1
|
Meanwell NA. The pyridazine heterocycle in molecular recognition and drug discovery. Med Chem Res 2023; 32:1-69. [PMID: 37362319 PMCID: PMC10015555 DOI: 10.1007/s00044-023-03035-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/06/2023] [Indexed: 03/17/2023]
Abstract
The pyridazine ring is endowed with unique physicochemical properties, characterized by weak basicity, a high dipole moment that subtends π-π stacking interactions and robust, dual hydrogen-bonding capacity that can be of importance in drug-target interactions. These properties contribute to unique applications in molecular recognition while the inherent polarity, low cytochrome P450 inhibitory effects and potential to reduce interaction of a molecule with the cardiac hERG potassium channel add additional value in drug discovery and development. The recent approvals of the gonadotropin-releasing hormone receptor antagonist relugolix (24) and the allosteric tyrosine kinase 2 inhibitor deucravacitinib (25) represent the first examples of FDA-approved drugs that incorporate a pyridazine ring. In this review, the properties of the pyridazine ring are summarized in comparison to the other azines and its potential in drug discovery is illustrated through vignettes that explore applications that take advantage of the inherent physicochemical properties as an approach to solving challenges associated with candidate optimization. Graphical Abstract
Collapse
|
2
|
Kazmierski WM, Miriyala N, Johnson DK, Baskaran S. The Discovery of Conformationally Constrained Bicyclic Peptidomimetics as Potent Hepatitis C NS5A Inhibitors. ACS Med Chem Lett 2021; 12:1649-1655. [PMID: 34790290 PMCID: PMC8591741 DOI: 10.1021/acsmedchemlett.1c00391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Indexed: 01/03/2023] Open
Abstract
![]()
HCV NS5A inhibitors are the backbone
of directly acting antiviral
treatments against the hepatitis C virus (HCV). While these therapies
are generally highly curative, they are less effective in some specific
HCV patient populations. In the search for broader-acting HCV NS5A
inhibitors that address these needs, we explored conformational restrictions
imposed by the [7,5]-azabicyclic lactam moiety incorporated into daclatasvir
(1) and related HCV NS5A inhibitors. Unexpectedly, compound 5 was identified as a potent HCV genotype 1a and 1b inhibitor.
Molecular modeling of 5 bound to HCV genotype 1a suggested
that the use of the conformationally restricted lactam moiety might
have resulted in reorientation of its N-terminal carbamate to expose
a new interaction with the NS5A pocket located between amino acids
P97 and Y93, which was not easily accessible to 1. The
results also suggest new chemistry directions that exploit the interactions
with the P97–Y93 site toward new and potentially improved HCV
NS5A inhibitors.
Collapse
Affiliation(s)
- Wieslaw M. Kazmierski
- GlaxoSmithKline, 5 Moore Drive, Research Triangle Park, North Carolina 27709-3398, United States
| | - Nagaraju Miriyala
- GlaxoSmithKline, 5 Moore Drive, Research Triangle Park, North Carolina 27709-3398, United States
| | - David K. Johnson
- Computational Chemical Biology Core and Molecular Graphics and Modeling Laboratory, University of Kansas, Lawrence, Kansas 66047, United States
| | - Sam Baskaran
- GlaxoSmithKline, 5 Moore Drive, Research Triangle Park, North Carolina 27709-3398, United States
| |
Collapse
|
3
|
Caron G, Kihlberg J, Goetz G, Ratkova E, Poongavanam V, Ermondi G. Steering New Drug Discovery Campaigns: Permeability, Solubility, and Physicochemical Properties in the bRo5 Chemical Space. ACS Med Chem Lett 2021; 12:13-23. [PMID: 33488959 PMCID: PMC7812602 DOI: 10.1021/acsmedchemlett.0c00581] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
An increasing number of drug discovery programs concern compounds in the beyond rule of 5 (bRo5) chemical space, such as cyclic peptides, macrocycles, and degraders. Recent results show that common paradigms of property-based drug design need revision to be applied to larger and more flexible compounds. A virtual event entitled "Solubility, permeability and physico-chemical properties in the bRo5 chemical space" was organized to provide preliminary guidance on how to make the discovery of oral drugs in the bRo5 space more effective. The four speakers emphasized the importance of the bRo5 space as a source of new oral drugs and provided examples of experimental and computational methods specifically tailored for design and optimization in this chemical space.
Collapse
Affiliation(s)
- Giulia Caron
- Molecular
Biotechnology and Health Sciences Department, University of Torino, Via Quarello, 15, 10135 Torino, Italy
| | - Jan Kihlberg
- Department
of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Gilles Goetz
- Hit
Discovery and Optimization, Discovery Sciences, WWRD, Pfizer Inc, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ekaterina Ratkova
- Medicinal
Chemistry, Research and Early Development, Cardiovascular, Renal and
Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | | | - Giuseppe Ermondi
- Molecular
Biotechnology and Health Sciences Department, University of Torino, Via Quarello, 15, 10135 Torino, Italy
| |
Collapse
|
4
|
Sofia MJ. The Discovery and Development of Daclatasvir: An Inhibitor of the Hepatitis C Virus NS5A Replication Complex. ACTA ACUST UNITED AC 2019. [PMCID: PMC7122418 DOI: 10.1007/7355_2018_47] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
5
|
Russo G, Barbato F, Grumetto L, Philippe L, Lynen F, Goetz GH. Entry of therapeutics into the brain: Influence of exposed polarity calculated in silico and measured in vitro by supercritical fluid chromatography. Int J Pharm 2019; 560:294-305. [DOI: 10.1016/j.ijpharm.2019.02.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 01/18/2019] [Accepted: 02/08/2019] [Indexed: 12/23/2022]
|
6
|
Determining molecular properties with differential mobility spectrometry and machine learning. Nat Commun 2018; 9:5096. [PMID: 30504922 PMCID: PMC6269546 DOI: 10.1038/s41467-018-07616-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 11/06/2018] [Indexed: 01/30/2023] Open
Abstract
The fast and accurate determination of molecular properties is highly desirable for many facets of chemical research, particularly in drug discovery where pre-clinical assays play an important role in paring down large sets of drug candidates. Here, we present the use of supervised machine learning to treat differential mobility spectrometry - mass spectrometry data for ten topological classes of drug candidates. We demonstrate that the gas-phase clustering behavior probed in our experiments can be used to predict the candidates' condensed phase molecular properties, such as cell permeability, solubility, polar surface area, and water/octanol distribution coefficient. All of these measurements are performed in minutes and require mere nanograms of each drug examined. Moreover, by tuning gas temperature within the differential mobility spectrometer, one can fine tune the extent of ion-solvent clustering to separate subtly different molecular geometries and to discriminate molecules of very similar physicochemical properties.
Collapse
|
7
|
Young RJ, Leeson PD. Mapping the Efficiency and Physicochemical Trajectories of Successful Optimizations. J Med Chem 2018; 61:6421-6467. [DOI: 10.1021/acs.jmedchem.8b00180] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Robert J. Young
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Paul D. Leeson
- Paul Leeson Consulting Ltd., The Malt House, Main Street, Congerstone, Nuneaton, Warwickshire CV13 6LZ, U.K
| |
Collapse
|
8
|
DeGoey DA, Chen HJ, Cox PB, Wendt MD. Beyond the Rule of 5: Lessons Learned from AbbVie’s Drugs and Compound Collection. J Med Chem 2017; 61:2636-2651. [DOI: 10.1021/acs.jmedchem.7b00717] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- David A. DeGoey
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Hui-Ju Chen
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Philip B. Cox
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Michael D. Wendt
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| |
Collapse
|
9
|
Moore TO, Paradowski M, Ward SE. An atom-efficient and convergent approach to the preparation of NS5A inhibitors by C-H activation. Org Biomol Chem 2016; 14:3307-13. [PMID: 26936019 DOI: 10.1039/c6ob00340k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A novel approach of the convergent functionalisation of aryl dibromides to form NS5A type inhibitors using C-H activation is reported. The focus of investigation was to reduce the formation of homodimeric side product, as well as to investigate the scope of different aryl dibromides that were tolerated under the reaction conditions. The C-H activation methodology was found to give a viable synthetic route to NS5A inhibitors, with late stage functionalisation of the core portion of the molecule, albeit with some chemical functionalities not tolerated.
Collapse
Affiliation(s)
- Thomas O Moore
- Sussex Drug Discovery Centre, University of Sussex, Brighton, England BN1 9QJ, UK.
| | - Michael Paradowski
- Sussex Drug Discovery Centre, University of Sussex, Brighton, England BN1 9QJ, UK.
| | - Simon E Ward
- Sussex Drug Discovery Centre, University of Sussex, Brighton, England BN1 9QJ, UK.
| |
Collapse
|
10
|
Matsson P, Doak BC, Over B, Kihlberg J. Cell permeability beyond the rule of 5. Adv Drug Deliv Rev 2016; 101:42-61. [PMID: 27067608 DOI: 10.1016/j.addr.2016.03.013] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/25/2016] [Accepted: 03/31/2016] [Indexed: 11/17/2022]
Abstract
Drug discovery for difficult targets that have large and flat binding sites is often better suited to compounds beyond the "rule of 5" (bRo5). However, such compounds carry higher pharmacokinetic risks, such as low solubility and permeability, and increased efflux and metabolism. Interestingly, recent drug approvals and studies suggest that cell permeable and orally bioavailable drugs can be discovered far into bRo5 space. Tactics such as reduction or shielding of polarity by N-methylation, bulky side chains and intramolecular hydrogen bonds may be used to increase cell permeability in this space, but often results in decreased solubility. Conformationally flexible compounds can, however, combine high permeability and solubility, properties that are keys for cell permeability and intestinal absorption. Recent developments in computational conformational analysis will aid design of such compounds and hence prediction of cell permeability. Transporter mediated efflux occurs for most investigated drugs in bRo5 space, however it is commonly overcome by high local intestinal concentrations on oral administration. In contrast, there is little data to support significant impact of transporter-mediated intestinal absorption in bRo5 space. Current knowledge of compound properties that govern transporter effects of bRo5 drugs is limited and requires further fundamental and comprehensive studies.
Collapse
Affiliation(s)
- Pär Matsson
- Department of Pharmacy, BMC, Uppsala University, Box 580, SE-751 23 Uppsala, Sweden
| | - Bradley C Doak
- Department of Medicinal Chemistry, MIPS, Monash University, 381 Royal Parade, Parkville, Victoria, Australia
| | - Björn Over
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden.
| |
Collapse
|
11
|
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
| |
Collapse
|
12
|
Novel benzidine and diaminofluorene prolinamide derivatives as potent hepatitis C virus NS5A inhibitors. Eur J Med Chem 2015; 101:163-78. [PMID: 26134551 DOI: 10.1016/j.ejmech.2015.06.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 06/14/2015] [Accepted: 06/15/2015] [Indexed: 12/21/2022]
Abstract
Our study describes the discovery of a series of highly potent hepatitis C virus (HCV) NS5A inhibitors based on symmetrical prolinamide derivatives of benzidine and diaminofluorene. Through modification of benzidine, l-proline, and diaminofluorene derivatives, we developed novel inhibitor structures, which allowed us to establish a library of potent HCV NS5A inhibitors. After optimizing the benzidine prolinamide backbone, we identified inhibitors embedding meta-substituted benzidine core structures that exhibited the most potent anti-HCV activities. Furthermore, through a battery of studies including hERG ligand binding assay, CYP450 binding assay, rat plasma stability test, human liver microsomal stability test, and pharmacokinetic studies, the identified compounds 24, 26, 27, 42, and 43 are found to be nontoxic, and are expected to be effective therapeutic anti-HCV agents.
Collapse
|
13
|
Goetz GH, Philippe L, Shapiro MJ. EPSA: A Novel Supercritical Fluid Chromatography Technique Enabling the Design of Permeable Cyclic Peptides. ACS Med Chem Lett 2014; 5:1167-72. [PMID: 25313332 DOI: 10.1021/ml500239m] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 08/04/2014] [Indexed: 12/23/2022] Open
Abstract
Most peptides are generally insufficiently permeable to be used as oral drugs. Designing peptides with improved permeability without reliable permeability monitoring is a challenge. We have developed a supercritical fluid chromatography technique for peptides, termed EPSA, which is shown here to enable improved permeability design. Through assessing the exposed polarity of a peptide, this technique can be used as a permeability surrogate.
Collapse
Affiliation(s)
- Gilles H. Goetz
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Laurence Philippe
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Michael J. Shapiro
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States
| |
Collapse
|
14
|
Doak B, Over B, Giordanetto F, Kihlberg J. Oral Druggable Space beyond the Rule of 5: Insights from Drugs and Clinical Candidates. ACTA ACUST UNITED AC 2014; 21:1115-42. [DOI: 10.1016/j.chembiol.2014.08.013] [Citation(s) in RCA: 282] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|