1
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Fagnani E, Bonì F, Seneci P, Gornati D, Muzio L, Mastrangelo E, Milani M. Stabilization of the retromer complex: Analysis of novel binding sites of bis-1,3-phenyl guanylhydrazone 2a to the VPS29/VPS35 interface. Comput Struct Biotechnol J 2024; 23:1088-1093. [PMID: 38487369 PMCID: PMC10937258 DOI: 10.1016/j.csbj.2024.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
The stabilization of the retromer protein complex can be effective in the treatment of different neurological disorders. Following the identification of bis-1,3-phenyl guanylhydrazone 2a as an effective new compound for the treatment of amyotrophic lateral sclerosis, in this work we analyze the possible binding sites of this molecule to the VPS35/VPS29 dimer of the retromer complex. Our results show that the affinity for different sites of the protein assembly depends on compound charge and therefore slight changes in the cell microenvironment could promote different binding states. Finally, we describe a novel binding site located in a deep cleft between VPS29 and VPS35 that should be further explored to select novel molecular chaperones for the stabilization of the retromer complex.
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Affiliation(s)
- Elisa Fagnani
- Biophysics Institute, CNR-IBF, Via Corti 12, I-20133 Milano, Italy
- Department of Bioscience, University of Milan, Via Celoria 26, I-20133 Milano, Italy
| | - Francesco Bonì
- Biophysics Institute, CNR-IBF, Via Corti 12, I-20133 Milano, Italy
- Department of Bioscience, University of Milan, Via Celoria 26, I-20133 Milano, Italy
| | - Pierfausto Seneci
- Department of Chemistry, University of Milan, Via Celoria 26, I-20133 Milano, Italy
| | - Davide Gornati
- Department of Chemistry, University of Milan, Via Celoria 26, I-20133 Milano, Italy
| | - Luca Muzio
- INSPE—Institute of Experimental Neurology, San Raffaele Scientific Institute, Via Olgettina 60, I–20132 Milano, Italy
| | - Eloise Mastrangelo
- Biophysics Institute, CNR-IBF, Via Corti 12, I-20133 Milano, Italy
- Department of Bioscience, University of Milan, Via Celoria 26, I-20133 Milano, Italy
| | - Mario Milani
- Biophysics Institute, CNR-IBF, Via Corti 12, I-20133 Milano, Italy
- Department of Bioscience, University of Milan, Via Celoria 26, I-20133 Milano, Italy
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2
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Braun MG, Ashkenazi A, Beveridge RE, Castanedo G, Wallweber HA, Beresini MH, Clark KR, De Bruyn T, Fu L, Gibbons P, Jiang F, Kaufman S, Kan D, Kiefer JR, Leclerc JP, Lemire A, Ly C, Segal E, Sims J, Wang W, Wei W, Zhao L, Schwarz JB, Rudolph J. Discovery of Potent, Selective, and Orally Available IRE1α Inhibitors Demonstrating Comparable PD Modulation to IRE1 Knockdown in a Multiple Myeloma Model. J Med Chem 2024; 67:8708-8729. [PMID: 38748820 DOI: 10.1021/acs.jmedchem.3c02425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
The lack of selective and safe in vivo IRE1α tool molecules has limited the evaluation of IRE1α as a viable target to treat multiple myeloma. Focus on improving the physicochemical properties of a literature compound by decreasing lipophilicity, molecular weight, and basicity allowed the discovery of a novel series with a favorable in vitro safety profile and good oral exposure. These efforts culminated in the identification of a potent and selective in vivo tool compound, G-5758, that was well tolerated following multiday oral administration of doses up to 500 mg/kg. G-5758 demonstrated comparable pharmacodynamic effects to induced IRE1 knockdown as measured by XBP1s levels in a multiple myeloma model (KMS-11).
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Affiliation(s)
| | - Avi Ashkenazi
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Georgette Castanedo
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Maureen H Beresini
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Kevin R Clark
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Tom De Bruyn
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Liqiang Fu
- WuXi AppTec Co., Ltd., Shanghai 200131, P. R. China
| | - Paul Gibbons
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Fan Jiang
- VIVA Biotech, No. 735, Ziping Road, Pudong New Area, Shanghai 201321, China
| | - Susan Kaufman
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - David Kan
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - James R Kiefer
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Alexandre Lemire
- Paraza Pharma Inc., 2525 Ave. Marie-Curie, Montreal, QC, Canada H4S 2E1
| | - Cuong Ly
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Ehud Segal
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jessica Sims
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Weiru Wang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Wentao Wei
- VIVA Biotech, No. 735, Ziping Road, Pudong New Area, Shanghai 201321, China
| | - Liang Zhao
- Paraza Pharma Inc., 2525 Ave. Marie-Curie, Montreal, QC, Canada H4S 2E1
| | - Jacob B Schwarz
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Joachim Rudolph
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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3
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Dorel R, Sun D, Carruthers N, Castanedo GM, Ung PMU, Factor DC, Li T, Baumann H, Janota D, Pang J, Salphati L, Meklemburg R, Korman AJ, Harper HE, Stubblefield S, Payandeh J, McHugh D, Lang BT, Tesar PJ, Dere E, Masureel M, Adams DJ, Volgraf M, Braun MG. Discovery and Optimization of Selective Brain-Penetrant EBP Inhibitors that Enhance Oligodendrocyte Formation. J Med Chem 2024. [PMID: 38470227 DOI: 10.1021/acs.jmedchem.3c02396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
The inhibition of emopamil binding protein (EBP), a sterol isomerase within the cholesterol biosynthesis pathway, promotes oligodendrocyte formation, which has been proposed as a potential therapeutic approach for treating multiple sclerosis. Herein, we describe the discovery and optimization of brain-penetrant, orally bioavailable inhibitors of EBP. A structure-based drug design approach from literature compound 1 led to the discovery of a hydantoin-based scaffold, which provided balanced physicochemical properties and potency and an improved in vitro safety profile. The long half-lives of early hydantoin-based EBP inhibitors in rodents prompted an unconventional optimization strategy, focused on increasing metabolic turnover while maintaining potency and a brain-penetrant profile. The resulting EBP inhibitor 11 demonstrated strong in vivo target engagement in the brain, as illustrated by the accumulation of EBP substrate zymostenol after repeated dosing. Furthermore, compound 11 enhanced the formation of oligodendrocytes in human cortical organoids, providing additional support for our therapeutic hypothesis.
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Affiliation(s)
- Ruth Dorel
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Dawei Sun
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Nicholas Carruthers
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | | | - Peter M-U Ung
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel C Factor
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Tianbo Li
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Hannah Baumann
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Danielle Janota
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Jodie Pang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Laurent Salphati
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Robert Meklemburg
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Allison J Korman
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Halie E Harper
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | | | - Jian Payandeh
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel McHugh
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Bradley T Lang
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Paul J Tesar
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Edward Dere
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Matthieu Masureel
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Drew J Adams
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Matthew Volgraf
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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4
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Koehler MFT, Chen YC, Chen Y, Chen Y, Crawford JJ, Durk MR, Garland K, Hanan EJ, Higuchi RI, Hu H, Ly CQ, Paraselli PG, Roberts TC, Schwarz JB, Smith PA, Yu Z, Heise CE. Lipid Tales: Optimizing Arylomycin Membrane Anchors. ACS Med Chem Lett 2023; 14:1524-1530. [PMID: 37974942 PMCID: PMC10641904 DOI: 10.1021/acsmedchemlett.3c00327] [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: 07/26/2023] [Accepted: 09/22/2023] [Indexed: 11/19/2023] Open
Abstract
Multidrug-resistant bacteria are spreading at alarming rates, and despite extensive efforts, no new antibiotic class with activity against Gram-negative bacteria has been approved in over 50 years. LepB inhibitors (LepBi) based on the arylomycin class of natural products are a novel class of antibiotics and function by inhibiting the bacterial type I signal peptidase (SPase) in Gram-negative bacteria. One critical aspect of LepBi development involves optimization of the membrane-anchored lipophilic portion of the molecule. We therefore developed an approach that assesses the effect of this portion on the complicated equilibria of plasma protein binding, crossing the outer membrane of Gram-negative bacteria and anchoring in the bacterial inner membrane to facilitate SPase binding. Our findings provide important insights into the development of antibacterial agents where the target is associated with the inner membrane of Gram-negative bacteria.
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Affiliation(s)
- Michael F. T. Koehler
- Department
of Discovery Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Yi-Chen Chen
- Department
of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, California 94080, United States
| | - Yongsheng Chen
- Department
of Chemistry, WuXi AppTec, Shanghai 200131, China
| | - Yuan Chen
- Department
of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, California 94080, United States
| | - James J. Crawford
- Department
of Discovery Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Matthew R. Durk
- Department
of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, California 94080, United States
| | - Keira Garland
- Department
of Discovery Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Emily J. Hanan
- Department
of Discovery Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | | | - Huiyong Hu
- Department
of Discovery Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Cuong Q. Ly
- Department
of Discovery Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | | | | | - Jacob B. Schwarz
- Department
of Discovery Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Peter A. Smith
- Department
of Infectious Disease, Genentech, Inc., South San Francisco, California 94080, United States
| | - Zhiyong Yu
- Department
of Chemistry, WuXi AppTec, Shanghai 200131, China
| | - Christopher E. Heise
- Department
of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
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5
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Tang K, Wang S, Gao W, Song Y, Yu B. Harnessing the cyclization strategy for new drug discovery. Acta Pharm Sin B 2022; 12:4309-4326. [PMID: 36562004 PMCID: PMC9764076 DOI: 10.1016/j.apsb.2022.09.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/07/2022] [Accepted: 09/23/2022] [Indexed: 12/25/2022] Open
Abstract
The design of new ligands with high affinity and specificity against the targets of interest has been a central focus in drug discovery. As one of the most commonly used methods in drug discovery, the cyclization represents a feasible strategy to identify new lead compounds by increasing structural novelty, scaffold diversity and complexity. Such strategy could also be potentially used for the follow-on drug discovery without patent infringement. In recent years, the cyclization strategy has witnessed great success in the discovery of new lead compounds against different targets for treating various diseases. Herein, we first briefly summarize the use of the cyclization strategy in the discovery of new small-molecule lead compounds, including the proteolysis targeting chimeras (PROTAC) molecules. Particularly, we focus on four main strategies including fused ring cyclization, chain cyclization, spirocyclization and macrocyclization and highlight the use of the cyclization strategy in lead generation. Finally, the challenges including the synthetic intractability, relatively poor pharmacokinetics (PK) profiles and the absence of the structural information for rational structure-based cyclization are also briefly discussed. We hope this review, not exhaustive, could provide a timely overview on the cyclization strategy for the discovery of new lead compounds.
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6
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Agarwal P, Huckle J, Newman J, Reid DL. Trends in small molecule drug properties: A developability molecule assessment perspective. Drug Discov Today 2022; 27:103366. [PMID: 36122862 DOI: 10.1016/j.drudis.2022.103366] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/10/2022] [Accepted: 09/13/2022] [Indexed: 11/18/2022]
Abstract
Developability molecule assessment is a key interfacial capability across the biopharmaceutical industry, screening and staging molecules discovered by medicinal chemists for successful chemistry manufacturing controls (CMC) development and launch. The breadth of responsibility and expertise such teams possess puts them in a unique position to understand the impact of the physicochemical properties of a drug during its initial discovery and subsequent development. However, most of the publications describing trends in physicochemical properties are written from a medicinal chemistry perspective with the aim to identify molecules with better ADMET profiles that are either lead-like or drug-like, failing to describe the impact these properties have on CMC development. To systematically uncover knowledge obtained from recent trends in physicochemical properties and the corresponding impact on CMC development, a comprehensive analysis was conducted on molecules in the drug repurposing hub dataset. The only physicochemical property that seems to have been preserved in FDA-approved oral molecules over the decades (1900-2020) is a constant H-bond donor count, highlighting the importance this property has on cell permeability and lattice energy. Pharmaceutical attrition analysis suggests that partition-distribution coefficient, H-bond acceptors, polar surface area and the fraction of sp3 carbons are properties that are associated with compound attrition. Looking at pharmaceutical attrition asynchronously with the temporal analysis of FDA-approved oral molecules highlights the opposing trends, risks and diminishing effects some of these physiochemical properties (cLogP, cLogD and Fsp3) have on describing compound attrition during the past decade. Trellising the dataset by target class suggests that certain formulation and drug delivery strategies can be anticipated or put into place based on target class of a molecule. For example, molecules binding to nuclear hormone receptors are amenable to lipid-based drug delivery systems with proven commercial success. Although the poor solubility of kinase inhibitors is a combination of hydrophobicity (due to aromaticity) required to bind to its target and high lattice energy (melting point), they are a challenging target class to formulate. The influence of drug targets on physicochemical properties and the temporal nature of these properties is highlighted when comparing molecules in the drug repurposing dataset to those developed at Amgen. An improved understanding of the impact of molecular properties on performance attributes can accelerate decisions and facilitate risk assessments during candidate selection and development.
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Affiliation(s)
- Prashant Agarwal
- Drug Product Technologies, Process Development, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA.
| | - James Huckle
- Drug Product Technologies, Process Development, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Jake Newman
- Drug Product Technologies, Process Development, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Darren L Reid
- Drug Product Technologies, Process Development, Amgen, 360 Binney St, Cambridge, MA 02142, USA.
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7
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Alford JS, Lampe JW, Brach D, Chesworth R, Cosmopoulos K, Duncan KW, Eckley ST, Kutok JL, Raimondi A, Riera TV, Shook B, Tang C, Totman J, Farrow NA. Conformational-Design-Driven Discovery of EZM0414: A Selective, Potent SETD2 Inhibitor for Clinical Studies. ACS Med Chem Lett 2022; 13:1137-1143. [PMID: 35859865 PMCID: PMC9290024 DOI: 10.1021/acsmedchemlett.2c00167] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
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SETD2, a lysine N-methyltransferase, is a histone
methyltransferase that plays an important role in various cellular
processes and was identified as a target of interest in multiple myeloma
that features a t(4,14) translocation. We recently reported the discovery
of a novel small-molecule SETD2 inhibitor tool compound that is suitable
for preclinical studies. Herein we describe the conformational-design-driven
evolution of the advanced chemistry lead, which resulted in compounds
appropriate for clinical evaluation. Further optimization of this
chemical series led to the discovery of EZM0414, which is a potent,
selective, and orally bioavailable inhibitor of SETD2 with good pharmacokinetic
properties and robust pharmacodynamic activity in a mouse xenograft
model.
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Affiliation(s)
- Joshua S. Alford
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - John W. Lampe
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Dorothy Brach
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Richard Chesworth
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Kat Cosmopoulos
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Kenneth W. Duncan
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Sean T. Eckley
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Jeffrey L. Kutok
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Alejandra Raimondi
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Thomas V. Riera
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Brian Shook
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Cuyue Tang
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Jennifer Totman
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
| | - Neil A. Farrow
- Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States
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8
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Darnowski MG, Lanosky TD, Labana P, Brazeau-Henrie JT, Calvert ND, Dornan MH, Natola C, Paquette AR, Shuhendler AJ, Boddy CN. Armeniaspirol analogues with more potent Gram-positive antibiotic activity show enhanced inhibition of the ATP-dependent proteases ClpXP and ClpYQ. RSC Med Chem 2022; 13:436-444. [PMID: 35647545 PMCID: PMC9020616 DOI: 10.1039/d1md00355k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/07/2022] [Indexed: 11/21/2022] Open
Abstract
Antibiotics with fundamentally new mechanisms of action such as the armeniaspirols, which target the ATP-dependent proteases ClpXP and ClpYQ, must be developed to combat antimicrobial resistance. While the mechanism of action of armeniaspirol against Gram-positive bacteria is understood, little is known about the structure-activity relationship for its antibiotic activity. Based on the preliminary data showing that modifications of armeniaspirol's N-methyl group increased antibiotic potency, we probed the structure-activity relationship of N-alkyl armeniaspirol derivatives. A series of focused derivatives were synthesized and evaluated for antibiotic activity against clinically relevant pathogens including methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus. Replacement of the N-methyl with N-hexyl, various N-benzyl, and N-phenethyl substituents led to substantial increases in antibiotic activity and potency for inhibition of both ClpYQ and ClpXP. Docking studies identified binding models for ClpXP and ClpYQ that were consistent with the inhibition data. This work confirms the role of ClpXP and ClpYQ in the mechanism of action of armeniaspirol and provides important lead compounds for further antibiotic development.
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Affiliation(s)
- Michael G. Darnowski
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Taylor D. Lanosky
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Puneet Labana
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Jordan T. Brazeau-Henrie
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Nicholas D. Calvert
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Mark H. Dornan
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Claudia Natola
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - André R. Paquette
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Adam J. Shuhendler
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Christopher N. Boddy
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
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9
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Kang SG, Morrone JA, Weber JK, Cornell WD. Analysis of Training and Seed Bias in Small Molecules Generated with a Conditional Graph-Based Variational Autoencoder─Insights for Practical AI-Driven Molecule Generation. J Chem Inf Model 2022; 62:801-816. [PMID: 35130440 DOI: 10.1021/acs.jcim.1c01545] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The application of deep learning to generative molecule design has shown early promise for accelerating lead series development. However, questions remain concerning how factors like training, data set, and seed bias impact the technology's utility to medicinal and computational chemists. In this work, we analyze the impact of seed and training bias on the output of an activity-conditioned graph-based variational autoencoder (VAE). Leveraging a massive, labeled data set corresponding to the dopamine D2 receptor, our graph-based generative model is shown to excel in producing desired conditioned activities and favorable unconditioned physical properties in generated molecules. We implement an activity-swapping method that allows for the activation, deactivation, or retention of activity of molecular seeds, and we apply independent deep learning classifiers to verify the generative results. Overall, we uncover relationships between noise, molecular seeds, and training set selection across a range of latent-space sampling procedures, providing important insights for practical AI-driven molecule generation.
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Affiliation(s)
- Seung-Gu Kang
- Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10594, United States
| | - Joseph A Morrone
- Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10594, United States
| | - Jeffrey K Weber
- Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10594, United States
| | - Wendy D Cornell
- Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10594, United States
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10
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11
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Polypharmacology: The science of multi-targeting molecules. Pharmacol Res 2022; 176:106055. [PMID: 34990865 DOI: 10.1016/j.phrs.2021.106055] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/23/2021] [Accepted: 12/31/2021] [Indexed: 12/28/2022]
Abstract
Polypharmacology is a concept where a molecule can interact with two or more targets simultaneously. It offers many advantages as compared to the conventional single-targeting molecules. A multi-targeting drug is much more efficacious due to its cumulative efficacy at all of its individual targets making it much more effective in complex and multifactorial diseases like cancer, where multiple proteins and pathways are involved in the onset and development of the disease. For a molecule to be polypharmacologic in nature, it needs to possess promiscuity which is the ability to interact with multiple targets; and at the same time avoid binding to antitargets which would otherwise result in off-target adverse effects. There are certain structural features and physicochemical properties which when present would help researchers to predict if the designed molecule would possess promiscuity or not. Promiscuity can also be identified via advanced state-of-the-art computational methods. In this review, we also elaborate on the methods by which one can intentionally incorporate promiscuity in their molecules and make them polypharmacologic. The polypharmacology paradigm of "one drug-multiple targets" has numerous applications especially in drug repurposing where an already established drug is redeveloped for a new indication. Though designing a polypharmacological drug is much more difficult than designing a single-targeting drug, with the current technologies and information regarding different diseases and chemical functional groups, it is plausible for researchers to intentionally design a polypharmacological drug and unlock its advantages.
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12
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Billings KJ, Grenier-Davies MC. Library Synthesis: Building Block Selection, Handling, and Tracking. Methods Mol Biol 2022; 2541:1-11. [PMID: 36083536 DOI: 10.1007/978-1-0716-2545-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Careful selection and manipulation of small molecule building blocks is crucial to the success of a DNA-encoded library. Building block selection impacts the quality of the hits arising out of a selection assay, while proper sample handling and tracking ensure follow-up synthetic work is done with the appropriate synthetic map in mind. In this chapter, possible strategies for building block selection are outlined, as well as best practices for handling and tracking samples to be used for validation and library synthesis.
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Affiliation(s)
| | - Melissa C Grenier-Davies
- Encoded Library Technologies/NCE Molecular Discovery, R & D Medicinal Science and Technology, GlaxoSmithKline, Cambridge, MA, USA
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13
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Structural Optimization and Biological Activity of Pyrazole Derivatives: Virtual Computational Analysis, Recovery Assay and 3D Culture Model as Potential Predictive Tools of Effectiveness against Trypanosoma cruzi. Molecules 2021; 26:molecules26216742. [PMID: 34771151 PMCID: PMC8587750 DOI: 10.3390/molecules26216742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 12/18/2022] Open
Abstract
Chagas disease, a chronic and silent disease caused by Trypanosoma cruzi, is currently a global public health problem. The treatment of this neglected disease relies on benznidazole and nifurtimox, two nitroheterocyclic drugs that show limited efficacy and severe side effects. The failure of potential drug candidates in Chagas disease clinical trials highlighted the urgent need to identify new effective chemical entities and more predictive tools to improve translational success in the drug development pipeline. In this study, we designed a small library of pyrazole derivatives (44 analogs) based on a hit compound, previously identified as a T. cruzi cysteine protease inhibitor. The in vitro phenotypic screening revealed compounds 3g, 3j, and 3m as promising candidates, with IC50 values of 6.09 ± 0.52, 2.75 ± 0.62, and 3.58 ± 0.25 µM, respectively, against intracellular amastigotes. All pyrazole derivatives have good oral bioavailability prediction. The structure–activity relationship (SAR) analysis revealed increased potency of 1-aryl-1H-pyrazole-imidazoline derivatives with the Br, Cl, and methyl substituents in the para-position. The 3m compound stands out for its trypanocidal efficacy in 3D microtissue, which mimics tissue microarchitecture and physiology, and abolishment of parasite recrudescence in vitro. Our findings encourage the progression of the promising candidate for preclinical in vivo studies.
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14
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Freeman-Cook KD, Hoffman RL, Behenna DC, Boras B, Carelli J, Diehl W, Ferre RA, He YA, Hui A, Huang B, Huser N, Jones R, Kephart SE, Lapek J, McTigue M, Miller N, Murray BW, Nagata A, Nguyen L, Niessen S, Ninkovic S, O'Doherty I, Ornelas MA, Solowiej J, Sutton SC, Tran K, Tseng E, Visswanathan R, Xu M, Zehnder L, Zhang Q, Zhang C, Dann S. Discovery of PF-06873600, a CDK2/4/6 Inhibitor for the Treatment of Cancer. J Med Chem 2021; 64:9056-9077. [PMID: 34110834 DOI: 10.1021/acs.jmedchem.1c00159] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Control of the cell cycle through selective pharmacological inhibition of CDK4/6 has proven beneficial in the treatment of breast cancer. Extending this level of control to additional cell cycle CDK isoforms represents an opportunity to expand to additional tumor types and potentially provide benefits to patients that develop tumors resistant to selective CDK4/6 inhibitors. However, broad-spectrum CDK inhibitors have a long history of failure due to safety concerns. In this approach, we describe the use of structure-based drug design and Free-Wilson analysis to optimize a series of CDK2/4/6 inhibitors. Further, we detail the use of molecular dynamics simulations to provide insights into the basis for selectivity against CDK9. Based on overall potency, selectivity, and ADME profile, PF-06873600 (22) was identified as a candidate for the treatment of cancer and advanced to phase 1 clinical trials.
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Affiliation(s)
- Kevin D Freeman-Cook
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Robert L Hoffman
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Douglas C Behenna
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Britton Boras
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Jordan Carelli
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Wade Diehl
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Rose Ann Ferre
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - You-Ai He
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Andrea Hui
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Buwen Huang
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Nanni Huser
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Rhys Jones
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Susan E Kephart
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - John Lapek
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Michele McTigue
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Nichol Miller
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Brion W Murray
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Asako Nagata
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Lisa Nguyen
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Sherry Niessen
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Sacha Ninkovic
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Inish O'Doherty
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Martha A Ornelas
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - James Solowiej
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Scott C Sutton
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Khanh Tran
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Elaine Tseng
- Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ravi Visswanathan
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Meirong Xu
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Luke Zehnder
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Qin Zhang
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Cathy Zhang
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Stephen Dann
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, California 92121, United States
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15
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Veale CGL. Into the Fray! A Beginner's Guide to Medicinal Chemistry. ChemMedChem 2021; 16:1199-1225. [PMID: 33591595 DOI: 10.1002/cmdc.202000929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Indexed: 12/31/2022]
Abstract
Modern medicinal chemistry is a complex, multidimensional discipline that operates at the interface of the chemical and biological sciences. The medicinal chemistry contribution to drug discovery is typically described in the context of the well-recited linear progression of the drug discovery pipeline. However, compound optimization is idiosyncratic to each project, and clear definitions of hit and lead molecules and the subsequent progress along the pipeline becomes easily blurred. In addition, this description lacks insight into the entangled relationship between chemical and pharmacological properties, and thus provides limited guidance on how innovative medicinal chemistry strategies can be applied to solve optimization problems, regardless of the stage in the pipeline. Through discussion and illustrative examples, this article seeks to provide insights into the finesse of medicinal chemistry and the subtlety of balancing chemical properties pharmacology. In so doing, it aims to serve as an accessible and simple-to-digest guide for anyone who wishes to learn about the underlying principles of medicinal chemistry, in a context that has been decoupled from the pipeline description.
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Affiliation(s)
- Clinton G L Veale
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Pietermaritzburg, Scottsville, 3209, South Africa
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16
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Miller RR, Madeira M, Wood HB, Geissler WM, Raab CE, Martin IJ. Integrating the Impact of Lipophilicity on Potency and Pharmacokinetic Parameters Enables the Use of Diverse Chemical Space during Small Molecule Drug Optimization. J Med Chem 2020; 63:12156-12170. [DOI: 10.1021/acs.jmedchem.9b01813] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Randy R. Miller
- Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Maria Madeira
- Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Harold B. Wood
- Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Wayne M. Geissler
- Business Development & Licensing, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Conrad E. Raab
- Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Iain J. Martin
- Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
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17
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White C, McGowan MA, Zhou H, Sciammetta N, Fradera X, Lim J, Joshi EM, Andrews C, Nickbarg EB, Cowley P, Trewick S, Augustin M, von Köenig K, Lesburg CA, Otte K, Knemeyer I, Woo H, Yu W, Cheng M, Spacciapoli P, Geda P, Song X, Smotrov N, Curran P, Heo MR, Abeywickrema P, Miller JR, Bennett DJ, Han Y. Strategic Incorporation of Polarity in Heme-Displacing Inhibitors of Indoleamine-2,3-dioxygenase-1 (IDO1). ACS Med Chem Lett 2020; 11:550-557. [PMID: 32292563 DOI: 10.1021/acsmedchemlett.0c00010] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/10/2020] [Indexed: 12/13/2022] Open
Abstract
Indoleamine-2,3-dioxygenase-1 (IDO1) has emerged as a target of significant interest to the field of cancer immunotherapy, as the upregulation of IDO1 in certain cancers has been linked to host immune evasion and poor prognosis for patients. In particular, IDO1 inhibition is of interest as a combination therapy with immune checkpoint inhibition. Through an Automated Ligand Identification System (ALIS) screen, a diamide class of compounds was identified as a promising lead for the inhibition of IDO1. While hit 1 possessed attractive cell-based potency, it suffered from a significant right-shift in a whole blood assay, poor solubility, and poor pharmacokinetic properties. Through a physicochemical property-based approach, including a focus on lowering AlogP98 via the strategic introduction of polar substitution, compound 13 was identified bearing a pyridyl oxetane core. Compound 13 demonstrated improved whole blood potency and solubility, and an improved pharmacokinetic profile resulting in a low predicted human dose.
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18
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Jones LH. Pharmacological Correction of Proteinopathies via Lysosomal Degradation. Biochemistry 2020; 59:727-728. [PMID: 31999102 DOI: 10.1021/acs.biochem.9b00942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lyn H Jones
- Center for Protein Degradation , Dana-Farber Cancer Institute , 360 Longwood Avenue , Boston , Massachusetts 02115 , United States
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19
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Modifying the lipophilic part of phenylthiazole antibiotics to control their drug-likeness. Eur J Med Chem 2019; 185:111830. [PMID: 31718945 DOI: 10.1016/j.ejmech.2019.111830] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/13/2019] [Accepted: 10/28/2019] [Indexed: 02/01/2023]
Abstract
Compounds with high lipophilic properties are often associated with bad physicochemical properties, triggering many off-targets, and less likely to pass clinical trials. Two metabolically stable phenylthiazole antibiotic scaffolds having notable high lipophilic characters, one with alkoxy side chain and the other one with alkynyl moiety, were derivatized by inserting a cyclic amine at the lipophilic tail with the objective of improving physicochemical properties and the overall pharmacokinetic behavior. Only alkynyl derivatives with 4- or 5-membered rings showed remarkable antibacterial activity. The azetidine-containing compound 8 was the most effective and it revealed a potent antibacterial effect against 15 multi-drug resistant (MDR)-Gram positive pathogens including Staphylococcus aureus, Streptococcus pneumoniae, Staphylococcus epidermidis and enterococci. Compound 8 was also highly effective in clearing 99.7% of the intracellular methicillin-resistant S. aureus (MRSA) harbored inside macrophages. In addition to the remarkable enhancement in aqueous solubility, the in vivo pharmacokinetic study in rats indicated that compound 8 can penetrate gut cells and reach plasma at a therapeutic concentration within 15 min and maintain effective plasma concentration for around 12 h. Interestingly, the main potential metabolite (compound 9) was also active as an antibacterial agent with potent antibiofilm activity.
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20
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Bunally SB, Luscombe CN, Young RJ. Using Physicochemical Measurements to Influence Better Compound Design. SLAS DISCOVERY 2019; 24:791-801. [PMID: 31429385 DOI: 10.1177/2472555219859845] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
During the past decade, the physicochemical quality of molecules under investigation at all stages of the drug discovery process has come under particular scrutiny. The issues associated with excessive lipophilicity and poor solubility in particular are many and varied, ranging from poor outcomes in screening campaigns to promiscuity, limited and/or poorly predictable pharmacokinetic exposure, and, ultimately, greater chances of clinical failure. In this review, contemporary methods to secure key measurements are described along with their relevance to understanding the behavior of molecules in environments pertinent to pharmacological activity. Together, the various measurements contribute to predictive models of both the physicochemical properties themselves and the outcomes they influence.
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Affiliation(s)
| | | | - Robert J Young
- 1 GlaxoSmithKline Medicines Research Centre, Stevenage, UK
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21
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Chen Y, Sit SY, Chen J, Swidorski JJ, Liu Z, Sin N, Venables BL, Parker DD, Nowicka-Sans B, Lin Z, Li Z, Terry BJ, Protack T, Rahematpura S, Hanumegowda U, Jenkins S, Krystal M, Dicker ID, Meanwell NA, Regueiro-Ren A. The design, synthesis and structure-activity relationships associated with C28 amine-based betulinic acid derivatives as inhibitors of HIV-1 maturation. Bioorg Med Chem Lett 2018; 28:1550-1557. [DOI: 10.1016/j.bmcl.2018.03.067] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/17/2018] [Accepted: 03/23/2018] [Indexed: 01/22/2023]
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22
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Zhang M, Wang Z, Zhang Y, Guo W, Ji H. Structure-Based Optimization of Small-Molecule Inhibitors for the β-Catenin/B-Cell Lymphoma 9 Protein-Protein Interaction. J Med Chem 2018; 61:2989-3007. [PMID: 29566337 DOI: 10.1021/acs.jmedchem.8b00068] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Structure-based optimization was conducted to improve the potency, selectivity, and cell-based activities of β-catenin/B-cell lymphoma 9 (BCL9) inhibitors based on the 4'-fluoro- N-phenyl-[1,1'-biphenyl]-3-carboxamide scaffold, which was designed to mimic the side chains of the hydrophobic α-helical hot spots at positions i, i + 3, and i + 7. Compound 29 was found to disrupt the β-catenin/BCL9 protein-protein interaction (PPI) with a Ki of 0.47 μM and >1900-fold selectivity for β-catenin/BCL9 over β-catenin/E-cadherin PPIs. The proposed binding mode of new inhibitors was consistent with the results of site-directed mutagenesis and structure-activity relationship studies. Cell-based studies indicated that 29 disrupted the β-catenin/BCL9 interaction without affecting the β-catenin/E-cadherin interaction, selectively suppressed transactivation of Wnt/β-catenin signaling, downregulated expression of Wnt target genes, and inhibited viability of Wnt/β-catenin-dependent cancer cells in dose-dependent manners. A comparison of the biochemical and cell-based assay results offered the directions for future inhibitor optimization.
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Affiliation(s)
- Min Zhang
- Drug Discovery Department , H. Lee Moffitt Cancer Center and Research Institute , Tampa , Florida 33612 , United States.,Departments of Oncologic Sciences and Chemistry , University of South Florida , Tampa , Florida 33620 , United States
| | - Zhen Wang
- Drug Discovery Department , H. Lee Moffitt Cancer Center and Research Institute , Tampa , Florida 33612 , United States.,Departments of Oncologic Sciences and Chemistry , University of South Florida , Tampa , Florida 33620 , United States
| | - Yongqiang Zhang
- Drug Discovery Department , H. Lee Moffitt Cancer Center and Research Institute , Tampa , Florida 33612 , United States.,Departments of Oncologic Sciences and Chemistry , University of South Florida , Tampa , Florida 33620 , United States
| | - Wenxing Guo
- Drug Discovery Department , H. Lee Moffitt Cancer Center and Research Institute , Tampa , Florida 33612 , United States.,Departments of Oncologic Sciences and Chemistry , University of South Florida , Tampa , Florida 33620 , United States
| | - Haitao Ji
- Drug Discovery Department , H. Lee Moffitt Cancer Center and Research Institute , Tampa , Florida 33612 , United States.,Departments of Oncologic Sciences and Chemistry , University of South Florida , Tampa , Florida 33620 , United States
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23
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Nakahata T, Tokumaru K, Ito Y, Ishii N, Setoh M, Shimizu Y, Harasawa T, Aoyama K, Hamada T, Kori M, Aso K. Design and synthesis of 1-(1-benzothiophen-7-yl)-1H-pyrazole, a novel series of G protein-coupled receptor 52 (GPR52) agonists. Bioorg Med Chem 2018; 26:1598-1608. [PMID: 29478803 DOI: 10.1016/j.bmc.2018.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/24/2018] [Accepted: 02/05/2018] [Indexed: 11/30/2022]
Abstract
G-protein-coupled receptor 52 (GPR52) is classified as an orphan Gs-coupled G-protein-coupled receptor. GPR52 cancels dopamine D2 receptor signaling and activates dopamine D1/N-methyl-d-aspartate receptors via intracellular cAMP accumulation. Therefore, GPR52 agonists are expected to alleviate symptoms of psychotic disorders. A novel series of 1-(benzothiophen-7-yl)-1H-pyrazole as GPR52 agonists was designed and synthesized based on compound 1b. Compound 1b has been reported by our group as the first orally active GPR52 agonist, but high lipophilicity and poor aqueous solubility still remained as issues for candidate selection. To resolve these issues, replacement of the benzene ring at the 7-positon of compound 1b with heterocylic rings, such as pyrazole and pyridine, was greatly expected to reduce lipophilicity to levels for which calculated logD values were lower than that of compound 1b. While evaluating the pyrazole derivatives, introduction of a methyl substituent at the 3-position of the pyrazole ring led to increased GPR52 agonistic activity. Moreover, additional methyl substituent at the 5-position of the pyrazole and further introduction of hydroxy group to lower logD led to significant improvement of solubility while maintaining the activity. As a result, we identified 3-methyl-5-hydroxymethyl-1H-pyrazole derivative 17 (GPR52 EC50 = 21 nM, Emax = 103%, logD = 2.21, Solubility at pH 6.8 = 21 μg/mL) with potent GPR52 agonistic activity and good solubility compared to compound 1b. Furthermore, this compound 17 dose-dependently suppressed methamphetamine-induced hyperlocomotion in mice.
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Affiliation(s)
- Takashi Nakahata
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., 26-1, Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.
| | - Kazuyuki Tokumaru
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., 26-1, Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yoshiteru Ito
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., 26-1, Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Naoki Ishii
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., 26-1, Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Masaki Setoh
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., 26-1, Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yuji Shimizu
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., 26-1, Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Toshiya Harasawa
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., 26-1, Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Kazunobu Aoyama
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., 26-1, Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Teruki Hamada
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., 26-1, Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Masakuni Kori
- Pharmaceutical Sciences, Takeda Pharmaceutical Company Ltd., 17-85, Jusohonmachi-2-chome, Yodogawa-ku, Osaka 532-8686, Japan
| | - Kazuyoshi Aso
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., 26-1, Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.
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24
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Ivanova T, Hardes K, Kallis S, Dahms SO, Than ME, Künzel S, Böttcher-Friebertshäuser E, Lindberg I, Jiao GS, Bartenschlager R, Steinmetzer T. Optimization of Substrate-Analogue Furin Inhibitors. ChemMedChem 2017; 12:1953-1968. [PMID: 29059503 DOI: 10.1002/cmdc.201700596] [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: 09/25/2017] [Revised: 10/19/2017] [Indexed: 12/21/2022]
Abstract
The proprotein convertase furin is a potential target for drug design, especially for the inhibition of furin-dependent virus replication. All effective synthetic furin inhibitors identified thus far are multibasic compounds; the highest potency was found for our previously developed inhibitor 4-(guanidinomethyl)phenylacetyl-Arg-Tle-Arg-4-amidinobenzylamide (MI-1148). An initial study in mice revealed a narrow therapeutic range for this tetrabasic compound, while significantly reduced toxicity was observed for some tribasic analogues. This suggests that the toxicity depends at least to some extent on the overall multibasic character of this inhibitor. Therefore, in a first approach, the C-terminal benzamidine of MI-1148 was replaced by less basic P1 residues. Despite decreased potency, a few compounds still inhibit furin in the low nanomolar range, but display negligible efficacy in cells. In a second approach, the P2 arginine was replaced by lysine; compared to MI-1148, this furin inhibitor has slightly decreased potency, but exhibits similar antiviral activity against West Nile and Dengue virus in cell culture and decreased toxicity in mice. These results provide a promising starting point for the development of efficacious and well-tolerated furin inhibitors.
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Affiliation(s)
- Teodora Ivanova
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6, 35032, Marburg, Germany
| | - Kornelia Hardes
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6, 35032, Marburg, Germany
| | - Stephanie Kallis
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany.,German Center for Infection Research, Heidelberg Partner Site, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
| | - Sven O Dahms
- Protein Crystallography Group, Leibniz Institute on Aging-Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.,Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria
| | - Manuel E Than
- Protein Crystallography Group, Leibniz Institute on Aging-Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Sebastian Künzel
- Faculty of Engineering Sciences, Hochschule Ansbach, Residenzstraße 8, 91522, Ansbach, Germany
| | | | - Iris Lindberg
- Department of Anatomy and Neurobiology, University of Maryland Medical School, Baltimore, MD, 21201, USA
| | - Guan-Sheng Jiao
- Department of Chemistry, Hawaii Biotech, Inc., Honolulu, HI, USA.,MedChem ShortCut LLC, Pearl City, HI, USA
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany.,German Center for Infection Research, Heidelberg Partner Site, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6, 35032, Marburg, Germany
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25
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Noël F, Nascimento-Viana JB, Romeiro LAS, Silva RO, Lemes LFN, Oliveira AS, Giorno TBS, Fernandes PD, Silva CLM. ADME studies and preliminary safety pharmacology of LDT5, a lead compound for the treatment of benign prostatic hyperplasia. ACTA ACUST UNITED AC 2017; 49:e5542. [PMID: 27901175 PMCID: PMC5188857 DOI: 10.1590/1414-431x20165542] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/26/2016] [Indexed: 02/06/2023]
Abstract
This study aimed to estimate the absorption, distribution, metabolism and excretion
(ADME) properties and safety of LDT5, a lead compound for oral treatment of benign
prostatic hyperplasia that has previously been characterized as a multi-target
antagonist of α1A-, α1D-adrenoceptors and 5-HT1A
receptors. The preclinical characterization of this compound comprised the evaluation
of its in vitro properties, including plasma, microsomal and
hepatocytes stability, cytochrome P450 metabolism and inhibition, plasma protein
binding, and permeability using MDCK-MDR1 cells. De-risking and preliminary safety
pharmacology assays were performed through screening of 44 off-target receptors and
in vivo tests in mice (rota-rod and single dose toxicity). LDT5
is stable in rat and human plasma, human liver microsomes and hepatocytes, but
unstable in rat liver microsomes and hepatocytes (half-life of 11 min). LDT5 is
highly permeable across the MDCK-MDR1 monolayer (Papp ∼32×10-6
cm/s), indicating good intestinal absorption and putative brain penetration. LDT5 is
not extensively protein-bound and is a substrate of human CYP2D6 and CYP2C19 but not
of CYP3A4 (half-life >60 min), and did not significantly influence the activities
of any of the human cytochrome P450 isoforms screened. LDT5 was considered safe
albeit new studies are necessary to rule out putative central adverse effects through
D2, 5-HT1A and 5-HT2B receptors, after chronic
use. This work highlights the drug-likeness properties of LDT5 and supports its
further preclinical development.
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Affiliation(s)
- F Noël
- Laboratório de Farmacologia Bioquímica e Molecular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - J B Nascimento-Viana
- Laboratório de Farmacologia Bioquímica e Molecular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - L A S Romeiro
- Departamento de Farmácia, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília, DF, Brasil
| | - R O Silva
- Departamento de Farmácia, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília, DF, Brasil.,Laboratório de Desenvolvimento de Estratégias Terapêuticas, Universidade Católica de Brasília, Brasília, DF, Brasil
| | - L F N Lemes
- Laboratório de Desenvolvimento de Estratégias Terapêuticas, Universidade Católica de Brasília, Brasília, DF, Brasil
| | - A S Oliveira
- Departamento de Farmácia, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília, DF, Brasil.,Laboratório de Desenvolvimento de Estratégias Terapêuticas, Universidade Católica de Brasília, Brasília, DF, Brasil
| | - T B S Giorno
- Laboratório de Farmacologia da Dor e Inflamação, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - P D Fernandes
- Laboratório de Farmacologia da Dor e Inflamação, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - C L M Silva
- Laboratório de Farmacologia Bioquímica e Molecular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
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26
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Chen D, Huang X, Zhou H, Luo H, Wang P, Chang Y, He X, Ni S, Shen Q, Cao G, Sun H, Wen X, Liu J. Discovery of pentacyclic triterpene 3β-ester derivatives as a new class of cholesterol ester transfer protein inhibitors. Eur J Med Chem 2017; 139:201-213. [DOI: 10.1016/j.ejmech.2017.08.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/08/2017] [Accepted: 08/03/2017] [Indexed: 01/06/2023]
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27
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Sebastián-Pérez V, Roca C, Awale M, Reymond JL, Martinez A, Gil C, Campillo NE. Medicinal and Biological Chemistry (MBC) Library: An Efficient Source of New Hits. J Chem Inf Model 2017; 57:2143-2151. [PMID: 28813151 DOI: 10.1021/acs.jcim.7b00401] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Identification of new hits is one of the biggest challenges in drug discovery. Creating a library of well-characterized drug-like compounds is a key step in this process. Our group has developed an in-house chemical library called the Medicinal and Biological Chemistry (MBC) library. This collection has been successfully used to start several medicinal chemistry programs and developed in an accumulation of more than 30 years of experience in drug design and discovery of new drugs for unmet diseases. It contains over 1000 compounds, mainly heterocyclic scaffolds. In this work, analysis of drug-like properties and comparative study with well-known libraries by using different computer software are presented here.
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Affiliation(s)
- Víctor Sebastián-Pérez
- Centro de Investigaciones Biológicas (CIB, CSIC) , Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Carlos Roca
- Centro de Investigaciones Biológicas (CIB, CSIC) , Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Mahendra Awale
- Department of Chemistry and Biochemistry, University of Bern , Freiestrasse 3, 3012 Bern, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Bern , Freiestrasse 3, 3012 Bern, Switzerland
| | - Ana Martinez
- Centro de Investigaciones Biológicas (CIB, CSIC) , Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Carmen Gil
- Centro de Investigaciones Biológicas (CIB, CSIC) , Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Nuria E Campillo
- Centro de Investigaciones Biológicas (CIB, CSIC) , Ramiro de Maeztu 9, 28040 Madrid, Spain
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28
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Monteleone S, Fuchs JE, Liedl KR. Molecular Connectivity Predefines Polypharmacology: Aliphatic Rings, Chirality, and sp 3 Centers Enhance Target Selectivity. Front Pharmacol 2017; 8:552. [PMID: 28894419 PMCID: PMC5581349 DOI: 10.3389/fphar.2017.00552] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/07/2017] [Indexed: 12/31/2022] Open
Abstract
Dark chemical matter compounds are small molecules that have been recently identified as highly potent and selective hits. For this reason, they constitute a promising class of possible candidates in the process of drug discovery and raise the interest of the scientific community. To this purpose, Wassermann et al. (2015) have described the application of 2D descriptors to characterize dark chemical matter. However, their definition was based on the number of reported positive assays rather than the number of known targets. As there might be multiple assays for one single target, the number of assays does not fully describe target selectivity. Here, we propose an alternative classification of active molecules that is based on the number of known targets. We cluster molecules in four classes: black, gray, and white compounds are active on one, two to four, and more than four targets respectively, whilst inactive compounds are found to be inactive in the considered assays. In this study, black and inactive compounds are found to have not only higher solubility, but also a higher number of chiral centers, sp3 carbon atoms and aliphatic rings. On the contrary, white compounds contain a higher number of double bonds and fused aromatic rings. Therefore, the design of a screening compound library should consider these molecular properties in order to achieve target selectivity or polypharmacology. Furthermore, analysis of four main target classes (GPCRs, kinases, proteases, and ion channels) shows that GPCR ligands are more selective than the other classes, as the number of black compounds is higher in this target superfamily. On the other side, ligands that hit kinases, proteases, and ion channels bind to GPCRs more likely than to other target classes. Consequently, depending on the target protein family, appropriate screening libraries can be designed in order to minimize the likelihood of unwanted side effects early in the drug discovery process. Additionally, synergistic effects may be obtained by library design toward polypharmacology.
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Affiliation(s)
| | | | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, Center of Molecular Biosciences, University of InnsbruckInnsbruck, Austria
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29
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Functional annotation of chemical libraries across diverse biological processes. Nat Chem Biol 2017; 13:982-993. [PMID: 28759014 PMCID: PMC6056180 DOI: 10.1038/nchembio.2436] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 06/13/2017] [Indexed: 11/08/2022]
Abstract
Chemical-genetic approaches offer the potential for unbiased functional annotation of chemical libraries. Mutations can alter the response of cells in the presence of a compound, revealing chemical-genetic interactions that can elucidate a compound's mode of action. We developed a highly parallel, unbiased yeast chemical-genetic screening system involving three key components. First, in a drug-sensitive genetic background, we constructed an optimized diagnostic mutant collection that is predictive for all major yeast biological processes. Second, we implemented a multiplexed (768-plex) barcode-sequencing protocol, enabling the assembly of thousands of chemical-genetic profiles. Finally, based on comparison of the chemical-genetic profiles with a compendium of genome-wide genetic interaction profiles, we predicted compound functionality. Applying this high-throughput approach, we screened seven different compound libraries and annotated their functional diversity. We further validated biological process predictions, prioritized a diverse set of compounds, and identified compounds that appear to have dual modes of action.
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30
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Rubio-Ruiz B, Ríos-Marco P, Carrasco-Jiménez MP, Espinosa A, Hurtado-Guerrero R, Marco C, Conejo-García A, Entrena A. Choline kinase inhibition and docking studies of a series of 6-(benzylthio)-9H-purin-9-yl-pyridinium derivatives. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1979-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Blagg J, Workman P. Choose and Use Your Chemical Probe Wisely to Explore Cancer Biology. Cancer Cell 2017; 32:9-25. [PMID: 28697345 PMCID: PMC5511331 DOI: 10.1016/j.ccell.2017.06.005] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/31/2017] [Accepted: 06/09/2017] [Indexed: 01/15/2023]
Abstract
Small-molecule chemical probes or tools have become progressively more important in recent years as valuable reagents to investigate fundamental biological mechanisms and processes causing disease, including cancer. Chemical probes have also achieved greater prominence alongside complementary biological reagents for target validation in drug discovery. However, there is evidence of widespread continuing misuse and promulgation of poor-quality and insufficiently selective chemical probes, perpetuating a worrisome and misleading pollution of the scientific literature. We discuss current challenges with the selection and use of chemical probes, and suggest how biologists can and should be more discriminating in the probes they employ.
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Affiliation(s)
- Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK.
| | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK.
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32
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Proschak E, Heitel P, Kalinowsky L, Merk D. Opportunities and Challenges for Fatty Acid Mimetics in Drug Discovery. J Med Chem 2017; 60:5235-5266. [PMID: 28252961 DOI: 10.1021/acs.jmedchem.6b01287] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Fatty acids beyond their role as an endogenous energy source and storage are increasingly considered as signaling molecules regulating various physiological effects in metabolism and inflammation. Accordingly, the molecular targets involved in formation and physiological activities of fatty acids hold significant therapeutic potential. A number of these fatty acid targets are addressed by some of the oldest and most widely used drugs such as cyclooxygenase inhibiting NSAIDs, whereas others remain unexploited. Compounds orthosterically binding to proteins that endogenously bind fatty acids are considered as fatty acid mimetics. On the basis of their structural resemblance, fatty acid mimetics constitute a family of bioactive compounds showing specific binding thermodynamics and following similar pharmacokinetic mechanisms. This perspective systematically evaluates targets for fatty acid mimetics, investigates their common structural characteristics, and highlights demands in their discovery and design. In summary, fatty acid mimetics share particularly favorable characteristics justifying the conclusion that their therapeutic potential vastly outweighs the challenges in their design.
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Affiliation(s)
- Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Pascal Heitel
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Lena Kalinowsky
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
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33
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Ford KA. Refinement, Reduction, and Replacement of Animal Toxicity Tests by Computational Methods. ILAR J 2017; 57:226-233. [DOI: 10.1093/ilar/ilw031] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 10/12/2016] [Indexed: 12/16/2022] Open
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34
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Dimova D, Gilberg E, Bajorath J. Identification and analysis of promiscuity cliffs formed by bioactive compounds and experimental implications. RSC Adv 2017. [DOI: 10.1039/c6ra27247a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
For three promiscuity cliffs (enclosed), cliff compounds, their promiscuity degrees (PDs), and color-coded substitution sites are shown. Comparison of these cliffs suggests the design of a new analog to further explore promiscuity.
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Affiliation(s)
- Dilyana Dimova
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
| | - Erik Gilberg
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
| | - Jürgen Bajorath
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
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35
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Lee ECY, Steeno G, Wassermann AM, Zhang L, Shah F, Price DA. Amine promiscuity and toxicology analysis. Bioorg Med Chem Lett 2016; 27:653-657. [PMID: 28011216 DOI: 10.1016/j.bmcl.2016.11.085] [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: 10/03/2016] [Revised: 11/27/2016] [Accepted: 11/28/2016] [Indexed: 12/22/2022]
Abstract
Drug discovery programs often face challenges to obtain sufficient duration of action of the drug (i.e. seek longer half-lives). If the pharmacodynamic response is driven by free plasma concentration of the drug then extending the plasma drug concentration is a valid approach. Half-life is dependent on the volume of distribution, which in turn can be dependent upon the ionization state of the molecule. Basic compounds tend to have a higher volume of distribution leading to longer half-lives. However, it has been shown that bases may also have higher promiscuity. In this work, we describe an analysis of in vitro pharmacological profiling and toxicology data investigating the role of primary, secondary, and tertiary amines in imparting promiscuity and thus off-target toxicity. Primary amines are found to be less promiscuous in in vitro assays and have improved profiles in in vivo toxicology studies compared to secondary and tertiary amines.
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Affiliation(s)
- Esther C Y Lee
- Medicine Design, Pfizer Worldwide Research & Development, Cambridge, MA 02139, United States.
| | - Gregory Steeno
- Research Statistics, Pfizer Worldwide Research & Development, Groton, CT 06340, United States
| | | | - Liying Zhang
- Computational Sciences, Pfizer Worldwide Research & Development, Cambridge, MA 02139, United States
| | - Falgun Shah
- Computational Sciences, Pfizer Worldwide Research & Development, Cambridge, MA 02139, United States
| | - David A Price
- Medicine Design, Pfizer Worldwide Research & Development, Cambridge, MA 02139, United States
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36
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Cortes Cabrera A, Lucena-Agell D, Redondo-Horcajo M, Barasoain I, Díaz JF, Fasching B, Petrone PM. Aggregated Compound Biological Signatures Facilitate Phenotypic Drug Discovery and Target Elucidation. ACS Chem Biol 2016; 11:3024-3034. [PMID: 27564241 DOI: 10.1021/acschembio.6b00358] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Predicting the cellular response of compounds is a challenge central to the discovery of new drugs. Compound biological signatures have risen as a way of representing the perturbation produced by a compound in the cell. However, their ability to encode specific phenotypic information and generating tangible predictions remains unknown, mainly because of the inherent noise in such data sets. In this work, we statistically aggregate signals from several compound biological signatures to find compounds that produce a desired phenotype in the cell. We exploit this method in two applications relevant for phenotypic screening in drug discovery programs: target-independent hit expansion and target identification. As a result, we present here (i) novel nanomolar inhibitors of cellular division that reproduce the phenotype and the mode of action of reference natural products and (ii) blockers of the NKCC1 cotransporter for autism spectrum disorders. Our results were confirmed in both cellular and biochemical assays of the respective projects. In addition, these examples provided novel insights on the information content and biological significance of compound biological signatures from HTS, and their applicability to drug discovery in general. For target identification, we show that novel targets can be predicted successfully for drugs by reporting new activities for nimedipine, fluspirilene, and pimozide and providing a rationale for repurposing and side effects. Our results highlight the opportunities of reusing public bioactivity data for prospective drug discovery, including scenarios where the effective target or mode of action of a particular molecule is not known, such as in phenotypic screening campaigns.
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Affiliation(s)
- Alvaro Cortes Cabrera
- Pharma Research & Early Development Informatics (pREDi), Roche Innovation Center Basel, Basel, Switzerland
| | - Daniel Lucena-Agell
- Laboratory
of Microtubule Stabilizing Agents, Department of Physical and Chemical
Biology, Centro de Investigaciones Biológicas, CIB, CSIC, Madrid, Spain
| | - Mariano Redondo-Horcajo
- Laboratory
of Microtubule Stabilizing Agents, Department of Physical and Chemical
Biology, Centro de Investigaciones Biológicas, CIB, CSIC, Madrid, Spain
| | - Isabel Barasoain
- Laboratory
of Microtubule Stabilizing Agents, Department of Physical and Chemical
Biology, Centro de Investigaciones Biológicas, CIB, CSIC, Madrid, Spain
| | - José Fernando Díaz
- Laboratory
of Microtubule Stabilizing Agents, Department of Physical and Chemical
Biology, Centro de Investigaciones Biológicas, CIB, CSIC, Madrid, Spain
| | - Bernhard Fasching
- Medicinal Chemistry, Pharma Research & Early Development (pRED), Roche Innovation Center Basel, Basel, Switzerland
| | - Paula M. Petrone
- Pharma Research & Early Development Informatics (pREDi), Roche Innovation Center Basel, Basel, Switzerland
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37
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Noji S, Seki N, Maeba T, Sakai T, Watanabe E, Maeda K, Fukushima K, Noguchi T, Ogawa K, Toyonaga Y, Negoro T, Kawasaki H, Shiozaki M. Concise SAR Exploration Based on the "Head-to-Tail" Approach: Discovery of PI4KIIIα Inhibitors Bearing Diverse Scaffolds. ACS Med Chem Lett 2016; 7:919-923. [PMID: 27774129 DOI: 10.1021/acsmedchemlett.6b00232] [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: 06/07/2016] [Accepted: 08/03/2016] [Indexed: 12/31/2022] Open
Abstract
In typical kinase inhibitor programs, a hinge binder showing best potency with preferential specificity is initially selected, followed by fine-tuning of the accompanying substituents on its core module. A shortcoming of this approach is that the exclusive focus on a single chemotype can endanger all the analogues in the series if a critical shortcoming is revealed. Thus, an early evaluation of structure-activity relationships (SARs) can mitigate unforeseen outcomes within a series of multiple compounds, although there have been very few examples to follow such a policy. PI4KIIIα is one of four mammalian phosphatidylinositol-4 kinases and has recently drawn significant attention as an emerging target for hepatitis C virus (HCV) treatment. In this letter, a novel "head-to-tail" approach to discover a diverse set of PI4KIIIα inhibitors is reported. We believe this method will generate distinct core scaffolds, a rational strategy to circumvent potential risks in general kinase programs.
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Affiliation(s)
- Satoru Noji
- Chemical Research Laboratories, §Biological Pharmacological Research Laboratories, and ‡Drug Metabolism & Pharmacokinetics Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Noriyoshi Seki
- Chemical Research Laboratories, §Biological Pharmacological Research Laboratories, and ‡Drug Metabolism & Pharmacokinetics Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Takaki Maeba
- Chemical Research Laboratories, §Biological Pharmacological Research Laboratories, and ‡Drug Metabolism & Pharmacokinetics Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Takayuki Sakai
- Chemical Research Laboratories, §Biological Pharmacological Research Laboratories, and ‡Drug Metabolism & Pharmacokinetics Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Eiichi Watanabe
- Chemical Research Laboratories, §Biological Pharmacological Research Laboratories, and ‡Drug Metabolism & Pharmacokinetics Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Katsuya Maeda
- Chemical Research Laboratories, §Biological Pharmacological Research Laboratories, and ‡Drug Metabolism & Pharmacokinetics Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Kyoko Fukushima
- Chemical Research Laboratories, §Biological Pharmacological Research Laboratories, and ‡Drug Metabolism & Pharmacokinetics Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Toru Noguchi
- Chemical Research Laboratories, §Biological Pharmacological Research Laboratories, and ‡Drug Metabolism & Pharmacokinetics Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Kazuya Ogawa
- Chemical Research Laboratories, §Biological Pharmacological Research Laboratories, and ‡Drug Metabolism & Pharmacokinetics Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Yukiyo Toyonaga
- Chemical Research Laboratories, §Biological Pharmacological Research Laboratories, and ‡Drug Metabolism & Pharmacokinetics Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Tamotsu Negoro
- Chemical Research Laboratories, §Biological Pharmacological Research Laboratories, and ‡Drug Metabolism & Pharmacokinetics Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Hisashi Kawasaki
- Chemical Research Laboratories, §Biological Pharmacological Research Laboratories, and ‡Drug Metabolism & Pharmacokinetics Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Makoto Shiozaki
- Chemical Research Laboratories, §Biological Pharmacological Research Laboratories, and ‡Drug Metabolism & Pharmacokinetics Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
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38
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Kell DB, Pretorius E. On the translocation of bacteria and their lipopolysaccharides between blood and peripheral locations in chronic, inflammatory diseases: the central roles of LPS and LPS-induced cell death. Integr Biol (Camb) 2016; 7:1339-77. [PMID: 26345428 DOI: 10.1039/c5ib00158g] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We have recently highlighted (and added to) the considerable evidence that blood can contain dormant bacteria. By definition, such bacteria may be resuscitated (and thus proliferate). This may occur under conditions that lead to or exacerbate chronic, inflammatory diseases that are normally considered to lack a microbial component. Bacterial cell wall components, such as the endotoxin lipopolysaccharide (LPS) of Gram-negative strains, are well known as potent inflammatory agents, but should normally be cleared. Thus, their continuing production and replenishment from dormant bacterial reservoirs provides an easy explanation for the continuing, low-grade inflammation (and inflammatory cytokine production) that is characteristic of many such diseases. Although experimental conditions and determinants have varied considerably between investigators, we summarise the evidence that in a great many circumstances LPS can play a central role in all of these processes, including in particular cell death processes that permit translocation between the gut, blood and other tissues. Such localised cell death processes might also contribute strongly to the specific diseases of interest. The bacterial requirement for free iron explains the strong co-existence in these diseases of iron dysregulation, LPS production, and inflammation. Overall this analysis provides an integrative picture, with significant predictive power, that is able to link these processes via the centrality of a dormant blood microbiome that can resuscitate and shed cell wall components.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry and The Manchester Institute of Biotechnology, The University of Manchester, 131, Princess St, Manchester M1 7DN, Lancs, UK.
| | - Etheresia Pretorius
- Department of Physiology, Faculty of Health Sciences, University of Pretoria, Arcadia 0007, South Africa.
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39
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Lee HM, Kim Y. Drug Repurposing Is a New Opportunity for Developing Drugs against Neuropsychiatric Disorders. SCHIZOPHRENIA RESEARCH AND TREATMENT 2016; 2016:6378137. [PMID: 27073698 PMCID: PMC4814692 DOI: 10.1155/2016/6378137] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/24/2016] [Indexed: 01/03/2023]
Abstract
Better the drugs you know than the drugs you do not know. Drug repurposing is a promising, fast, and cost effective method that can overcome traditional de novo drug discovery and development challenges of targeting neuropsychiatric and other disorders. Drug discovery and development targeting neuropsychiatric disorders are complicated because of the limitations in understanding pathophysiological phenomena. In addition, traditional de novo drug discovery and development are risky, expensive, and time-consuming processes. One alternative approach, drug repurposing, has emerged taking advantage of off-target effects of the existing drugs. In order to identify new opportunities for the existing drugs, it is essential for us to understand the mechanisms of action of drugs, both biologically and pharmacologically. By doing this, drug repurposing would be a more effective method to develop drugs against neuropsychiatric and other disorders. Here, we review the difficulties in drug discovery and development in neuropsychiatric disorders and the extent and perspectives of drug repurposing.
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Affiliation(s)
- Hyeong-Min Lee
- Department of Cell Biology & Physiology, School of Medicine, University of North Carolina, 115 Mason Farm Road, Chapel Hill, NC 27599, USA
| | - Yuna Kim
- Department of Pediatrics, School of Medicine, Duke University, 905 S. LaSalle Street, Durham, NC 27710, USA
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40
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Meanwell NA. Improving Drug Design: An Update on Recent Applications of Efficiency Metrics, Strategies for Replacing Problematic Elements, and Compounds in Nontraditional Drug Space. Chem Res Toxicol 2016; 29:564-616. [DOI: 10.1021/acs.chemrestox.6b00043] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicholas A. Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research & Development, Wallingford, Connecticut 06492, United States
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41
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Swidorski JJ, Liu Z, Sit SY, Chen J, Chen Y, Sin N, Venables BL, Parker DD, Nowicka-Sans B, Terry BJ, Protack T, Rahematpura S, Hanumegowda U, Jenkins S, Krystal M, Dicker IB, Meanwell NA, Regueiro-Ren A. Inhibitors of HIV-1 maturation: Development of structure-activity relationship for C-28 amides based on C-3 benzoic acid-modified triterpenoids. Bioorg Med Chem Lett 2016; 26:1925-30. [PMID: 26988305 DOI: 10.1016/j.bmcl.2016.03.019] [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: 01/11/2016] [Revised: 03/05/2016] [Accepted: 03/07/2016] [Indexed: 12/27/2022]
Abstract
We have recently reported on the discovery of a C-3 benzoic acid (1) as a suitable replacement for the dimethyl succinate side chain of bevirimat (2), an HIV-1 maturation inhibitor that reached Phase II clinical trials before being discontinued. Recent SAR studies aimed at improving the antiviral properties of 2 have shown that the benzoic acid moiety conferred topographical constraint to the pharmacophore and was associated with a lower shift in potency in the presence of human serum albumin. In this manuscript, we describe efforts to improve the polymorphic coverage of the C-3 benzoic acid chemotype through modifications at the C-28 position of the triterpenoid core. The dimethylaminoethyl amides 17 and 23 delivered improved potency toward bevirimat-resistant viruses while increasing C24 in rat oral PK studies.
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Affiliation(s)
- Jacob J Swidorski
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA.
| | - Zheng Liu
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Sing-Yuen Sit
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Jie Chen
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Yan Chen
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Ny Sin
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Brian L Venables
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Dawn D Parker
- Department of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Beata Nowicka-Sans
- Department of Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Brian J Terry
- Department of Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Tricia Protack
- Department of Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Sandhya Rahematpura
- Department of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Umesh Hanumegowda
- Department of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Susan Jenkins
- Department of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Mark Krystal
- Department of Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Ira B Dicker
- Department of Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Nicholas A Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Alicia Regueiro-Ren
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
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Kirmeier T, Gopalakrishnan R, Gormanns V, Werner AM, Cuboni S, Rudolf GC, Höfner G, Wanner KT, Sieber SA, Schmidt U, Holsboer F, Rein T, Hausch F. Azidobupramine, an Antidepressant-Derived Bifunctional Neurotransmitter Transporter Ligand Allowing Covalent Labeling and Attachment of Fluorophores. PLoS One 2016; 11:e0148608. [PMID: 26863431 PMCID: PMC4749225 DOI: 10.1371/journal.pone.0148608] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 01/20/2016] [Indexed: 12/21/2022] Open
Abstract
The aim of this study was to design, synthesize and validate a multifunctional antidepressant probe that is modified at two distinct positions. The purpose of these modifications was to allow covalent linkage of the probe to interaction partners, and decoration of probe-target complexes with fluorescent reporter molecules. The strategy for the design of such a probe (i.e., azidobupramine) was guided by the need for the introduction of additional functional groups, conveying the required properties while keeping the additional moieties as small as possible. This should minimize the risk of changing antidepressant-like properties of the new probe azidobupramine. To control for this, we evaluated the binding parameters of azidobupramine to known target sites such as the transporters for serotonin (SERT), norepinephrine (NET), and dopamine (DAT). The binding affinities of azidobupramine to SERT, NET, and DAT were in the range of structurally related and clinically active antidepressants. Furthermore, we successfully visualized azidobupramine-SERT complexes not only in SERT-enriched protein material but also in living cells stably overexpressing SERT. To our knowledge, azidobupramine is the first structural analogue of a tricyclic antidepressant that can be covalently linked to target structures and further attached to reporter molecules while preserving antidepressant-like properties and avoiding radioactive isotopes.
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Affiliation(s)
- Thomas Kirmeier
- Max Planck Institute of Psychiatry, Clinical Department, Munich, Germany
| | - Ranganath Gopalakrishnan
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
| | - Vanessa Gormanns
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
| | - Anna M. Werner
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
| | - Serena Cuboni
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
| | - Georg C. Rudolf
- Technical University Munich, IAS, CIPSM, Department of Chemistry, Garching, Germany
| | - Georg Höfner
- Department Pharmazie Zentrum für Pharmaforschung, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Klaus T. Wanner
- Department Pharmazie Zentrum für Pharmaforschung, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stephan A. Sieber
- Technical University Munich, IAS, CIPSM, Department of Chemistry, Garching, Germany
| | - Ulrike Schmidt
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
| | - Florian Holsboer
- Max Planck Institute of Psychiatry, Clinical Department, Munich, Germany
| | - Theo Rein
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
- * E-mail: (TR); (F. Hausch)
| | - Felix Hausch
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
- * E-mail: (TR); (F. Hausch)
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Ndubaku CO, Crawford JJ, Drobnick J, Aliagas I, Campbell D, Dong P, Dornan LM, Duron S, Epler J, Gazzard L, Heise CE, Hoeflich KP, Jakubiak D, La H, Lee W, Lin B, Lyssikatos JP, Maksimoska J, Marmorstein R, Murray LJ, O’Brien T, Oh A, Ramaswamy S, Wang W, Zhao X, Zhong Y, Blackwood E, Rudolph J. Design of Selective PAK1 Inhibitor G-5555: Improving Properties by Employing an Unorthodox Low-pK a Polar Moiety. ACS Med Chem Lett 2015; 6:1241-6. [PMID: 26713112 DOI: 10.1021/acsmedchemlett.5b00398] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 10/31/2015] [Indexed: 11/28/2022] Open
Abstract
Signaling pathways intersecting with the p21-activated kinases (PAKs) play important roles in tumorigenesis and cancer progression. By recognizing that the limitations of FRAX1036 (1) were chiefly associated with the highly basic amine it contained, we devised a mitigation strategy to address several issues such as hERG activity. The 5-amino-1,3-dioxanyl moiety was identified as an effective means of reducing pK a and logP simultaneously. When positioned properly within the scaffold, this group conferred several benefits including potency, pharmacokinetics, and selectivity. Mouse xenograft PK/PD studies were carried out using an advanced compound, G-5555 (12), derived from this approach. These studies concluded that dose-dependent pathway modulation was achievable and paves the way for further in vivo investigations of PAK1 function in cancer and other diseases.
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Affiliation(s)
- Chudi O. Ndubaku
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - James J. Crawford
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Joy Drobnick
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Ignacio Aliagas
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - David Campbell
- Afraxis, Inc., 6605 Nancy Ridge
Road, Suite 224, San Diego, California 92121, United States
| | - Ping Dong
- Shanghai ChemPartner, 576 Libing
Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai 201203, PRC
| | - Laura M. Dornan
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Sergio Duron
- Afraxis, Inc., 6605 Nancy Ridge
Road, Suite 224, San Diego, California 92121, United States
| | - Jennifer Epler
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Lewis Gazzard
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Christopher E. Heise
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Klaus P. Hoeflich
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Diana Jakubiak
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Hank La
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Wendy Lee
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Baiwei Lin
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Joseph P. Lyssikatos
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jasna Maksimoska
- Perelman
School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104, United States
| | - Ronen Marmorstein
- Perelman
School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104, United States
| | - Lesley J. Murray
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Thomas O’Brien
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Angela Oh
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Sreemathy Ramaswamy
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Weiru Wang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Xianrui Zhao
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Yu Zhong
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Elizabeth Blackwood
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Joachim Rudolph
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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Abstract
Attrition due to nonclinical safety represents a major issue for the productivity of pharmaceutical research and development (R&D) organizations, especially during the compound optimization stages of drug discovery and the early stages of clinical development. Focusing on decreasing nonclinical safety-related attrition is not a new concept, and various approaches have been experimented with over the last two decades. Front-loading testing funnels in Discovery with in vitro toxicity assays designed to rapidly identify unfavorable molecules was the approach adopted by most pharmaceutical R&D organizations a few years ago. However, this approach has also a non-negligible opportunity cost. Hence, significant refinements to the "fail early, fail often" paradigm have been proposed recently to reflect the complexity of accurately categorizing compounds with early data points without taking into account other important contextual aspects, in particular efficacious systemic and tissue exposures. This review provides an overview of toxicology approaches and models that can be used in pharmaceutical Discovery at the series/lead identification and lead optimization stages to guide and inform chemistry efforts, as well as a personal view on how to best use them to meet nonclinical safety-related attrition objectives consistent with a sustainable pharmaceutical R&D model. The scope of this review is limited to small molecules, as large molecules are associated with challenges that are quite different. Finally, a perspective on how several emerging technologies may impact toxicity evaluation is also provided.
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Affiliation(s)
- Eric A G Blomme
- Global Preclinical Safety, AbbVie Inc. , 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Yvonne Will
- Drug Safety Research and Development, Pfizer , Eastern Point Road, Groton, Connecticut 06340, United States
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45
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Camp D, Garavelas A, Campitelli M. Analysis of Physicochemical Properties for Drugs of Natural Origin. JOURNAL OF NATURAL PRODUCTS 2015; 78:1370-1382. [PMID: 26039921 DOI: 10.1021/acs.jnatprod.5b00255] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The impact of time, therapy area, and route of administration on 13 physicochemical properties calculated for 664 drugs developed from a natural prototype was investigated. The mean values for the majority of properties sampled over five periods from pre-1900 to 2013 were found to change in a statistically significant manner. In contrast, lipophilicity and aromatic ring count remained relatively constant, suggesting that these parameters are the most important for successful prosecution of a natural product drug discovery program if the route of administration is not focused exclusively on oral availability. An examination by therapy area revealed that anti-infective agents had the most differences in physicochemical property profiles compared with other areas, particularly with respect to lipophilicity. However, when this group was removed, the variation between the mean values for lipophilicity and aromatic ring count across the remaining therapy areas was again found not to change in a meaningful manner, further highlighting the importance of these two parameters. The vast majority of drugs with a natural progenitor were formulated for either oral and/or injectable administration. Injectables were, on average, larger and more polar than drugs developed for oral, topical, and inhalation routes.
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Affiliation(s)
| | | | - Marc Campitelli
- §QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
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46
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Waring MJ, Arrowsmith J, Leach AR, Leeson PD, Mandrell S, Owen RM, Pairaudeau G, Pennie WD, Pickett SD, Wang J, Wallace O, Weir A. An analysis of the attrition of drug candidates from four major pharmaceutical companies. Nat Rev Drug Discov 2015; 14:475-86. [PMID: 26091267 DOI: 10.1038/nrd4609] [Citation(s) in RCA: 805] [Impact Index Per Article: 89.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The pharmaceutical industry remains under huge pressure to address the high attrition rates in drug development. Attempts to reduce the number of efficacy- and safety-related failures by analysing possible links to the physicochemical properties of small-molecule drug candidates have been inconclusive because of the limited size of data sets from individual companies. Here, we describe the compilation and analysis of combined data on the attrition of drug candidates from AstraZeneca, Eli Lilly and Company, GlaxoSmithKline and Pfizer. The analysis reaffirms that control of physicochemical properties during compound optimization is beneficial in identifying compounds of candidate drug quality and indicates for the first time a link between the physicochemical properties of compounds and clinical failure due to safety issues. The results also suggest that further control of physicochemical properties is unlikely to have a significant effect on attrition rates and that additional work is required to address safety-related failures. Further cross-company collaborations will be crucial to future progress in this area.
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Affiliation(s)
| | | | | | - Paul D Leeson
- 1] GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, UK. [2] Paul Leeson Consulting, The Malt House, Main Street, Congerstone, Nuneaton, Warwickshire CV13 6LZ, UK
| | - Sam Mandrell
- Thomson Reuters, 77 Hatton Garden, London EC1N 8JS, UK
| | | | | | - William D Pennie
- 1] Pfizer, Groton, Connecticut 06340, USA. [2] Takeda Pharmaceuticals, Cambridge, Massachusetts 02139, USA
| | | | - Jibo Wang
- Eli Lilly, Indianapolis, Indiana 46285, USA
| | - Owen Wallace
- 1] Eli Lilly, Indianapolis, Indiana 46285, USA. [2] Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Alex Weir
- Thomson Reuters, 77 Hatton Garden, London EC1N 8JS, UK
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47
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Wang X, Dong Y, Cal M, Kaiser M, Wittlin S, Vennerstrom JL. Antiprotozoal Selectivity of Diimidazoline N-Phenylbenzamides. ACS Infect Dis 2015; 1:135-9. [PMID: 27622464 DOI: 10.1021/id500034v] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We discovered three diimidazolines with high antiplasmodial selectivity that had IC50 values of 1.9-28 nM against cultured Plasmodium falciparum. We also identified a gem-dimethyl diimidazoline with high antitrypanosomal selectivity that had an IC50 value of 26 nM against cultured Trypanosoma brucei rhodesiense. Two 2-imidazoline heterocycles in a para orientation on a N-phenylbenzamide or similar core structure were required for high antiprotozoal activity. Ring expansion of the imidazoline as well as heterocyclic variants with pKa values of <7 all decreased activity significantly.
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Affiliation(s)
- Xiaofang Wang
- College
of Pharmacy, 986025 Nebraska Medical Center, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
| | - Yuxiang Dong
- College
of Pharmacy, 986025 Nebraska Medical Center, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
| | - Monica Cal
- Swiss Tropical and Public Health Institute, Socinstrasse 57, CH-4002 Basel, Switzerland
- University of Basel, CH-4003 Basel, Switzerland
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Socinstrasse 57, CH-4002 Basel, Switzerland
- University of Basel, CH-4003 Basel, Switzerland
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Socinstrasse 57, CH-4002 Basel, Switzerland
- University of Basel, CH-4003 Basel, Switzerland
| | - Jonathan L. Vennerstrom
- College
of Pharmacy, 986025 Nebraska Medical Center, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
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Lemurell M, Ulander J, Winiwarter S, Dahlén A, Davidsson Ö, Emtenäs H, Broddefalk J, Swanson M, Hovdal D, Plowright AT, Pettersen A, Rydén-Landergren M, Barlind J, Llinas A, Herslöf M, Drmota T, Sigfridsson K, Moses S, Whatling C. Discovery of AZD6642, an Inhibitor of 5-Lipoxygenase Activating Protein (FLAP) for the Treatment of Inflammatory Diseases. J Med Chem 2014; 58:897-911. [DOI: 10.1021/jm501531v] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Malin Lemurell
- Cardiovascular & Metabolic Diseases iMed, ‡Respiratory, Inflammation & Autoimmune Diseases iMed, §Drug Safety & Metabolism, and ∥Pharmaceutical Development, AstraZeneca, Pepparedsleden 1, Mölndal, 43183, Sweden
| | - Johan Ulander
- Cardiovascular & Metabolic Diseases iMed, ‡Respiratory, Inflammation & Autoimmune Diseases iMed, §Drug Safety & Metabolism, and ∥Pharmaceutical Development, AstraZeneca, Pepparedsleden 1, Mölndal, 43183, Sweden
| | - Susanne Winiwarter
- Cardiovascular & Metabolic Diseases iMed, ‡Respiratory, Inflammation & Autoimmune Diseases iMed, §Drug Safety & Metabolism, and ∥Pharmaceutical Development, AstraZeneca, Pepparedsleden 1, Mölndal, 43183, Sweden
| | - Anders Dahlén
- Cardiovascular & Metabolic Diseases iMed, ‡Respiratory, Inflammation & Autoimmune Diseases iMed, §Drug Safety & Metabolism, and ∥Pharmaceutical Development, AstraZeneca, Pepparedsleden 1, Mölndal, 43183, Sweden
| | - Öjvind Davidsson
- Cardiovascular & Metabolic Diseases iMed, ‡Respiratory, Inflammation & Autoimmune Diseases iMed, §Drug Safety & Metabolism, and ∥Pharmaceutical Development, AstraZeneca, Pepparedsleden 1, Mölndal, 43183, Sweden
| | - Hans Emtenäs
- Cardiovascular & Metabolic Diseases iMed, ‡Respiratory, Inflammation & Autoimmune Diseases iMed, §Drug Safety & Metabolism, and ∥Pharmaceutical Development, AstraZeneca, Pepparedsleden 1, Mölndal, 43183, Sweden
| | - Johan Broddefalk
- Cardiovascular & Metabolic Diseases iMed, ‡Respiratory, Inflammation & Autoimmune Diseases iMed, §Drug Safety & Metabolism, and ∥Pharmaceutical Development, AstraZeneca, Pepparedsleden 1, Mölndal, 43183, Sweden
| | - Marianne Swanson
- Cardiovascular & Metabolic Diseases iMed, ‡Respiratory, Inflammation & Autoimmune Diseases iMed, §Drug Safety & Metabolism, and ∥Pharmaceutical Development, AstraZeneca, Pepparedsleden 1, Mölndal, 43183, Sweden
| | - Daniel Hovdal
- Cardiovascular & Metabolic Diseases iMed, ‡Respiratory, Inflammation & Autoimmune Diseases iMed, §Drug Safety & Metabolism, and ∥Pharmaceutical Development, AstraZeneca, Pepparedsleden 1, Mölndal, 43183, Sweden
| | - Alleyn T. Plowright
- Cardiovascular & Metabolic Diseases iMed, ‡Respiratory, Inflammation & Autoimmune Diseases iMed, §Drug Safety & Metabolism, and ∥Pharmaceutical Development, AstraZeneca, Pepparedsleden 1, Mölndal, 43183, Sweden
| | - Anna Pettersen
- Cardiovascular & Metabolic Diseases iMed, ‡Respiratory, Inflammation & Autoimmune Diseases iMed, §Drug Safety & Metabolism, and ∥Pharmaceutical Development, AstraZeneca, Pepparedsleden 1, Mölndal, 43183, Sweden
| | - Marie Rydén-Landergren
- Cardiovascular & Metabolic Diseases iMed, ‡Respiratory, Inflammation & Autoimmune Diseases iMed, §Drug Safety & Metabolism, and ∥Pharmaceutical Development, AstraZeneca, Pepparedsleden 1, Mölndal, 43183, Sweden
| | - Jonas Barlind
- Cardiovascular & Metabolic Diseases iMed, ‡Respiratory, Inflammation & Autoimmune Diseases iMed, §Drug Safety & Metabolism, and ∥Pharmaceutical Development, AstraZeneca, Pepparedsleden 1, Mölndal, 43183, Sweden
| | - Antonio Llinas
- Cardiovascular & Metabolic Diseases iMed, ‡Respiratory, Inflammation & Autoimmune Diseases iMed, §Drug Safety & Metabolism, and ∥Pharmaceutical Development, AstraZeneca, Pepparedsleden 1, Mölndal, 43183, Sweden
| | - Margareta Herslöf
- Cardiovascular & Metabolic Diseases iMed, ‡Respiratory, Inflammation & Autoimmune Diseases iMed, §Drug Safety & Metabolism, and ∥Pharmaceutical Development, AstraZeneca, Pepparedsleden 1, Mölndal, 43183, Sweden
| | - Tomas Drmota
- Cardiovascular & Metabolic Diseases iMed, ‡Respiratory, Inflammation & Autoimmune Diseases iMed, §Drug Safety & Metabolism, and ∥Pharmaceutical Development, AstraZeneca, Pepparedsleden 1, Mölndal, 43183, Sweden
| | - Kalle Sigfridsson
- Cardiovascular & Metabolic Diseases iMed, ‡Respiratory, Inflammation & Autoimmune Diseases iMed, §Drug Safety & Metabolism, and ∥Pharmaceutical Development, AstraZeneca, Pepparedsleden 1, Mölndal, 43183, Sweden
| | - Sara Moses
- Cardiovascular & Metabolic Diseases iMed, ‡Respiratory, Inflammation & Autoimmune Diseases iMed, §Drug Safety & Metabolism, and ∥Pharmaceutical Development, AstraZeneca, Pepparedsleden 1, Mölndal, 43183, Sweden
| | - Carl Whatling
- Cardiovascular & Metabolic Diseases iMed, ‡Respiratory, Inflammation & Autoimmune Diseases iMed, §Drug Safety & Metabolism, and ∥Pharmaceutical Development, AstraZeneca, Pepparedsleden 1, Mölndal, 43183, Sweden
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49
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Trieselmann T, Wagner H, Fuchs K, Hamprecht D, Berta D, Cremonesi P, Streicher R, Luippold G, Volz A, Markert M, Nar H. Potent cholesteryl ester transfer protein inhibitors of reduced lipophilicity: 1,1'-spiro-substituted hexahydrofuroquinoline derivatives. J Med Chem 2014; 57:8766-76. [PMID: 25265559 DOI: 10.1021/jm500431d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A series of 1,1'-spiro-substituted hexahydrofuroquinoline derivatives exhibiting potent cholesteryl ester transfer protein (CETP) inhibition at reduced lipophilicity was identified. A focused structure-activity relationship (SAR) exploration led to the potent and comparatively polar CETP inhibitor 26 showing robust high density lipoprotein-cholesterol (HDL-C) elevation and low density lipoprotein-cholesterol (LDL-C) reduction in transgenic hCETP/hApoB-100 mice. Compound 26 was also shown to positively differentiate from highly lipophilic CETP inhibitors in its complete elimination from fat tissue in hCETP transgenic mice as evident within 21 days after cessation of treatment. In addition, compound 26 showed no significant effects on aldosterone secretion from H295R cells, as well as no significant effects on blood pressure and electrocardiogram parameters in telemetrized cynomolgus monkeys.
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Affiliation(s)
- Thomas Trieselmann
- Departments of Medicinal Chemistry, §Cardiometabolic Diseases, ⊥Drug Discovery Support, and ∥Lead Identification, Boehringer Ingelheim Pharma GmbH & Co. KG , Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany
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50
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Charifson PS, Walters WP. Acidic and Basic Drugs in Medicinal Chemistry: A Perspective. J Med Chem 2014; 57:9701-17. [DOI: 10.1021/jm501000a] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Paul S. Charifson
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue Boston, Massachusetts 02210, United States
| | - W. Patrick Walters
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue Boston, Massachusetts 02210, United States
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