1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Ouyang Y, Huang JJ, Wang YL, Zhong H, Song BA, Hao GF. In Silico Resources of Drug-Likeness as a Mirror: What Are We Lacking in Pesticide-Likeness? JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:10761-10773. [PMID: 34516106 DOI: 10.1021/acs.jafc.1c01460] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Unfavorable bioavailability is an important aspect underlying the failure of drug candidates. Computational approaches for evaluating drug-likeness can minimize these risks. Over the past decades, computational approaches for evaluating drug-likeness have sped up the process of drug development and were also quickly derived to pesticide-likeness. As a result of many critical differences between drugs and pesticides, many kinds of methods for drug-likeness cannot be used for pesticide-likeness. Therefore, it is crucial to comprehensively compare and analyze the differences between drug-likeness and pesticide-likeness, which may provide a basis for solving the problems encountered during the evaluation of pesticide-likeness. Here, we systematically collected the recent advances of drug-likeness and pesticide-likeness and compared their characteristics. We also evaluated the current lack of studies on pesticide-likeness, the molecular descriptors and parameters adopted, the pesticide-likeness model on pesticide target organisms, and comprehensive analysis tools. This work may guide researchers to use appropriate methods for developing pesticide-likeness models. It may also aid non-specialists to understand some important concepts in drug-likeness and pesticide-likeness.
Collapse
Affiliation(s)
- Yan Ouyang
- Guizhou Engineering Laboratory for Synthetic Drugs, Key Laboratory of Guizhou Fermentation Engineering and Biomedicine, School of Pharmaceutical Sciences, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
| | - Jun-Jie Huang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
| | - Yu-Liang Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
- International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Hang Zhong
- Guizhou Engineering Laboratory for Synthetic Drugs, Key Laboratory of Guizhou Fermentation Engineering and Biomedicine, School of Pharmaceutical Sciences, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
| | - Bao-An Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
| | - Ge-Fei Hao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
| |
Collapse
|
3
|
Bhanot A, Sundriyal S. Physicochemical Profiling and Comparison of Research Antiplasmodials and Advanced Stage Antimalarials with Oral Drugs. ACS OMEGA 2021; 6:6424-6437. [PMID: 33718733 PMCID: PMC7948433 DOI: 10.1021/acsomega.1c00104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/18/2021] [Indexed: 06/12/2023]
Abstract
To understand the property space of antimalarials, we collated a large dataset of research antiplasmodial (RAP) molecules with known in vitro potencies and advanced stage antimalarials (ASAMs) with established oral bioavailability. While RAP molecules are "non-druglike", ASAM molecules display properties closer to Lipinski's and Veber's thresholds. Comparison within the different potency groups of RAP molecules indicates that the in vitro potency is positively correlated to the molecular weight, the calculated octanol-water partition coefficient (clog P), aromatic ring counts (#Ar), and hydrogen bond acceptors. Despite both categories being bioavailable, the ASAM molecules are relatively larger and more lipophilic, have a lower polar surface area, and possess a higher count of heteroaromatic rings than oral drugs. Also, antimalarials are found to have a higher proportion of aromatic (#ArN) and basic nitrogen (#BaN) counts, features implicitly used in the design of antimalarial molecules but not well studied hitherto. We also propose using descriptors scaled by the sum of #ArN and #BaN (SBAN) to define an antimalarial property space. Together, these results may have important applications in the identification and optimization of future antimalarials.
Collapse
Affiliation(s)
- Amritansh Bhanot
- Department of Pharmacy, Birla
Institute of Technology and Science Pilani, Pilani Campus,
Vidya Vihar, Pilani, Rajasthan 333 031, India
| | - Sandeep Sundriyal
- Department of Pharmacy, Birla
Institute of Technology and Science Pilani, Pilani Campus,
Vidya Vihar, Pilani, Rajasthan 333 031, India
| |
Collapse
|
4
|
Ichikawa Y, Hiramatsu M, Mita Y, Makishima M, Matsumoto Y, Masumoto Y, Muranaka A, Uchiyama M, Hashimoto Y, Ishikawa M. meta-Non-flat substituents: a novel molecular design to improve aqueous solubility in small molecule drug discovery. Org Biomol Chem 2021; 19:446-456. [PMID: 33331380 DOI: 10.1039/d0ob02083d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Aqueous solubility is a key requirement for small-molecule drug candidates. Here, we investigated the regioisomer-physicochemical property relationships of disubstituted benzenes. We found that meta-isomers bearing non-flat substituents tend to possess the lowest melting point and the highest thermodynamic aqueous solubility among the regioisomers. The examination of pharmaceutical compounds containing a disubstituted benzene moiety supported the idea that the introduction of a non-flat substituent at the meta position of a benzene substructure would be a promising approach for medicinal chemists aiming to improve the thermodynamic aqueous solubility of drug candidates, even though it might not be universally effective.
Collapse
Affiliation(s)
- Yuki Ichikawa
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Michiaki Hiramatsu
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yusuke Mita
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Makoto Makishima
- Nihon University School of Medicine, 30-1 Oyaguchi-kamicho, Itabashi-ku, Tokyo 173-8610, Japan
| | - Yotaro Matsumoto
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Yui Masumoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Atsuya Muranaka
- Advanced Elements Chemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan and Advanced Elements Chemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Yuichi Hashimoto
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Minoru Ishikawa
- Graduate School of Life Sciences, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Fournier JF, Bhurruth-Alcor Y, Musicki B, Aubert J, Aurelly M, Bouix-Peter C, Bouquet K, Chantalat L, Delorme M, Drean B, Duvert G, Fleury-Bregeot N, Gauthier B, Grisendi K, Harris CS, Hennequin LF, Isabet T, Joly F, Lafitte G, Millois C, Morgentin R, Pascau J, Piwnica D, Rival Y, Soulet C, Thoreau É, Tomas L. Squaramides as novel class I and IIB histone deacetylase inhibitors for topical treatment of cutaneous t-cell lymphoma. Bioorg Med Chem Lett 2018; 28:2985-2992. [PMID: 30122227 DOI: 10.1016/j.bmcl.2018.06.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/26/2018] [Accepted: 06/15/2018] [Indexed: 10/14/2022]
Abstract
A series of squaramide-based hydroxamic acids were designed, synthesized and evaluated against human HDAC enzyme. Squaramides were found to be potent in the Hut78 cell line, but initially suffered from low solubility. Leads with improved solubility and metabolic profiles were shown to be class I, IIB and IV selective.
Collapse
Affiliation(s)
- Jean-François Fournier
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France.
| | - Yushma Bhurruth-Alcor
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Branislav Musicki
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Jérome Aubert
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Michèle Aurelly
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Claire Bouix-Peter
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Karinne Bouquet
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Laurent Chantalat
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Marion Delorme
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Bénédicte Drean
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Gwenaelle Duvert
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | | | - Blanche Gauthier
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Karine Grisendi
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Craig S Harris
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Laurent F Hennequin
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Tatiana Isabet
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin - BP 48, 91192 Gif-sur-Yvette Cedex, France
| | - Florence Joly
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Guillaume Lafitte
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Corinne Millois
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | | | - Jonathan Pascau
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - David Piwnica
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Yves Rival
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Catherine Soulet
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Étienne Thoreau
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Loïc Tomas
- Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| |
Collapse
|
7
|
Fournier JF, Clary L, Chambon S, Dumais L, Harris CS, Millois C, Pierre R, Talano S, Thoreau É, Aubert J, Aurelly M, Bouix-Peter C, Brethon A, Chantalat L, Christin O, Comino C, El-Bazbouz G, Ghilini AL, Isabet T, Lardy C, Luzy AP, Mathieu C, Mebrouk K, Orfila D, Pascau J, Reverse K, Roche D, Rodeschini V, Hennequin LF. Rational Drug Design of Topically Administered Caspase 1 Inhibitors for the Treatment of Inflammatory Acne. J Med Chem 2018; 61:4030-4051. [DOI: 10.1021/acs.jmedchem.8b00067] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jean-François Fournier
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Laurence Clary
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Sandrine Chambon
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Laurence Dumais
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Craig Steven Harris
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Corinne Millois
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Romain Pierre
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Sandrine Talano
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Étienne Thoreau
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Jérome Aubert
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Michèle Aurelly
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Claire Bouix-Peter
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Anne Brethon
- Edelris, 115 Avenue Lacassagne, 69003 Lyon, France
| | - Laurent Chantalat
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Olivier Christin
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Catherine Comino
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Ghizlane El-Bazbouz
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Anne-Laurence Ghilini
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Tatiana Isabet
- Synchrotron Soleil, L’Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette Cedex, France
| | - Claude Lardy
- Edelris, 115 Avenue Lacassagne, 69003 Lyon, France
| | - Anne-Pascale Luzy
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Céline Mathieu
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Kenny Mebrouk
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Danielle Orfila
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Jonathan Pascau
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Kevin Reverse
- Nestlé Skin Health R&D, 2400 Route des Colles, BP 87, 06902 Sophia-Antipolis Cedex, France
| | - Didier Roche
- Edelris, 115 Avenue Lacassagne, 69003 Lyon, France
| | | | | |
Collapse
|
8
|
Withnall M, Chen H, Tetko IV. Matched Molecular Pair Analysis on Large Melting Point Datasets: A Big Data Perspective. ChemMedChem 2018; 13:599-606. [PMID: 28650584 PMCID: PMC5900986 DOI: 10.1002/cmdc.201700303] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 06/26/2017] [Indexed: 11/11/2022]
Abstract
A matched molecular pair (MMP) analysis was used to examine the change in melting point (MP) between pairs of similar molecules in a set of ∼275k compounds. We found many cases in which the change in MP (ΔMP) of compounds correlates with changes in functional groups. In line with the results of a previous study, correlations between ΔMP and simple molecular descriptors, such as the number of hydrogen bond donors, were identified. In using a larger dataset, covering a wider chemical space and range of melting points, we observed that this method remains stable and scales well with larger datasets. This MMP-based method could find use as a simple privacy-preserving technique to analyze large proprietary databases and share findings between participating research groups.
Collapse
Affiliation(s)
- Michael Withnall
- Helmholtz Zentrum München—German Research Center for Environmental Health, GmbHInstitute of Structural BiologyNeuherbergGermany
| | - Hongming Chen
- External Sciences, Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D GothenburgMölndal43183Sweden
| | - Igor V. Tetko
- Helmholtz Zentrum München—German Research Center for Environmental Health, GmbHInstitute of Structural BiologyNeuherbergGermany
- BIGCHEM GmbHIngolstädter Landstraße 1, b. 60w85764NeuherbergGermany
- Institute of Structural Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, GmbHIngolstädter Landstraße 185764NeuherbergGermany
| |
Collapse
|
9
|
Kopsida M, Barron GA, Bermano G, Kong Thoo Lin P, Goua M. Novel bisnaphthalimidopropyl (BNIPs) derivatives as anticancer compounds targeting DNA in human breast cancer cells. Org Biomol Chem 2018; 14:9780-9789. [PMID: 27722499 DOI: 10.1039/c6ob01850e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Bisnaphthalimidopropyl (BNIP) derivatives are a family of compounds that exert anti-cancer activities in vitro and, according to previous studies, variations in the linker sequence have increased their DNA binding and cytotoxic activities. By modifying the linker sequence of bisnaphthalimidopropyl diaminodicyclohexylmethane (BNIPDaCHM), a previously synthesised BNIP derivative with anti-cancer properties, three novel BNIP derivatives were designed. Bisnaphthalimidopropyl-piperidylpropane (BNIPPiProp), a structural isomer of BNIPDaCHM, bisnaphthalimidopropyl ethylenedipiperidine dihydrobromide (BNIPPiEth), an isoform of BNIPDaCHM with a shorter linker chain, and (trans(trans))-bisnaphthalimidopropyl diaminodicyclohexylmethane (trans,trans-BNIPDaCHM), a stereoisomer of BNIPDaCHM, were successfully synthesised (72.3-29.5% yield) and characterised by nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS). Competitive displacement of ethidium bromide (EtBr) and UV binding studies were used to study the interactions of BNIP derivatives with Calf Thymus DNA. The cytotoxicity of these derivatives was assessed against human breast cancer MDA-MB-231 and SKBR-3 cells by MTT assay. Propidium iodide (PI) flow cytometry was conducted in order to evaluate the cellular DNA content in both breast cancer cell lines before and after treatment with BNIPs. The results showed that all novel BNIPs exhibit strong DNA binding properties in vitro, and strong cytotoxicity, with IC50 values in the range of 0.2-3.3 μM after 24 hours drug treatment. Two of the novel BNIP derivatives, BNIPPiEth and trans,trans-BNIPDaCHM, exhibited greater cytotoxicity against the two breast cancer cell lines studied, compared to BNIPDaCHM. By synthesising enantiopures and reducing the length of the linker sequence, the cytotoxicity of the BNIP derivatives was significantly improved compared to BNIPDaCHM, while maintaining DNA binding and bis-intercalating properties. In addition, cell cycle studies indicated that trans,trans-BNIPDaCHM, the most cytotoxic BNIP derivative, induced sub-G1 cell cycle arrest, indicative of apoptotic cell death. Based on these findings, further investigation is under way to assess the potential efficacy of trans,trans-BNIPDaCHM and BNIPPiEth in treating human breast cancer.
Collapse
Affiliation(s)
- Maria Kopsida
- School of Pharmacy and Life Sciences, Robert Gordon University, Garthdee Road, Aberdeen, AB10 7GJ, Scotland, UK.
| | - Gemma A Barron
- School of Pharmacy and Life Sciences, Robert Gordon University, Garthdee Road, Aberdeen, AB10 7GJ, Scotland, UK. and Centre for Obesity Research and Education (CORE), Faculty of Health and Social Care, Robert Gordon University, Garthdee Road, Aberdeen, AB10 7GJ, Scotland, UK
| | - Giovanna Bermano
- Centre for Obesity Research and Education (CORE), Faculty of Health and Social Care, Robert Gordon University, Garthdee Road, Aberdeen, AB10 7GJ, Scotland, UK
| | - Paul Kong Thoo Lin
- School of Pharmacy and Life Sciences, Robert Gordon University, Garthdee Road, Aberdeen, AB10 7GJ, Scotland, UK.
| | - Marie Goua
- School of Pharmacy and Life Sciences, Robert Gordon University, Garthdee Road, Aberdeen, AB10 7GJ, Scotland, UK.
| |
Collapse
|
10
|
Lukac I, Zarnecka J, Griffen EJ, Dossetter AG, St-Gallay SA, Enoch SJ, Madden JC, Leach AG. Turbocharging Matched Molecular Pair Analysis: Optimizing the Identification and Analysis of Pairs. J Chem Inf Model 2017; 57:2424-2436. [DOI: 10.1021/acs.jcim.7b00335] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Iva Lukac
- School
of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, U.K
| | - Joanna Zarnecka
- School
of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, U.K
| | | | | | | | - Steven J. Enoch
- School
of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, U.K
| | - Judith C. Madden
- School
of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, U.K
| | - Andrew G. Leach
- School
of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, U.K
- MedChemica Ltd., BioHub, Alderley
Park, Macclesfield SK10
4TG, U.K
| |
Collapse
|
11
|
Boiteau JG, Ouvry G, Arlabosse JM, Astri S, Beillard A, Bhurruth-Alcor Y, Bonnary L, Bouix-Peter C, Bouquet K, Bourotte M, Cardinaud I, Comino C, Deprez B, Duvert D, Féret A, Hacini-Rachinel F, Harris CS, Luzy AP, Mathieu A, Millois C, Orsini N, Pascau J, Pinto A, Piwnica D, Polge G, Reitz A, Reversé K, Rodeville N, Rossio P, Spiesse D, Tabet S, Taquet N, Tomas L, Vial E, Hennequin LF. Discovery and process development of a novel TACE inhibitor for the topical treatment of psoriasis. Bioorg Med Chem 2017; 26:945-956. [PMID: 28818461 DOI: 10.1016/j.bmc.2017.07.054] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/17/2017] [Accepted: 07/28/2017] [Indexed: 01/15/2023]
Abstract
Targeting the TNFα pathway is a validated approach to the treatment of psoriasis. In this pathway, TACE stands out as a druggable target and has been the focus of in-house research programs. In this article, we present the discovery of clinical candidate 26a. Starting from hits plagued with poor solubility or genotoxicity, 26a was identified through thorough multiparameter optimisation. Showing robust in vivo activity in an oxazolone-mediated inflammation model, the compound was selected for development. Following a polymorph screen, the hydrochloride salt was selected and the synthesis was efficiently developed to yield the API in 47% overall yield.
Collapse
Affiliation(s)
- Jean-Guy Boiteau
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France.
| | - Gilles Ouvry
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France.
| | | | - Stéphanie Astri
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Audrey Beillard
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | | | - Laetitia Bonnary
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Claire Bouix-Peter
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Karine Bouquet
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Marilyne Bourotte
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Isabelle Cardinaud
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Catherine Comino
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Benoît Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Denis Duvert
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Angélique Féret
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | | | - Craig S Harris
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Anne-Pascale Luzy
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Arnaud Mathieu
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Corinne Millois
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Nicolas Orsini
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Jonathan Pascau
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Artur Pinto
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - David Piwnica
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Gaëlle Polge
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Arnaud Reitz
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Kevin Reversé
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Nicolas Rodeville
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Patricia Rossio
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Delphine Spiesse
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Samuel Tabet
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Nathalie Taquet
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Loïc Tomas
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Emmanuel Vial
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| | - Laurent F Hennequin
- Nestlé Skin Health R&D, Les Templiers 2400 Route des Colles, 06410 Biot, France
| |
Collapse
|
12
|
Umei K, Nishigaya Y, Kondo A, Tatani K, Tanaka N, Kohno Y, Seto S. Novel pyrazolo[1,5- a ]pyridines as orally active EP 1 receptor antagonists: Synthesis, structure-activity relationship studies, and biological evaluation. Bioorg Med Chem 2017; 25:2635-2642. [DOI: 10.1016/j.bmc.2017.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 02/27/2017] [Accepted: 03/03/2017] [Indexed: 10/20/2022]
|
13
|
Fucke K, McIntyre GJ, Lemée-Cailleau MH, Wilkinson C, Edwards AJ, Howard JAK, Steed JW. Insights into the crystallisation process from anhydrous, hydrated and solvated crystal forms of diatrizoic acid. Chemistry 2015; 21:1036-47. [PMID: 25370384 DOI: 10.1002/chem.201404693] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Indexed: 11/11/2022]
Abstract
Diatrizoic acid (DTA), a clinically used X-ray contrast agent, crystallises in two hydrated, three anhydrous and nine solvated solid forms, all of which have been characterised by X-ray crystallography. Single-crystal neutron structures of DTA dihydrate and monosodium DTA tetrahydrate have been determined. All of the solid-state structures have been analysed using partial atomic charges and hardness algorithm (PACHA) calculations. Even though in general all DTA crystal forms reveal similar intermolecular interactions, the overall crystal packing differs considerably from form to form. The water of the dihydrate is encapsulated between a pair of host molecules, which calculations reveal to be an extraordinarily stable motif. DTA presents functionalities that enable hydrogen and halogen bonding, and whilst an extended hydrogen-bonding network is realised in all crystal forms, halogen bonding is not present in the hydrated crystal forms. This is due to the formation of a hydrogen-bonding network based on individual enclosed water squares, which is not amenable to the concomitant formation of halogen bonds. The main interaction in the solvates involves the carboxylic acid, which corroborates the hypothesis that this strong interaction is the last one to be broken during the crystal desolvation and nucleation process.
Collapse
Affiliation(s)
- Katharina Fucke
- School of Medicine, Pharmacy and Health, Durham University, University Boulevard, Stockton-on-Tees, TS17 6BH (United Kingdom).
| | | | | | | | | | | | | |
Collapse
|
14
|
|
15
|
Nicolaou KC. Advancing the Drug Discovery and Development Process. Angew Chem Int Ed Engl 2014; 53:9128-40. [DOI: 10.1002/anie.201404761] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Indexed: 11/05/2022]
|
16
|
Kramer C, Fuchs JE, Whitebread S, Gedeck P, Liedl KR. Matched Molecular Pair Analysis: Significance and the Impact of Experimental Uncertainty. J Med Chem 2014; 57:3786-802. [DOI: 10.1021/jm500317a] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Christian Kramer
- Department
of Theoretical Chemistry, Faculty for Chemistry and Pharmacy, Center
for Molecular Biosciences Innsbruck (CMBI), Leopold-Franzens University Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Julian E. Fuchs
- Department
of Theoretical Chemistry, Faculty for Chemistry and Pharmacy, Center
for Molecular Biosciences Innsbruck (CMBI), Leopold-Franzens University Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Steven Whitebread
- Preclinical
Safety Profiling, Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Peter Gedeck
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, No. 05-01 Chromos, Singapore 138670, Singapore
| | - Klaus R. Liedl
- Department
of Theoretical Chemistry, Faculty for Chemistry and Pharmacy, Center
for Molecular Biosciences Innsbruck (CMBI), Leopold-Franzens University Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| |
Collapse
|
17
|
Stepan AF, Kauffman GW, Keefer CE, Verhoest PR, Edwards M. Evaluating the Differences in Cycloalkyl Ether Metabolism Using the Design Parameter “Lipophilic Metabolism Efficiency” (LipMetE) and a Matched Molecular Pairs Analysis. J Med Chem 2013; 56:6985-90. [DOI: 10.1021/jm4008642] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Antonia F. Stepan
- Pfizer Worldwide Research & Development, 700 Main Street, Cambridge, Massachusetts 02139, United States
| | - Gregory W. Kauffman
- Pfizer Worldwide Research & Development, 700 Main Street, Cambridge, Massachusetts 02139, United States
| | - Christopher E. Keefer
- Pfizer Worldwide Research & Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Patrick R. Verhoest
- Pfizer Worldwide Research & Development, 700 Main Street, Cambridge, Massachusetts 02139, United States
| | - Martin Edwards
- Pfizer Worldwide Research & Development, 10770 Science Center Drive, La Jolla, California 92121, United States
| |
Collapse
|
18
|
Dossetter AG, Griffen EJ, Leach AG. Matched Molecular Pair Analysis in drug discovery. Drug Discov Today 2013; 18:724-31. [DOI: 10.1016/j.drudis.2013.03.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/15/2013] [Accepted: 03/25/2013] [Indexed: 01/07/2023]
|
19
|
Papadatos G, Brown N. In silico
applications of bioisosterism in contemporary medicinal chemistry practice. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1148] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
20
|
Wassermann AM, Dimova D, Iyer P, Bajorath J. Advances in Computational Medicinal Chemistry: Matched Molecular Pair Analysis. Drug Dev Res 2012. [DOI: 10.1002/ddr.21045] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Anne Mai Wassermann
- Department of Life Science Informatics; B-IT; LIMES Program Unit Chemical Biology and Medicinal Chemistry; Rheinische Friedrich-Wilhelms-Universität Bonn; Dahlmannstr. 2; D-53113; Bonn; Germany
| | - Dilyana Dimova
- Department of Life Science Informatics; B-IT; LIMES Program Unit Chemical Biology and Medicinal Chemistry; Rheinische Friedrich-Wilhelms-Universität Bonn; Dahlmannstr. 2; D-53113; Bonn; Germany
| | - Preeti Iyer
- Department of Life Science Informatics; B-IT; LIMES Program Unit Chemical Biology and Medicinal Chemistry; Rheinische Friedrich-Wilhelms-Universität Bonn; Dahlmannstr. 2; D-53113; Bonn; Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics; B-IT; LIMES Program Unit Chemical Biology and Medicinal Chemistry; Rheinische Friedrich-Wilhelms-Universität Bonn; Dahlmannstr. 2; D-53113; Bonn; Germany
| |
Collapse
|
21
|
Fucke K, Howard JAK, Steed JW. Overcoming the solvation shell during the crystallisation of diatrizoic acid from dimethylsulfoxide. Chem Commun (Camb) 2012; 48:12065-7. [DOI: 10.1039/c2cc35995b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|