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Marshall CM, Federice JG, Bell CN, Cox PB, Njardarson JT. An Update on the Nitrogen Heterocycle Compositions and Properties of U.S. FDA-Approved Pharmaceuticals (2013-2023). J Med Chem 2024. [PMID: 38995264 DOI: 10.1021/acs.jmedchem.4c01122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
This Perspective is a continuation of our analysis of U.S. FDA-approved small-molecule drugs (1938-2012) containing nitrogen heterocycles. In this study we report drug structure and property analyses of 321 unique new small-molecule drugs approved from January 2013 to December 2023 as well as information about frequency of important heteroatoms such as sulfur and fluorine and key small nitrogen substituents (CN and NO2). The most notable change is an incredible increase in drugs containing at least one nitrogen heterocycle─82%, compared to 59% from preceding decades─as well as a significant increase in the number of nitrogen heterocycles per drug. Pyridine has claimed the #1 high-frequency nitrogen heterocycle occurrence spot from piperidine (#2), with pyrimidine (#5), pyrazole (#6), and morpholine (#9) being the big top 10 climbers. Also notable is high number of fused nitrogen heterocycles, apparently driven largely by newly approved cancer drugs.
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Affiliation(s)
- Christopher M Marshall
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - John G Federice
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Chloe N Bell
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Philip B Cox
- Discovery Research, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Jon T Njardarson
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
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2
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Heinzke AL, Pahl A, Zdrazil B, Leach AR, Waldmann H, Young RJ, Leeson PD. Occurrence of "Natural Selection" in Successful Small Molecule Drug Discovery. J Med Chem 2024; 67:11226-11241. [PMID: 38949112 PMCID: PMC11247505 DOI: 10.1021/acs.jmedchem.4c00811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/08/2024] [Accepted: 06/13/2024] [Indexed: 07/02/2024]
Abstract
Published compounds from ChEMBL version 32 are used to seek evidence for the occurrence of "natural selection" in drug discovery. Three measures of natural product (NP) character were applied, to compare time- and target-matched compounds reaching the clinic (clinical compounds in phase 1-3 development and approved drugs) with background compounds (reference compounds). Pseudo-NPs (PNPs), containing NP fragments combined in ways inaccessible by nature, are increasing over time, reaching 67% of clinical compounds first disclosed since 2010. PNPs are 54% more likely to be found in post-2008 clinical versus reference compounds. The majority of target classes show increased clinical compound NP character versus their reference compounds. Only 176 NP fragments appear in >1000 clinical compounds published since 2008, yet these make up on average 63% of the clinical compound's core scaffolds. There is untapped potential awaiting exploitation, by applying nature's building blocks─"natural intelligence"─to drug design.
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Affiliation(s)
- A. Lina Heinzke
- European
Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Genome Campus, Hinxton CB10 1SD, Cambridgeshire, U.K.
| | - Axel Pahl
- Compound
Management and Screening Center, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Barbara Zdrazil
- European
Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Genome Campus, Hinxton CB10 1SD, Cambridgeshire, U.K.
| | - Andrew R. Leach
- European
Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Genome Campus, Hinxton CB10 1SD, Cambridgeshire, U.K.
| | - Herbert Waldmann
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
- Faculty
of Chemistry and Chemical Biology, Technical
University Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | | | - Paul D. Leeson
- Paul Leeson
Consulting Ltd., Nuneaton CV13 6LZ, Warwickshire, U.K.
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3
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Pennington LD, Hesse MJ, Koester DC, McAtee RC, Qunies AM, Hu DX. Property-Based Drug Design Merits a Nobel Prize. J Med Chem 2024. [PMID: 38940466 DOI: 10.1021/acs.jmedchem.4c01345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Affiliation(s)
| | | | | | - Rory C McAtee
- Drug Hunter, Happy Valley, Oregon 97086, United States
| | | | - Dennis X Hu
- Drug Hunter, Happy Valley, Oregon 97086, United States
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4
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Hirst DJ, Bamborough P, Al-Mahdi N, Angell DC, Barnett HA, Baxter A, Bit RA, Brown JA, Chung CW, Craggs PD, Davis RP, Demont EH, Ferrie A, Gordon LJ, Harada I, Ho TCT, Holyer ID, Hooper-Greenhill E, Jones KL, Lindon MJ, Lovatt C, Lugo D, Maller C, McGonagle G, Messenger C, Mitchell DJ, Pascoe DD, Patel VK, Patten C, Poole DL, Shah RR, Rioja I, Stafford KAJ, Tape D, Taylor S, Theodoulou NH, Tomlinson L, Wall ID, Wellaway CR, White G, Prinjha RK, Humphreys PG. Structure- and Property-Based Optimization of Efficient Pan-Bromodomain and Extra Terminal Inhibitors to Identify Oral and Intravenous Candidate I-BET787. J Med Chem 2024; 67:10464-10489. [PMID: 38866424 DOI: 10.1021/acs.jmedchem.4c00959] [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 bromodomain and extra terminal (BET) family of bromodomain-containing proteins are important epigenetic regulators that elicit their effect through binding histone tail N-acetyl lysine (KAc) post-translational modifications. Recognition of such markers has been implicated in a range of oncology and immune diseases and, as such, small-molecule inhibition of the BET family bromodomain-KAc protein-protein interaction has received significant interest as a therapeutic strategy, with several potential medicines under clinical evaluation. This work describes the structure- and property-based optimization of a ligand and lipophilic efficient pan-BET bromodomain inhibitor series to deliver candidate I-BET787 (70) that demonstrates efficacy in a mouse model of inflammation and suitable properties for both oral and intravenous (IV) administration. This focused two-phase explore-exploit medicinal chemistry effort delivered the candidate molecule in 3 months with less than 100 final compounds synthesized.
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Affiliation(s)
- David J Hirst
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Paul Bamborough
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Niam Al-Mahdi
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Davina C Angell
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Heather A Barnett
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Andrew Baxter
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Rino A Bit
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Jack A Brown
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Chun-Wa Chung
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Peter D Craggs
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Robert P Davis
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Emmanuel H Demont
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Alan Ferrie
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Laurie J Gordon
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Isobel Harada
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Tim C T Ho
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Ian D Holyer
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | - Katherine L Jones
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Matthew J Lindon
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Cerys Lovatt
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - David Lugo
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Claire Maller
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Grant McGonagle
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Cassie Messenger
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Darren J Mitchell
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - David D Pascoe
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | | | - Darren L Poole
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Rishi R Shah
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Inmaculada Rioja
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | - Daniel Tape
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Simon Taylor
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | - Laura Tomlinson
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Ian D Wall
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | - Gemma White
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Rab K Prinjha
- GSK Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
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Gallego RA, Edwards MP, Montgomery TP. An update on lipophilic efficiency as an important metric in drug design. Expert Opin Drug Discov 2024:1-15. [PMID: 38919130 DOI: 10.1080/17460441.2024.2368744] [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: 05/10/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024]
Abstract
INTRODUCTION Lipophilic efficiency (LipE) and lipophilic metabolic efficiency (LipMetE) are valuable tools that can be utilized as part of a multiparameter optimization process to advance a hit to a clinical quality compound. AREAS COVERED This review covers recent, effective use cases of LipE and LipMetE that have been published in the literature over the past 5 years. These use cases resulted in the delivery of high-quality molecules that were brought forward to in vivo work and/or to clinical studies. The authors discuss best-practices for using LipE and LipMetE analysis, combined with lipophilicity-focused compound design strategies, to increase the speed and effectiveness of the hit to clinical quality compound optimization process. EXPERT OPINION It has become well established that increasing LipE and LipMetE within a series of analogs facilitates the improvement of broad selectivity, clearance, solubility, and permeability and, through this optimization, also facilitates the achievement of desired pharmacokinetic properties, efficacy, and tolerability. Within this article, we discuss lipophilic efficiency-focused optimization as a tool to yield high-quality potential clinical candidates. It is suggested that LipE/LipMetE-focused optimization can facilitate and accelerate the drug-discovery process.
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Adessi TG, Wagner PM, Bisogno FR, Nicotra VE, Guido ME, García ME. Enhancing structural diversity through chemical engineering of Ambrosia tenuifolia extract for novel anti-glioblastoma compounds. Sci Rep 2024; 14:14229. [PMID: 38902325 PMCID: PMC11190268 DOI: 10.1038/s41598-024-63639-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 05/30/2024] [Indexed: 06/22/2024] Open
Abstract
Natural products are an unsurpassed source of leading structures in drug discovery. The biosynthetic machinery of the producing organism offers an important source for modifying complex natural products, leading to analogs that are unattainable by chemical semisynthesis or total synthesis. In this report, through the combination of natural products chemistry and diversity-oriented synthesis, a diversity-enhanced extracts approach is proposed using chemical reactions that remodel molecular scaffolds directly on extracts of natural resources. This method was applied to subextract enriched in sesquiterpene lactones from Ambrosia tenuifolia (Fam. Asteraceae) using acid media conditions (p-toluenesulfonic acid) to change molecular skeletons. The chemically modified extract was then fractionated by a bioguided approach to obtain the pure compounds responsible for the anti-glioblastoma (GBM) activity in T98G cell cultures. Indeed, with the best candidate, chronobiological experiments were performed to evaluate temporal susceptibility to the treatment on GBM cell cultures to define the best time to apply the therapy. Finally, bioinformatics tools were used to supply qualitative and quantitative information on the physicochemical properties, chemical space, and structural similarity of the compound library obtained. As a result, natural products derivatives containing new molecular skeletons were obtained, with possible applications as chemotherapeutic agents against human GBM T98G cell cultures.
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Affiliation(s)
- Tonino G Adessi
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Edificio de Ciencias Químicas 2, Haya de la Torre y Medina Allende, Ciudad Universitaria, CP X5000HUA, Córdoba, Argentina
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Paula M Wagner
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Edificio de Ciencias Químicas 2, Haya de la Torre y Medina Allende, Ciudad Universitaria, CP X5000HUA, Córdoba, Argentina
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC-CONICET), Córdoba, Argentina
| | - Fabricio R Bisogno
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Edificio de Ciencias Químicas 2, Haya de la Torre y Medina Allende, Ciudad Universitaria, CP X5000HUA, Córdoba, Argentina
- Instituto de Investigaciones en Físico-Química de Córdoba (INFIQC-CONICET), Córdoba, Argentina
| | - Viviana E Nicotra
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Edificio de Ciencias Químicas 2, Haya de la Torre y Medina Allende, Ciudad Universitaria, CP X5000HUA, Córdoba, Argentina
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Mario E Guido
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Edificio de Ciencias Químicas 2, Haya de la Torre y Medina Allende, Ciudad Universitaria, CP X5000HUA, Córdoba, Argentina
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC-CONICET), Córdoba, Argentina
| | - Manuela E García
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Edificio de Ciencias Químicas 2, Haya de la Torre y Medina Allende, Ciudad Universitaria, CP X5000HUA, Córdoba, Argentina.
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina.
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7
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Lanne A, Bardelle C, Davies G, Turberville A, Semple H, Moore R, Holdgate GA. POLARISED views and FRETting about probe modulation assays: Learning from High Throughput Screening. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100156. [PMID: 38642710 DOI: 10.1016/j.slasd.2024.100156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/28/2024] [Accepted: 04/14/2024] [Indexed: 04/22/2024]
Abstract
Fluorescent probe modulation assays are a widely used approach to monitor displacement or stabilisation of fluorescently labelled tool ligands by test compounds. These assays allow an optical read-out of probe-receptor binding and can be used to detect compounds that compete with the labelled ligand, either directly or indirectly. Probes for both orthosteric and allosteric sites are often employed. The method can also be used to identify test compounds that may stabilise the ternary complex, offering an opportunity to discover novel molecular glues. The utility of these fluorescence-based assays within high-throughput screening has been facilitated by the use of streptavidin labelled terbium as a donor and access to a range of different acceptor fluorophores. During 2023, the High-throughput Screening group at AstraZeneca carried out 8 high-throughput screens using these approaches. In this manuscript we will present the types of assays used, an overview of the timelines for assay development and screening, the application of orthogonal artefact methods to aid hit finding and the results of the screens in terms of hit rate and the number of compounds identified with IC50 values of better than 30 µM. Learning across the development, execution and analysis of these screens will be presented.
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Affiliation(s)
- Alice Lanne
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Catherine Bardelle
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, Macclesfield, UK
| | - Gareth Davies
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, Macclesfield, UK
| | | | - Hannah Semple
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Rachel Moore
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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8
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Daina A, Zoete V. Testing the predictive power of reverse screening to infer drug targets, with the help of machine learning. Commun Chem 2024; 7:105. [PMID: 38724725 PMCID: PMC11082207 DOI: 10.1038/s42004-024-01179-2] [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: 04/06/2023] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
Estimating protein targets of compounds based on the similarity principle-similar molecules are likely to show comparable bioactivity-is a long-standing strategy in drug research. Having previously quantified this principle, we present here a large-scale evaluation of its predictive power for inferring macromolecular targets by reverse screening an unprecedented vast external test set of more than 300,000 active small molecules against another bioactivity set of more than 500,000 compounds. We show that machine-learning can predict the correct targets, with the highest probability among 2069 proteins, for more than 51% of the external molecules. The strong enrichment thus obtained demonstrates its usefulness in supporting phenotypic screens, polypharmacology, or repurposing. Moreover, we quantified the impact of the bioactivity knowledge available for proteins in terms of number and diversity of actives. Finally, we advise that developers of such approaches follow an application-oriented benchmarking strategy and use large, high-quality, non-overlapping datasets as provided here.
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Affiliation(s)
- Antoine Daina
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland
| | - Vincent Zoete
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland.
- Computer-Aided Molecular Engineering, Department of Oncology UNIL-CHUV, Ludwig Institute for Cancer Research Lausanne Branch, University of Lausanne, Lausanne, Switzerland.
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9
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Sinha P, Yadav AK. Unraveling the anti-breast cancer activity of Cimicifugae rhizoma using biological network pathways and molecular dynamics simulation. Mol Divers 2024:10.1007/s11030-024-10847-3. [PMID: 38615110 DOI: 10.1007/s11030-024-10847-3] [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: 02/06/2024] [Accepted: 03/12/2024] [Indexed: 04/15/2024]
Abstract
Cimicifugae is a commonly used treatment for breast cancer, but the specific molecular mechanisms underlying its effectiveness remain unclear. In this research, we employ a combination of network pharmacology, molecular docking, and molecular dynamics simulations to uncover the most potent phytochemical within Cimicifugae rhizoma in order to delve into its interaction with the target protein in breast cancer treatment. We identified 18 active compounds and 89 associated targets, primarily associated to various biological processes such as lipid metabolism, the signaling pathway in diabetes, viral infections, and cancer-related pathways. Molecular docking analysis revealed that the two most active compounds, Formononetin and Cimigenol, exhibit strong binding to the target protein AKT1. Through molecular dynamics simulations, we found that the Cimigenol-AKT1 complex exhibits greater structural stability and lower interaction energy compared to the stigmasterol-AKT1 complex. Our study demonstrates that Cimicifugae rhizoma exerts its effects in breast cancer treatment through a multi-component, multi-target synergistic approach. Furthermore, we propose that Cimigenol, targeting AKT-1, represents the most effective compound, offering valuable insights into the molecular mechanisms underpinning its role in breast cancer therapy.
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Affiliation(s)
- Prashasti Sinha
- Department of Physics, School of Physical & Decision Science, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, 226025, India
| | - Anil Kumar Yadav
- Department of Physics, School of Physical & Decision Science, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, 226025, India.
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10
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Le Roch M, Renault J, Argouarch G, Lenci E, Trabocchi A, Roisnel T, Gouault N, Lalli C. Synthesis and Chemoinformatic Analysis of Fluorinated Piperidines as 3D Fragments for Fragment-Based Drug Discovery. J Org Chem 2024; 89:4932-4946. [PMID: 38451837 DOI: 10.1021/acs.joc.4c00143] [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: 03/09/2024]
Abstract
The concise synthesis of a small library of fluorinated piperidines from readily available dihydropyridinone derivatives has been described. The effect of the fluorination on different positions has then been evaluated by chemoinformatic tools. In particular, the compounds' pKa's have been calculated, revealing that the fluorine atoms notably lowered their basicity, which is correlated to the affinity for hERG channels resulting in cardiac toxicity. The "lead-likeness" and three-dimensionality have also been evaluated to assess their ability as useful fragments for drug design. A random screening on a panel of representative proteolytic enzymes was then carried out and revealed that one scaffold is recognized by the catalytic pocket of 3CLPro (main protease of SARS-CoV-2 coronavirus).
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Affiliation(s)
- Myriam Le Roch
- Univ Rennes, CNRS, ISCR-UMR 6226, Rennes F-35000, France
| | | | | | - Elena Lenci
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, Sesto Fiorentino, Florence 50019, Italy
| | - Andrea Trabocchi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, Sesto Fiorentino, Florence 50019, Italy
| | - Thierry Roisnel
- Univ Rennes, Centre de Diffractométrie X (CDIFX), ISCR-UMR 6226, Rennes F-35000, France
| | | | - Claudia Lalli
- Univ Rennes, CNRS, ISCR-UMR 6226, Rennes F-35000, France
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11
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Raghu MS, Yogesh Kumar K, Shamala T, Alharti FA, Prashanth MK, Jeon BH. Synthesis, antitubercular profile and molecular docking studies of quinazolinone-based pyridine derivatives against drug-resistant tuberculosis. J Biomol Struct Dyn 2024; 42:3307-3317. [PMID: 37261798 DOI: 10.1080/07391102.2023.2217928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/03/2023] [Indexed: 06/02/2023]
Abstract
The promising quinazolinone-based pyridine derivatives (4a-j) were synthesized and subsequently tested for their antimycobacterial activities against the various drug-sensitive and drug-resistant Mycobacterium tuberculosis (Mtb) strains to combat infectious diseases and address growing concerns about the devastating effects of tuberculosis (TB). Utilizing 1H NMR, 13C NMR, and mass spectra, the structural and molecular confirmation of the synthesized compounds were deciphered. With minimum inhibitory concentration (MIC) values ranging from 0.31 to 19.13 μM, the results showed that compounds 4e and 4f showed promise anti-TB action against both drug-sensitive and drug-resistant TB strains. To study the cytotoxicity of synthesized molecules, normal Vero and mouse macrophage (RAW264.7) cell lines were utilized. Remarkably, it was revealed that at the highest concentration tested, none of the newly synthesized molecules were toxic to the Vero cell line. The binding patterns of the potent compounds 4b, 4e and 4f in the active site of the mycobacterial membrane protein Large 3 (MmpL3) protein are also revealed by molecular docking studies, which has contributed to the development of a structural rationale for Mtb inhibition. The physicochemical characteristics of the compounds were then predicted using theoretical calculations. Overall, the molecular docking results, physiochemical properties, and observed antimycobacterial activity all point to compound 4e with trifluoromethyl and compound 4f with nitro moiety as potential quinazolinone linked pyridine-based MmpL3 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- M S Raghu
- Department of Chemistry, New Horizon College of Engineering, Bengaluru, India
| | - K Yogesh Kumar
- Department of Chemistry, Faculty of Engineering and Technology, Jain University, Ramanagara, India
| | - T Shamala
- Department of Chemistry, B N M Institute of Technology, Bengaluru, India
| | - Fahad A Alharti
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - M K Prashanth
- Department of Chemistry, B N M Institute of Technology, Bengaluru, India
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul, Republic of Korea
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12
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Toscano G, Höfurthner T, Nagl B, Beier A, Mayer M, Geist L, McConnell DB, Weinstabl H, Konrat R, Lichtenecker RJ. 13 Cβ-Valine and 13 Cγ-Leucine Methine Labeling To Probe Protein Ligand Interaction. Chembiochem 2024; 25:e202300762. [PMID: 38294275 DOI: 10.1002/cbic.202300762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/01/2024]
Abstract
Precise information regarding the interaction between proteins and ligands at molecular resolution is crucial for effectively guiding the optimization process from initial hits to lead compounds in early stages of drug development. In this study, we introduce a novel aliphatic side chain isotope-labeling scheme to directly probe interactions between ligands and aliphatic sidechains using NMR techniques. To demonstrate the applicability of this method, we selected a set of Brd4-BD1 binders and analyzed 1 H chemical shift perturbation resulting from CH-π interaction of Hβ -Val and Hγ -Leu as CH donors with corresponding ligand aromatic moieties as π acceptors.
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Affiliation(s)
- Giorgia Toscano
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Institute of Organic Chemistry, University of Vienna, Währingerstraße 38, 1090, Vienna, Austria
- Vienna Doctoral School of Chemistry, University of Vienna, Währingerstr. 38, 1090, Vienna, Austria
| | - Theresa Höfurthner
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Max Perutz Laboratories, Department of Structural and Computational Biology, Campus Vienna Biocenter 5, 1030, Vienna, Austria
- Vienna Doctoral School of Chemistry, University of Vienna, Währingerstr. 38, 1090, Vienna, Austria
| | - Benjamin Nagl
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Institute of Organic Chemistry, University of Vienna, Währingerstraße 38, 1090, Vienna, Austria
| | - Andreas Beier
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Max Perutz Laboratories, Department of Structural and Computational Biology, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer, Gasse 5-Wien, 11, 1121, Vienna
| | - Leonhard Geist
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer, Gasse 5-Wien, 11, 1121, Vienna
| | - Darryl B McConnell
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer, Gasse 5-Wien, 11, 1121, Vienna
| | - Harald Weinstabl
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer, Gasse 5-Wien, 11, 1121, Vienna
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Max Perutz Laboratories, Department of Structural and Computational Biology, Campus Vienna Biocenter 5, 1030, Vienna, Austria
- MAG-LAB, Karl-Farkas Gasse 22, 1030, Vienna
| | - Roman J Lichtenecker
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Institute of Organic Chemistry, University of Vienna, Währingerstraße 38, 1090, Vienna, Austria
- MAG-LAB, Karl-Farkas Gasse 22, 1030, Vienna
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13
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Reese TC, Devineni A, Smith T, Lalami I, Ahn JM, Raj GV. Evaluating physiochemical properties of FDA-approved orally administered drugs. Expert Opin Drug Discov 2024; 19:225-238. [PMID: 37921049 DOI: 10.1080/17460441.2023.2275617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023]
Abstract
INTRODUCTION Analyses of orally administered FDA-approved drugs from 1990 to 1993 enabled the identification of a set of physiochemical properties known as Lipinski's Rule of Five (Ro5). The original Ro5 and extended versions still remain the reference criteria for drug development programs. Since many bioactive compounds do not conform to the Ro5, we validated the relevance of and adherence to these rulesets in a contemporary cohort of FDA-approved drugs. AREAS COVERED The authors noted that a significant proportion of FDA-approved orally administered parent compounds from 2011 to 2022 deviate from the original Ro5 criteria (~38%) or the Ro5 with extensions (~53%). They then evaluated if a contemporary Ro5 criteria (cRo5) could be devised to better predict oral bioavailability. Furthermore, they discuss many case studies showcasing the need for and benefit of increasing the size of certain compounds and cover several evolving strategies for improving oral bioavailability. EXPERT OPINION Despite many revisions to the Ro5, the authors find that no single proposed physiochemical rule has universal concordance with absolute oral bioavailability. Innovations in drug delivery and formulation have dramatically expanded the range of physicochemical properties and the chemical diversity for oral administration.
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Affiliation(s)
- Tanner C Reese
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, USA
| | - Anvita Devineni
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, USA
| | - Tristan Smith
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, USA
| | - Ismail Lalami
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, USA
| | - Jung-Mo Ahn
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, USA
| | - Ganesh V Raj
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, USA
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14
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Roskoski R. Properties of FDA-approved small molecule protein kinase inhibitors: A 2024 update. Pharmacol Res 2024; 200:107059. [PMID: 38216005 DOI: 10.1016/j.phrs.2024.107059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/14/2024]
Abstract
Owing to the dysregulation of protein kinase activity in many diseases including cancer, this enzyme family has become one of the most important drug targets in the 21st century. There are 80 FDA-approved therapeutic agents that target about two dozen different protein kinases and seven of these drugs were approved in 2023. Of the approved drugs, thirteen target protein-serine/threonine protein kinases, four are directed against dual specificity protein kinases (MEK1/2), twenty block nonreceptor protein-tyrosine kinases, and 43 inhibit receptor protein-tyrosine kinases. The data indicate that 69 of these drugs are prescribed for the treatment of neoplasms. Six drugs (abrocitinib, baricitinib, deucravacitinib, ritlecitinib, tofacitinib, upadacitinib) are used for the treatment of inflammatory diseases (atopic dermatitis, rheumatoid arthritis, psoriasis, alopecia areata, and ulcerative colitis). Of the 80 approved drugs, nearly two dozen are used in the treatment of multiple diseases. The following seven drugs received FDA approval in 2023: capivasertib (HER2-positive breast cancer), fruquintinib (metastatic colorectal cancer), momelotinib (myelofibrosis), pirtobrutinib (mantle cell lymphoma, chronic lymphocytic leukemia, small lymphocytic lymphoma), quizartinib (Flt3-mutant acute myelogenous leukemia), repotrectinib (ROS1-positive lung cancer), and ritlecitinib (alopecia areata). All of the FDA-approved drugs are orally effective with the exception of netarsudil, temsirolimus, and trilaciclib. This review summarizes the physicochemical properties of all 80 FDA-approved small molecule protein kinase inhibitors including the molecular weight, number of hydrogen bond donors/acceptors, polar surface area, potency, solubility, lipophilic efficiency, and ligand efficiency.
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Affiliation(s)
- Robert Roskoski
- Blue Ridge Institute for Medical Research, 221 Haywood Knolls Drive, Hendersonville, NC 28791, United States.
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15
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Takarada JE, Cunha MR, Almeida VM, Vasconcelos SNS, Santiago AS, Godoi PH, Salmazo A, Ramos PZ, Fala AM, de Souza LR, Da Silva IEP, Bengtson MH, Massirer KB, Couñago RM. Discovery of pyrazolo[3,4-d]pyrimidines as novel mitogen-activated protein kinase kinase 3 (MKK3) inhibitors. Bioorg Med Chem 2024; 98:117561. [PMID: 38157838 DOI: 10.1016/j.bmc.2023.117561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/06/2023] [Accepted: 12/17/2023] [Indexed: 01/03/2024]
Abstract
The dual-specificity protein kinase MKK3 has been implicated in tumor cell proliferation and survival, yet its precise role in cancer remains inconclusive. A critical step in elucidating the kinase's involvement in disease biology is the identification of potent, cell-permeable kinase inhibitors. Presently, MKK3 lacks a dedicated tool compound for these purposes, along with validated methods for the facile screening, identification, and optimization of inhibitors. In this study, we have developed a TR-FRET-based enzymatic assay for the detection of MKK3 activity in vitro and a BRET-based assay to assess ligand binding to this enzyme within intact human cells. These assays were instrumental in identifying hit compounds against MKK3 that share a common chemical scaffold, sourced from a library of bioactive kinase inhibitors. Initial hits were subsequently expanded through the synthesis of novel analogs. The resulting structure-activity relationship (SAR) was rationalized using molecular dynamics simulations against a homology model of MKK3. We expect our findings to expedite the development of novel, potent, selective, and bioactive inhibitors, thus facilitating investigations into MKK3's role in various cancers.
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Affiliation(s)
- Jéssica E Takarada
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Micael R Cunha
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Vitor M Almeida
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Stanley N S Vasconcelos
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - André S Santiago
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Paulo H Godoi
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Anita Salmazo
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Priscila Z Ramos
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Angela M Fala
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Lucas R de Souza
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Italo E P Da Silva
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil; Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Mario H Bengtson
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil; Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Katlin B Massirer
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Rafael M Couñago
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil; Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, United States.
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16
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Wang P, Raja A, Luscombe VB, Bataille CJR, Lucy D, Rogga VV, Greaves DR, Russell AJ. Development of Highly Potent, G-Protein Pathway Biased, Selective, and Orally Bioavailable GPR84 Agonists. J Med Chem 2024; 67:110-137. [PMID: 38146625 PMCID: PMC10788923 DOI: 10.1021/acs.jmedchem.3c00951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 11/06/2023] [Accepted: 11/20/2023] [Indexed: 12/27/2023]
Abstract
Orphan G-protein-coupled receptor 84 (GPR84) is a receptor that has been linked to cancer, inflammatory, and fibrotic diseases. We have reported DL-175 as a biased agonist at GPR84 which showed differential signaling via Gαi/cAMP and β-arrestin, but which is rapidly metabolized. Herein, we describe an optimization of DL-175 through a systematic structure-activity relationship (SAR) analysis. This reveals that the replacement of the naphthalene group improved metabolic stability and the addition of a 5-hydroxy substituent to the pyridine N-oxide group, yielding compounds 68 (OX04528) and 69 (OX04529), enhanced the potency for cAMP signaling by 3 orders of magnitude to low picomolar values. Neither compound showed detectable effects on β-arrestin recruitment up to 80 μM. Thus, the new GPR84 agonists 68 and 69 displayed excellent potency, high G-protein signaling bias, and an appropriate in vivo pharmacokinetic profile that will allow investigation of GPR84 biased agonist activity in vivo.
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Affiliation(s)
- Pinqi Wang
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
- Department
of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K.
| | - Arun Raja
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
- Department
of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K.
| | - Vincent B. Luscombe
- Sir
William Dunn School of Pathology, University
of Oxford, South Parks Road, Oxford OX1 3RE, U.K.
| | - Carole J. R. Bataille
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
- Department
of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K.
| | - Daniel Lucy
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
- Sir
William Dunn School of Pathology, University
of Oxford, South Parks Road, Oxford OX1 3RE, U.K.
| | - Vanessa V. Rogga
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - David R. Greaves
- Sir
William Dunn School of Pathology, University
of Oxford, South Parks Road, Oxford OX1 3RE, U.K.
| | - Angela J. Russell
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
- Department
of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K.
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17
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Zdrazil B, Felix E, Hunter F, Manners EJ, Blackshaw J, Corbett S, de Veij M, Ioannidis H, Lopez DM, Mosquera J, Magarinos M, Bosc N, Arcila R, Kizilören T, Gaulton A, Bento A, Adasme M, Monecke P, Landrum G, Leach A. The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods. Nucleic Acids Res 2024; 52:D1180-D1192. [PMID: 37933841 PMCID: PMC10767899 DOI: 10.1093/nar/gkad1004] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/09/2023] [Accepted: 10/23/2023] [Indexed: 11/08/2023] Open
Abstract
ChEMBL (https://www.ebi.ac.uk/chembl/) is a manually curated, high-quality, large-scale, open, FAIR and Global Core Biodata Resource of bioactive molecules with drug-like properties, previously described in the 2012, 2014, 2017 and 2019 Nucleic Acids Research Database Issues. Since its introduction in 2009, ChEMBL's content has changed dramatically in size and diversity of data types. Through incorporation of multiple new datasets from depositors since the 2019 update, ChEMBL now contains slightly more bioactivity data from deposited data vs data extracted from literature. In collaboration with the EUbOPEN consortium, chemical probe data is now regularly deposited into ChEMBL. Release 27 made curated data available for compounds screened for potential anti-SARS-CoV-2 activity from several large-scale drug repurposing screens. In addition, new patent bioactivity data have been added to the latest ChEMBL releases, and various new features have been incorporated, including a Natural Product likeness score, updated flags for Natural Products, a new flag for Chemical Probes, and the initial annotation of the action type for ∼270 000 bioactivity measurements.
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Affiliation(s)
- Barbara Zdrazil
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Eloy Felix
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Fiona Hunter
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Emma J Manners
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - James Blackshaw
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Sybilla Corbett
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Marleen de Veij
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Harris Ioannidis
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - David Mendez Lopez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Juan F Mosquera
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Maria Paula Magarinos
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Nicolas Bosc
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Ricardo Arcila
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Tevfik Kizilören
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Anna Gaulton
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - A Patrícia Bento
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Melissa F Adasme
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Peter Monecke
- Sanofi, R&D, Preclinical Safety, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Gregory A Landrum
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Andrew R Leach
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
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18
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Choi K. The Structure-property Relationships of Clinically Approved Protease Inhibitors. Curr Med Chem 2024; 31:1441-1463. [PMID: 37031455 DOI: 10.2174/0929867330666230409232655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 01/17/2023] [Accepted: 02/24/2023] [Indexed: 04/11/2023]
Abstract
BACKGROUND Proteases play important roles in the regulation of many physiological processes, and protease inhibitors have become one of the important drug classes. Especially because the development of protease inhibitors often starts from a substrate- based peptidomimetic strategy, many of the initial lead compounds suffer from pharmacokinetic liabilities. OBJECTIVE To reduce drug attrition rates, drug metabolism and pharmacokinetics studies are fully integrated into modern drug discovery research, and the structure-property relationship illustrates how the modification of the chemical structure influences the pharmacokinetic and toxicological properties of drug compounds. Understanding the structure- property relationships of clinically approved protease inhibitor drugs and their analogues could provide useful information on the lead-to-candidate optimization strategies. METHODS About 70 inhibitors against human or pathogenic viral proteases have been approved until the end of 2021. In this review, 17 inhibitors are chosen for the structure- property relationship analysis because detailed pharmacological and/or physicochemical data have been disclosed in the medicinal chemistry literature for these inhibitors and their close analogues. RESULTS The compiled data are analyzed primarily focusing on the pharmacokinetic or toxicological deficiencies found in lead compounds and the structural modification strategies used to generate candidate compounds. CONCLUSION The structure-property relationships hereby summarized how the overall druglike properties could be successfully improved by modifying the structure of protease inhibitors. These specific examples are expected to serve as useful references and guidance for developing new protease inhibitor drugs in the future.
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Affiliation(s)
- Kihang Choi
- Department of Chemistry, Korea University, Seoul, 02841, Korea (ROK)
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19
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Tautermann CS, Borghardt JM, Pfau R, Zentgraf M, Weskamp N, Sauer A. Towards holistic Compound Quality Scores: Extending ligand efficiency indices with compound pharmacokinetic characteristics. Drug Discov Today 2023; 28:103758. [PMID: 37660984 DOI: 10.1016/j.drudis.2023.103758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/17/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023]
Abstract
The suitability of small molecules as oral drugs is often assessed by simple physicochemical rules, the application of ligand efficiency scores or by composite scores based on physicochemical compound properties. These rules and scores are empirical and typically lack mechanistic background, such as information on pharmacokinetics (PK). We introduce new types of Compound Quality Scores (CQS, specifically called dose scores and cmax scores), which explicitly include predicted or, when available, experimental PK parameters and combine these with on-target potency. These CQS scores are surrogates for an estimated dose and corresponding cmax and allow prioritizing of compounds within test cascades as well as before synthesis. We demonstrate the complementarity and, in most cases, superior performance relative to existing efficiency metrics by project examples.
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Affiliation(s)
- Christofer S Tautermann
- Boehringer Ingelheim Pharma GmbH & Co. KG, Medicinal Chemistry, Birkendorfer Strasse 65, Biberach 88397, Germany; Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck 6020, Austria.
| | - Jens M Borghardt
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Strasse 65, Biberach 88397, Germany.
| | - Roland Pfau
- Boehringer Ingelheim Pharma GmbH & Co. KG, Medicinal Chemistry, Birkendorfer Strasse 65, Biberach 88397, Germany; Boehringer Ingelheim Pharma GmbH & Co. KG, CNS Research, Birkendorfer Strasse 65, Biberach 88397, Germany.
| | - Matthias Zentgraf
- Boehringer Ingelheim Pharma GmbH & Co. KG, Discovery Research Coordination Germany, Birkendorfer Strasse 65, Biberach 88397, Germany.
| | - Nils Weskamp
- Boehringer Ingelheim Pharma GmbH & Co. KG, Medicinal Chemistry, Birkendorfer Strasse 65, Biberach 88397, Germany.
| | - Achim Sauer
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Strasse 65, Biberach 88397, Germany.
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20
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Maus H, Müller P, Meta M, Hoba SN, Hammerschmidt SJ, Zimmermann RA, Zimmer C, Fuchs N, Schirmeister T, Barthels F. Next Generation of Fluorometric Protease Assays: 7-Nitrobenz-2-oxa-1,3-diazol-4-yl-amides (NBD-Amides) as Class-Spanning Protease Substrates. Chemistry 2023; 29:e202301855. [PMID: 37313627 DOI: 10.1002/chem.202301855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/15/2023]
Abstract
Fluorometric assays are one of the most frequently used methods in medicinal chemistry. Over the last 50 years, the reporter molecules for the detection of protease activity have evolved from first-generation colorimetric p-nitroanilides, through FRET substrates, and 7-amino-4-methyl coumarin (AMC)-based substrates. The aim of further substrate development is to increase sensitivity and reduce vulnerability to assay interferences. Herein, we describe a new generation of substrates for protease assays based on 7-nitrobenz-2-oxa-1,3-diazol-4-yl-amides (NBD-amides). In this study, we synthesized and tested substrates for 10 different proteases from the serine-, cysteine-, and metalloprotease classes. Enzyme- and substrate-specific parameters as well as the inhibitory activity of literature-known inhibitors confirmed their suitability for application in fluorometric assays. Hence, we were able to present NBD-based alternatives for common protease substrates. In conclusion, these NBD substrates are not only less susceptible to common assay interference, but they are also able to replace FRET-based substrates with the requirement of a prime site amino acid residue.
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Affiliation(s)
- Hannah Maus
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Patrick Müller
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Mergim Meta
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Sabrina N Hoba
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Stefan J Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Collin Zimmer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Natalie Fuchs
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Fabian Barthels
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
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21
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Roskoski R. Small molecule protein kinase inhibitors approved by regulatory agencies outside of the United States. Pharmacol Res 2023; 194:106847. [PMID: 37454916 DOI: 10.1016/j.phrs.2023.106847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Owing to genetic alterations and overexpression, the dysregulation of protein kinases plays a significant role in the pathogenesis of many autoimmune and neoplastic disorders and protein kinase antagonists have become an important drug target. Although the efficacy of imatinib in the treatment of chronic myelogenous leukemia in the United States in 2001 was the main driver of protein kinase inhibitor drug discovery, this was preceded by the approval of fasudil (a ROCK antagonist) in Japan in 1995 for the treatment of cerebral vasospasm. There are 21 small molecule protein kinase inhibitors that are approved in China, Japan, Europe, and South Korea that are not approved in the United Sates and 75 FDA-approved inhibitors in the United States. Of the 21 agents, eleven target receptor protein-tyrosine kinases, eight inhibit nonreceptor protein-tyrosine kinases, and two block protein-serine/threonine kinases. All 21 drugs are orally bioavailable or topically effective. Of the non-FDA approved drugs, sixteen are prescribed for the treatment of neoplastic diseases, three are directed toward inflammatory disorders, one is used for glaucoma, and fasudil is used in the management of vasospasm. The leading targets of kinase inhibitors approved by both international regulatory agencies and by the FDA are members of the EGFR family, the VEGFR family, and the JAK family. One-third of the 21 internationally approved drugs are not compliant with Lipinski's rule of five for orally bioavailable drugs. The rule of five relies on four parameters including molecular weight, number of hydrogen bond donors and acceptors, and the Log of the partition coefficient.
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Affiliation(s)
- Robert Roskoski
- Blue Ridge Institute for Medical Research, 221 Haywood Knolls Drive, Hendersonville, NC 28791-8717, United States.
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Wen Z, Pramanik A, Lewicki SA, Jung YH, Gao ZG, Randle JCR, Cronin C, Chen Z, Giancotti LA, Whitehead GS, Liang BT, Breton S, Salvemini D, Cook DN, Jacobson KA. Alicyclic Ring Size Variation of 4-Phenyl-2-naphthoic Acid Derivatives as P2Y 14 Receptor Antagonists. J Med Chem 2023; 66:9076-9094. [PMID: 37382926 PMCID: PMC10407959 DOI: 10.1021/acs.jmedchem.3c00664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
P2Y14 receptor (P2Y14R) is activated by extracellular UDP-glucose, a damage-associated molecular pattern that promotes inflammation in the kidney, lung, fat tissue, and elsewhere. Thus, selective P2Y14R antagonists are potentially useful for inflammatory and metabolic diseases. The piperidine ring size of potent, competitive P2Y14R antagonist (4-phenyl-2-naphthoic acid derivative) PPTN 1 was varied from 4- to 8-membered rings, with bridging/functional substitution. Conformationally and sterically modified isosteres included N-containing spirocyclic (6-9), fused (11-13), and bridged (14, 15) or large (16-20) ring systems, either saturated or containing alkene or hydroxy/methoxy groups. The alicyclic amines displayed structural preference. An α-hydroxyl group increased the affinity of 4-(4-((1R,5S,6r)-6-hydroxy-3-azabicyclo[3.1.1]heptan-6-yl)phenyl)-7-(4-(trifluoromethyl)phenyl)-2-naphthoic acid 15 (MRS4833) compared to 14 by 89-fold. 15 but not its double prodrug 50 reduced airway eosinophilia in a protease-mediated asthma model, and orally administered 15 and prodrugs reversed chronic neuropathic pain (mouse CCI model). Thus, we identified novel drug leads having in vivo efficacy.
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Affiliation(s)
- Zhiwei Wen
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Asmita Pramanik
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Sarah A Lewicki
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Young-Hwan Jung
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Zhan-Guo Gao
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - John C R Randle
- Random Walk Ventures, LLC, 108 Lincoln Street Unit 6B, Boston, Massachusetts 02111, United States
| | - Chunxia Cronin
- Pat and Jim Calhoun Cardiology Center, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Zhoumou Chen
- Department of Pharmacology and Physiology and the Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University School of Medicine, 1402 South Grand Blvd., St. Louis, Missouri 63104, United States
| | - Luigino A Giancotti
- Department of Pharmacology and Physiology and the Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University School of Medicine, 1402 South Grand Blvd., St. Louis, Missouri 63104, United States
| | - Gregory S Whitehead
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, United States
| | - Bruce T Liang
- Pat and Jim Calhoun Cardiology Center, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Sylvie Breton
- Centre de Recherche du CHU de Québec, Département d'Obstétrique, de Gynécologie et Reproduction, Faculté de Médecine, Université Laval, Laval, Québec G1V 4G2, Canada
| | - Daniela Salvemini
- Department of Pharmacology and Physiology and the Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University School of Medicine, 1402 South Grand Blvd., St. Louis, Missouri 63104, United States
| | - Donald N Cook
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, United States
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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Ren Q, Fan Y, Yang L, Shan M, Shi W, Qian H. An updated patent review of GPR40/ FFAR1 modulators (2020 - present). Expert Opin Ther Pat 2023; 33:565-577. [PMID: 37947382 DOI: 10.1080/13543776.2023.2272649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/04/2023] [Indexed: 11/12/2023]
Abstract
INTRODUCTION Free fatty acid receptor 1 (FFAR1) is a potential therapeutic target for type 2 diabetes mellitus (T2DM) because it could clinically stimulate insulin release in a glucose-dependent manner without inducing hypoglycemia. In both the pharmaceutical industry and academic community, FFAR1 agonists have attracted considerable attention. AREAS COVERED The review presents a patent overview of FFAR1 modulators in 2020-2023, along with chemical structures, the biological activities and therapeutic applications of the representative compounds. Our patent survey used the major electronic databases, namely SciFinder, and Web of Science and Innojoy. EXPERT OPINION Although FFAR1 agonists exhibit outstanding advantages, they are also associated with significant challenges. At present, reducing the molecular weight and overall lipophilicity and developing tissue-specific FFAR1 agonists may be the strategies for alleviating hepatotoxicity.
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Affiliation(s)
- Qiang Ren
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, PR China
| | - Yiqing Fan
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, PR China
| | - Lixin Yang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, PR China
| | - Mayu Shan
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, PR China
| | - Wei Shi
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, PR China
| | - Hai Qian
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, PR China
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, China Pharmaceutical University, Nanjing, PR China
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Young RJ. Today's drug discovery and the shadow of the rule of 5. Expert Opin Drug Discov 2023; 18:965-972. [PMID: 37378429 DOI: 10.1080/17460441.2023.2228199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023]
Abstract
INTRODUCTION The rule of 5 developed by Lipinski et al., a landmark and prescient piece of scholarship, focused the minds of drug hunters by systematically characterizing the physical make-up of drug molecules for the first time, noting many sub-optimal compounds identified by high-throughput screening practices. Its profound influence on thinking and practices, whilst providing benefit, perhaps etched the guidelines too strongly in the minds of some drug hunters who applied the bounds too literally without understanding the implications of the underlying statistics. AREAS COVERED This opinion is based on recent key developments that take thinking, measurements, and standards beyond those first set out, particularly the influences of molecular weight and the understanding, measurement, and calculation of lipophilicity. EXPERT OPINION Techniques and technologies for physicochemical estimations set new standards. It is timely to celebrate the significance and influence of the rule of 5, whilst taking thinking to new levels with better characterizations. The shadow of the rule of 5 may be long, but it is not dark, as new measurements, predictions and principles emerge as guiding lights in the design and prioritization of higher-quality molecules redefining the meaning of beyond the rule of 5.
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Affiliation(s)
- Robert J Young
- Blue Burgundy (Drug Discovery Consultancy) Ltd, Bedford, UK
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25
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Prabhakaran P, Hebbani AV, Menon SV, Paital B, Murmu S, Kumar S, Singh MK, Sahoo DK, Desai PPD. Insilico generation of novel ligands for the inhibition of SARS-CoV-2 main protease (3CL pro) using deep learning. Front Microbiol 2023; 14:1194794. [PMID: 37448573 PMCID: PMC10338188 DOI: 10.3389/fmicb.2023.1194794] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/05/2023] [Indexed: 07/15/2023] Open
Abstract
The recent emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the coronavirus disease (COVID-19) has become a global public health crisis, and a crucial need exists for rapid identification and development of novel therapeutic interventions. In this study, a recurrent neural network (RNN) is trained and optimized to produce novel ligands that could serve as potential inhibitors to the SARS-CoV-2 viral protease: 3 chymotrypsin-like protease (3CLpro). Structure-based virtual screening was performed through molecular docking, ADMET profiling, and predictions of various molecular properties were done to evaluate the toxicity and drug-likeness of the generated novel ligands. The properties of the generated ligands were also compared with current drugs under various phases of clinical trials to assess the efficacy of the novel ligands. Twenty novel ligands were selected that exhibited good drug-likeness properties, with most ligands conforming to Lipinski's rule of 5, high binding affinity (highest binding affinity: -9.4 kcal/mol), and promising ADMET profile. Additionally, the generated ligands complexed with 3CLpro were found to be stable based on the results of molecular dynamics simulation studies conducted over a 100 ns period. Overall, the findings offer a promising avenue for the rapid identification and development of effective therapeutic interventions to treat COVID-19.
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Affiliation(s)
- Prejwal Prabhakaran
- Department of Biotechnology, New Horizon College of Engineering, Bangalore, India
- Faculty of Biology, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany
| | - Ananda Vardhan Hebbani
- Department of Biochemistry, Indian Academy Degree College (Autonomous), Bangalore, India
| | - Soumya V. Menon
- Department of Chemistry and Biochemistry, School of Sciences, Jain (Deemed-to-be) University, Bangalore, India
| | - Biswaranjan Paital
- Redox Regulation Laboratory, Department of Zoology, College of Basic Science and Humanities, Odisha University of Agriculture and Technology, Bhubaneswar, India
| | - Sneha Murmu
- ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, India
| | - Sunil Kumar
- ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, India
| | | | - Dipak Kumar Sahoo
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
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Zhang Z, Zhang SL, Wu C, Li HH, Zha L, Shi J, Liu X, Qin HL, Tang W. Sulfur-fluoride exchange (SuFEx)-enabled lead discovery of AChE inhibitors by fragment linking strategies. Eur J Med Chem 2023; 257:115502. [PMID: 37224761 DOI: 10.1016/j.ejmech.2023.115502] [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: 04/04/2023] [Revised: 05/06/2023] [Accepted: 05/16/2023] [Indexed: 05/26/2023]
Abstract
SuFEx click chemistry has been a method for the rapid synthesis of functional molecules with desirable properties. Here, we demonstrated a workflow that allows for in situ synthesis of sulfonamide inhibitors based on SuFEx reaction for high-throughput testing of their cholinesterase activity. According to fragment-based drug discovery (FBDD), sulfonyl fluorides [R-SO2F] with moderate activity were identified as fragment hits, rapidly diversified into 102 analogs in SuFEx reactions, and the sulfonamides were directly screened to yield drug-like inhibitors with 70-fold higher potency (IC50 = 94 nM). Moreover, the improved molecule J8-A34 can ameliorate cognitive function in Aβ1-42-induced mouse model. Since this SuFEx linkage reaction succeeds on picomole scale for direct screening, this methodology can accelerate the development of robust biological probes and drug candidates.
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Affiliation(s)
- Ziwen Zhang
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, 230032, China
| | - Shi-Long Zhang
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, 230032, China
| | - Chengyao Wu
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, 230032, China
| | - Huan-Huan Li
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, 230032, China
| | - Liang Zha
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, 230032, China
| | - Jingbo Shi
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, 230032, China
| | - Xinhua Liu
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, 230032, China.
| | - Hua-Li Qin
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, 430070, China.
| | - Wenjian Tang
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, 230032, China.
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Roskoski R. Rule of five violations among the FDA-approved small molecule protein kinase inhibitors. Pharmacol Res 2023; 191:106774. [PMID: 37075870 DOI: 10.1016/j.phrs.2023.106774] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 04/16/2023] [Indexed: 04/21/2023]
Abstract
Because genetic alterations including mutations, overexpression, translocations, and dysregulation of protein kinases are involved in the pathogenesis of many illnesses, this enzyme family is the target of many drug discovery programs in the pharmaceutical industry. Overall, the US FDA has approved 74 small molecule protein kinase inhibitors, nearly all of which are orally effective. Of the 74 approved drugs, forty block receptor protein-tyrosine kinases, eighteen target nonreceptor protein-tyrosine kinases, twelve are directed against protein-serine/threonine protein kinases, and four target dual specificity protein kinases. The data indicate that 63 of these medicinals are approved for the management of neoplasms (51 against solid tumors such as breast, colon, and lung cancers, eight against nonsolid tumors such as leukemia, and four against both types of tumors). Seven of the FDA-approved kinase inhibitors form covalent bonds with their target enzymes and they are accordingly classified as TCIs (targeted covalent inhibitors). Medicinal chemists have examined the physicochemical properties of drugs that are orally effective. Lipinski's rule of five (Ro5) is a computational procedure that is used to estimate solubility, membrane permeability, and pharmacological effectiveness in the drug-discovery setting. It relies on four parameters including molecular weight, number of hydrogen bond donors and acceptors, and the Log of the partition coefficient. Other important descriptors include the lipophilic efficiency, the polar surface area, and the number of rotatable bonds and aromatic rings. We tabulated these and other properties of the FDA-approved kinase inhibitors. Of the 74 approved drugs, 30 fail to comply with the rule of five.
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Affiliation(s)
- Robert Roskoski
- Blue Ridge Institute for Medical Research, 221 Haywood Knolls Drive, Hendersonville, NC 28791-8717, United States.
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28
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Shaaban S, Abdou A, Alhamzani AG, Abou-Krisha MM, Al-Qudah MA, Alaasar M, Youssef I, Yousef TA. Synthesis and in Silico Investigation of Organoselenium-Clubbed Schiff Bases as Potential Mpro Inhibitors for the SARS-CoV-2 Replication. Life (Basel) 2023; 13:life13040912. [PMID: 37109441 PMCID: PMC10141725 DOI: 10.3390/life13040912] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
Since the first report of the organoselenium compound, ebselen, as a potent inhibitor of the SARS-CoV-2 Mpro main protease by Z. Jin et al. (Nature, 2020), different OSe analogs have been developed and evaluated for their anti-COVID-19 activities. Herein, organoselenium-clubbed Schiff bases were synthesized in good yields (up to 87%) and characterized using different spectroscopic techniques. Their geometries were studied by DFT using the B3LYP/6–311 (d, p) approach. Ten FDA-approved drugs targeting COVID-19 were used as model pharmacophores to interpret the binding requirements of COVID-19 inhibitors. The antiviral efficiency of the novel organoselenium compounds was assessed by molecular docking against the 6LU7 protein to investigate their possible interactions. Our results showed that the COVID-19 primary protease bound to organoselenium ligands with high binding energy scores ranging from −8.19 to −7.33 Kcal/mol for 4c and 4a to −6.10 to −6.20 Kcal/mol for 6b and 6a. Furthermore, the docking data showed that 4c and 4a are good Mpro inhibitors. Moreover, the drug-likeness studies, including Lipinski’s rule and ADMET properties, were also assessed. Interestingly, the organoselenium candidates manifested solid pharmacokinetic qualities in the ADMET studies. Overall, the results demonstrated that the organoselenium-based Schiff bases might serve as possible drugs for the COVID-19 epidemic.
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Wang L, Sun Y, Wang J, Xue Y, Sun Y, Qin Q, Sun Y, Zhao D, Cheng M. Design, synthesis, and biological evaluation of a potent PLK4 inhibitor WY29 with 1H-pyrazolo[3,4-d]pyrimidine scaffold. Arch Pharm (Weinheim) 2023; 356:e2200490. [PMID: 36442843 DOI: 10.1002/ardp.202200490] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/26/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022]
Abstract
Centriole duplication occurs once per cell cycle and is regulated by Polo-like kinase 4 (PLK4). Overexpression of PLK4 in somatic cells can lead to the excessive formation of centrioles, directly causing chromosome segregation errors and tumorigenesis. In this study, we described our efforts to develop a series of PLK4 inhibitors with 1H-pyrazolo[3,4-d]pyrimidine core, and further structure- and receptor-based design and optimization resulted in a potent inhibitor WY29 (IC50 = 0.027 μM), which exhibited good selectivity to other PLK family members (PLK1-3). At the cellular level, compound WY29 showed excellent antiproliferative activity against three breast cancer cell lines (MCF-7, BT474, and MDA-MB-231) while weak inhibitory activity was found on normal cell line HUVECs. In addition, the in vitro preliminary drug-like properties evaluation of compound WY29 showed outstanding stability in human plasma and liver microsomes, and weak inhibitory activity against the major subtypes of human cytochrome P450. Also, the drug-like properties prediction of compound WY29 displayed remarkable drug-like properties (drug-likeness mode score: 1.06). In conclusion, these results support the further development of compound WY29 as a lead compound for PLK4-targeted anticancer drug discovery.
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Affiliation(s)
- Lin Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Yu Sun
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Jingkai Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Yanli Xue
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Yin Sun
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Qiaohua Qin
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Yixiang Sun
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
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Mahmoudi A, Butler AE, Banach M, Jamialahmadi T, Sahebkar A. Identification of Potent Small-Molecule PCSK9 Inhibitors Based on Quantitative Structure-Activity Relationship, Pharmacophore Modeling, and Molecular Docking Procedure. Curr Probl Cardiol 2023; 48:101660. [PMID: 36841313 DOI: 10.1016/j.cpcardiol.2023.101660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 02/17/2023] [Indexed: 02/27/2023]
Abstract
The leading cause of atherosclerotic cardiovascular disease (ASCVD) is elevated low-density lipoprotein cholesterol (LDL-C). Proprotein convertase subtilisin/kexin type 9 (PCSK9) attaches to the domain of LDL receptor (LDLR), diminishing LDL-C influx and LDLR cell surface presentation in hepatocytes, resulting in higher circulating LDL-C levels. PCSK9 dysfunction has been linked to lower levels of plasma LDLC and a decreased risk of coronary heart disease (CHD). Herein, using virtual screening tools, we aimed to identify a potent small-molecule PCSK9 inhibitor in compounds that are currently being studied in clinical trials. We first performed chemical absorption, distribution, metabolism, excretion, and toxicity (ADMET) filtering of 9800 clinical trial compounds obtained from the ZINC 15 database using Lipinski's rule of 5 and achieved 3853 compounds. Two-dimensional (2D) quantitative structure-activity relationship (QSAR) was initiated by computing molecular descriptors and selecting important descriptors of 23 PCSK9 inhibitors. Multivariate calibration was performed with the partial least square regression (PLS) method with 18 compounds for training to design the QSAR model and 5 compounds for the test set to assess the model. The best latent variables (LV) (LV=6) with the lowest value of Root-Mean-Square Error of Cross-Validation (RMSECV) of 0.48 and leave-one-out cross-validation correlation coefficient (R2CV) = 0.83 were obtained for the QSAR model. The low RMSEC (0.21) with high R²cal (0.966) indicates the probability of fit between the experimental data and the calibration model. Using QSAR analysis of 3853 compounds, 2635 had a pIC50<1 and were considered for pharmacophore screening. The PHASE module (a complete package for pharmacophore modeling) designed the pharmacophore hypothesis through multiple ligands. The top 14 compounds (pIC50>1) were defined as active, whereas 9 (pIC50<1) were considered as an inactive set. Three five-point pharmacophore hypotheses achieved the highest score: DHHRR1, DHHRR2, and DHRRR1. The highest and best model with survival scores (5.365) was DHHRR1, comprising 1 hydrogen donor (D), 2 hydrophobic groups (H), and 2 rings of aromatic (R) features. We selected the molecules with a higher 1.5 fitness score (257 compounds) in pharmacophore screening (DHHRR1) for molecular docking screening. Molecular docking indicates that ZINC000051951669, with a binding affinity: of -13.2 kcal/mol and 2 H-bonds, has the highest binding to the PCSK9 protein. ZINC000011726230 with energy binding: -11.4 kcal/mol and 3 H-bonds, ZINC000068248147 with binding affinity: -10.7 kcal/mol and 1 H-bond, ZINC000029134440 with a binding affinity: -10.6 kcal/mol and 4 H-bonds were ranked next, respectively. To conclude, the archived molecules identified as inhibitory PCSK9 candidates, and especially ZINC000051951669 may therefore significantly inhibit PCSK9 and should be considered in the newly designed trials.
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Affiliation(s)
- Ali Mahmoudi
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Iran
| | - Alexandra E Butler
- Research Department, Royal College of Surgeons in Ireland Bahrain, Adliya, Bahrain
| | - Maciej Banach
- Department of Preventive Cardiology and Lipidology, Medical University of Lodz (MUL) Lodz, Poland; Cardiovascular Research Centre, University of Zielona Gora, Zielona Gora, Poland; Department of Cardiology and Congenital Diseases of Adults, Polish Mother's Memorial Hospital Research institute (PMMHRI), Lodz, Poland; Ciccarone Center for the Prevention of Cardiovascular Disease, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Tannaz Jamialahmadi
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; School of Medicine, The University of Western Australia, Perth, Australia; Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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31
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O'Brien Laramy MN, Luthra S, Brown MF, Bartlett DW. Delivering on the promise of protein degraders. Nat Rev Drug Discov 2023; 22:410-427. [PMID: 36810917 DOI: 10.1038/s41573-023-00652-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2023] [Indexed: 02/23/2023]
Abstract
Over the past 3 years, the first bivalent protein degraders intentionally designed for targeted protein degradation (TPD) have advanced to clinical trials, with an initial focus on established targets. Most of these clinical candidates are designed for oral administration, and many discovery efforts appear to be similarly focused. As we look towards the future, we propose that an oral-centric discovery paradigm will overly constrain the chemical designs that are considered and limit the potential to drug novel targets. In this Perspective, we summarize the current state of the bivalent degrader modality and propose three categories of degrader designs, based on their likely route of administration and requirement for drug delivery technologies. We then describe a vision for how parenteral drug delivery, implemented early in research and supported by pharmacokinetic-pharmacodynamic modelling, can enable exploration of a broader drug design space, expand the scope of accessible targets and deliver on the promise of protein degraders as a therapeutic modality.
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Affiliation(s)
| | - Suman Luthra
- Discovery Pharmaceutical Sciences, Merck & Co., Inc., Boston, MA, USA
| | - Matthew F Brown
- Discovery Sciences, Worldwide Research, Development, and Medical, Pfizer Inc., Groton, CT, USA
| | - Derek W Bartlett
- Pharmacokinetics, Dynamics, & Metabolism, Worldwide Research, Development, and Medical, Pfizer Inc., San Diego, CA, USA
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Qi Y, Wang K, Long B, Yue H, Wu Y, Yang D, Tong M, Shi X, Hou Y, Zhao Y. Discovery of novel 7,7-dimethyl-6,7-dihydro-5H-pyrrolo[3,4-d]pyrimidines as ATR inhibitors based on structure-based drug design. Eur J Med Chem 2023; 246:114945. [PMID: 36462444 DOI: 10.1016/j.ejmech.2022.114945] [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: 10/24/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 11/27/2022]
Abstract
ATR kinase is essential to the viability of replicating cells responding to the accumulation of single-strand breaks in DNA, which is an attractive anticancer drug target based on synthetic lethality. Herein we design, synthesize, and evaluate a novel series of fused pyrimidine derivatives as ATR inhibitors. As a result, compound 48f, with an IC50 value of 0.0030 μM against ATR, displayed strong monotherapy efficacy in ataxia-telangiectasia mutated (ATM) kinase-deficient tumor cells LoVo, SW620, OVCAR-3 cell lines with IC50 values of 0.040 μM, 0.095 μM, 0.098 μM, respectively. More importantly, the combination of 48f with AZD-1390, cisplatin, oxaliplatin, and olaparib respectively resulted in synergistic activity against HT-29, HCT116, A549, MCF-7, MDA-MB-231 cells. Moreover, 48f showed a favorable pharmacokinetic profile with a bioavailability of 30.0% in SD rats, acceptable PPB, high permeability (Papp A to B = 8.23 cm s-1 × 10-6), and low risk of drug-drug interactions. Collectively, compound 48f could be a promising compound for further investigation.
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Affiliation(s)
- Yinliang Qi
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning, 110016, China
| | - Kun Wang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning, 110016, China
| | - Bin Long
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning, 110016, China
| | - Hao Yue
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning, 110016, China
| | - Yongshuo Wu
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning, 110016, China
| | - Dexiao Yang
- 3D BioOptima, 1338 Wuzhong Avenue, Suzhou, 215104, China
| | - Minghui Tong
- 3D BioOptima, 1338 Wuzhong Avenue, Suzhou, 215104, China
| | - Xuan Shi
- 3D BioOptima, 1338 Wuzhong Avenue, Suzhou, 215104, China
| | - Yunlei Hou
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning, 110016, China.
| | - Yanfang Zhao
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning, 110016, China.
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Thakur M, Bateman A, Brooksbank C, Freeberg M, Harrison M, Hartley M, Keane T, Kleywegt G, Leach A, Levchenko M, Morgan S, McDonagh E, Orchard S, Papatheodorou I, Velankar S, Vizcaino J, Witham R, Zdrazil B, McEntyre J. EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022. Nucleic Acids Res 2023; 51:D9-D17. [PMID: 36477213 PMCID: PMC9825486 DOI: 10.1093/nar/gkac1098] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 10/21/2022] [Accepted: 10/31/2022] [Indexed: 12/13/2022] Open
Abstract
The European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) is one of the world's leading sources of public biomolecular data. Based at the Wellcome Genome Campus in Hinxton, UK, EMBL-EBI is one of six sites of the European Molecular Biology Laboratory (EMBL), Europe's only intergovernmental life sciences organisation. This overview summarises the status of services that EMBL-EBI data resources provide to scientific communities globally. The scale, openness, rich metadata and extensive curation of EMBL-EBI added-value databases makes them particularly well-suited as training sets for deep learning, machine learning and artificial intelligence applications, a selection of which are described here. The data resources at EMBL-EBI can catalyse such developments because they offer sustainable, high-quality data, collected in some cases over decades and made openly availability to any researcher, globally. Our aim is for EMBL-EBI data resources to keep providing the foundations for tools and research insights that transform fields across the life sciences.
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Affiliation(s)
| | - Alex Bateman
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Cath Brooksbank
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Mallory Freeberg
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Melissa Harrison
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Matthew Hartley
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Thomas Keane
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Gerard Kleywegt
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Andrew Leach
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Mariia Levchenko
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Sarah Morgan
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Ellen M McDonagh
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
- OpenTargets, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Sandra Orchard
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Irene Papatheodorou
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Sameer Velankar
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Juan Antonio Vizcaino
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Rick Witham
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Barbara Zdrazil
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
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34
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Properties of FDA-approved small molecule protein kinase inhibitors: A 2023 update. Pharmacol Res 2023; 187:106552. [PMID: 36403719 DOI: 10.1016/j.phrs.2022.106552] [Citation(s) in RCA: 108] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022]
Abstract
Owing to the dysregulation of protein kinase activity in many diseases including cancer, this enzyme family has become one of the most important drug targets in the 21st century. There are 72 FDA-approved therapeutic agents that target about two dozen different protein kinases and three of these drugs were approved in 2022. Of the approved drugs, twelve target protein-serine/threonine protein kinases, four are directed against dual specificity protein kinases (MEK1/2), sixteen block nonreceptor protein-tyrosine kinases, and 40 target receptor protein-tyrosine kinases. The data indicate that 62 of these drugs are prescribed for the treatment of neoplasms (57 against solid tumors including breast, lung, and colon, ten against nonsolid tumors such as leukemia, and four against both solid and nonsolid tumors: acalabrutinib, ibrutinib, imatinib, and midostaurin). Four drugs (abrocitinib, baricitinib, tofacitinib, upadacitinib) are used for the treatment of inflammatory diseases (atopic dermatitis, psoriatic arthritis, rheumatoid arthritis, Crohn disease, and ulcerative colitis). Of the 72 approved drugs, eighteen are used in the treatment of multiple diseases. The following three drugs received FDA approval in 2022 for the treatment of these specified diseases: abrocitinib (atopic dermatitis), futibatinib (cholangiocarcinomas), pacritinib (myelofibrosis). All of the FDA-approved drugs are orally effective with the exception of netarsudil, temsirolimus, and trilaciclib. This review summarizes the physicochemical properties of all 72 FDA-approved small molecule protein kinase inhibitors including lipophilic efficiency and ligand efficiency.
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35
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Beckers M, Fechner N, Stiefl N. 25 Years of Small-Molecule Optimization at Novartis: A Retrospective Analysis of Chemical Series Evolution. J Chem Inf Model 2022; 62:6002-6021. [PMID: 36351293 DOI: 10.1021/acs.jcim.2c00785] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In the drug development process, optimization of properties and biological activities of small molecules is an important task to obtain drug candidates with optimal efficacy when first applied in subsequent clinical studies. However, despite its importance, large-scale investigations of the optimization process in early drug discovery are lacking, likely due to the absence of historical records of different chemical series used in past projects. Here, we report a retrospective reconstruction of ∼3000 chemical series from the Novartis compound database, which allows us to characterize the general properties of chemical series as well as the time evolution of structural properties, ADMET properties, and target activities. Our data-driven approach allows us to substantiate common MedChem knowledge. We find that size, fraction of sp3-hybridized carbon atoms (Fsp3), and the density of stereocenters tend to increase during optimization, while the aromaticity of the compounds decreases. On the ADMET side, solubility tends to increase and permeability decreases, while safety-related properties tend to improve. Importantly, while ligand efficiency decreases due to molecular growth over time, target activities and lipophilic efficiency tend to improve. This emphasizes the heavy-atom count and log D as important parameters to monitor, especially as we further show that the decrease in permeability can be explained with the increase in molecular size. We highlight overlaps, shortcomings, and differences of the computationally reconstructed chemical series compared to the series used in recent internal drug discovery projects and investigate the relation to historical projects.
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Affiliation(s)
- Maximilian Beckers
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Postfach, 4002Basel, Switzerland
| | - Nikolas Fechner
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Postfach, 4002Basel, Switzerland
| | - Nikolaus Stiefl
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Postfach, 4002Basel, Switzerland
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36
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Young RJ, Flitsch SL, Grigalunas M, Leeson PD, Quinn RJ, Turner NJ, Waldmann H. The Time and Place for Nature in Drug Discovery. JACS AU 2022; 2:2400-2416. [PMID: 36465532 PMCID: PMC9709949 DOI: 10.1021/jacsau.2c00415] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/06/2022] [Accepted: 10/06/2022] [Indexed: 05/31/2023]
Abstract
The case for a renewed focus on Nature in drug discovery is reviewed; not in terms of natural product screening, but how and why biomimetic molecules, especially those produced by natural processes, should deliver in the age of artificial intelligence and screening of vast collections both in vitro and in silico. The declining natural product-likeness of licensed drugs and the consequent physicochemical implications of this trend in the context of current practices are noted. To arrest these trends, the logic of seeking new bioactive agents with enhanced natural mimicry is considered; notably that molecules constructed by proteins (enzymes) are more likely to interact with other proteins (e.g., targets and transporters), a notion validated by natural products. Nature's finite number of building blocks and their interactions necessarily reduce potential numbers of structures, yet these enable expansion of chemical space with their inherent diversity of physical characteristics, pertinent to property-based design. The feasible variations on natural motifs are considered and expanded to encompass pseudo-natural products, leading to the further logical step of harnessing bioprocessing routes to access them. Together, these offer opportunities for enhancing natural mimicry, thereby bringing innovation to drug synthesis exploiting the characteristics of natural recognition processes. The potential for computational guidance to help identifying binding commonalities in the route map is a logical opportunity to enable the design of tailored molecules, with a focus on "organic/biological" rather than purely "synthetic" structures. The design and synthesis of prototype structures should pay dividends in the disposition and efficacy of the molecules, while inherently enabling greener and more sustainable manufacturing techniques.
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Affiliation(s)
| | - Sabine L. Flitsch
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Michael Grigalunas
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn Strasse 11, 44227 Dortmund, Germany
| | - Paul D. Leeson
- Paul
Leeson Consulting Limited, The Malt House, Main Street, Congerstone, Nuneaton, Warwickshire CV13 6LZ, U.K.
| | - Ronald J. Quinn
- Griffith
Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Nicholas J. Turner
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Herbert Waldmann
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn Strasse 11, 44227 Dortmund, Germany
- Faculty of
Chemistry and Chemical Biology, Technical
University of Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
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37
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Humphreys PG, Anderson NA, Bamborough P, Baxter A, Chung CW, Cookson R, Craggs PD, Dalton T, Fournier JCL, Gordon LJ, Gray HF, Gray MW, Gregory R, Hirst DJ, Jamieson C, Jones KL, Kessedjian H, Lugo D, McGonagle G, Patel VK, Patten C, Poole DL, Prinjha RK, Ramirez-Molina C, Rioja I, Seal G, Stafford KAJ, Shah RR, Tape D, Theodoulou NH, Tomlinson L, Ukuser S, Wall ID, Wellaway N, White G. Identification and Optimization of a Ligand-Efficient Benzoazepinone Bromodomain and Extra Terminal (BET) Family Acetyl-Lysine Mimetic into the Oral Candidate Quality Molecule I-BET432. J Med Chem 2022; 65:15174-15207. [DOI: 10.1021/acs.jmedchem.2c01102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | - Niall A. Anderson
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Paul Bamborough
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Andrew Baxter
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Chun-wa Chung
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Rosa Cookson
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Peter D. Craggs
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Toryn Dalton
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | - Laurie J. Gordon
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Heather F. Gray
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Matthew W. Gray
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Richard Gregory
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - David J. Hirst
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Craig Jamieson
- WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K
| | | | | | - David Lugo
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Grant McGonagle
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | | | - Darren L. Poole
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Rab K. Prinjha
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | - Inmaculada Rioja
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Gail Seal
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | - Rishi R. Shah
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Daniel Tape
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | - Laura Tomlinson
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Sabri Ukuser
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Ian D. Wall
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Natalie Wellaway
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Gemma White
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
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38
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Scheiber N, Blaser G, Pferschy-Wenzig EM, Kaiser M, Mäser P, Presser A. Efficient Oxidative Dearomatisations of Substituted Phenols Using Hypervalent Iodine (III) Reagents and Antiprotozoal Evaluation of the Resulting Cyclohexadienones against T. b. rhodesiense and P. falciparum Strain NF54. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196559. [PMID: 36235096 PMCID: PMC9573667 DOI: 10.3390/molecules27196559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/21/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022]
Abstract
Quinones and quinols are secondary metabolites of higher plants that are associated with many biological activities. The oxidative dearomatization of phenols induced by hypervalent iodine(III) reagents has proven to be a very useful synthetic approach for the preparation of these compounds, which are also widely used in organic synthesis and medicinal chemistry. Starting from several substituted phenols and naphthols, a series of cyclohexadienone and naphthoquinone derivatives were synthesized using different hypervalent iodine(III) reagents and evaluated for their in vitro antiprotozoal activity. Antiprotozoal activity was assessed against Plasmodium falciparum NF54 and Trypanosoma brucei rhodesiense STIB900. Cytotoxicity of all compounds towards L6 cells was evaluated and the respective selectivity indices (SI) were calculated. We found that benzyl naphthoquinone 5c was the most active and selective molecule against T. brucei rhodesiense (IC50 = 0.08 μM, SI = 275). Furthermore, the antiprotozoal assays revealed no specific effects. In addition, some key physicochemical parameters of the synthesised compounds were calculated.
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Affiliation(s)
- Nina Scheiber
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Schubertstrasse 1, 8010 Graz, Austria
| | - Gregor Blaser
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Schubertstrasse 1, 8010 Graz, Austria
| | - Eva-Maria Pferschy-Wenzig
- Institute of Pharmaceutical Sciences, Pharmacognosy, University of Graz, Beethovenstrasse 8, 8010 Graz, Austria
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
- Swiss Tropical and Public Health Institute, University of Basel, Petersplatz 1, 4001 Basel, Switzerland
| | - Pascal Mäser
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
- Swiss Tropical and Public Health Institute, University of Basel, Petersplatz 1, 4001 Basel, Switzerland
| | - Armin Presser
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Schubertstrasse 1, 8010 Graz, Austria
- Correspondence: ; Tel.: +43-316-380-5369
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39
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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: 11] [Impact Index Per Article: 5.5] [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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40
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Liu W, Jiang J, Lin Y, You Q, Wang L. Insight into Thermodynamic and Kinetic Profiles in Small-Molecule Optimization. J Med Chem 2022; 65:10809-10847. [PMID: 35969687 DOI: 10.1021/acs.jmedchem.2c00682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-activity relationships (SARs) and structure-property relationships (SPRs) have been considered the most important factors during the drug optimization process. For medicinal chemists, improvements in the potencies and druglike properties of small molecules are regarded as their major goals. Among them, the binding affinity and selectivity of small molecules on their targets are the most important indicators. In recent years, there has been growing interest in using thermodynamic and kinetic profiles to analyze ligand-receptor interactions, which could provide not only binding affinities but also detailed binding parameters for small-molecule optimization. In this perspective, we are trying to provide an insight into thermodynamic and kinetic profiles in small-molecule optimization. Through a highlight of strategies on the small-molecule optimization with specific cases, we aim to put forward the importance of structure-thermodynamic relationships (STRs) and structure-kinetic relationships (SKRs), which could provide more guidance to find safe and effective small-molecule drugs.
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jingsheng Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yating Lin
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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41
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Roskoski R. Janus kinase (JAK) inhibitors in the treatment of neoplastic and inflammatory disorders. Pharmacol Res 2022; 183:106362. [PMID: 35878738 DOI: 10.1016/j.phrs.2022.106362] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 02/07/2023]
Abstract
The Janus kinase (JAK) family of nonreceptor protein-tyrosine kinases consists of JAK1, JAK2, JAK3, and TYK2 (Tyrosine Kinase 2). Each of these proteins contains a JAK homology pseudokinase (JH2) domain that interacts with and regulates the activity of the adjacent protein kinase domain (JH1). The Janus kinase family is regulated by numerous cytokines including interferons, interleukins, and hormones such as erythropoietin and thrombopoietin. Ligand binding to cytokine receptors leads to the activation of associated Janus kinases, which then catalyze the phosphorylation of the receptors. The SH2 domain of signal transducers and activators of transcription (STAT) binds to the cytokine receptor phosphotyrosines thereby promoting STAT phosphorylation and activation by the Janus kinases. STAT dimers are then translocated into the nucleus where they participate in the regulation and expression of dozens of proteins. JAK1/3 signaling participates in the pathogenesis of inflammatory disorders while JAK1/2 signaling contributes to the development of myeloproliferative neoplasms as well as several malignancies including leukemias and lymphomas. An activating JAK2 V617F mutation occurs in 95% of people with polycythemia vera and about 50% of cases of myelofibrosis and essential thrombocythemia. Abrocitinib, ruxolitinib, and upadacitinib are JAK inhibitors that are FDA-approved for the treatment of atopic dermatitis. Baricitinib is used for the treatment of rheumatoid arthritis and covid 19. Tofacitinib and upadacitinib are JAK antagonists that are used for the treatment of rheumatoid arthritis and ulcerative colitis. Additionally, ruxolitinib is approved for the treatment of polycythemia vera while fedratinib, pacritinib, and ruxolitinib are approved for the treatment of myelofibrosis.
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Affiliation(s)
- Robert Roskoski
- Blue Ridge Institute for Medical Research, 3754 Brevard Road, Suite 106, Box 19, Horse Shoe, NC 28742, United States.
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42
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Willis N, Mahy W, Sipthorp J, Zhao Y, Woodward HL, Atkinson BN, Bayle ED, Svensson F, Frew S, Jeganathan F, Monaghan A, Benvegnù S, Jolly S, Vecchia L, Ruza RR, Kjær S, Howell S, Snijders AP, Bictash M, Salinas PC, Vincent JP, Jones EY, Whiting P, Fish PV. Design of a Potent, Selective, and Brain-Penetrant Inhibitor of Wnt-Deactivating Enzyme Notum by Optimization of a Crystallographic Fragment Hit. J Med Chem 2022; 65:7212-7230. [PMID: 35536179 PMCID: PMC9150124 DOI: 10.1021/acs.jmedchem.2c00162] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Indexed: 12/26/2022]
Abstract
Notum is a carboxylesterase that suppresses Wnt signaling through deacylation of an essential palmitoleate group on Wnt proteins. There is a growing understanding of the role Notum plays in human diseases such as colorectal cancer and Alzheimer's disease, supporting the need to discover improved inhibitors, especially for use in models of neurodegeneration. Here, we have described the discovery and profile of 8l (ARUK3001185) as a potent, selective, and brain-penetrant inhibitor of Notum activity suitable for oral dosing in rodent models of disease. Crystallographic fragment screening of the Diamond-SGC Poised Library for binding to Notum, supported by a biochemical enzyme assay to rank inhibition activity, identified 6a and 6b as a pair of outstanding hits. Fragment development of 6 delivered 8l that restored Wnt signaling in the presence of Notum in a cell-based reporter assay. Assessment in pharmacology screens showed 8l to be selective against serine hydrolases, kinases, and drug targets.
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Affiliation(s)
- Nicky
J. Willis
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - William Mahy
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - James Sipthorp
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Yuguang Zhao
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine,
Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Hannah L. Woodward
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Benjamin N. Atkinson
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Elliott D. Bayle
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Fredrik Svensson
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Sarah Frew
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Fiona Jeganathan
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Amy Monaghan
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Stefano Benvegnù
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Sarah Jolly
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Luca Vecchia
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine,
Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Reinis R. Ruza
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine,
Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Svend Kjær
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Steven Howell
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | | | - Magda Bictash
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Patricia C. Salinas
- Department
of Cell and Developmental Biology, Laboratory for Molecular and Cellular
Biology, University College London, London WC1E 6BT, U.K.
| | - Jean-Paul Vincent
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - E. Yvonne Jones
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine,
Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Paul Whiting
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Paul V. Fish
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
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Panda SS, Tran QL, Rajpurohit P, Pillai GG, Thomas SJ, Bridges AE, Capito JE, Thangaraju M, Lokeshwar BL. Design, Synthesis, and Molecular Docking Studies of Curcumin Hybrid Conjugates as Potential Therapeutics for Breast Cancer. Pharmaceuticals (Basel) 2022; 15:ph15040451. [PMID: 35455448 PMCID: PMC9028889 DOI: 10.3390/ph15040451] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 02/06/2023] Open
Abstract
Curcumin (CUR) has received great attention over the past two decades due to its anticancer, anti-inflammatory, and antioxidant properties. Similarly, Dichloroacetate (DCA), an pyruvate dehydrogenase kinase 1 (PKD1) inhibitor, has gained huge attention as a potential anticancer drug. However, the clinical utility of these two agents is very limited because of the poor bioavailability and unsolicited side effects, respectively. We have synthesized fusion conjugates of CUR and DCA with an amino acids linker to overcome these limitations by utilizing the molecular hybridization approach. The molecular docking studies showed the potential targets of Curcumin-Modified Conjugates (CMCs) in breast cancer cells. We synthesized six hybrid conjugates named CMC1-6. These six CMC conjugates do not show any significant toxicity in a human normal immortalized mammary epithelial cell line (MCF10A) in vitro and C57BL/6 mice in vivo. However, treatment with CMC1 and CMC2 significantly reduced the growth and clonogenic survival by colony-formation assays in several human breast cancer cells (BC). Treatment by oral gavage of a transgenic mouse BC and metastatic BC tumor-bearing mice with CMC2 significantly reduced tumor growth and metastasis. Overall, our study provides strong evidence that CUR and DCA conjugates have a significant anticancer properties at a sub-micromolar concentration and overcome the clinical limitation of using CUR and DCA as potential anticancer drugs.
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Affiliation(s)
- Siva S. Panda
- Department of Chemistry and Physics, Augusta University, Augusta, GA 30912, USA; (Q.L.T.); (S.J.T.); (J.E.C.)
- Correspondence: (S.S.P.); (M.T.)
| | - Queen L. Tran
- Department of Chemistry and Physics, Augusta University, Augusta, GA 30912, USA; (Q.L.T.); (S.J.T.); (J.E.C.)
| | - Pragya Rajpurohit
- Department of Biochemistry and Molecular Biology, Augusta University, Augusta, GA 30912, USA; (P.R.); (A.E.B.); (B.L.L.)
- Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA
| | | | - Sean J. Thomas
- Department of Chemistry and Physics, Augusta University, Augusta, GA 30912, USA; (Q.L.T.); (S.J.T.); (J.E.C.)
| | - Allison E. Bridges
- Department of Biochemistry and Molecular Biology, Augusta University, Augusta, GA 30912, USA; (P.R.); (A.E.B.); (B.L.L.)
- Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA
| | - Jason E. Capito
- Department of Chemistry and Physics, Augusta University, Augusta, GA 30912, USA; (Q.L.T.); (S.J.T.); (J.E.C.)
| | - Muthusamy Thangaraju
- Department of Biochemistry and Molecular Biology, Augusta University, Augusta, GA 30912, USA; (P.R.); (A.E.B.); (B.L.L.)
- Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA
- Correspondence: (S.S.P.); (M.T.)
| | - Bal L. Lokeshwar
- Department of Biochemistry and Molecular Biology, Augusta University, Augusta, GA 30912, USA; (P.R.); (A.E.B.); (B.L.L.)
- Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
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44
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Targeting BCR-Abl in the treatment of Philadelphia-chromosome positive chronic myelogenous leukemia. Pharmacol Res 2022; 178:106156. [DOI: 10.1016/j.phrs.2022.106156] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/02/2022] [Indexed: 02/07/2023]
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45
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Zhang TJ, Zhang Y, Zhang ZH, Wang ZR, Zhang X, Hu SS, Lu PF, Guo S, Meng FH. Discovery of 4-(phenoxymethyl)-1H-1,2,3-triazole derivatives as novel xanthine oxidase inhibitors. Bioorg Med Chem Lett 2022; 60:128582. [DOI: 10.1016/j.bmcl.2022.128582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/23/2021] [Accepted: 01/18/2022] [Indexed: 12/20/2022]
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46
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Roskoski R. Properties of FDA-approved small molecule protein kinase inhibitors: A 2022 update. Pharmacol Res 2021; 175:106037. [PMID: 34921994 DOI: 10.1016/j.phrs.2021.106037] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/12/2021] [Indexed: 01/03/2023]
Abstract
Owing to the dysregulation of protein kinase activity in many diseases including cancer, this enzyme family has become one of the most important drug targets in the 21st century. There are 68 FDA-approved therapeutic agents that target about two dozen different protein kinases and six of these drugs were approved in 2021. Of the approved drugs, twelve target protein-serine/threonine protein kinases, four are directed against dual specificity protein kinases (MEK1/2), thirteen block nonreceptor protein-tyrosine kinases, and 39 target receptor protein-tyrosine kinases. The data indicate that 58 of these drugs are prescribed for the treatment of neoplasms (49 against solid tumors including breast, lung, and colon, five against nonsolid tumors such as leukemias, and four against both solid and nonsolid tumors: acalabrutinib, ibrutinib, imatinib, and midostaurin). Three drugs (baricitinib, tofacitinib, upadacitinib) are used for the treatment of inflammatory diseases including rheumatoid arthritis. Of the 68 approved drugs, eighteen are used in the treatment of multiple diseases. The following six drugs received FDA approval in 2021 for the treatment of these specified diseases: belumosudil (graft vs. host disease), infigratinib (cholangiocarcinomas), mobocertinib and tepotinib (specific forms of non-small cell lung cancer), tivozanib (renal cell carcinoma), and trilaciclib (to decrease chemotherapy-induced myelosuppression). All of the FDA-approved drugs are orally effective with the exception of netarsudil, temsirolimus, and the newly approved trilaciclib. This review summarizes the physicochemical properties of all 68 FDA-approved small molecule protein kinase inhibitors including lipophilic efficiency and ligand efficiency.
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Affiliation(s)
- Robert Roskoski
- Blue Ridge Institute for Medical Research, 3754 Brevard Road, Suite 106, Box 19, Horse Shoe, NC 28742-8814, United States.
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47
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de Oliveira RG, Cruz LR, Mollo MC, Dias LC, Kratz JM. Chagas Disease Drug Discovery in Latin America-A Mini Review of Antiparasitic Agents Explored Between 2010 and 2021. Front Chem 2021; 9:771143. [PMID: 34778217 PMCID: PMC8581468 DOI: 10.3389/fchem.2021.771143] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 10/15/2021] [Indexed: 11/13/2022] Open
Abstract
Chagas disease is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi that endangers almost 70 million people worldwide. The only two drugs that are currently approved for its treatment, benznidazole and nifurtimox, have controversial efficacy in adults and restricting safety issues, leaving thousands of patients without a suitable treatment. The neglect of Chagas disease is further illustrated by the lack of a robust and diverse drug discovery and development portfolio of new chemical entities, and it is of paramount importance to build a strong research and development network for antichagasic drugs. Focusing on drug discovery programs led by scientists based in Latin America, the main endemic region for this disease, we discuss herein what has been published in the last decade in terms of identification of new antiparasitic drugs to treat Chagas disease, shining a spotlight on the origin, chemical diversity, level of characterization of hits, and strategies used for optimization of lead compounds. Finally, we identify strengths and weaknesses in these drug discovery campaigns and highlight the importance of multidisciplinary collaboration and knowledge sharing.
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Affiliation(s)
- Ramon G. de Oliveira
- Laboratory of Synthetic Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Brazil
| | - Luiza R. Cruz
- Laboratory of Synthetic Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Brazil
| | - María C. Mollo
- Laboratory of Synthetic Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Brazil
| | - Luiz C. Dias
- Laboratory of Synthetic Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Brazil
| | - Jadel M. Kratz
- Drugs for Neglected Diseases Initiative (DNDi) Latin America, Rio de Janeiro, Brazil
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48
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Zhou Y, Zhang Y, Lian X, Li F, Wang C, Zhu F, Qiu Y, Chen Y. Therapeutic target database update 2022: facilitating drug discovery with enriched comparative data of targeted agents. Nucleic Acids Res 2021; 50:D1398-D1407. [PMID: 34718717 PMCID: PMC8728281 DOI: 10.1093/nar/gkab953] [Citation(s) in RCA: 289] [Impact Index Per Article: 96.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 11/14/2022] Open
Abstract
Drug discovery relies on the knowledge of not only drugs and targets, but also the comparative agents and targets. These include poor binders and non-binders for developing discovery tools, prodrugs for improved therapeutics, co-targets of therapeutic targets for multi-target strategies and off-target investigations, and the collective structure-activity and drug-likeness landscapes of enhanced drug feature. However, such valuable data are inadequately covered by the available databases. In this study, a major update of the Therapeutic Target Database, previously featured in NAR, was therefore introduced. This update includes (a) 34 861 poor binders and 12 683 non-binders of 1308 targets; (b) 534 prodrug-drug pairs for 121 targets; (c) 1127 co-targets of 672 targets regulated by 642 approved and 624 clinical trial drugs; (d) the collective structure-activity landscapes of 427 262 active agents of 1565 targets; (e) the profiles of drug-like properties of 33 598 agents of 1102 targets. Moreover, a variety of additional data and function are provided, which include the cross-links to the target structure in PDB and AlphaFold, 159 and 1658 newly emerged targets and drugs, and the advanced search function for multi-entry target sequences or drug structures. The database is accessible without login requirement at: https://idrblab.org/ttd/.
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Affiliation(s)
- Ying Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, China
| | - Yintao Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xichen Lian
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chaoxin Wang
- Department of Computer Science, Kansas State University, Manhattan 66506, USA
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Yunqing Qiu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, China
| | - Yuzong Chen
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, The Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
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