Químicas Aplicadas, Universidad Autónoma de Chile, El Llano Subercaseaux, San Miguel, 2801, Santiago, Chile
| | - Yunier Perera-Sardiña
- Laboratorio de Bioinformática Y Química Computacional, Escuela de Química Y Farmacia, Facultad de Medicina, Universidad Católica de Maule, Talca, Chile
| | - Erix W Hernández-Rodríguez
- Laboratorio de Bioinformática Y Química Computacional, Escuela de Química Y Farmacia, Facultad de Medicina, Universidad Católica de Maule, Talca, Chile
| | - Yovani Marrero-Ponce
- Grupo de Medicina Molecular Y Traslacional (MeM & T), Escuela de Medicina, Universidad San Francisco de Quito, Edificio de Especialidades Médicas, Av. Interoceánica Km 12½, Quito, Ecuador
| | - Francisco Torrens
- Institut Universitari de Ciència Molecular, Universitat de València, Edifici D'Instituts de Paterna, P.O. Box 22085, 46071, València, Spain
| | - Juan A Castillo-Garit
- Unidad de Toxicología Experimental, Universidad de Ciencias Médicas de Villa Clara, Carretera a Acueducto Y Circunvalación, CP: 50200, Santa Clara, Villa Clara, Cuba.
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3
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Cañizares-Carmenate Y, Alcántara Cárdenas A, Roche Llerena V, Torrens F, Castillo-Garit JA. Computational approach to the discovery of potential neprilysin inhibitors compounds for cardiovascular diseases treatment. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02529-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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4
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Kawanami T, Karki RG, Cody E, Liu Q, Liang G, Ksander GM, Rigel DF, Schiering N, Gong Y, Coppola GM, Iwaki Y, Sun R, Neubert A, Fan L, Ingles S, D’Arcy A, Villard F, Ramage P, Jeng AY, Leung-Chu J, Liu J, Beil M, Fu F, Chen W, Cumin F, Wiesmann C, Mogi M. Structure-Guided Design of Substituted Biphenyl Butanoic Acid Derivatives as Neprilysin Inhibitors. ACS Med Chem Lett 2020; 11:188-194. [PMID: 32071687 DOI: 10.1021/acsmedchemlett.9b00578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/27/2020] [Indexed: 12/11/2022] Open
Abstract
Inhibition of neprilysin (NEP) is widely studied as a therapeutic target for the treatment of hypertension, heart failure, and kidney disease. Sacubitril/valsartan (LCZ696) is a drug approved to reduce the risk of cardiovascular death in heart failure patients with reduced ejection fraction. LBQ657 is the active metabolite of sacubitril and an inhibitor of NEP. Previously, we have reported the crystal structure of NEP bound with LBQ657, whereby we noted the presence of a subsite in S1' that has not been explored before. We were also intrigued by the zinc coordination made by one of the carboxylic acids of LBQ657, leading us to explore alternative linkers to efficiently engage zinc for NEP inhibition. Structure-guided design culminated in the synthesis of selective, orally bioavailable, and subnanomolar inhibitors of NEP. A 17-fold boost in biochemical potency was observed upon addition of a chlorine atom that occupied the newly found subsite in S1'. We report herein the discovery and preclinical profiling of compound 13, which paved the path to our clinical candidate.
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Affiliation(s)
- Toshio Kawanami
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Rajeshri G. Karki
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Emma Cody
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Qian Liu
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Guiqing Liang
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Gary M. Ksander
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Dean F. Rigel
- Novartis Pharmaceuticals Corporation, One Health Plaza, East Hanover, New Jersey 07936-1080, United States
| | - Nikolaus Schiering
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Yongjin Gong
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Gary M. Coppola
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Yuki Iwaki
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Robert Sun
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Alan Neubert
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Li Fan
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Sara Ingles
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Allan D’Arcy
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Frederic Villard
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Paul Ramage
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Arco Y. Jeng
- Novartis Pharmaceuticals Corporation, One Health Plaza, East Hanover, New Jersey 07936-1080, United States
| | - Jennifer Leung-Chu
- Novartis Pharmaceuticals Corporation, One Health Plaza, East Hanover, New Jersey 07936-1080, United States
| | - Jing Liu
- Novartis Pharmaceuticals Corporation, One Health Plaza, East Hanover, New Jersey 07936-1080, United States
| | - Michael Beil
- Novartis Pharmaceuticals Corporation, One Health Plaza, East Hanover, New Jersey 07936-1080, United States
| | - Fumin Fu
- Novartis Pharmaceuticals Corporation, One Health Plaza, East Hanover, New Jersey 07936-1080, United States
| | - Wei Chen
- Novartis Pharmaceuticals Corporation, One Health Plaza, East Hanover, New Jersey 07936-1080, United States
| | - Frederic Cumin
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Christian Wiesmann
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Muneto Mogi
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
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5
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Arendse LB, Danser AHJ, Poglitsch M, Touyz RM, Burnett JC, Llorens-Cortes C, Ehlers MR, Sturrock ED. Novel Therapeutic Approaches Targeting the Renin-Angiotensin System and Associated Peptides in Hypertension and Heart Failure. Pharmacol Rev 2019; 71:539-570. [PMID: 31537750 PMCID: PMC6782023 DOI: 10.1124/pr.118.017129] [Citation(s) in RCA: 204] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Despite the success of renin-angiotensin system (RAS) blockade by angiotensin-converting enzyme (ACE) inhibitors and angiotensin II type 1 receptor (AT1R) blockers, current therapies for hypertension and related cardiovascular diseases are still inadequate. Identification of additional components of the RAS and associated vasoactive pathways, as well as new structural and functional insights into established targets, have led to novel therapeutic approaches with the potential to provide improved cardiovascular protection and better blood pressure control and/or reduced adverse side effects. The simultaneous modulation of several neurohumoral mediators in key interconnected blood pressure-regulating pathways has been an attractive approach to improve treatment efficacy, and several novel approaches involve combination therapy or dual-acting agents. In addition, increased understanding of the complexity of the RAS has led to novel approaches aimed at upregulating the ACE2/angiotensin-(1-7)/Mas axis to counter-regulate the harmful effects of the ACE/angiotensin II/angiotensin III/AT1R axis. These advances have opened new avenues for the development of novel drugs targeting the RAS to better treat hypertension and heart failure. Here we focus on new therapies in preclinical and early clinical stages of development, including novel small molecule inhibitors and receptor agonists/antagonists, less conventional strategies such as gene therapy to suppress angiotensinogen at the RNA level, recombinant ACE2 protein, and novel bispecific designer peptides.
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Affiliation(s)
- Lauren B Arendse
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa (L.B.A., E.D.S.); Division of Pharmacology, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands (A.H.J.D.); Attoquant Diagnostics, Vienna, Austria (M.P.); Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom (R.M.T.); Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota (J.C.B.); Institut National de la Santé et de la Recherche Médicale, Paris, France (C.L.-C.); and Clinical Trials Group, Immune Tolerance Network, San Francisco, California (M.R.E.)
| | - A H Jan Danser
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa (L.B.A., E.D.S.); Division of Pharmacology, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands (A.H.J.D.); Attoquant Diagnostics, Vienna, Austria (M.P.); Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom (R.M.T.); Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota (J.C.B.); Institut National de la Santé et de la Recherche Médicale, Paris, France (C.L.-C.); and Clinical Trials Group, Immune Tolerance Network, San Francisco, California (M.R.E.)
| | - Marko Poglitsch
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa (L.B.A., E.D.S.); Division of Pharmacology, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands (A.H.J.D.); Attoquant Diagnostics, Vienna, Austria (M.P.); Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom (R.M.T.); Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota (J.C.B.); Institut National de la Santé et de la Recherche Médicale, Paris, France (C.L.-C.); and Clinical Trials Group, Immune Tolerance Network, San Francisco, California (M.R.E.)
| | - Rhian M Touyz
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa (L.B.A., E.D.S.); Division of Pharmacology, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands (A.H.J.D.); Attoquant Diagnostics, Vienna, Austria (M.P.); Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom (R.M.T.); Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota (J.C.B.); Institut National de la Santé et de la Recherche Médicale, Paris, France (C.L.-C.); and Clinical Trials Group, Immune Tolerance Network, San Francisco, California (M.R.E.)
| | - John C Burnett
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa (L.B.A., E.D.S.); Division of Pharmacology, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands (A.H.J.D.); Attoquant Diagnostics, Vienna, Austria (M.P.); Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom (R.M.T.); Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota (J.C.B.); Institut National de la Santé et de la Recherche Médicale, Paris, France (C.L.-C.); and Clinical Trials Group, Immune Tolerance Network, San Francisco, California (M.R.E.)
| | - Catherine Llorens-Cortes
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa (L.B.A., E.D.S.); Division of Pharmacology, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands (A.H.J.D.); Attoquant Diagnostics, Vienna, Austria (M.P.); Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom (R.M.T.); Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota (J.C.B.); Institut National de la Santé et de la Recherche Médicale, Paris, France (C.L.-C.); and Clinical Trials Group, Immune Tolerance Network, San Francisco, California (M.R.E.)
| | - Mario R Ehlers
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa (L.B.A., E.D.S.); Division of Pharmacology, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands (A.H.J.D.); Attoquant Diagnostics, Vienna, Austria (M.P.); Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom (R.M.T.); Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota (J.C.B.); Institut National de la Santé et de la Recherche Médicale, Paris, France (C.L.-C.); and Clinical Trials Group, Immune Tolerance Network, San Francisco, California (M.R.E.)
| | - Edward D Sturrock
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa (L.B.A., E.D.S.); Division of Pharmacology, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands (A.H.J.D.); Attoquant Diagnostics, Vienna, Austria (M.P.); Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom (R.M.T.); Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota (J.C.B.); Institut National de la Santé et de la Recherche Médicale, Paris, France (C.L.-C.); and Clinical Trials Group, Immune Tolerance Network, San Francisco, California (M.R.E.)
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6
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Moss S, Subramanian V, Acharya KR. Crystal structure of peptide-bound neprilysin reveals key binding interactions. FEBS Lett 2019; 594:327-336. [PMID: 31514225 DOI: 10.1002/1873-3468.13602] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 11/09/2022]
Abstract
Neprilysin (NEP) is a promiscuous zinc metalloprotease with broad substrate specificity and cleaves a remarkable diversity of substrates through endopeptidase action. Two of these - amyloid-β and natriuretic peptides - implicate the enzyme in both Alzheimer's disease and cardiovascular disease, respectively. Here, we report the creation of a catalytically inactive NEP (E584D) to determine the first peptide-bound crystal structure at 2.6 Å resolution. The structure reveals key interactions involved in substrate binding which we have identified to be conserved in other known zinc metalloproteases. In addition, the structure provides evidence for a potential exosite within the central cavity that may play a critical role in substrate positioning. Together, these results contribute to our understanding of the molecular function of NEP.
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Affiliation(s)
- Stephen Moss
- Department of Biology and Biochemistry, Claverton Down, University of Bath, UK
| | - Vasanta Subramanian
- Department of Biology and Biochemistry, Claverton Down, University of Bath, UK
| | - K Ravi Acharya
- Department of Biology and Biochemistry, Claverton Down, University of Bath, UK
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7
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Labiuk SL, Sygusch J, Grochulski P. Structures of soluble rabbit neprilysin complexed with phosphoramidon or thiorphan. Acta Crystallogr F Struct Biol Commun 2019; 75:405-411. [PMID: 31204686 PMCID: PMC6572095 DOI: 10.1107/s2053230x19006046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 04/30/2019] [Indexed: 12/15/2022] Open
Abstract
Neutral endopeptidase (neprilysin; NEP) is a proteinase that cleaves a wide variety of peptides and has been implicated in Alzheimer's disease, cardiovascular conditions, arthritis and other inflammatory diseases. The structure of the soluble extracellular domain (residues 55-750) of rabbit neprilysin was solved both in its native form at 2.1 Å resolution, and bound to the inhibitors phosphoramidon and thiorphan at 2.8 and 3.0 Å resolution, respectively. Consistent with the extracellular domain of human neprilysin, the structure reveals a large central cavity which contains the active site and the location for inhibitor binding.
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Affiliation(s)
- Shaunivan L. Labiuk
- Canadian Light Source, 44 Innovation Boulevard, Saskatoon, SK S7N 2V3, Canada
| | - Jurgen Sygusch
- Biochimie et Médecine Moléculaire, Université de Montréal, CP 6128, Station Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Pawel Grochulski
- Canadian Light Source, 44 Innovation Boulevard, Saskatoon, SK S7N 2V3, Canada
- College of Pharmacy and Nutrition, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
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8
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Cozier GE, Arendse LB, Schwager SL, Sturrock ED, Acharya KR. Molecular Basis for Multiple Omapatrilat Binding Sites within the ACE C-Domain: Implications for Drug Design. J Med Chem 2018; 61:10141-10154. [PMID: 30372620 DOI: 10.1021/acs.jmedchem.8b01309] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Omapatrilat was designed as a vasopeptidase inhibitor with dual activity against the zinc metallopeptidases angiotensin-1 converting enzyme (ACE) and neprilysin (NEP). ACE has two homologous catalytic domains (nACE and cACE), which exhibit different substrate specificities. Here, we report high-resolution crystal structures of omapatrilat in complex with nACE and cACE and show omapatrilat has subnanomolar affinity for both domains. The structures show nearly identical binding interactions for omapatrilat in each domain, explaining the lack of domain selectivity. The cACE complex structure revealed an omapatrilat dimer occupying the cavity beyond the S2 subsite, and this dimer had low micromolar inhibition of nACE and cACE. These results highlight residues beyond the S2 subsite that could be exploited for domain selective inhibition. In addition, it suggests the possibility of either domain specific allosteric inhibitors that bind exclusively to the nonprime cavity or the potential for targeting specific substrates rather than completely inhibiting the enzyme.
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Affiliation(s)
- Gyles E Cozier
- Department of Biology and Biochemistry , University of Bath , Claverton Down , Bath BA2 7AY , United Kingdom
| | - Lauren B Arendse
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine , University of Cape Town , Observatory , 7925 Cape Town , Republic of South Africa
| | - Sylva L Schwager
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine , University of Cape Town , Observatory , 7925 Cape Town , Republic of South Africa
| | - Edward D Sturrock
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine , University of Cape Town , Observatory , 7925 Cape Town , Republic of South Africa
| | - K Ravi Acharya
- Department of Biology and Biochemistry , University of Bath , Claverton Down , Bath BA2 7AY , United Kingdom
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9
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High resolution crystal structure of substrate-free human neprilysin. J Struct Biol 2018; 204:19-25. [PMID: 29906506 DOI: 10.1016/j.jsb.2018.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/09/2018] [Accepted: 06/11/2018] [Indexed: 11/23/2022]
Abstract
Neprilysin is a transmembrane M13 zinc metalloprotease responsible for the degradation of several biologically active peptides including insulin, enkephalin, substance P, bradykinin, endothelin-1, neurotensin and amyloid-β. The protein has received attention for its role in modulating blood pressure responses with its inhibition producing an antihypertensive response. To date, several inhibitor bound crystal structures of the human neprilysin extracellular domain have been determined, but, a structure free of bound inhibitor or substrate has yet to be reported. Here, we report the first crystal structure free of substrate or inhibitor for the extracellular catalytic domain of human neprilysin at 1.9 Å resolution. This structure will provide a reference point for comparisons to future inhibitor or substrate bound structures. The neprilysin structure also reveals that a closed protein conformation can be adopted in protein crystals absent of bound substrate or inhibitor.
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10
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Schiering N, D'Arcy A, Villard F, Ramage P, Logel C, Cumin F, Ksander GM, Wiesmann C, Karki RG, Mogi M. Structure of neprilysin in complex with the active metabolite of sacubitril. Sci Rep 2016; 6:27909. [PMID: 27302413 PMCID: PMC4908401 DOI: 10.1038/srep27909] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/26/2016] [Indexed: 02/06/2023] Open
Abstract
Sacubitril is an ethyl ester prodrug of LBQ657, the active neprilysin (NEP) inhibitor, and a component of LCZ696 (sacubitril/valsartan). We report herein the three-dimensional structure of LBQ657 in complex with human NEP at 2 Å resolution. The crystal structure unravels the binding mode of the compound occupying the S1, S1’ and S2’ sub-pockets of the active site, consistent with a competitive inhibition mode. An induced fit conformational change upon binding of the P1’-biphenyl moiety of the inhibitor suggests an explanation for its selectivity against structurally homologous zinc metallopeptidases.
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Affiliation(s)
- Nikolaus Schiering
- Novartis Institutes for BioMedical Research Inc., Fabrikstrasse 16, CH-4002 Basel, Switzerland
| | - Allan D'Arcy
- Novartis Institutes for BioMedical Research Inc., Fabrikstrasse 16, CH-4002 Basel, Switzerland
| | - Frederic Villard
- Novartis Institutes for BioMedical Research Inc., Fabrikstrasse 16, CH-4002 Basel, Switzerland
| | - Paul Ramage
- Novartis Institutes for BioMedical Research Inc., Fabrikstrasse 16, CH-4002 Basel, Switzerland
| | - Claude Logel
- Novartis Institutes for BioMedical Research Inc., Fabrikstrasse 16, CH-4002 Basel, Switzerland
| | - Frederic Cumin
- Novartis Institutes for BioMedical Research Inc., Fabrikstrasse 16, CH-4002 Basel, Switzerland
| | - Gary M Ksander
- Novartis Institutes for BioMedical Research Inc., 100 Technology Square, Cambridge, Massachusetts, 02139, United States
| | - Christian Wiesmann
- Novartis Institutes for BioMedical Research Inc., Fabrikstrasse 16, CH-4002 Basel, Switzerland
| | - Rajeshri G Karki
- Novartis Institutes for BioMedical Research Inc., 100 Technology Square, Cambridge, Massachusetts, 02139, United States
| | - Muneto Mogi
- Novartis Institutes for BioMedical Research Inc., 100 Technology Square, Cambridge, Massachusetts, 02139, United States
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11
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Webster CI, Burrell M, Olsson LL, Fowler SB, Digby S, Sandercock A, Snijder A, Tebbe J, Haupts U, Grudzinska J, Jermutus L, Andersson C. Engineering neprilysin activity and specificity to create a novel therapeutic for Alzheimer's disease. PLoS One 2014; 9:e104001. [PMID: 25089527 PMCID: PMC4121237 DOI: 10.1371/journal.pone.0104001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 07/05/2014] [Indexed: 02/07/2023] Open
Abstract
Neprilysin is a transmembrane zinc metallopeptidase that degrades a wide range of peptide substrates. It has received attention as a potential therapy for Alzheimer’s disease due to its ability to degrade the peptide amyloid beta. However, its broad range of peptide substrates has the potential to limit its therapeutic use due to degradation of additional peptides substrates that tightly regulate many physiological processes. We sought to generate a soluble version of the ectodomain of neprilysin with improved activity and specificity towards amyloid beta as a potential therapeutic for Alzheimer’s disease. Extensive amino acid substitutions were performed at positions surrounding the active site and inner surface of the enzyme and variants screened for activity on amyloid beta 1–40, 1–42 and a variety of other physiologically relevant peptides. We identified several mutations that modulated and improved both enzyme selectivity and intrinsic activity. Neprilysin variant G399V/G714K displayed an approximately 20-fold improved activity on amyloid beta 1–40 and up to a 3,200-fold reduction in activity on other peptides. Along with the altered peptide substrate specificity, the mutant enzyme produced a markedly altered series of amyloid beta cleavage products compared to the wild-type enzyme. Crystallisation of the mutant enzyme revealed that the amino acid substitutions result in alteration of the shape and size of the pocket containing the active site compared to the wild-type enzyme. The mutant enzyme offers the potential for the more efficient degradation of amyloid beta in vivo as a therapeutic for the treatment of Alzheimer’s disease.
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Affiliation(s)
- Carl I. Webster
- Antibody Discovery and Protein Engineering, MedImmune, Cambridge, United Kingdom
- * E-mail:
| | - Matthew Burrell
- Antibody Discovery and Protein Engineering, MedImmune, Cambridge, United Kingdom
| | | | - Susan B. Fowler
- Antibody Discovery and Protein Engineering, MedImmune, Cambridge, United Kingdom
| | - Sarah Digby
- Antibody Discovery and Protein Engineering, MedImmune, Cambridge, United Kingdom
| | - Alan Sandercock
- Antibody Discovery and Protein Engineering, MedImmune, Cambridge, United Kingdom
| | - Arjan Snijder
- Discovery Sciences, AstraZeneca R & D, Mölndal, Sweden
| | - Jan Tebbe
- Global Drug Discovery, Global Biologics, Bayer HealthCare AG, Cologne, Germany
| | - Ulrich Haupts
- Global Drug Discovery, Global Biologics, Bayer HealthCare AG, Cologne, Germany
| | - Joanna Grudzinska
- Global Drug Discovery, Global Biologics, Bayer HealthCare AG, Cologne, Germany
| | - Lutz Jermutus
- Antibody Discovery and Protein Engineering, MedImmune, Cambridge, United Kingdom
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Pope D, Madura JD, Cascio M. β-Amyloid and neprilysin computational studies identify critical residues implicated in binding specificity. J Chem Inf Model 2014; 54:1157-65. [PMID: 24650257 DOI: 10.1021/ci500015m] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The zinc metalloprotease neprilysin (NEP) promiscuously degrades small bioactive peptides. NEP is among a select group of metalloenzymes that degrade the amyloid beta-peptide (Aβ) in vivo and in situ. Since accumulation of neurotoxic Aβ aggregates in the brain appears to be a causative agent in the pathophysiology of Alzheimer's disease (AD), increased clearance of Aβ resulting from overexpression of NEP exhibits therapeutic potential for AD. However, higher NEP peptidase activity may be harmful without an increased specificity for Aβ over other competing substrates. Crystal structures of NEP-inhibitor complexes and their characterization have highlighted potential amino acid interactions involved in substrate binding and are used as templates to guide our methodology in docking Aβ in NEP. Results from protein-ligand docking calculations predict S2' subsite residues Arg 102 and Arg 110 of NEP participate in specific interactions with Aβ. These interactions provide insight into developing NEP specificity for Aβ.
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Affiliation(s)
- Darrick Pope
- Department of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University , 600 Forbes Avenue, 331 Mellon Hall, Pittsburgh, Pennsylvania 15282, United States
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El Bakali J, Maingot L, Dumont J, Host H, Hocine A, Cousaert N, Dassonneville S, Leroux F, Deprez B, Deprez-Poulain R. Novel selective inhibitors of neutral endopeptidase: discovery by screening and hit-to-lead optimisation. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md00287f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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