1
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Bobrovs R, Basens EE, Drunka L, Kanepe I, Matisone S, Velins KK, Andrianov V, Leitis G, Zelencova-Gopejenko D, Rasina D, Jirgensons A, Jaudzems K. Exploring Aspartic Protease Inhibitor Binding to Design-Selective Antimalarials. J Chem Inf Model 2022; 62:3263-3273. [PMID: 35712895 DOI: 10.1021/acs.jcim.2c00422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Selectivity is a major issue in the development of drugs targeting pathogen aspartic proteases. Here, we explore the selectivity-determining factors by studying specifically designed malaria aspartic protease (plasmepsin) open-flap inhibitors. Metadynamics simulations are used to uncover the complex binding/unbinding pathways of these inhibitors and describe the critical transition states in atomistic resolution. The simulation results are compared with experimentally determined enzymatic activities. Our findings demonstrate that plasmepsin inhibitor selectivity can be achieved by targeting the flap loop with hydrophobic substituents that enable ligand binding under the flap loop, as such a behavior is not observed for several other aspartic proteases. The ability to estimate the selectivity of compounds before they are synthesized is of considerable importance in drug design; therefore, we expect that our approach will be useful in selective inhibitor designs against not only aspartic proteases but also other enzyme classes.
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Affiliation(s)
- Raitis Bobrovs
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | | | - Laura Drunka
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Iveta Kanepe
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Sofija Matisone
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | | | - Victor Andrianov
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Gundars Leitis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | | | - Dace Rasina
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Aigars Jirgensons
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
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2
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Tetrahydroisoquinoline-Based Non-Peptidomimetic Plasmepsin Inhibitors. Chem Heterocycl Compd (N Y) 2020. [DOI: 10.1007/s10593-020-02623-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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3
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Bobrovs R, Jaudzems K, Jirgensons A. Exploiting Structural Dynamics To Design Open-Flap Inhibitors of Malarial Aspartic Proteases. J Med Chem 2019; 62:8931-8950. [DOI: 10.1021/acs.jmedchem.9b00184] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Raitis Bobrovs
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Aigars Jirgensons
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
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4
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Brennecke P, Rasina D, Aubi O, Herzog K, Landskron J, Cautain B, Vicente F, Quintana J, Mestres J, Stechmann B, Ellinger B, Brea J, Kolanowski JL, Pilarski R, Orzaez M, Pineda-Lucena A, Laraia L, Nami F, Zielenkiewicz P, Paruch K, Hansen E, von Kries JP, Neuenschwander M, Specker E, Bartunek P, Simova S, Leśnikowski Z, Krauss S, Lehtiö L, Bilitewski U, Brönstrup M, Taskén K, Jirgensons A, Lickert H, Clausen MH, Andersen JH, Vicent MJ, Genilloud O, Martinez A, Nazaré M, Fecke W, Gribbon P. EU-OPENSCREEN: A Novel Collaborative Approach to Facilitate Chemical Biology. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2019; 24:398-413. [PMID: 30616481 PMCID: PMC6764006 DOI: 10.1177/2472555218816276] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/11/2018] [Accepted: 11/08/2018] [Indexed: 12/27/2022]
Abstract
Compound screening in biological assays and subsequent optimization of hits is indispensable for the development of new molecular research tools and drug candidates. To facilitate such discoveries, the European Research Infrastructure EU-OPENSCREEN was founded recently with the support of its member countries and the European Commission. Its distributed character harnesses complementary knowledge, expertise, and instrumentation in the discipline of chemical biology from 20 European partners, and its open working model ensures that academia and industry can readily access EU-OPENSCREEN's compound collection, equipment, and generated data. To demonstrate the power of this collaborative approach, this perspective article highlights recent projects from EU-OPENSCREEN partner institutions. These studies yielded (1) 2-aminoquinazolin-4(3 H)-ones as potential lead structures for new antimalarial drugs, (2) a novel lipodepsipeptide specifically inducing apoptosis in cells deficient for the pVHL tumor suppressor, (3) small-molecule-based ROCK inhibitors that induce definitive endoderm formation and can potentially be used for regenerative medicine, (4) potential pharmacological chaperones for inborn errors of metabolism and a familiar form of acute myeloid leukemia (AML), and (5) novel tankyrase inhibitors that entered a lead-to-candidate program. Collectively, these findings highlight the benefits of small-molecule screening, the plethora of assay designs, and the close connection between screening and medicinal chemistry within EU-OPENSCREEN.
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Affiliation(s)
- Philip Brennecke
- EU-OPENSCREEN, Leibniz Research
Institute for Molecular Pharmacology, Berlin, Germany
| | - Dace Rasina
- Organic Synthesis Methodology Group,
Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Oscar Aubi
- Department of Biomedicine, University of
Bergen, Bergen, Norway
| | - Katja Herzog
- EU-OPENSCREEN, Leibniz Research
Institute for Molecular Pharmacology, Berlin, Germany
| | - Johannes Landskron
- Centre for Molecular Medicine
Norway–Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - Bastien Cautain
- Fundación MEDINA, Health Sciences
Technology Park, Granada, Spain
| | | | - Jordi Quintana
- Department of Experimental and Health
Sciences, Universitat Pompeu Fabra, Barcelona, Catalunya, Spain
| | - Jordi Mestres
- Department of Experimental and Health
Sciences, Universitat Pompeu Fabra, Barcelona, Catalunya, Spain
- IMIM Hospital del Mar Medical Research
Institute, Research Program on Biomedical Informatics (GRIB), Barcelona, Spain
| | - Bahne Stechmann
- EU-OPENSCREEN, Leibniz Research
Institute for Molecular Pharmacology, Berlin, Germany
| | - Bernhard Ellinger
- Fraunhofer Institute for Molecular
Biology and Applied Ecology IME, Screening Port, Hamburg, Germany
| | - Jose Brea
- Institute for Research in Molecular
Medicine and Chronic Diseases—BioFarma Research Group, University of Santiago de
Compostela, Santiago de Compostela, Spain
| | - Jacek L. Kolanowski
- Department of Molecular Probes and
Prodrugs, Institute of Bioorganic Chemistry—Polish Academy of Sciences, Poznan,
Poland
| | - Radosław Pilarski
- Department of Molecular Probes and
Prodrugs, Institute of Bioorganic Chemistry—Polish Academy of Sciences, Poznan,
Poland
| | - Mar Orzaez
- Screening Platform, Principe Felipe
Research Center, Valencia, Spain
| | | | - Luca Laraia
- Center for Nanomedicine and
Theranostics, Department of Chemistry, Technical University of Denmark, Lyngby,
Denmark
- Technical University of Denmark,
DK-OPENSCREEN, Lyngby, Denmark
| | - Faranak Nami
- Center for Nanomedicine and
Theranostics, Department of Chemistry, Technical University of Denmark, Lyngby,
Denmark
- Technical University of Denmark,
DK-OPENSCREEN, Lyngby, Denmark
| | - Piotr Zielenkiewicz
- Department of Bioinformatics,
Institute of Biochemistry and Biophysics—Polish Academy of Sciences, Warsaw,
Poland
| | - Kamil Paruch
- Department of Chemistry—CZ-OPENSCREEN,
Masaryk University, Brno, Czech Republic
| | - Espen Hansen
- The Arctic University of Norway,
University of Tromsø, Marbio, Tromsø, Norway
| | - Jens P. von Kries
- Screening Unit, Leibniz Research
Institute for Molecular Pharmacology, Berlin, Germany
| | - Martin Neuenschwander
- Screening Unit, Leibniz Research
Institute for Molecular Pharmacology, Berlin, Germany
| | - Edgar Specker
- Medicinal Chemistry Research Group,
Leibniz Research Institute for Molecular Pharmacology, Berlin, Germany
| | - Petr Bartunek
- Institute of Molecular Genetics of the
ASCR, CZ-OPENSCREEN, Prague, Czech Republic
| | - Sarka Simova
- Institute of Molecular Genetics of the
ASCR, CZ-OPENSCREEN, Prague, Czech Republic
| | - Zbigniew Leśnikowski
- Laboratory of Molecular Virology and
Biological Chemistry, Institute of Medical Biology—Polish Academy of Sciences, Łódź,
Poland
| | - Stefan Krauss
- Department of Immunology and
Transfusion Medicine, Oslo University Hospital, Oslo, Norway
- Hybrid Technology Hub—Centre of
Excellence—Institute of Basic Medical Sciences, University of Oslo, Oslo,
Norway
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular
Medicine—Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Ursula Bilitewski
- Working Group Compound Profiling and
Screening, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Mark Brönstrup
- Department of Chemical Biology,
Helmholtz Centre for Infection Research, Brunswick, Germany
- German Center for Infection Research
(DZIF), partner site Hannover-Brunswick, Brunswick, Germany
| | - Kjetil Taskén
- Centre for Molecular Medicine
Norway–Nordic EMBL Partnership, University of Oslo, Oslo, Norway
- Department of Cancer
Immunology—Institute for Cancer Research, Oslo University Hospital, Oslo,
Norway
- K.G. Jebsen Centre for Cancer
Immunotherapy—Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- K.G. Jebsen Centre for B Cell
Malignancies—Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Aigars Jirgensons
- Organic Synthesis Methodology Group,
Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Heiko Lickert
- Institute of Diabetes and Regeneration
Research, Helmholtz Centre Munich German Research Center for Environmental Health,
Neuherberg, Germany
| | - Mads H. Clausen
- Center for Nanomedicine and
Theranostics, Department of Chemistry, Technical University of Denmark, Lyngby,
Denmark
- Technical University of Denmark,
DK-OPENSCREEN, Lyngby, Denmark
| | | | - Maria J. Vicent
- Screening Platform, Principe Felipe
Research Center, Valencia, Spain
| | - Olga Genilloud
- Fundación MEDINA, Health Sciences
Technology Park, Granada, Spain
| | - Aurora Martinez
- Department of Biomedicine, University of
Bergen, Bergen, Norway
| | - Marc Nazaré
- Medicinal Chemistry Research Group,
Leibniz Research Institute for Molecular Pharmacology, Berlin, Germany
| | | | - Philip Gribbon
- Fraunhofer Institute for Molecular
Biology and Applied Ecology IME, Screening Port, Hamburg, Germany
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5
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Kinena L, Leitis G, Kanepe-Lapsa I, Bobrovs R, Jaudzems K, Ozola V, Suna E, Jirgensons A. Azole-based non-peptidomimetic plasmepsin inhibitors. Arch Pharm (Weinheim) 2018; 351:e1800151. [DOI: 10.1002/ardp.201800151] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/21/2018] [Accepted: 06/29/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Linda Kinena
- Latvian Institute of Organic Synthesis; Riga Latvia
| | | | | | | | | | - Vita Ozola
- Latvian Institute of Organic Synthesis; Riga Latvia
| | - Edgars Suna
- Latvian Institute of Organic Synthesis; Riga Latvia
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6
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Mishra V, Rathore I, Arekar A, Sthanam LK, Xiao H, Kiso Y, Sen S, Patankar S, Gustchina A, Hidaka K, Wlodawer A, Yada RY, Bhaumik P. Deciphering the mechanism of potent peptidomimetic inhibitors targeting plasmepsins - biochemical and structural insights. FEBS J 2018; 285:3077-3096. [PMID: 29943906 DOI: 10.1111/febs.14598] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/10/2018] [Accepted: 06/22/2018] [Indexed: 11/28/2022]
Abstract
Malaria is a deadly disease killing worldwide hundreds of thousands people each year and the responsible parasite has acquired resistance to the available drug combinations. The four vacuolar plasmepsins (PMs) in Plasmodium falciparum involved in hemoglobin (Hb) catabolism represent promising targets to combat drug resistance. High antimalarial activities can be achieved by developing a single drug that would simultaneously target all the vacuolar PMs. We have demonstrated for the first time the use of soluble recombinant plasmepsin II (PMII) for structure-guided drug discovery with KNI inhibitors. Compounds used in this study (KNI-10742, 10743, 10395, 10333, and 10343) exhibit nanomolar inhibition against PMII and are also effective in blocking the activities of PMI and PMIV with the low nanomolar Ki values. The high-resolution crystal structures of PMII-KNI inhibitor complexes reveal interesting features modulating their differential potency. Important individual characteristics of the inhibitors and their importance for potency have been established. The alkylamino analog, KNI-10743, shows intrinsic flexibility at the P2 position that potentiates its interactions with Asp132, Leu133, and Ser134. The phenylacetyl tripeptides, KNI-10333 and KNI-10343, accommodate different ρ-substituents at the P3 phenylacetyl ring that determine the orientation of the ring, thus creating novel hydrogen-bonding contacts. KNI-10743 and KNI-10333 possess significant antimalarial activity, block Hb degradation inside the food vacuole, and show no cytotoxicity on human cells; thus, they can be considered as promising candidates for further optimization. Based on our structural data, novel KNI derivatives with improved antimalarial activity could be designed for potential clinical use. DATABASE: Structural data are available in the PDB under the accession numbers 5YIE, 5YIB, 5YID, 5YIC, and 5YIA.
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Affiliation(s)
- Vandana Mishra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ishan Rathore
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Anagha Arekar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Lakshmi Kavitha Sthanam
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Huogen Xiao
- Department of Molecular and Cellular Biology, University of Guelph, ON, Canada
| | - Yoshiaki Kiso
- Laboratory of Peptide Sciences, Nagahama Institute of Bio-Science and Technology, Japan
| | - Shamik Sen
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Swati Patankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Alla Gustchina
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Koushi Hidaka
- Division of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Kobe Gakuin University, Japan
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Rickey Y Yada
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, Canada
| | - Prasenjit Bhaumik
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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7
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Liu RH, Wang ZQ, Wei BY, Zhang JW, Zhou B, Han B. Cu-Catalyzed Aminoacyloxylation of Unactivated Alkenes of Unsaturated Hydrazones with Manifold Carboxylic Acids toward Ester-Functionalized Pyrazolines. Org Lett 2018; 20:4183-4186. [DOI: 10.1021/acs.orglett.8b01507] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Rui-Hua Liu
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, PR China
| | - Zi-Qing Wang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, PR China
| | - Bang-Yi Wei
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, PR China
| | - Jian-Wu Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, PR China
| | - Bo Zhou
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, PR China
| | - Bing Han
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, PR China
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8
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Kumar Singh A, Rajendran V, Singh S, Kumar P, Kumar Y, Singh A, Miller W, Potemkin V, Poonam, Grishina M, Gupta N, Kempaiah P, Durvasula R, Singh BK, Dunn BM, Rathi B. Antiplasmodial activity of hydroxyethylamine analogs: Synthesis, biological activity and structure activity relationship of plasmepsin inhibitors. Bioorg Med Chem 2018; 26:3837-3844. [PMID: 29983285 DOI: 10.1016/j.bmc.2018.06.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 06/26/2018] [Accepted: 06/28/2018] [Indexed: 01/08/2023]
Abstract
Malaria, particularly in endemic countries remains a threat to the human health and is the leading the cause of mortality in the tropical and sub-tropical areas. Herein, we explored new C2 symmetric hydroxyethylamine analogs as the potential inhibitors of Plasmodium falciparum (P. falciparum; 3D7) in in-vitro cultures. All the listed compounds were also evaluated against crucial drug targets, plasmepsin II (Plm II) and IV (Plm IV), enzymes found in the digestive vacuole of the P. falciparum. Analog 10f showed inhibitory activities against both the enzymes Plm II and Plm IV (Ki, 1.93 ± 0.29 µM for Plm II; Ki, 1.99 ± 0.05 µM for Plm IV). Among all these analogs, compounds 10g selectively inhibited the activity of Plm IV (Ki, 0.84 ± 0.08 µM). In the in vitro screening assay, the growth inhibition of P. falciparum by both the analogs (IC50, 2.27 ± 0.95 µM for 10f; IC50, 3.11 ± 0.65 µM for 10g) displayed marked killing effect. A significant growth inhibition of the P. falciparum was displayed by analog 12c with IC50 value of 1.35 ± 0.85 µM, however, it did not show inhibitory activity against either Plms. The hemolytic assay suggested that the active compounds selectively inhibit the growth of the parasite. Further, potent analogs (10f and 12c) were evaluated for their cytotoxicity towards mammalian HepG2 and vero cells. The selectivity index (SI) values were noticed greater than 10 for both the analogs that suggested their poor toxicity. The present study indicates these analogs as putative lead structures and could serve as crucial for the development of new drug molecules.
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Affiliation(s)
- Amit Kumar Singh
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Vinoth Rajendran
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Snigdha Singh
- Department of Chemistry, University of Delhi, Delhi 110007, India; Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi 110007, India
| | - Prashant Kumar
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Yogesh Kumar
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi 110007, India
| | - Archana Singh
- Department of Botany, Hansraj College University Enclave, University of Delhi, Delhi 110007, India
| | - Whelton Miller
- Department of Chemistry & Physics, Lincoln University, Lincoln University, PA 19352, USA; Department of Chemical & Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Vladimir Potemkin
- South Ural State University, Laboratory of Computational Modeling of Drugs, 454080, Russia
| | - Poonam
- South Ural State University, Laboratory of Computational Modeling of Drugs, 454080, Russia; Department of Chemistry, Miranda House University Enclave, University of Delhi, Delhi 110007 India
| | - Maria Grishina
- South Ural State University, Laboratory of Computational Modeling of Drugs, 454080, Russia
| | - Nikesh Gupta
- Special Centre for Nanosciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Prakasha Kempaiah
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Ravi Durvasula
- Department of Medicine, Loyola University Stritch School of Medicine, Maywood, IL 60153, USA
| | | | - Ben M Dunn
- Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, P.O. Box 100245, Gainesville, FL, USA
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi 110007, India; South Ural State University, Laboratory of Computational Modeling of Drugs, 454080, Russia.
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9
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Abiri A. Plerixafor and related macrocyclic amines are potential drug candidates in treatment of malaria by "filling the flap" region of plasmepsin enzymes. Med Hypotheses 2018; 118:68-73. [PMID: 30037618 DOI: 10.1016/j.mehy.2018.06.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/24/2018] [Accepted: 06/19/2018] [Indexed: 11/30/2022]
Abstract
Death by Plasmodium falsiparum, the leading cause of malaria, is going to remain a major obstacle among the infectious diseases. Plasmepsin aspartic proteases are key proteins in the pathogenesis of plasmodium species which break down the hemoglobin and exploit it as a source of amino acids. These enzymes are one of the favorite targeting agents for medicinal chemists to design new drugs. Plasmepsin proteins show a "flap" region in their N-terminal domain, predisposing them to a good "filler" drug with an exceptional affinity to this enzyme. Plerixafor (Mozobil®, AMD3100), a CXCR4 antagonist with a bicyclam ring, historically discovered as an impurity in a mixture which had anti-HIV properties, is now a FDA approved drug for mobilizing haematopoietic stem cells in cancer patients. In this hypothesis, we focused on the similarity of the structure of plerixafor and its analogues with heme functional group of hemoglobin, the main substrate of plasmepsin, and also with some other recent azamacrocyclic compounds demonstrating antimalarial activity, to test whether these compounds are capable of exhibiting antimalarial activity by inhibiting plasmepsin or not. A preliminary in silico docking study was used to evaluate this hypothesis and docking results indicated that macrocyclic cyclams and cyclens can reliably act as potent lead drug or central pharmacophore in developing new plasmepsin inhibitors as compared with previously designed plasmepsin II inhibitors.
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Affiliation(s)
- Ardavan Abiri
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran; Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran.
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10
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Rasina D, Stakanovs G, Borysov OV, Pantelejevs T, Bobrovs R, Kanepe-Lapsa I, Tars K, Jaudzems K, Jirgensons A. 2-Aminoquinazolin-4(3H)-one based plasmepsin inhibitors with improved hydrophilicity and selectivity. Bioorg Med Chem 2018; 26:2488-2500. [PMID: 29636223 DOI: 10.1016/j.bmc.2018.04.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/29/2018] [Accepted: 04/03/2018] [Indexed: 11/15/2022]
Abstract
2-Aminoquinazolin-4(3H)-ones were previously discovered as perspective leads for antimalarial drug development targeting the plasmepsins. Here we report the lead optimization studies with the aim to reduce inhibitor lipophilicity and increase selectivity versus the human aspartic protease Cathepsin D. Exploiting the solvent exposed area of the enzyme provides an option to install polar groups (R1) the 5-position of 2-aminoquinazolin-4(3H)-one to inhibitors such as carboxylic acid without scarifying enzymatic potency. Moreover, introduction of R1 substituents increased selectivity factors of compounds in this series up to 100-fold for Plm II, IV vs CatD inhibition. The introduction of flap pocket substituent (R2) at 7-postion of 2-aminoquinazolin-4(3H)-one allows to remove Ph group from THF ring without notably impairing Plm inhibitory potency. Based on these findings, inhibitors were developed, which show Plm II and IV inhibitory potency in low nanomolar range and remarkable selectivity against Cathepsin D along with decreased lipophilicity and increased solubility.
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Affiliation(s)
- Dace Rasina
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Georgijs Stakanovs
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Oleksandr V Borysov
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Teodors Pantelejevs
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Raitis Bobrovs
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Iveta Kanepe-Lapsa
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Kaspars Tars
- Biomedical Research and Study Centre, Ratsupites 1, Riga LV-1067, Latvia
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Aigars Jirgensons
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia.
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11
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Mukherjee B, Tessaro F, Vahokoski J, Kursula I, Marq JB, Scapozza L, Soldati-Favre D. Modeling and resistant alleles explain the selectivity of antimalarial compound 49c towards apicomplexan aspartyl proteases. EMBO J 2018. [PMID: 29519896 DOI: 10.15252/embj.201798047] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Toxoplasma gondii aspartyl protease 3 (TgASP3) phylogenetically clusters with Plasmodium falciparum Plasmepsins IX and X (PfPMIX, PfPMX). These proteases are essential for parasite survival, acting as key maturases for secreted proteins implicated in invasion and egress. A potent antimalarial peptidomimetic inhibitor (49c) originally developed against Plasmepsin II selectively targets TgASP3, PfPMIX, and PfPMX To unravel the molecular basis for the selectivity of 49c, we constructed homology models of PfPMIX, PfPMX, and TgASP3 that were first validated by identifying the determinants of microneme and rhoptry substrate recognition. The flap and flap-like structures of several reported Plasmepsins are highly flexible and critically modulate the access to the binding cavity. Molecular docking of 49c to TgASP3, PfPMIX, and PfPMX models predicted that the conserved phenylalanine residues in the flap, F344, F291, and F305, respectively, account for the sensitivity toward 49c. Concordantly, phenylalanine mutations in the flap of the three proteases increase twofold to 15-fold the IC50 values of 49c. Compellingly the selection of mutagenized T. gondii resistant strains to 49c reproducibly converted F344 to a cysteine residue.
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Affiliation(s)
- Budhaditya Mukherjee
- Department of Microbiology and Molecular Medicine, University of Geneva CMU, Geneva 4, Switzerland
| | - Francesca Tessaro
- Pharmaceutical Biochemistry, School of Pharmaceutical Sciences, University of Lausanne University of Geneva CMU, Geneva, Switzerland
| | - Juha Vahokoski
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Inari Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Jean-Baptiste Marq
- Department of Microbiology and Molecular Medicine, University of Geneva CMU, Geneva 4, Switzerland
| | - Leonardo Scapozza
- Pharmaceutical Biochemistry, School of Pharmaceutical Sciences, University of Lausanne University of Geneva CMU, Geneva, Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, University of Geneva CMU, Geneva 4, Switzerland
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Bule MH, Ahmed I, Maqbool F, Zia MA. Quinazolinone Derivatives as a Potential Class of Compounds in Malaria Drug Discovery. INT J PHARMACOL 2017. [DOI: 10.3923/ijp.2017.818.831] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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13
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Roy KK. Targeting the active sites of malarial proteases for antimalarial drug discovery: approaches, progress and challenges. Int J Antimicrob Agents 2017; 50:287-302. [PMID: 28668681 DOI: 10.1016/j.ijantimicag.2017.04.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 04/12/2017] [Accepted: 04/27/2017] [Indexed: 02/08/2023]
Abstract
Malaria is an infectious disease causing vast mortality and morbidity worldwide. Although antimalarial drugs are effective in several parts of the world, there is a serious threat to malaria control as malaria parasites are continuously developing widespread resistance against currently available antimalarial drugs, including artemisinin. Such widespread antimalarial drug resistance confirms the need to improve the efficacy of existing or new drugs as well as to develop alternative treatments through the identification of novel drug targets and the development of candidate drugs. Similar to proteases in other parasitic diseases such as leishmaniasis, schistosomiasis, Chagas disease and African sleeping sickness, malarial proteases constitute the major virulence factors in malaria. Malarial proteases belong to several classes and many of them have been targeted for the design and discovery of antimalarial agents. This review summarises the approaches, progress and challenges in the design of small-molecule inhibitors as antimalarial drugs targeting the inhibition of various malarial proteases.
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Affiliation(s)
- Kuldeep K Roy
- National Institute of Pharmaceutical Education and Research (NIPER), 4 Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India.
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14
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Cunico W, Ferreira MDLG, Wardell JL, Harrison WTA. Different intra- and inter-molecular hydrogen-bonding patterns in (3 S,4a S,8a S)-2-[(2 R,3 S)-3-(2,5- X2-benzamido)-2-(2,5- X2-benzo-yloxy)-4-phenyl-butyl]- N- tert-butyldeca-hydro-iso-quinoline-3-carboxamides ( X = H or Cl): compounds with moderate aspartyl protease inhibition activity. Acta Crystallogr E Crystallogr Commun 2017; 73:913-917. [PMID: 28638658 PMCID: PMC5458323 DOI: 10.1107/s2056989017007800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 05/25/2017] [Indexed: 11/26/2022]
Abstract
The crystal structures of (3S,4aS,8aS)-2-[(2R,3S)-3-benzamido-2-benzo-yloxy-4-phenyl-but-yl]-N-tert-butyldeca-hydro-iso-quinoline-3-carboxamide, C38H47N3O4, (I), and (3S,4aS,8aS)-2-[(2R,3S)-3-(2,5-di-chloro-benzamido)-2-(2,5-di-chloro-benzo-yloxy)-4-phenyl-but-yl]-N-tert-butyldeca-hydro-iso-quinoline-3-carboxamide, C38H43Cl4N3O4, (II), are described. Despite their chemical similarity, they adopt different conformations in the solid state: (I) features a bifurcated intra-molecular N-H⋯(N,O) hydrogen bond from the tert-butylamide NH group to the piperidine N atom and the benzoate O atom, whereas (II) has an intra-molecular N-H⋯O link from the benzamide NH group to the tert-butyl-amide O atom. In the crystal of (I), mol-ecules are linked by C(4) amide N-H⋯O hydrogen bonds into chains propagating in the [010] direction, with both donor and acceptor parts of the benzamide group. In the extended structure of (II), C(11) N-H⋯O chains propagating in the [010] direction arise, with the donor being the tert-butylamide NH group and the acceptor being the O atom of the benzamide group.
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Affiliation(s)
- Wilson Cunico
- Departamento de Química Orgânica, Universidade Federal de Pelotas (UFPel), Campus Universitário, s/n, Caixa Postal 354, 96010-900 Pelotas, RS, Brazil
| | - Maria de Lourdes G. Ferreira
- Instituto de Tecnologia em Fármacos – Farmanguinhos, Fiocruz. R. Sizenando, Nabuco, 100, Manguinhos, 21041-250, Rio de Janeiro, RJ, Brazil
| | - James L. Wardell
- Instituto de Tecnologia em Fármacos – Farmanguinhos, Fiocruz. R. Sizenando, Nabuco, 100, Manguinhos, 21041-250, Rio de Janeiro, RJ, Brazil
- Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland
| | - William T. A. Harrison
- Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland
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15
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Saturated Heterocycles with Applications in Medicinal Chemistry. ADVANCES IN HETEROCYCLIC CHEMISTRY 2017. [DOI: 10.1016/bs.aihch.2016.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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16
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Cassone A, Vecchiarelli A, Hube B. Aspartyl Proteinases of Eukaryotic Microbial Pathogens: From Eating to Heating. PLoS Pathog 2016; 12:e1005992. [PMID: 28005981 PMCID: PMC5179018 DOI: 10.1371/journal.ppat.1005992] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Antonio Cassone
- Polo d’innovazione della Genomica, Genetica e Biologia, University of Perugia, Perugia, Italy
| | - Anna Vecchiarelli
- Microbiology Section, Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knoell Institute, Jena, Germany
- Center for Sepsis Control and Care, University Hospital Jena, Jena, Germany
- Friedrich-Schiller-Universität, Jena, Germany
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17
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The prosegment catalyzes native folding of Plasmodium falciparum plasmepsin II. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1356-62. [DOI: 10.1016/j.bbapap.2016.06.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/29/2016] [Accepted: 06/30/2016] [Indexed: 01/15/2023]
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18
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Starkl Renar K, Iskra J, Križaj I. Understanding malarial toxins. Toxicon 2016; 119:319-29. [PMID: 27353131 DOI: 10.1016/j.toxicon.2016.06.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/26/2016] [Accepted: 06/24/2016] [Indexed: 10/21/2022]
Abstract
Recognized since antiquity, malaria is one of the most infamous and widespread infectious diseases in humans and, although the death rate during the last century has been diminishing, it still accounts for more than a half million deaths annually. It is caused by the Plasmodium parasite and typical symptoms include fever, shivering, headache, diaphoresis and nausea, all resulting from an excessive inflammatory response induced by malarial toxins released into the victim's bloodstream. These toxins are hemozoin and glycosylphosphatidylinositols. The former is the final product of the parasite's detoxification of haeme, a by-product of haemoglobin catabolism, while the latter anchor proteins to the Plasmodium cell surface or occur as free molecules. Currently, only two groups of antimalarial toxin drugs exist on the market, quinolines and artemisinins. As we describe, they both target biosynthesis of hemozoin. Other substances, currently in various phases of clinical trials, are directed towards biosynthesis of glycosylphosphatidylinositol, formation of hemozoin, or attenuation of the inflammatory response of the patient. Among the innovative approaches to alleviating the effects of malarial toxins, is the development of antimalarial toxin vaccines. In this review the most important lessons learned from the use of treatments directed against the action of malarial toxins in antimalarial therapy are emphasized and the most relevant and promising directions for future research in obtaining novel antimalarial agents acting on malarial toxins are discussed.
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Affiliation(s)
- Katarina Starkl Renar
- Laboratory of Organic and Bioorganic Chemistry, Department of Physical and Organic Chemistry, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova 39, 1000 Ljubljana, Slovenia.
| | - Jernej Iskra
- Laboratory of Organic and Bioorganic Chemistry, Department of Physical and Organic Chemistry, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Igor Križaj
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia; Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia.
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19
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Rasina D, Otikovs M, Leitans J, Recacha R, Borysov OV, Kanepe-Lapsa I, Domraceva I, Pantelejevs T, Tars K, Blackman MJ, Jaudzems K, Jirgensons A. Fragment-Based Discovery of 2-Aminoquinazolin-4(3H)-ones As Novel Class Nonpeptidomimetic Inhibitors of the Plasmepsins I, II, and IV. J Med Chem 2015; 59:374-87. [PMID: 26670264 DOI: 10.1021/acs.jmedchem.5b01558] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
2-Aminoquinazolin-4(3H)-ones were identified as a novel class of malaria digestive vacuole plasmepsin inhibitors by using NMR-based fragment screening against Plm II. Initial fragment hit optimization led to a submicromolar inhibitor, which was cocrystallized with Plm II to produce an X-ray structure of the complex. The structure showed that 2-aminoquinazolin-4(3H)-ones bind to the open flap conformation of the enzyme and provided clues to target the flap pocket. Further improvement in potency was achieved via introduction of hydrophobic substituents occupying the flap pocket. Most of the 2-aminoquinazolin-4(3H)-one based inhibitors show a similar activity against digestive Plms I, II, and IV and >10-fold selectivity versus CatD, although varying the flap pocket substituent led to one Plm IV selective inhibitor. In cell-based assays, the compounds show growth inhibition of Plasmodium falciparum 3D7 with IC50 ∼ 1 μM. Together, these results suggest 2-aminoquinazolin-4(3H)-ones as perspective leads for future development of an antimalarial agent.
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Affiliation(s)
- Dace Rasina
- Latvian Institute of Organic Synthesis , Aizkraukles 21, Riga LV-1006, Latvia
| | - Martins Otikovs
- Latvian Institute of Organic Synthesis , Aizkraukles 21, Riga LV-1006, Latvia
| | - Janis Leitans
- Biomedical Research and Study Centre , Ratsupites 1, Riga LV-1067, Latvia
| | - Rosario Recacha
- Latvian Institute of Organic Synthesis , Aizkraukles 21, Riga LV-1006, Latvia
| | - Oleksandr V Borysov
- Latvian Institute of Organic Synthesis , Aizkraukles 21, Riga LV-1006, Latvia
| | - Iveta Kanepe-Lapsa
- Latvian Institute of Organic Synthesis , Aizkraukles 21, Riga LV-1006, Latvia
| | - Ilona Domraceva
- Latvian Institute of Organic Synthesis , Aizkraukles 21, Riga LV-1006, Latvia
| | - Teodors Pantelejevs
- Latvian Institute of Organic Synthesis , Aizkraukles 21, Riga LV-1006, Latvia
| | - Kaspars Tars
- Biomedical Research and Study Centre , Ratsupites 1, Riga LV-1067, Latvia
| | - Michael J Blackman
- The Francis Crick Institute, Mill Hill Laboratory , The Ridgeway, Mill Hill, London NW7 1AA, U.K
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis , Aizkraukles 21, Riga LV-1006, Latvia
| | - Aigars Jirgensons
- Latvian Institute of Organic Synthesis , Aizkraukles 21, Riga LV-1006, Latvia
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