1
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Zell L, Hofer TS, Schubert M, Popoff A, Höll A, Marschhofer M, Huber-Cantonati P, Temml V, Schuster D. Impact of 2-hydroxypropyl-β-cyclodextrin inclusion complex formation on dopamine receptor-ligand interaction - A case study. Biochem Pharmacol 2024; 226:116340. [PMID: 38848779 DOI: 10.1016/j.bcp.2024.116340] [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: 02/08/2024] [Revised: 05/10/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
The octanol-water distribution coefficient (logP), used as a measure of lipophilicity, plays a major role in the drug design and discovery processes. While average logP values remain unchanged in approved oral drugs since 1983, current medicinal chemistry trends towards increasingly lipophilic compounds that require adapted analytical workflows and drug delivery systems. Solubility enhancers like cyclodextrins (CDs), especially 2-hydroxypropyl-β-CD (2-HP-β-CD), have been studied in vitro and in vivo investigating their ADMET (adsorption, distribution, metabolism, excretion and toxicity)-related properties. However, data is scarce regarding the applicability of CD inclusion complexes (ICs) in vitro compared to pure compounds. In this study, dopamine receptor (DR) ligands were used as a case study, utilizing a combined in silico/in vitro workflow. Media-dependent solubility and IC stoichiometry were investigated using HPLC. NMR was used to observe IC formation-caused chemical shift deviations while in silico approaches utilizing basin hopping global minimization were used to propose putative IC binding modes. A cell-based in vitro homogeneous time-resolved fluorescence (HTRF) assay was used to quantify ligand binding affinity at the DR subtype 2 (D2R). While all ligands showed increased solubility using 2-HP-β-CD, they differed regarding IC stoichiometry and receptor binding affinity. This case study shows that IC-formation was ligand-dependent and sometimes altering in vitro binding. Therefore, IC complex formation can't be recommended as a general means of improving compound solubility for in vitro studies as they may alter ligand binding.
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Affiliation(s)
- Lukas Zell
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; Research and Innovation Center for Novel Therapies and Regenerative Medicine, Austria
| | - Thomas S Hofer
- Institute of General, Inorganic and Theoretical Chemistry, Center for Biochemistry and Biomedicine, University of Innsbruck, 6020 Innsbruck, Austria
| | - Mario Schubert
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; Department of Chemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Alexander Popoff
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; Research and Innovation Center for Novel Therapies and Regenerative Medicine, Austria
| | - Anna Höll
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; Research and Innovation Center for Novel Therapies and Regenerative Medicine, Austria
| | - Moritz Marschhofer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; Research and Innovation Center for Novel Therapies and Regenerative Medicine, Austria
| | - Petra Huber-Cantonati
- Department of Pharmaceutical Biology, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; Research and Innovation Center for Novel Therapies and Regenerative Medicine, Austria
| | - Veronika Temml
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; Research and Innovation Center for Novel Therapies and Regenerative Medicine, Austria
| | - Daniela Schuster
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; Research and Innovation Center for Novel Therapies and Regenerative Medicine, Austria.
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2
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Jorgensen C, Troendle EP, Ulmschneider JP, Searson PC, Ulmschneider MB. A least-squares-fitting procedure for an efficient preclinical ranking of passive transport across the blood-brain barrier endothelium. J Comput Aided Mol Des 2023; 37:537-549. [PMID: 37573260 PMCID: PMC10505096 DOI: 10.1007/s10822-023-00525-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/24/2023] [Indexed: 08/14/2023]
Abstract
The treatment of various disorders of the central nervous system (CNS) is often impeded by the limited brain exposure of drugs, which is regulated by the human blood-brain barrier (BBB). The screening of lead compounds for CNS penetration is challenging due to the biochemical complexity of the BBB, while experimental determination of permeability is not feasible for all types of compounds. Here we present a novel method for rapid preclinical screening of libraries of compounds by utilizing advancements in computing hardware, with its foundation in transition-based counting of the flux. This method has been experimentally validated for in vitro permeabilities and provides atomic-level insights into transport mechanisms. Our approach only requires a single high-temperature simulation to rank a compound relative to a library, with a typical simulation time converging within 24 to 72 h. The method offers unbiased thermodynamic and kinetic information to interpret the passive transport of small-molecule drugs across the BBB.
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Affiliation(s)
- Christian Jorgensen
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark.
| | | | | | - Peter C Searson
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD, USA
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3
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Mugnaini C, Kostrzewa M, Casini M, Kumar P, Catallo V, Allarà M, Guastaferro L, Brizzi A, Paolino M, Tafi A, Kapatais C, Giorgi G, Vacondio F, Mor M, Corelli F, Ligresti A. Systematic Modification of the Substitution Pattern of the 7-Hydroxy-5-oxopyrazolo[4,3- b]pyridine-6-carboxamide Scaffold Enabled the Discovery of New Ligands with High Affinity and Selectivity for the Cannabinoid Type 2 Receptor. Molecules 2023; 28:4958. [PMID: 37446625 DOI: 10.3390/molecules28134958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Selective ligands of the CB2 receptor are receiving considerable attention due to their potential as therapeutic agents for a variety of diseases. Recently, 7-hydroxy-5-oxopyrazolo[4,3-b]pyridine-6-carboxamide derivatives were shown to act at the CB2 receptor either as agonists or as inverse agonists/antagonists in vitro and to have anti-osteoarthritic activity in vivo. In this article, we report the synthesis, pharmacological profile, and molecular modeling of a series of twenty-three new 7-hydroxy-5-oxopyrazolo[4,3-b]pyridine-6-carboxamides with the aim of further developing this new class of selective CB2 ligands. In addition to these compounds, seven other analogs that had been previously synthesized were included in this study to better define the structure-activity relationship (SAR). Ten of the new compounds studied were found to be potent and selective ligands of the CB2 receptor, with Ki values ranging from 48.46 to 0.45 nM and CB1/CB2 selectivity indices (SI) ranging from >206 to >4739. In particular, compounds 54 and 55 were found to be high-affinity CB2 inverse agonists that were not active at all at the CB1 receptor, whereas 57 acted as an agonist. The functional activity profile of the compounds within this structural class depends mainly on the substitution pattern of the pyrazole ring.
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Affiliation(s)
- Claudia Mugnaini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Magdalena Kostrzewa
- National Research Council of Italy, Institute of Biomolecular Chemistry, 80078 Pozzuoli, Italy
| | - Marta Casini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Poulami Kumar
- National Research Council of Italy, Institute of Biomolecular Chemistry, 80078 Pozzuoli, Italy
| | - Valeria Catallo
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Marco Allarà
- National Research Council of Italy, Institute of Biomolecular Chemistry, 80078 Pozzuoli, Italy
| | - Laura Guastaferro
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Antonella Brizzi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Marco Paolino
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Andrea Tafi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Christelos Kapatais
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Gianluca Giorgi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Federica Vacondio
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Marco Mor
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Federico Corelli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Alessia Ligresti
- National Research Council of Italy, Institute of Biomolecular Chemistry, 80078 Pozzuoli, Italy
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4
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Wang Z, Felstead HR, Troup RI, Linclau B, Williamson PTF. Lipophilicity Modulations by Fluorination Correlate with Membrane Partitioning. Angew Chem Int Ed Engl 2023; 62:e202301077. [PMID: 36932824 PMCID: PMC10946813 DOI: 10.1002/anie.202301077] [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: 01/20/2023] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 03/19/2023]
Abstract
Bioactive compounds generally need to cross membranes to arrive at their site of action. The octanol-water partition coefficient (lipophilicity, logPOW ) has proven to be an excellent proxy for membrane permeability. In modern drug discovery, logPOW and bioactivity are optimized simultaneously, for which fluorination is one of the relevant strategies. The question arises as to which extent the often subtle logP modifications resulting from different aliphatic fluorine-motif introductions also lead to concomitant membrane permeability changes, given the difference in molecular environment between octanol and (anisotropic) membranes. It was found that for a given compound class, there is excellent correlation between logPOW values with the corresponding membrane molar partitioning coefficients (logKp ); a study enabled by novel solid-state 19 F NMR MAS methodology using lipid vesicles. Our results show that the factors that cause modulation of octanol-water partition coefficients similarly affect membrane permeability.
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Affiliation(s)
- Zhong Wang
- School of ChemistryUniversity of Southampton HighfieldSouthamptonSO17 1BJUK
| | - Hannah R. Felstead
- School of ChemistryUniversity of Southampton HighfieldSouthamptonSO17 1BJUK
| | - Robert I. Troup
- School of ChemistryUniversity of Southampton HighfieldSouthamptonSO17 1BJUK
| | - Bruno Linclau
- School of ChemistryUniversity of Southampton HighfieldSouthamptonSO17 1BJUK
- Department of Organic and Macromolecular ChemistryGhent University Campus SterreKrijgslaan 281-S49000GhentBelgium
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5
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Hirlekar BU, Nuthi A, Singh KD, Murty US, Dixit VA. An overview of compound properties, multiparameter optimization, and computational drug design methods for PARP-1 inhibitor drugs. Eur J Med Chem 2023; 252:115300. [PMID: 36989813 DOI: 10.1016/j.ejmech.2023.115300] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023]
Abstract
Breast cancer treatment with PARP-1 inhibitors remains challenging due to emerging toxicities, drug resistance, and unaffordable costs of treatment options. How do we invent strategies to design better anti-cancer drugs? A part of the answer is in optimized compound properties, desirability functions, and modern computational drug design methods that drive selectivity and toxicity and have not been reviewed for PARP-1 inhibitors. Nonetheless, comparisons of these compound properties for PARP-1 inhibitors are not available in the literature. In this review, we analyze the physchem, PKPD space to identify inherent desirability functions characteristic of approved drugs that can be valuable for the design of better candidates. Recent literature utilizing ligand, structure-based drug design strategies and matched molecular pair analysis (MMPA) for the discovery of novel PARP-1 inhibitors are also reviewed. Thus, this perspective provides valuable insights into the medchem and multiparameter optimization of PARP-1 inhibitors that might be useful to other medicinal chemists.
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6
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Agarwal P, Huckle J, Newman J, Reid DL. Trends in small molecule drug properties: A developability molecule assessment perspective. Drug Discov Today 2022; 27:103366. [PMID: 36122862 DOI: 10.1016/j.drudis.2022.103366] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [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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7
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Hill J, Crich D. The N,N,O-Trisubstituted Hydroxylamine Isostere and Its Influence on Lipophilicity and Related Parameters. ACS Med Chem Lett 2022; 13:799-806. [PMID: 35586423 PMCID: PMC9109164 DOI: 10.1021/acsmedchemlett.1c00713] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/13/2022] [Indexed: 11/28/2022] Open
Abstract
The influence of substitution of an N,N,O-trisubstituted hydroxylamine (-NR-OR'-) unit for a hydrocarbon (-CHR-CH2-), ether (-CHR-OR'-), or amine (-NR-CHR'-) moiety on lipophilicity and other ADME parameters is described. A matched molecular pair analysis was conducted across five series of compounds, which showed that the replacement of carbon-carbon bonds by N,N,O-trisubstituted hydroxylamines typically leads to a reduction in logP comparable to that achieved with a tertiary amine group. In contrast, the weakly basic N,N,O-trisubstituted hydroxylamines have greater logD 7.4 values than tertiary amines. It is also demonstrated that the N,N,O-trisubstituted hydroxylamine moiety can improve metabolic stability and reduce human plasma protein binding relative to the corresponding hydrocarbon and ether units. Coupled with recent synthetic methods for hydroxylamine assembly by N-O bond formation, these results provide support for the re-evaluation of the N,N,O-trisubstituted hydroxylamine moiety in small-molecule optimization schemes in medicinal chemistry.
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Affiliation(s)
- Jarvis Hill
- Department
of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, Georgia 30602, United
States
- Department
of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
| | - David Crich
- Department
of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, Georgia 30602, United
States
- Department
of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend
Road, Athens, Georgia 30602, United States
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8
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Jorgensen C, Ulmschneider MB, Searson PC. Atomistic Model of Solute Transport across the Blood-Brain Barrier. ACS OMEGA 2022; 7:1100-1112. [PMID: 35036773 PMCID: PMC8757349 DOI: 10.1021/acsomega.1c05679] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/25/2021] [Indexed: 06/14/2023]
Abstract
The blood-brain barrier remains a major roadblock to the delivery of drugs to the brain. While in vitro and in vivo measurements of permeability are widely used to predict brain penetration, very little is known about the mechanisms of passive transport. Detailed insight into interactions between solutes and cell membranes could provide new insight into drug design and screening. Here, we perform unbiased atomistic MD simulations to visualize translocation of a library of 24 solutes across a lipid bilayer representative of brain microvascular endothelial cells. A temperature bias is used to achieve steady state of all solutes, including those with low permeability. Based on free-energy surface profiles, we show that the solutes can be classified into three groups that describe distinct mechanisms of transport across the bilayer. Simulations down to 310 K for solutes with fast permeability were used to justify the extrapolation of values at 310 K from higher temperatures. Comparison of permeabilities at 310 K to experimental values obtained from in vitro transwell measurements and in situ brain perfusion revealed that permeabilities obtained from simulations vary from close to the experimental values to more than 3 orders of magnitude faster. The magnitude of the difference was dependent on the group defined by free-energy surface profiles. Overall, these results show that MD simulations can provide new insight into the mechanistic details of brain penetration and provide a new approach for drug discovery.
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Affiliation(s)
- Christian Jorgensen
- Institute
for Nanobiotechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | | | - Peter C. Searson
- Institute
for Nanobiotechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department
of Materials Science and Engineering, Johns
Hopkins University, Baltimore, Maryland 21218, United States
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9
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Ross-Hellauer T, Reichmann S, Cole NL, Fessl A, Klebel T, Pontika N. Dynamics of cumulative advantage and threats to equity in open science: a scoping review. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211032. [PMID: 35116143 PMCID: PMC8767192 DOI: 10.1098/rsos.211032] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Open Science holds the promise to make scientific endeavours more inclusive, participatory, understandable, accessible and re-usable for large audiences. However, making processes open will not per se drive wide reuse or participation unless also accompanied by the capacity (in terms of knowledge, skills, financial resources, technological readiness and motivation) to do so. These capacities vary considerably across regions, institutions and demographics. Those advantaged by such factors will remain potentially privileged, putting Open Science's agenda of inclusivity at risk of propagating conditions of 'cumulative advantage'. With this paper, we systematically scope existing research addressing the question: 'What evidence and discourse exists in the literature about the ways in which dynamics and structures of inequality could persist or be exacerbated in the transition to Open Science, across disciplines, regions and demographics?' Aiming to synthesize findings, identify gaps in the literature and inform future research and policy, our results identify threats to equity associated with all aspects of Open Science, including Open Access, Open and FAIR Data, Open Methods, Open Evaluation, Citizen Science, as well as its interfaces with society, industry and policy. Key threats include: stratifications of publishing due to the exclusionary nature of the author-pays model of Open Access; potential widening of the digital divide due to the infrastructure-dependent, highly situated nature of open data practices; risks of diminishing qualitative methodologies as 'reproducibility' becomes synonymous with quality; new risks of bias and exclusion in means of transparent evaluation; and crucial asymmetries in the Open Science relationships with industry and the public, which privileges the former and fails to fully include the latter.
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Affiliation(s)
- Tony Ross-Hellauer
- Know-Center GmbH, Graz, Austria
- Open and Reproducible Research Group, Graz University of Technology, Inffeldgasse 13, 8010 Graz, Austria
| | - Stefan Reichmann
- Open and Reproducible Research Group, Graz University of Technology, Inffeldgasse 13, 8010 Graz, Austria
| | - Nicki Lisa Cole
- Know-Center GmbH, Graz, Austria
- Open and Reproducible Research Group, Graz University of Technology, Inffeldgasse 13, 8010 Graz, Austria
| | - Angela Fessl
- Know-Center GmbH, Graz, Austria
- Open and Reproducible Research Group, Graz University of Technology, Inffeldgasse 13, 8010 Graz, Austria
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10
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Kok LY, Bannigan P, Sanaee F, Evans JC, Dunne M, Regenold M, Ahmed L, Dubins D, Allen C. Development and pharmacokinetic evaluation of a self-nanoemulsifying drug delivery system for the oral delivery of cannabidiol. Eur J Pharm Sci 2022; 168:106058. [PMID: 34763088 DOI: 10.1016/j.ejps.2021.106058] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/18/2021] [Accepted: 11/02/2021] [Indexed: 02/02/2023]
Abstract
The number of lipophilic drug candidates in pharmaceutical discovery pipelines has increased in recent years. These drugs often possess physicochemical properties that result in poor oral bioavailability, and their clinical potential may be limited without adequate formulation strategies. Cannabidiol (CBD) is an excellent example of a highly lipophilic compound with poor oral bioavailability, due to low water solubility and extensive first-pass metabolism. An approach that may overcome these limitations is formulation of the drug in self-nanoemulsifying drug delivery systems (SNEDDS). Herein, CBD-SNEDDS formulations were prepared and evaluated in vitro. Promising formulations (F2, F4) were administered to healthy female Sprague-Dawley rats via oral gavage (20 mg/kg CBD). Resulting pharmacokinetic parameters of CBD were compared to those obtained following administration of CBD in two oil-based formulations: a medium-chain triglyceride oil vehicle (MCT-CBD), and a sesame oil-based formulation similar in composition to an FDA-approved formulation of CBD, Epidiolex® (SO-CBD). Compared to MCT-CBD, administration of the SNEDDS formulations led to more rapid absorption of CBD (median Tmax values: 0.5 h (F2), 1 h (F4), 6 h (MCT-CBD)). Administration of F2 and F4 formulations also improved the systemic exposure to CBD by 2.2 and 2.8-fold compared to MCT-CBD; however, no improvement was found compared to SO-CBD.
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Affiliation(s)
- Lie Yun Kok
- Leslie Dan Faculty of Pharmacy, University of Toronto, Canada
| | - Pauric Bannigan
- Leslie Dan Faculty of Pharmacy, University of Toronto, Canada
| | - Forugh Sanaee
- Leslie Dan Faculty of Pharmacy, University of Toronto, Canada
| | - James C Evans
- Leslie Dan Faculty of Pharmacy, University of Toronto, Canada
| | - Michael Dunne
- Leslie Dan Faculty of Pharmacy, University of Toronto, Canada
| | | | - Lubabah Ahmed
- Leslie Dan Faculty of Pharmacy, University of Toronto, Canada
| | - David Dubins
- Leslie Dan Faculty of Pharmacy, University of Toronto, Canada.
| | - Christine Allen
- Leslie Dan Faculty of Pharmacy, University of Toronto, Canada.
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11
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Dombrowski AW, Aguirre AL, Shrestha A, Sarris KA, Wang Y. The Chosen Few: Parallel Library Reaction Methodologies for Drug Discovery. J Org Chem 2021; 87:1880-1897. [PMID: 34780177 DOI: 10.1021/acs.joc.1c01427] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Parallel library synthesis is an important tool for drug discovery because it enables the synthesis of closely related analogues in parallel via robust and general synthetic transformations. In this perspective, we analyzed the synthetic methodologies used in >5000 parallel libraries representing 15 prevalent synthetic transformations. The library data set contains complex substrates and diverse arrays of building blocks used over the last 14 years at AbbVie. The library synthetic methodologies that have demonstrated robustness and generality with proven success are described along with their substrate scopes. The evolution of the synthetic methodologies for library synthesis over the past decade is discussed. We also highlight that the combination of parallel library synthesis with high-throughput experimentation will continue to facilitate the discovery of library-amenable synthetic methodologies in drug discovery.
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Affiliation(s)
- Amanda W Dombrowski
- Advanced Chemistry Technologies Group, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Ana L Aguirre
- Advanced Chemistry Technologies Group, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Anurupa Shrestha
- Advanced Chemistry Technologies Group, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Kathy A Sarris
- Advanced Chemistry Technologies Group, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Ying Wang
- Advanced Chemistry Technologies Group, AbbVie, Inc., North Chicago, Illinois 60064, United States
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12
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Leeson PD, Bento AP, Gaulton A, Hersey A, Manners EJ, Radoux CJ, Leach AR. Target-Based Evaluation of "Drug-Like" Properties and Ligand Efficiencies. J Med Chem 2021; 64:7210-7230. [PMID: 33983732 PMCID: PMC7610969 DOI: 10.1021/acs.jmedchem.1c00416] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Physicochemical descriptors commonly used to define "drug-likeness" and ligand efficiency measures are assessed for their ability to differentiate marketed drugs from compounds reported to bind to their efficacious target or targets. Using ChEMBL version 26, a data set of 643 drugs acting on 271 targets was assembled, comprising 1104 drug-target pairs having ≥100 published compounds per target. Taking into account changes in their physicochemical properties over time, drugs are analyzed according to their target class, therapy area, and route of administration. Recent drugs, approved in 2010-2020, display no overall differences in molecular weight, lipophilicity, hydrogen bonding, or polar surface area from their target comparator compounds. Drugs are differentiated from target comparators by higher potency, ligand efficiency (LE), lipophilic ligand efficiency (LLE), and lower carboaromaticity. Overall, 96% of drugs have LE or LLE values, or both, greater than the median values of their target comparator compounds.
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Affiliation(s)
- Paul D Leeson
- Paul Leeson Consulting Ltd, The Malt House, Main Street, Congerstone, Nuneaton, Warkwickshire CV13 6LZ, United Kingdom
| | - A Patricia Bento
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Anna Gaulton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Anne Hersey
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Emma J Manners
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Chris J Radoux
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Andrew R Leach
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
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13
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Perera S, Fernando A, Dallman J, Weeramange C, Lansakara A, Nguyen T, Rafferty RJ. Construction and Biological Evaluation of Small Libraries Based on the Intermediates within the Total Synthesis of Uvaretin. ChemMedChem 2021; 16:1631-1639. [PMID: 33491867 DOI: 10.1002/cmdc.202001010] [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: 12/30/2020] [Indexed: 11/12/2022]
Abstract
Discovering therapeutic agents: New bioactive agents, either as sole or combinational agents, have been constructed through the synthetic manipulation of the intermediates within the total synthesis of the uvaretin class of natural products. It was found that increasing the hydrophobic character of the phenolic core correlates to a decrease in sole agent cytotoxicity. The synthesis of new, small chemical screening libraries (CSL) constructed from the intermediates of our total synthesis route of the uvaretin class of natural products is demonstrated herein. Numerous chalcone-based CSLs with various substitution on the phenolic groups within the chalcone core were assembled. Through cytotoxicity investigations, it was found that the level of hydrophobicity of the phenolic core of the chalcones gives biases: less cytotoxicity with more hydrophobic cores. In addition, it was observed that the potentiation, evaluated with 6-thiopurine in the pancreatic cancer cell line MIA PaCa-2, is tunable by the inclusion of less-hydrophobic character on the phenolic core. The role of the o-hydroxybenzyl group, present within the uvaretin family, was revealed to be cytotoxic in character. Merging all of the structure-activity relationship studies performed on the CSLs constructed in this effort led to the construction of a new chalcone hybrid possessing both a cytotoxic enone group and a small-molecule-potentiating, reduced enone group.
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Affiliation(s)
- Shashika Perera
- Department of Chemistry, Kansas State University, 1212 Mid-Campus Drive North, Manhattan, KS 66506, USA
| | - Asantha Fernando
- Department of Chemistry, Kansas State University, 1212 Mid-Campus Drive North, Manhattan, KS 66506, USA
| | - Johnathan Dallman
- Department of Chemistry, Kansas State University, 1212 Mid-Campus Drive North, Manhattan, KS 66506, USA
| | - Chamitha Weeramange
- Department of Chemistry, Kansas State University, 1212 Mid-Campus Drive North, Manhattan, KS 66506, USA
| | - Ashabha Lansakara
- Department of Chemistry, Kansas State University, 1212 Mid-Campus Drive North, Manhattan, KS 66506, USA
| | - Thi Nguyen
- Department of Chemistry, Kansas State University, 1212 Mid-Campus Drive North, Manhattan, KS 66506, USA
| | - Ryan J Rafferty
- Department of Chemistry, Kansas State University, 1212 Mid-Campus Drive North, Manhattan, KS 66506, USA
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14
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Vinarov Z, Abrahamsson B, Artursson P, Batchelor H, Berben P, Bernkop-Schnürch A, Butler J, Ceulemans J, Davies N, Dupont D, Flaten GE, Fotaki N, Griffin BT, Jannin V, Keemink J, Kesisoglou F, Koziolek M, Kuentz M, Mackie A, Meléndez-Martínez AJ, McAllister M, Müllertz A, O'Driscoll CM, Parrott N, Paszkowska J, Pavek P, Porter CJH, Reppas C, Stillhart C, Sugano K, Toader E, Valentová K, Vertzoni M, De Wildt SN, Wilson CG, Augustijns P. Current challenges and future perspectives in oral absorption research: An opinion of the UNGAP network. Adv Drug Deliv Rev 2021; 171:289-331. [PMID: 33610694 DOI: 10.1016/j.addr.2021.02.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/12/2021] [Accepted: 02/01/2021] [Indexed: 02/06/2023]
Abstract
Although oral drug delivery is the preferred administration route and has been used for centuries, modern drug discovery and development pipelines challenge conventional formulation approaches and highlight the insufficient mechanistic understanding of processes critical to oral drug absorption. This review presents the opinion of UNGAP scientists on four key themes across the oral absorption landscape: (1) specific patient populations, (2) regional differences in the gastrointestinal tract, (3) advanced formulations and (4) food-drug interactions. The differences of oral absorption in pediatric and geriatric populations, the specific issues in colonic absorption, the formulation approaches for poorly water-soluble (small molecules) and poorly permeable (peptides, RNA etc.) drugs, as well as the vast realm of food effects, are some of the topics discussed in detail. The identified controversies and gaps in the current understanding of gastrointestinal absorption-related processes are used to create a roadmap for the future of oral drug absorption research.
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Affiliation(s)
- Zahari Vinarov
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium; Department of Chemical and Pharmaceutical Engineering, Sofia University, Sofia, Bulgaria
| | - Bertil Abrahamsson
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg, Sweden
| | - Per Artursson
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Hannah Batchelor
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Philippe Berben
- Pharmaceutical Development, UCB Pharma SA, Braine- l'Alleud, Belgium
| | - Andreas Bernkop-Schnürch
- Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - James Butler
- GlaxoSmithKline Research and Development, Ware, United Kingdom
| | | | - Nigel Davies
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | | | - Gøril Eide Flaten
- Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
| | - Nikoletta Fotaki
- Department of Pharmacy and Pharmacology, University of Bath, Bath, United Kingdom
| | | | | | | | | | | | - Martin Kuentz
- Institute for Pharma Technology, University of Applied Sciences and Arts Northwestern Switzerland, Basel, Switzerland
| | - Alan Mackie
- School of Food Science & Nutrition, University of Leeds, Leeds, United Kingdom
| | | | | | - Anette Müllertz
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Petr Pavek
- Faculty of Pharmacy, Charles University, Hradec Králové, Czech Republic
| | | | - Christos Reppas
- Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Kiyohiko Sugano
- College of Pharmaceutical Sciences, Ritsumeikan University, Shiga, Japan
| | - Elena Toader
- Faculty of Medicine, University of Medicine and Pharmacy of Iasi, Romania
| | - Kateřina Valentová
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Maria Vertzoni
- Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Saskia N De Wildt
- Department of Pharmacology and Toxicology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Clive G Wilson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Patrick Augustijns
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium.
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15
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Chachulski L, Windshügel B. LEADS-FRAG: A Benchmark Data Set for Assessment of Fragment Docking Performance. J Chem Inf Model 2020; 60:6544-6554. [PMID: 33289563 DOI: 10.1021/acs.jcim.0c00693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fragment-based drug design is a popular approach in drug discovery, which makes use of computational methods such as molecular docking. To assess fragment placement performance of molecular docking programs, we constructed LEADS-FRAG, a benchmark data set containing 93 high-quality protein-fragment complexes that were selected from the Protein Data Bank using a rational and unbiased process. The data set contains fully prepared protein and fragment structures and is publicly available. Moreover, we used LEADS-FRAG for evaluating the small-molecule docking programs AutoDock, AutoDock Vina, FlexX, and GOLD for their fragment docking performance. GOLD in combination with the scoring function ChemPLP and AutoDock Vina performed best and generated near-native conformations (root mean square deviation <1.5 Å) for more than 50% of the data set considering the top-ranked docking pose. Taking into account all docking poses, the tested programs generated near-native conformations for up to 86% of the fragments in LEADS-FRAG. By rescoring all docking poses with the GOLD scoring functions and the Protein-Ligand Informatics force field, the number of near-native conformations increased up to 40% with respect to the top-rescored poses. Our results show that conventional small-molecule docking programs achieve a satisfactory fragment docking performance when utilizing rescoring.
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Affiliation(s)
- Laura Chachulski
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, ScreeningPort, Hamburg 22525, Germany.,Jacobs University Bremen gGmbH, Bremen 28759, Germany
| | - Björn Windshügel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, ScreeningPort, Hamburg 22525, Germany.,Institute for Biochemistry and Molecular Biology, Department of Chemistry, Universität Hamburg, Hamburg 20146, Germany
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16
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Agarwal P, Ishida K, Reid DL, Gupta A. Clearance prediction for Amgen molecules against Extended Clearance Classification System (ECCS) and future directions. Drug Discov Today 2020; 26:10-16. [PMID: 33075472 DOI: 10.1016/j.drudis.2020.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 09/17/2020] [Accepted: 10/12/2020] [Indexed: 10/23/2022]
Abstract
Early prediction of elimination pathways for new chemical entities can have a profound impact on drug discovery programs. The recently proposed Extended Clearance Classification System (ECCS) is a step in the right direction, providing a framework to help identify the major elimination pathway of a drug. A list of 42 Amgen small molecules was evaluated against the ECCS framework to assess its performance in retrospectively predicting their major elimination pathway. Here, we present a critical analysis of the chemical space defined by the ECCS framework with the aim of identifying its applicability and constraints. This evaluation highlights the critical need for periodic review and revision of ECCS, given that target constraints are moving molecules away from the traditional 'drug-like' physicochemical space.
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Affiliation(s)
- Prashant Agarwal
- Drug Product Technologies, Process Development, Amgen, Inc., 360 Binney St, Cambridge, MA 02142 USA
| | - Kazuya Ishida
- Pharmacokinetics and Drug Metabolism, Amgen Research, Amgen Inc., 360 Binney St, Cambridge, MA 02142 USA
| | - Darren L Reid
- Drug Product Technologies, Process Development, Amgen, Inc., 360 Binney St, Cambridge, MA 02142 USA
| | - Anshul Gupta
- Pharmacokinetics and Drug Metabolism, Amgen Research, Amgen Inc., 360 Binney St, Cambridge, MA 02142 USA.
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17
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Ferrera-Suanzes M, Prieto V, Medina-Olivera AJ, Botubol-Ares JM, Galán-Sánchez F, Rodríguez-Iglesias MA, Hernández-Galán R, Durán-Peña MJ. Synthesis of Degraded Limonoid Analogs as New Antibacterial Scaffolds against Staphylococcus aureus. Antibiotics (Basel) 2020; 9:antibiotics9080488. [PMID: 32781770 PMCID: PMC7459938 DOI: 10.3390/antibiotics9080488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/26/2020] [Accepted: 08/04/2020] [Indexed: 12/21/2022] Open
Abstract
Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (MRSA) have become serious infections in humans and ruminants. S. aureus strains are showing rapid changes to develop resistance in traditional antibiotic-containing systems. In the continuous fierce fight against the emergent multi-drug resistant bacterial strains, straightforward and scalable synthetic procedures to produce new active molecules are in demand. Analysis of molecular properties points to degraded limonoids as promising candidates. In this article, we report a simple synthetic approach to obtain degraded limonoid analogs as scaffolds for new antibacterial molecules. The minimum inhibitory concentrations against S. aureus were evaluated for the stereoisomer mixtures by the broth microdilution method. Analysis of results showed that the acetylated derivatives were the most active of them all.
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Affiliation(s)
- Marta Ferrera-Suanzes
- Department of Organic Chemistry, Faculty of Sciences, Campus Universitario Río San Pedro s/n, Torre Sur, 4; planta, University of Cádiz, 11510 Puerto Real, 11009 Cádiz, Spain; (M.F.-S.); (A.J.M.-O.); (J.M.B.-A.); (R.H.-G.)
| | - Victoria Prieto
- Department of Biomedicine, Biotechnology and Public Health, Hospital Puerta del Mar, University of Cádiz, 11009 Cádiz, Spain; (V.P.); (F.G.-S.); (M.A.R.-I.)
| | - Antonio J. Medina-Olivera
- Department of Organic Chemistry, Faculty of Sciences, Campus Universitario Río San Pedro s/n, Torre Sur, 4; planta, University of Cádiz, 11510 Puerto Real, 11009 Cádiz, Spain; (M.F.-S.); (A.J.M.-O.); (J.M.B.-A.); (R.H.-G.)
| | - José Manuel Botubol-Ares
- Department of Organic Chemistry, Faculty of Sciences, Campus Universitario Río San Pedro s/n, Torre Sur, 4; planta, University of Cádiz, 11510 Puerto Real, 11009 Cádiz, Spain; (M.F.-S.); (A.J.M.-O.); (J.M.B.-A.); (R.H.-G.)
| | - Fátima Galán-Sánchez
- Department of Biomedicine, Biotechnology and Public Health, Hospital Puerta del Mar, University of Cádiz, 11009 Cádiz, Spain; (V.P.); (F.G.-S.); (M.A.R.-I.)
- Instituto de investigación e Innovación Biomédica de Cádiz (INIBICA), 11009 Cádiz, Spain
| | - Manuel A. Rodríguez-Iglesias
- Department of Biomedicine, Biotechnology and Public Health, Hospital Puerta del Mar, University of Cádiz, 11009 Cádiz, Spain; (V.P.); (F.G.-S.); (M.A.R.-I.)
- Instituto de investigación e Innovación Biomédica de Cádiz (INIBICA), 11009 Cádiz, Spain
| | - Rosario Hernández-Galán
- Department of Organic Chemistry, Faculty of Sciences, Campus Universitario Río San Pedro s/n, Torre Sur, 4; planta, University of Cádiz, 11510 Puerto Real, 11009 Cádiz, Spain; (M.F.-S.); (A.J.M.-O.); (J.M.B.-A.); (R.H.-G.)
- Instituto de investigación e Innovación Biomédica de Cádiz (INIBICA), 11009 Cádiz, Spain
| | - María Jesús Durán-Peña
- Department of Organic Chemistry, Faculty of Sciences, Campus Universitario Río San Pedro s/n, Torre Sur, 4; planta, University of Cádiz, 11510 Puerto Real, 11009 Cádiz, Spain; (M.F.-S.); (A.J.M.-O.); (J.M.B.-A.); (R.H.-G.)
- Correspondence: ; Tel.: +34-956-016-583
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18
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Huang W, Czuba LC, Isoherranen N. Mechanistic PBPK Modeling of Urine pH Effect on Renal and Systemic Disposition of Methamphetamine and Amphetamine. J Pharmacol Exp Ther 2020; 373:488-501. [PMID: 32198137 PMCID: PMC7250368 DOI: 10.1124/jpet.120.264994] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 03/18/2020] [Indexed: 02/03/2023] Open
Abstract
The effect of urine pH on renal excretion and systemic disposition has been observed for many drugs and metabolites. When urine pH is altered, tubular ionization, passive reabsorption, renal clearance, and systemic exposure of drugs and metabolites may all change dramatically, raising clinically significant concerns. Surprisingly, the urine pH effect on drug disposition is not routinely explored in humans, and regulatory agencies have neither developed guidance on this issue nor required industry to conduct pertinent human trials. In this study, we hypothesized that physiologically based pharmacokinetic (PBPK) modeling could be used as a cost-effective method to examine potential urine pH effect on drug and metabolite disposition. Our previously developed and verified mechanistic kidney model was integrated with a full-body PBPK model to simulate renal clearance and area under the plasma concentration-time curve (AUC) with varying urine pH statuses using methamphetamine and amphetamine as model compounds. We first developed and verified drug models for methamphetamine and amphetamine under normal urine pH condition [absolute average fold error (AAFE) < 1.25 at study level]. Then, acidic and alkaline urine scenarios were simulated. Our simulation results show that the renal excretion and plasma concentration-time profiles for methamphetamine and amphetamine could be recapitulated under different urine pH (AAFE < 2 at individual level). The methamphetamine-amphetamine parent-metabolite full-body PBPK model also successfully simulated amphetamine plasma concentration-time profiles (AAFE < 1.25 at study level) and amphetamine/methamphetamine urinary concentration ratios (AAFE < 2 at individual level) after dosing methamphetamine. This demonstrates that our mechanistic PBPK model can predict urine pH effect on systemic and urinary disposition of drugs and metabolites. SIGNIFICANCE STATEMENT: Our study shows that integrating mechanistic kidney model with full-body physiologically based pharmacokinetic model can predict the magnitude of alteration in renal excretion and area under the plasma concentration-time curve (AUC) of drugs and metabolites when urine pH is changed. This provides a cost-effective method to evaluate the likelihood of renal and systemic disposition changes due to varying urine pH. This is important because multiple drugs and diseases can alter urine pH, leading to quantitatively and clinically significant changes in drug and metabolite disposition that may require adjustment of therapy.
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Affiliation(s)
- Weize Huang
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington
| | - Lindsay C Czuba
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington
| | - Nina Isoherranen
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington
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19
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Tinworth CP, Young RJ. Facts, Patterns, and Principles in Drug Discovery: Appraising the Rule of 5 with Measured Physicochemical Data. J Med Chem 2020; 63:10091-10108. [PMID: 32324397 DOI: 10.1021/acs.jmedchem.9b01596] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The rule of 5 was designed to estimate the likelihood of poor absorption or permeation, noting the impact of poor solubility. This Perspective explores the impact of various physicochemical descriptors and contemporary lipophilicity measurements on permeability and solubility, showing that the distribution coefficient log D7.4 (rather than log P) is the most impactful parameter. Molecular weight, almost invariably the defining characteristic of "beyond the rule of 5" compounds, has little impact on solubility when log D7.4 measurements and aromaticity are considered. Predicting permeation is more complex, given passive and carrier transport mechanisms; however, notable patterns of behavior are apparent, giving insight even "beyond the rule of 5". Recommended best practices should involve using the facts (measurements) and the patterns they reveal to establish informative principles rather than fastidious rules.
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Affiliation(s)
- Christopher P Tinworth
- Medicinal Sciences and Technology, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Robert J Young
- Medicinal Sciences and Technology, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.,Blue Burgundy Ltd., Bedford, Bedfordshire MK45 2AD, U.K
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20
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Saganuwan SA. Chirality of Central Nervous System (CNS) Acting Drugs: A Formidable Therapeutic Hurdle Against CNS Diseases. Cent Nerv Syst Agents Med Chem 2020; 19:171-179. [PMID: 31232237 DOI: 10.2174/1871524919666190624150214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 05/31/2019] [Accepted: 06/10/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Over fifty percent of drugs being used clinically are chiral and 90% of them are racemates. Unfortunately, they have both adverse and beneficial effects on body systems. METHODS Because of the erratic effects of chiral compounds on body functional systems, literature search was carried out with a view to identify CNS chiral drugs, their clinical advantages and disadvantages, unique physicochemical properties and structural modifications into safer drugs. RESULTS Findings have shown that majority of CNS and non-CNS acting drugs have chiral functional groups that may occur as either dextrorotatory (clockwise) or levorotatory (anticlockwise) or racemates which are inert. Sometimes, the enantiomers (optical isomers) could undergo keto-enol tautomerism, appearing in either acidic or basic or inert form. Chiral CNS acting drugs have agonistic and antagonistic effects, clinical advantages, disadvantages, and special clinical applications, possible modifications for better therapeutic effects and possible synthesis of more potent drugs from racemates. Clockwise chirality may be more effective and safer than the drugs with anticlockwise chirality. When chiral drugs are in racemate state they become inert and may be safer than when they are single. Also, diastereoisomers may be more dangerous than stereoisomers. CONCLUSION Therefore, chiral compounds should be adequately studied in lab rodents and primates, and their mechanisms of actions should be comprehensively understood before being used in clinical setting. Since many of them are toxic, their use should be based on principle of individualized medicine. Their molecular weights, functional groups, metabolites, polymers and stereoisomers could be valuable tools for their modifications.
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Affiliation(s)
- Saganuwan Alhaji Saganuwan
- Department of Veterinary Physiology, Pharmacology and Biochemistry, College of Veterinary Medicine, Federal University of Agriculture, P.M.B. 2373, Makurdi, Benue State, Nigeria
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21
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Yukawa T, Naven R. Utility of Physicochemical Properties for the Prediction of Toxicological Outcomes: Takeda Perspective. ACS Med Chem Lett 2020; 11:203-209. [PMID: 32071689 DOI: 10.1021/acsmedchemlett.9b00536] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/29/2020] [Indexed: 01/17/2023] Open
Abstract
The role that physicochemical properties play toward increasing the likelihood of toxicity findings in in vivo studies has been well reported, albeit sometimes with different conclusions. We decided to understand the role that physicochemical properties play toward the prediction of in vivo toxicological outcomes for Takeda chemistry using 284 internal compounds. In support of the previously reported "3/75 rule", reducing lipophilicity of molecules decreases toxicity odds noticeably; however, we also found that the trend of toxicity odds is different between compounds classified by their ionization state. For basic molecules, the odds of in vivo toxicity outcomes were significantly impacted by both lipophilicity and polar surface area, whereas neutral molecules were impacted less so. Through an analysis of several project-related compounds, we herein demonstrate that the utilization of the 3/75 rule coupled with consideration of ionization state is a rational strategy for medicinal chemistry design of safer drugs.
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Affiliation(s)
- Tomoya Yukawa
- Drug Safety Research and Evaluation, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 35 Landsdowne Street, Cambridge, Massachusetts 02139, United States
- Drug Safety Research and Evaluation, Pharmaceutical Research Division, Takeda Pharmaceuticals International Company Limited, 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Russell Naven
- Drug Safety Research and Evaluation, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 35 Landsdowne Street, Cambridge, Massachusetts 02139, United States
- Drug Safety Research and Evaluation, Pharmaceutical Research Division, Takeda Pharmaceuticals International Company Limited, 9625 Towne Centre Drive, San Diego, California 92121, United States
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22
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De Rycker M, Horn D, Aldridge B, Amewu RK, Barry CE, Buckner FS, Cook S, Ferguson MAJ, Gobeau N, Herrmann J, Herrling P, Hope W, Keiser J, Lafuente-Monasterio MJ, Leeson PD, Leroy D, Manjunatha UH, McCarthy J, Miles TJ, Mizrahi V, Moshynets O, Niles J, Overington JP, Pottage J, Rao SPS, Read KD, Ribeiro I, Silver LL, Southern J, Spangenberg T, Sundar S, Taylor C, Van Voorhis W, White NJ, Wyllie S, Wyatt PG, Gilbert IH. Setting Our Sights on Infectious Diseases. ACS Infect Dis 2020; 6:3-13. [PMID: 31808676 PMCID: PMC6958537 DOI: 10.1021/acsinfecdis.9b00371] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In
May 2019, the Wellcome Centre for Anti-Infectives Research (WCAIR) at the University of Dundee, UK, held an international
conference with the aim of discussing some key questions around discovering
new medicines for infectious diseases and a particular focus on diseases
affecting Low and Middle Income Countries. There is an urgent need
for new drugs to treat most infectious diseases. We were keen to see
if there were lessons that we could learn across different disease
areas and between the preclinical and clinical phases with the aim
of exploring how we can improve and speed up the drug discovery, translational,
and clinical development processes. We started with an introductory
session on the current situation and then worked backward from clinical
development to combination therapy, pharmacokinetic/pharmacodynamic
(PK/PD) studies, drug discovery pathways, and new starting points
and targets. This Viewpoint aims to capture some of the learnings.
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Affiliation(s)
- Manu De Rycker
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - David Horn
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Bree Aldridge
- Tufts University School of Medicine, 136 Harrison Avenue, Boston, Massachusetts 02111, United States
| | - Richard K. Amewu
- Department of Chemistry, University of Ghana, P.O. Box LG56, Legon, Accra, Ghana
| | - Clifton E. Barry
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Frederick S. Buckner
- Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, MS 358061, 750 Republican Street, Rm E-606, Seattle, Washington 98109-4766, United States
| | - Sarah Cook
- School of Humanities, University of Glasgow, 1 University Gardens, Glasgow G12 8QQ, United Kingdom
| | - Michael A. J. Ferguson
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Nathalie Gobeau
- Medicines for Malaria Venture (MMV), PO Box 1826, 20 Route de Pré-Bois, 1215 Geneva 15, Switzerland
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland, Department Microbial Natural Products, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Centre for Infection Research, partner
site Hannover-Braunschweig, Germany
| | | | - William Hope
- Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - Jennifer Keiser
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, CH-4051 Basel, Switzerland
- University of Basel, CH-4001 Basel, Switzerland
| | | | | | - Didier Leroy
- Medicines for Malaria Venture (MMV), PO Box 1826, 20 Route de Pré-Bois, 1215 Geneva 15, Switzerland
| | - Ujjini H. Manjunatha
- Novartis Institute for Tropical Diseases (NITD), Novartis Institutes for BioMedical Research (NIBR), 5300 Chiron Way, Emeryville, California 94608, United States
| | - James McCarthy
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Hertson, Queensland 4006, Australia
| | - Timothy J. Miles
- Tres Cantos Medicines Development Campus, Diseases of the Developing World (DDW), GlaxoSmithKline, Tres Cantos, Spain
| | - Valerie Mizrahi
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine and Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town, Observatory, Cape Town 7925, South Africa
| | - Olena Moshynets
- Biofilm Study Group, Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, 150 Zabolotnoho Street, Kiev 03143, Ukraine
| | - Jacquin Niles
- School of Engineering, Massachusetts Institute of Technology, Building 1-206, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, United States
| | - John P. Overington
- Medicines Discovery Catapult, Alderley
Park, Alderley Edge, Cheshire SK10 4TG, United Kingdom
| | - John Pottage
- ViiV Healthcare, 980 Great West Road, Brentford, Middlesex TW8 9GS, United Kingdom
| | - Srinivasa P. S. Rao
- Novartis Institute for Tropical Diseases (NITD), Novartis Institutes for BioMedical Research (NIBR), 5300 Chiron Way, Emeryville, California 94608, United States
| | - Kevin D. Read
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Isabela Ribeiro
- Drugs for Neglected Diseases Initiative (DNDi), Chemin Louis-Dunant 15, 1202 Genève, Switzerland
| | | | - Jen Southern
- Lancaster Institute for the Contemporary Arts (LICA), The LICA Building, Lancaster University, Lancaster LA1 4YW, United Kingdom
| | - Thomas Spangenberg
- Global Health Institute of Merck, Ares Trading S.A., a subsidiary
of Merck KGaA Darmstadt Germany, Route de Crassier 1, 1262 Eysins, Switzerland
| | - Shyam Sundar
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Caitlin Taylor
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine and Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town, Observatory, Cape Town 7925, South Africa
| | - Wes Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, MS 358061, 750 Republican Street, Rm E-606, Seattle, Washington 98109-4766, United States
| | - Nicholas J. White
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, 3/F, 60th Anniversary Chalermprakiat Building, 420/6 Rajvithi Road, Bangkok 10400, Thailand
| | - Susan Wyllie
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Paul G. Wyatt
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Ian H. Gilbert
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
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Affiliation(s)
- Sonia Lobo
- Department of Medical Education, Geisinger Commonwealth School of Medicine, Scranton, PA, USA
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Wang G, Cui P, Bai H, Wei S, Li S. Late-Stage C-H Functionalization of Nicotinamides for the Expedient Discovery of Novel Antifungal Leads. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:11901-11910. [PMID: 31584275 DOI: 10.1021/acs.jafc.9b05349] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Encouraged by the successful flexible modifications of the succinate dehydrogenase inhibitors, antifungal activity guided by the divergent synthesis of nicotinamides of the prevalidated pharmacophore 2-(2-oxazolinyl)aniline was conducted. The work highlighted the first utilization of the late-stage C-H functionalization assisted by the innate pharmacophore for the discovery of promising agrochemicals. New synthetic methodology and antifungal exploration of alkoxylated nicotinamides were accomplished. Fifty-five functionalized nicotinamides of 7 types were rationally designed and efficiently prepared through C-H functionalization, which facilitated the acquirement of four N-para aryloxylated nicotinamides (E3, E13, E19, and E22) as potential antifungal candidates against Botrytis cinerea, with the EC50 values lower than 5 mg/L. In vivo/vitro biotest, molecular docking, and structural analysis reconfirmed the novelty and practical potential of the antifungal candidates E3 and E19. This operationally simple platform will provide various "polar parts" and offer intriguing opportunities for the optimization of the carboxamide fungicides and structure-related pharmaceuticals.
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Affiliation(s)
- Guotong Wang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application , Nanjing Agricultural University , Nanjing 210095 , China
| | - Pengcheng Cui
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application , Nanjing Agricultural University , Nanjing 210095 , China
| | - Hongjin Bai
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin , Tarim University , Alaer 843300 , China
| | - Sanyue Wei
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application , Nanjing Agricultural University , Nanjing 210095 , China
| | - Shengkun Li
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application , Nanjing Agricultural University , Nanjing 210095 , China
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin , Tarim University , Alaer 843300 , China
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25
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Bunally SB, Luscombe CN, Young RJ. Using Physicochemical Measurements to Influence Better Compound Design. SLAS DISCOVERY 2019; 24:791-801. [PMID: 31429385 DOI: 10.1177/2472555219859845] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
During the past decade, the physicochemical quality of molecules under investigation at all stages of the drug discovery process has come under particular scrutiny. The issues associated with excessive lipophilicity and poor solubility in particular are many and varied, ranging from poor outcomes in screening campaigns to promiscuity, limited and/or poorly predictable pharmacokinetic exposure, and, ultimately, greater chances of clinical failure. In this review, contemporary methods to secure key measurements are described along with their relevance to understanding the behavior of molecules in environments pertinent to pharmacological activity. Together, the various measurements contribute to predictive models of both the physicochemical properties themselves and the outcomes they influence.
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Affiliation(s)
| | | | - Robert J Young
- 1 GlaxoSmithKline Medicines Research Centre, Stevenage, UK
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26
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Arisawa M. Development of Metal Nanoparticle Catalysis toward Drug Discovery. Chem Pharm Bull (Tokyo) 2019; 67:733-771. [PMID: 31366825 DOI: 10.1248/cpb.c19-00157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Transition-metal nanoparticles (NPs) catalysts supported on solid material represent one of the most important subjects in organic synthesis due to their reliable carbon-carbon or carbon-heteroatom bond-forming cross-coupling reactions. Therefore methodologically and conceptually novel immobilization methods for nonprecious transition-metal NPs are currently required for the development of organic, inorganic, green, materials, and medicinal chemistry. We discovered a self-assembled Au-supported Pd NPs catalyst (SAPd(0)) and applied it as a catalyst to Suzuki-Miyaura coupling, Buchwald-Hartwig reaction, Carbon(sp2 and sp3)-Hydrogen bond functionalization, double carbonylation, removal of the allyl protecting groups of allyl esters, and redox switching. SAPd(0) comprises approximately 10 layers of self-assembled Pd(0) NPs, whose size is less than 5 nm on the surface of a sulfur-modified Au. The Pd NPs are wrapped in a sulfated p-xylene polymer matrix. We thought that the self-assembled Au-supported Pd NPs could be made by in situ metal NP and nanospace simultaneous organization (PSSO). This methodology involves 4 kinds of simultaneous procedures: i) reduction of a higher valence metal salt, ii) growth of metal NPs with appropriate size, iii) growth of a matrix with appropriate pores, and iv) wrapping of the metal NPs by matrix nanopores. This methodology is different from previously reported metal NPs-immobilizing methods, which use solid supports with preformed pores or coordination sites. We also applied the in situ PSSO method to prepare various immobilized transition-metal NPs, including base metals. For example, the in situ PSSO method can be applicable to easily prepare Ni, Ru, and Fe NPs with good recyclability and low metal leaching for use in organic synthesis.
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Abstract
A common motivation for increasing open access to research findings and data is the potential to create economic benefits—but evidence is patchy and diverse. This study systematically reviewed the evidence on what kinds of economic impacts (positive and negative) open science can have, how these comes about, and how benefits could be maximized. Use of open science outputs often leaves no obvious trace, so most evidence of impacts is based on interviews, surveys, inference based on existing costs, and modelling approaches. There is indicative evidence that open access to findings/data can lead to savings in access costs, labour costs and transaction costs. There are examples of open science enabling new products, services, companies, research and collaborations. Modelling studies suggest higher returns to R&D if open access permits greater accessibility and efficiency of use of findings. Barriers include lack of skills capacity in search, interpretation and text mining, and lack of clarity around where benefits accrue. There are also contextual considerations around who benefits most from open science (e.g., sectors, small vs. larger companies, types of dataset). Recommendations captured in the review include more research, monitoring and evaluation (including developing metrics), promoting benefits, capacity building and making outputs more audience-friendly.
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Successful oral delivery of poorly water-soluble drugs both depends on the intraluminal behavior of drugs and of appropriate advanced drug delivery systems. Eur J Pharm Sci 2019; 137:104967. [PMID: 31252052 DOI: 10.1016/j.ejps.2019.104967] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/27/2019] [Accepted: 06/21/2019] [Indexed: 12/11/2022]
Abstract
Poorly water-soluble drugs continue to be a problematic, yet important class of pharmaceutical compounds for treatment of a wide range of diseases. Their prevalence in discovery is still high, and their development is usually limited by our lack of a complete understanding of how the complex chemical, physiological and biochemical processes that occur between administration and absorption individually and together impact on bioavailability. This review defines the challenge presented by these drugs, outlines contemporary strategies to solve this challenge, and consequent in silico and in vitro evaluation of the delivery technologies for poorly water-soluble drugs. The next steps and unmet needs are proposed to present a roadmap for future studies for the field to consider enabling progress in delivery of poorly water-soluble compounds.
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29
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Offline preparative 2-D polar-copolymerized reversed-phase chromatography × zwitterionic hydrophilic interaction chromatography for effective purification of polar compounds from Caulis Polygoni Multiflori. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1118-1119:70-77. [DOI: 10.1016/j.jchromb.2019.04.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 04/17/2019] [Accepted: 04/17/2019] [Indexed: 12/21/2022]
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Multi-targeted anti-leukemic drug design with the incorporation of silicon into Nelarabine: How silicon increases bioactivity. Eur J Pharm Sci 2019; 134:266-273. [PMID: 31028821 DOI: 10.1016/j.ejps.2019.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/19/2019] [Accepted: 04/04/2019] [Indexed: 12/23/2022]
Abstract
Acute Lymphoblastic Leukemia (ALL) represents 30% of all childhood cancers and children younger than 5 years old have the highest risk for developing ALL. Existing ALL drugs do not respond in approximately 20% of treatment. Therefore, drug development studies against ALL must be continued with either developing existing drugs or discovering new ones. In this study, we evaluated the U.S Food and Drug Administration (FDA) approved ALL drugs according to their physicochemical and pharmaceutical properties, and Nelarabine was found to have the highest bioactivity score. Using the key strategy of bioisosterism commonly accepted by medicinal chemists, we investigated in silico ADME properties, drug-likeness, and biological activity of new designed twenty-four compounds including Nelarabine. The results were evaluated in terms of two classifications: broad spectrum biological activity and filtering of five different drug likeness criteria of the literature including Lipinski's rule of five. We interestingly observed that silicon incorporated compounds exhibited better performance on both criteria by targeting broader spectrum of drug receptors including G-protein coupled receptor (GPCR), ion channel modulator, kinase inhibitor, protease and enzyme inhibitor and by satisfying all of five different drug-likeness criteria reported in the literature. Design compound C19 appeared as a potential drug candidate for further pharmacological research.
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31
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Konaklieva MI. Addressing Antimicrobial Resistance through New Medicinal and Synthetic Chemistry Strategies. SLAS DISCOVERY 2018; 24:419-439. [PMID: 30523713 DOI: 10.1177/2472555218812657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Over the past century, a multitude of derivatives of structural scaffolds with established antimicrobial potential have been prepared and tested, and a variety of new scaffolds have emerged. The effectiveness of antibiotics, however, is in sharp decline because of the emergence of drug-resistant microorganisms. The prevalence of drug resistance, both in clinical and community settings, is a consequence of bacterial ingenuity in altering pathways and/or cell morphology, making it a persistent threat to human health. The fundamental ability of pathogens to survive in a multitude of habitats can be triggered by recognition of chemical signals that warn organisms of exposure to a potentially harmful environment. Host immune defenses, including reactive oxygen intermediates and antibacterial substances, are among the multitude of chemical signals that can subsequently trigger expression of phenotypes better adapted for survival in that hostile environment. Thus, resistance development appears to be unavoidable, which leads to the conclusion that developing an alternative perspective for treatment options is vital. This review will discuss emerging medicinal chemistry approaches for addressing the global multidrug resistance in the 21st century.
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Naylor MR, Ly AM, Handford MJ, Ramos DP, Pye CR, Furukawa A, Klein VG, Noland RP, Edmondson Q, Turmon AC, Hewitt WM, Schwochert J, Townsend CE, Kelly CN, Blanco MJ, Lokey RS. Lipophilic Permeability Efficiency Reconciles the Opposing Roles of Lipophilicity in Membrane Permeability and Aqueous Solubility. J Med Chem 2018; 61:11169-11182. [DOI: 10.1021/acs.jmedchem.8b01259] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Matthew R. Naylor
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Andrew M. Ly
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Mason J. Handford
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Daniel P. Ramos
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Cameron R. Pye
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Akihiro Furukawa
- Modality Research Laboratories, Daiichi Sankyo Company, Ltd., 1-2-58 Hiromachi, Shingawa-ku, Tokyo 140-8710, Japan
| | - Victoria G. Klein
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Ryan P. Noland
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Quinn Edmondson
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Alexandra C. Turmon
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - William M. Hewitt
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Joshua Schwochert
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Chad E. Townsend
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Colin N. Kelly
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Maria-Jesus Blanco
- Sage Therapeutics, 215 First Street, Suite 220, Cambridge, Massachusetts 02142, United States
| | - R. Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
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Valeur E, Jimonet P. New Modalities, Technologies, and Partnerships in Probe and Lead Generation: Enabling a Mode-of-Action Centric Paradigm. J Med Chem 2018; 61:9004-9029. [DOI: 10.1021/acs.jmedchem.8b00378] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Eric Valeur
- Medicinal Chemistry, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal 431 83, Sweden
| | - Patrick Jimonet
- External Innovation Drug Discovery, Global Business Development & Licensing, Sanofi, 13 quai Jules Guesde, 94400 Vitry-sur-Seine, France
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35
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Leeson PD. Impact of Physicochemical Properties on Dose and Hepatotoxicity of Oral Drugs. Chem Res Toxicol 2018; 31:494-505. [PMID: 29722540 DOI: 10.1021/acs.chemrestox.8b00044] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A database containing maximum daily doses of 1841 marketed oral drugs was used to examine the influence of physicochemical properties on dose and hepatotoxicity (drug induced liver injury, DILI). Drugs in the highest ∼20% dose range had significantly reduced mean lipophilicity and molecular weight, increased fractional surface area, increased % of acids, and decreased % of bases versus drugs in the lower ∼60% dose range. Drugs in the ∼20-40% dose range had intermediate mean properties, similar to the mean values for the full drug set. Drugs that are both large and highly lipophilic almost invariably do not have doses in the upper ∼20% range. The results show that oral druglike physicochemical properties are different according to these dose ranges, and this is consistent with maintenance of acceptable safety profiles as efficacious exposure increases. Verified DILI annotations from a compilation of >1000 approved drugs (Chen, M.; et al. Drug Discov. Today, 2016, 21, 648 ) were used. The drugs classified as "No DILI" ( n = 163) had significantly lower dose and lipophilicity, and higher Fsp3 (fraction of carbon atoms that are sp3 hybridized) versus the "Most DILI" ( n = 163) drugs. The percentages of acids were reduced and bases increased in the "No DILI" versus the "Most DILI" groups. Drugs classified as "Less DILI" or "Ambiguous DILI" had intermediate mean values of dose, lipophilicity, Fsp3, and % acids and bases. The impact of lipophilicity and Fsp3 on DILI increases in the upper 20% versus the lower 80% dose range, and a simple decision tree model predicted "No DILI" versus "Most DILI" outcomes with 82% accuracy. The model correctly classified 19 of 22 drugs (86%) that failed in development due to human hepatotoxicity. Because many oral drugs lacking DILI annotations are predicted to be "Most DILI", the model is best used preclinically in conjunction with experimental DILI mitigation.
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Affiliation(s)
- Paul D Leeson
- Paul Leeson Consulting Ltd , The Malt House, Main Street, Congerstone , Nuneaton, Warks CV13 6LZ , U.K
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36
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Young RJ, Leeson PD. Mapping the Efficiency and Physicochemical Trajectories of Successful Optimizations. J Med Chem 2018; 61:6421-6467. [DOI: 10.1021/acs.jmedchem.8b00180] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Robert J. Young
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Paul D. Leeson
- Paul Leeson Consulting Ltd., The Malt House, Main Street, Congerstone, Nuneaton, Warwickshire CV13 6LZ, U.K
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Forster AB, Abeywickrema P, Bunda J, Cox CD, Cabalu TD, Egbertson M, Fay J, Getty K, Hall D, Kornienko M, Lu J, Parthasarathy G, Reid J, Sharma S, Shipe WD, Smith SM, Soisson S, Stachel SJ, Su HP, Wang D, Berger R. The identification of a novel lead class for phosphodiesterase 2 inhibition by fragment-based drug design. Bioorg Med Chem Lett 2017; 27:5167-5171. [DOI: 10.1016/j.bmcl.2017.10.054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/18/2017] [Accepted: 10/22/2017] [Indexed: 01/25/2023]
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38
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Zhang S, Li D, Song Z, Zang C, Zhang L, Song X, Li S. "Carbon Assimilation" Inspired Design and Divergent Synthesis of Drimane Meroterpenoid Mimics as Novel Fungicidal Leads. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:9013-9021. [PMID: 28949528 DOI: 10.1021/acs.jafc.7b03126] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
With structural diversity and versatile biological properties, drimane meroterpenoids have drawn remarkable attention in drug development. The stagnant progress made in the structure optimization and SAR study of this kind of natural product for agrochemicals was mainly a result of inefficient construction. Compared with the reported challenging coupling reaction ("1 + 1" tactic), "carbon assimilation" was conceived and used for the rapid construction of drimanyl meroterpenoid mimics, in which the newly formed covalent bond was directly from the old one of the drimanyl subunit ("2 + 0" tactic), which features atom economy, step economy, and facile preparation. The accompanying introduction of versatile heterocycles and application of easily available feedstocks are beneficial for novel green agrochemical discovery, in view of economic efficiency and improvement of physicochemical properities. Heterocyclic mimics 3a and 3c are presented as potent fungicidal leads with novel skeletons against Botrytis cinerea, >25-fold and >40-fold more promising than the commercial fungicide carbendazim, respectively. Our design was also rationalized by the 6-step synthesis and antifungal assay of the original model of natural meroterpenoids. This tactic can also be fostered or transferred directly to the design of novel natural product mimics for medicinal chemistry or other related biological exploration.
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Affiliation(s)
- Shasha Zhang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University , Weigang 1, Xuanwu District, Nanjing 210095, People's Republic of China
| | - Dangdang Li
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University , Weigang 1, Xuanwu District, Nanjing 210095, People's Republic of China
| | - Zehua Song
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University , Weigang 1, Xuanwu District, Nanjing 210095, People's Republic of China
| | - Chuanli Zang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University , Weigang 1, Xuanwu District, Nanjing 210095, People's Republic of China
| | - Lu Zhang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University , Weigang 1, Xuanwu District, Nanjing 210095, People's Republic of China
| | - Xiushi Song
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University , Weigang 1, Xuanwu District, Nanjing 210095, People's Republic of China
| | - Shengkun Li
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University , Weigang 1, Xuanwu District, Nanjing 210095, People's Republic of China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University , Guiyang 550025, People's Republic of China
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Morrison J, Nophsker M, Elzinga P, Donoso M, Park H, Haskell R. A polychromatic turbidity microplate assay to distinguish discovery stage drug molecules with beneficial precipitation properties. Int J Pharm 2017; 531:24-34. [DOI: 10.1016/j.ijpharm.2017.07.086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/19/2017] [Accepted: 07/31/2017] [Indexed: 02/03/2023]
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40
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DeGoey DA, Chen HJ, Cox PB, Wendt MD. Beyond the Rule of 5: Lessons Learned from AbbVie’s Drugs and Compound Collection. J Med Chem 2017; 61:2636-2651. [DOI: 10.1021/acs.jmedchem.7b00717] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- David A. DeGoey
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Hui-Ju Chen
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Philip B. Cox
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Michael D. Wendt
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
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41
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Polanski J, Tkocz A, Kucia U. Beware of ligand efficiency (LE): understanding LE data in modeling structure-activity and structure-economy relationships. J Cheminform 2017; 9:49. [PMID: 29086197 PMCID: PMC5593805 DOI: 10.1186/s13321-017-0236-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 09/04/2017] [Indexed: 12/19/2022] Open
Abstract
Background On the one hand, ligand efficiency (LE) and the binding efficiency index (BEI), which are binding properties (B) averaged versus the heavy atom count (HAC: LE) or molecular weight (MW: BEI), have recently been declared a novel universal tool for drug design. On the other hand, questions have been raised about the mathematical validity of the LE approach. Results In fact, neither the critics nor the advocates are precise enough to provide a generally understandable and accepted chemistry of the LE metrics. In particular, this refers to the puzzle of the LE trends for small and large molecules. In this paper, we explain the chemistry and mathematics of the LE type of data. Because LE is a weight metrics related to binding per gram, its hyperbolic decrease with an increasing number of heavy atoms can be easily understood by its 1/MW dependency. Accordingly, we analyzed how this influences the LE trends for ligand-target binding, economic big data or molecular descriptor data. In particular, we compared the trends for the thermodynamic ∆G data of a series of ligands that interact with 14 different target classes, which were extracted from the BindingDB database with the market prices of a commercial compound library of ca. 2.5 mln synthetic building blocks. Conclusions An interpretation of LE and BEI that clearly explains the observed trends for these parameters are presented here for the first time. Accordingly, we show that the main misunderstanding of the chemical meaning of the BEI and LE parameters is their interpretation as molecular descriptors that are connected with a single molecule, while binding is a statistical effect in which a population of ligands limits the formation of ligand-receptor complexes. Therefore, LE (BEI) should not be interpreted as a molecular (physicochemical) descriptor that is connected with a single molecule but as a property (binding per gram). Accordingly, the puzzle of the surprising behavior of LE is explained by the 1/MW dependency. This effect clearly explains the hyperbolic LE trend not as a real increase in binding potency but as a physical limitation due to the different population of ligands with different MWs in a 1 g sample available for the formation of ligand-receptor complexes.. ![]()
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Affiliation(s)
- Jaroslaw Polanski
- Institute of Chemistry, University of Silesia, 9 Szkolna Street, 40-006, Katowice, Poland.
| | - Aleksandra Tkocz
- Institute of Chemistry, University of Silesia, 9 Szkolna Street, 40-006, Katowice, Poland
| | - Urszula Kucia
- Institute of Chemistry, University of Silesia, 9 Szkolna Street, 40-006, Katowice, Poland
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Cavalluzzi MM, Mangiatordi GF, Nicolotti O, Lentini G. Ligand efficiency metrics in drug discovery: the pros and cons from a practical perspective. Expert Opin Drug Discov 2017; 12:1087-1104. [PMID: 28814111 DOI: 10.1080/17460441.2017.1365056] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Ligand efficiency metrics are almost universally accepted as a valuable indicator of compound quality and an aid to reduce attrition. Areas covered: In this review, the authors describe ligand efficiency metrics giving a balanced overview on their merits and points of weakness in order to enable the readers to gain an informed opinion. Relevant theoretical breakthroughs and drug-like properties are also illustrated. Several recent exemplary case studies are discussed in order to illustrate the main fields of application of ligand efficiency metrics. Expert opinion: As a medicinal chemist guide, ligand efficiency metrics perform in a context- and chemotype-dependent manner; thus, they should not be used as a magic box. Since the 'big bang' of efficiency metrics occurred more or less ten years ago and the average time to develop a new drug is over the same period, the next few years will give a clearer outlook on the increased rate of success, if any, gained by means of these new intriguing tools.
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Affiliation(s)
| | | | - Orazio Nicolotti
- a Department of Pharmacy - Drug Sciences , University of Bari Aldo Moro , Bari , Italy
| | - Giovanni Lentini
- a Department of Pharmacy - Drug Sciences , University of Bari Aldo Moro , Bari , Italy
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Edueng K, Mahlin D, Bergström CAS. The Need for Restructuring the Disordered Science of Amorphous Drug Formulations. Pharm Res 2017; 34:1754-1772. [PMID: 28523384 PMCID: PMC5533858 DOI: 10.1007/s11095-017-2174-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 05/01/2017] [Indexed: 11/25/2022]
Abstract
The alarming numbers of poorly soluble discovery compounds have centered the efforts towards finding strategies to improve the solubility. One of the attractive approaches to enhance solubility is via amorphization despite the stability issue associated with it. Although the number of amorphous-based research reports has increased tremendously after year 2000, little is known on the current research practice in designing amorphous formulation and how it has changed after the concept of solid dispersion was first introduced decades ago. In this review we try to answer the following questions: What model compounds and excipients have been used in amorphous-based research? How were these two components selected and prepared? What methods have been used to assess the performance of amorphous formulation? What methodology have evolved and/or been standardized since amorphous-based formulation was first introduced and to what extent have we embraced on new methods? Is the extent of research mirrored in the number of marketed amorphous drug products? We have summarized the history and evolution of amorphous formulation and discuss the current status of amorphous formulation-related research practice. We also explore the potential uses of old experimental methods and how they can be used in tandem with computational tools in designing amorphous formulation more efficiently than the traditional trial-and-error approach.
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Affiliation(s)
- Khadijah Edueng
- Department of Pharmacy, Uppsala University, Uppsala Biomedical Centre, P.O. Box 580, SE-75123, Uppsala, Sweden
- Kulliyyah of Pharmacy,, International Islamic University Malaysia, Jalan Istana, 25200, Bandar Indera Mahkota, Pahang, Malaysia
| | - Denny Mahlin
- Department of Pharmacy, Uppsala University, Uppsala Biomedical Centre, P.O. Box 580, SE-75123, Uppsala, Sweden
| | - Christel A S Bergström
- Department of Pharmacy, Uppsala University, Uppsala Biomedical Centre, P.O. Box 580, SE-75123, Uppsala, Sweden.
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Quality guidelines for oral drug candidates: dose, solubility and lipophilicity. Drug Discov Today 2016; 21:1719-1727. [DOI: 10.1016/j.drudis.2016.07.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 06/01/2016] [Accepted: 07/07/2016] [Indexed: 12/30/2022]
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Kell DB, Pretorius E. On the translocation of bacteria and their lipopolysaccharides between blood and peripheral locations in chronic, inflammatory diseases: the central roles of LPS and LPS-induced cell death. Integr Biol (Camb) 2016; 7:1339-77. [PMID: 26345428 DOI: 10.1039/c5ib00158g] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We have recently highlighted (and added to) the considerable evidence that blood can contain dormant bacteria. By definition, such bacteria may be resuscitated (and thus proliferate). This may occur under conditions that lead to or exacerbate chronic, inflammatory diseases that are normally considered to lack a microbial component. Bacterial cell wall components, such as the endotoxin lipopolysaccharide (LPS) of Gram-negative strains, are well known as potent inflammatory agents, but should normally be cleared. Thus, their continuing production and replenishment from dormant bacterial reservoirs provides an easy explanation for the continuing, low-grade inflammation (and inflammatory cytokine production) that is characteristic of many such diseases. Although experimental conditions and determinants have varied considerably between investigators, we summarise the evidence that in a great many circumstances LPS can play a central role in all of these processes, including in particular cell death processes that permit translocation between the gut, blood and other tissues. Such localised cell death processes might also contribute strongly to the specific diseases of interest. The bacterial requirement for free iron explains the strong co-existence in these diseases of iron dysregulation, LPS production, and inflammation. Overall this analysis provides an integrative picture, with significant predictive power, that is able to link these processes via the centrality of a dormant blood microbiome that can resuscitate and shed cell wall components.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry and The Manchester Institute of Biotechnology, The University of Manchester, 131, Princess St, Manchester M1 7DN, Lancs, UK.
| | - Etheresia Pretorius
- Department of Physiology, Faculty of Health Sciences, University of Pretoria, Arcadia 0007, South Africa.
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Norton RS, Leung EWW, Chandrashekaran IR, MacRaild CA. Applications of (19)F-NMR in Fragment-Based Drug Discovery. Molecules 2016; 21:molecules21070860. [PMID: 27438818 PMCID: PMC6273323 DOI: 10.3390/molecules21070860] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/21/2016] [Accepted: 06/21/2016] [Indexed: 11/16/2022] Open
Abstract
(19)F-NMR has proved to be a valuable tool in fragment-based drug discovery. Its applications include screening libraries of fluorinated fragments, assessing competition among elaborated fragments and identifying the binding poses of promising hits. By observing fluorine in both the ligand and the target protein, useful information can be obtained on not only the binding pose but also the dynamics of ligand-protein interactions. These applications of (19)F-NMR will be illustrated in this review with studies from our fragment-based drug discovery campaigns against protein targets in parasitic and infectious diseases.
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Affiliation(s)
- Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia.
| | - Eleanor W W Leung
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia.
| | - Indu R Chandrashekaran
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia.
| | - Christopher A MacRaild
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia.
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Abstract
After 20 years of sometimes quiet growth, fragment-based drug discovery (FBDD) has become mainstream. More than 30 drug candidates derived from fragments have entered the clinic, with two approved and several more in advanced trials. FBDD has been widely applied in both academia and industry, as evidenced by the large number of papers from universities, non-profit research institutions, biotechnology companies and pharmaceutical companies. Moreover, FBDD draws on a diverse range of disciplines, from biochemistry and biophysics to computational and medicinal chemistry. As the promise of FBDD strategies becomes increasingly realized, now is an opportune time to draw lessons and point the way to the future. This Review briefly discusses how to design fragment libraries, how to select screening techniques and how to make the most of information gleaned from them. It also shows how concepts from FBDD have permeated and enhanced drug discovery efforts.
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Bergström CAS, Yazdanian M. Lipophilicity in Drug Development: Too Much or Not Enough? AAPS JOURNAL 2016; 18:1095-1100. [PMID: 27393481 DOI: 10.1208/s12248-016-9947-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/03/2016] [Indexed: 11/30/2022]
Abstract
A round table discussion was held during the AAPS Annual Meeting on October 27, 2015, with the somewhat provocative topic of whether we need more or less lipophilic compounds in drug development. The session was attended by more than 250 participants, and the feedback was very positive as this round table became a forum for the exchange of ideas from scientists within the academia and industry. Most importantly, the discussion highlighted the difference in approaches to compound selection and development strategies in various companies and organizations. As moderators of this session, we are writing this report to highlight the points and counterpoints made at the session and to bring the importance of the dialogue and debate to the forefront of discussions on how to select the best drug development candidates to enable efficient delivery and, hence, treatment of diseases.
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Affiliation(s)
- Christel A S Bergström
- Department of Pharmacy, Uppsala University, Uppsala Biomedical Centre, P.O. Box 580, SE-751 23, Uppsala, Sweden.
| | - Mehran Yazdanian
- Pharmaceutics Department, Teva Branded Pharmaceutical R&D Inc, West Chester, Pennsylvania, USA
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Villoutreix B. Combining bioinformatics, chemoinformatics and experimental approaches to design chemical probes: Applications in the field of blood coagulation. ANNALES PHARMACEUTIQUES FRANÇAISES 2016; 74:253-66. [DOI: 10.1016/j.pharma.2016.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/21/2016] [Accepted: 03/21/2016] [Indexed: 11/08/2022]
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Bergström CAS, Charman WN, Porter CJH. Computational prediction of formulation strategies for beyond-rule-of-5 compounds. Adv Drug Deliv Rev 2016; 101:6-21. [PMID: 26928657 DOI: 10.1016/j.addr.2016.02.005] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/11/2016] [Accepted: 02/17/2016] [Indexed: 12/12/2022]
Abstract
The physicochemical properties of some contemporary drug candidates are moving towards higher molecular weight, and coincidentally also higher lipophilicity in the quest for biological selectivity and specificity. These physicochemical properties move the compounds towards beyond rule-of-5 (B-r-o-5) chemical space and often result in lower water solubility. For such B-r-o-5 compounds non-traditional delivery strategies (i.e. those other than conventional tablet and capsule formulations) typically are required to achieve adequate exposure after oral administration. In this review, we present the current status of computational tools for prediction of intestinal drug absorption, models for prediction of the most suitable formulation strategies for B-r-o-5 compounds and models to obtain an enhanced understanding of the interplay between drug, formulation and physiological environment. In silico models are able to identify the likely molecular basis for low solubility in physiologically relevant fluids such as gastric and intestinal fluids. With this baseline information, a formulation scientist can, at an early stage, evaluate different orally administered, enabling formulation strategies. Recent computational models have emerged that predict glass-forming ability and crystallisation tendency and therefore the potential utility of amorphous solid dispersion formulations. Further, computational models of loading capacity in lipids, and therefore the potential for formulation as a lipid-based formulation, are now available. Whilst such tools are useful for rapid identification of suitable formulation strategies, they do not reveal drug localisation and molecular interaction patterns between drug and excipients. For the latter, Molecular Dynamics simulations provide an insight into the interplay between drug, formulation and intestinal fluid. These different computational approaches are reviewed. Additionally, we analyse the molecular requirements of different targets, since these can provide an early signal that enabling formulation strategies will be required. Based on the analysis we conclude that computational biopharmaceutical profiling can be used to identify where non-conventional gateways, such as prediction of 'formulate-ability' during lead optimisation and early development stages, are important and may ultimately increase the number of orally tractable contemporary targets.
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Affiliation(s)
- Christel A S Bergström
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia; Department of Pharmacy, Uppsala University, Uppsala Biomedical Center, P.O. Box 580, SE-751 23 Uppsala, Sweden.
| | - William N Charman
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Christopher J H Porter
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia; ARC Centre of Excellence in Convergent Nano-Bio Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
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