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Abstract
An analysis of 156 published clinical candidates from the Journal of Medicinal Chemistry between 2018 and 2021 was conducted to identify lead generation strategies most frequently employed leading to drug candidates. As in a previous publication, the most frequent lead generation strategies resulting in clinical candidates were from known compounds (59%) followed by random screening approaches (21%). The remainder of the approaches included directed screening, fragment screening, DNA-encoded library screening (DEL), and virtual screening. An analysis of similarity was also conducted based on Tanimoto-MCS and revealed most clinical candidates were distant from their original hits; however, most shared a key pharmacophore that translated from hit-to-clinical candidate. An examination of frequency of oxygen, nitrogen, fluorine, chlorine, and sulfur incorporation in clinical candidates was also conducted. The three most similar and least similar hit-to-clinical pairs from random screening were examined to provide perspective on changes that occur that lead to successful clinical candidates.
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Affiliation(s)
- Dean G Brown
- Jnana Therapeutics, One Design Center Pl Suite 19-400, Boston, Massachusetts 02210, United States
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2
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Zhang S, Liu Y, Javeed A, Jian C, Sun J, Wu S, Han B. Treatment of allergy: Overview of synthetic anti-allergy small molecules in medicinal chemistry. Eur J Med Chem 2023; 249:115151. [PMID: 36731273 DOI: 10.1016/j.ejmech.2023.115151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/30/2023]
Abstract
The prevalence of allergic diseases has been continuously increasing over the past few decades, affecting approximately 20-30% of the global population. Allergic reactions to infection of respiratory tract, digestive tract, and skin system involve multiple different targets. The main difficulty of anti-allergy research is how to develop drugs with good curative effect and less side effects by adopting new multi-targets and mechanisms according to the clinical characteristics of different allergic populations and different allergens. This review focuses on information concerning potential therapeutic targets as well as the synthetic anti-allergy small molecules with respect to their medicinal chemistry. The structure-activity relationship and the mechanism of compound-target interaction were highlighted with perspective to histamine-1/4 receptor antagonists, leukotriene biosynthesis, Th2 cytokines inhibitors, and calcium channel blockers. We hope that the study of chemical scaffold modification and optimization for different lead compounds summarized in this review not only lays the foundation for improvement of success rate and efficiency of virtual screening of antiallergic drugs, but also can provide valuable reference for the drug design of related promising research such as allergy, inflammation, and cancer.
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Affiliation(s)
- Shanshan Zhang
- Zhejiang Key Laboratory of Silkworm Bioreactor and Biomedicine, Laboratory of Antiallergy Functional Molecules, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Yi Liu
- Hangzhou Zheda Dixun Biological Gene Engineering Co., LTD., Hangzhou, China
| | - Ansar Javeed
- Zhejiang Key Laboratory of Silkworm Bioreactor and Biomedicine, Laboratory of Antiallergy Functional Molecules, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Cuiqin Jian
- Zhejiang Key Laboratory of Silkworm Bioreactor and Biomedicine, Laboratory of Antiallergy Functional Molecules, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jinlyu Sun
- Department of Allergy, Beijing Key Laboratory of Precision Medicine for Diagnosis and Treatment of Allergic Diseases, National Clinical Research Center for Dermatologic and Immunologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100730, China
| | - Shandong Wu
- Hangzhou Zheda Dixun Biological Gene Engineering Co., LTD., Hangzhou, China
| | - Bingnan Han
- Zhejiang Key Laboratory of Silkworm Bioreactor and Biomedicine, Laboratory of Antiallergy Functional Molecules, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
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Haeggström JZ, Newcomer ME. Structures of Leukotriene Biosynthetic Enzymes and Development of New Therapeutics. Annu Rev Pharmacol Toxicol 2023; 63:407-428. [PMID: 36130059 DOI: 10.1146/annurev-pharmtox-051921-085014] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Leukotrienes are potent immune-regulating lipid mediators with patho-genic roles in inflammatory and allergic diseases, particularly asthma. These autacoids also contribute to low-grade inflammation, a hallmark of cardiovascular, neurodegenerative, metabolic, and tumor diseases. Biosynthesis of leukotrienes involves release and oxidative metabolism of arachidonic acid and proceeds via a set of cytosolic and integral membrane enzymes that are typically expressed by cells of the innate immune system. In activated cells, these enzymes traffic and assemble at the endoplasmic and perinuclear membrane, together comprising a biosynthetic complex. Here we describe recent advances in our molecular understanding of the protein components of the leukotriene-synthesizing enzyme machinery and also briefly touch upon the leukotriene receptors. Moreover, we discuss emerging opportunities for pharmacological intervention and development of new therapeutics.
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Affiliation(s)
- Jesper Z Haeggström
- Department of Medical Biochemistry and Biophysics, Division of Chemistry 2, Karolinska Institutet, Stockholm, Sweden;
| | - Marcia E Newcomer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA;
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4
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Ergül AG, Maz TG, Kretzer C, Olğaç A, Jordan PM, Çalışkan B, Werz O, Banoglu E. Novel potent benzimidazole-based microsomal prostaglandin E2 Synthase-1 (mPGES-1) inhibitors derived from BRP-201 that also inhibit leukotriene C4 synthase. Eur J Med Chem 2022; 231:114167. [DOI: 10.1016/j.ejmech.2022.114167] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/22/2022] [Accepted: 01/29/2022] [Indexed: 01/27/2023]
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5
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Cheng X, Ma L. Enzymatic synthesis of fluorinated compounds. Appl Microbiol Biotechnol 2021; 105:8033-8058. [PMID: 34625820 PMCID: PMC8500828 DOI: 10.1007/s00253-021-11608-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/16/2021] [Accepted: 09/18/2021] [Indexed: 12/31/2022]
Abstract
Fluorinated compounds are widely used in the fields of molecular imaging, pharmaceuticals, and materials. Fluorinated natural products in nature are rare, and the introduction of fluorine atoms into organic compound molecules can give these compounds new functions and make them have better performance. Therefore, the synthesis of fluorides has attracted more and more attention from biologists and chemists. Even so, achieving selective fluorination is still a huge challenge under mild conditions. In this review, the research progress of enzymatic synthesis of fluorinated compounds is summarized since 2015, including cytochrome P450 enzymes, aldolases, fluoroacetyl coenzyme A thioesterases, lipases, transaminases, reductive aminases, purine nucleoside phosphorylases, polyketide synthases, fluoroacetate dehalogenases, tyrosine phenol-lyases, glycosidases, fluorinases, and multienzyme system. Of all enzyme-catalyzed synthesis methods, the direct formation of the C-F bond by fluorinase is the most effective and promising method. The structure and catalytic mechanism of fluorinase are introduced to understand fluorobiochemistry. Furthermore, the distribution, applications, and future development trends of fluorinated compounds are also outlined. Hopefully, this review will help researchers to understand the significance of enzymatic methods for the synthesis of fluorinated compounds and find or create excellent fluoride synthase in future research.Key points• Fluorinated compounds are distributed in plants and microorganisms, and are used in imaging, medicine, materials science.• Enzyme catalysis is essential for the synthesis of fluorinated compounds.• The loop structure of fluorinase is the key to forming the C-F bond.
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Affiliation(s)
- Xinkuan Cheng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Laboratory of Metabolic Control Fermentation Technology, College of Biotechnology, Tianjin University of Science & Technology, No. 29, Thirteenth Street, Binhai New District, Tianjin, 300457, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Laboratory of Metabolic Control Fermentation Technology, College of Biotechnology, Tianjin University of Science & Technology, No. 29, Thirteenth Street, Binhai New District, Tianjin, 300457, China.
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6
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Gilbert NC, Newcomer ME, Werz O. Untangling the web of 5-lipoxygenase-derived products from a molecular and structural perspective: The battle between pro- and anti-inflammatory lipid mediators. Biochem Pharmacol 2021; 193:114759. [PMID: 34487716 PMCID: PMC8865081 DOI: 10.1016/j.bcp.2021.114759] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/29/2021] [Accepted: 09/01/2021] [Indexed: 12/31/2022]
Abstract
Arachidonic acid (AA) is the precursor to leukotrienes (LT), potent mediators of the inflammatory response. In the 35 + years since cysteinyl-LTs were reported to mediate antigen-induced constriction of bronchi in tissue from asthma patients, numerous cellular responses evoked by the LTs, such as chemoattraction and G protein-coupled receptor (GPCR) activation, have been elucidated and revealed a potential for 5-lipoxygenase (5-LOX) as a promising drug target that goes beyond asthma. We describe herein early work identifying 5-LOX as the key enzyme that initiates LT biosynthesis and the discovery of its membrane-embedded helper protein required to execute the two-step reaction that transforms AA to the progenitor leukotriene A4 (LTA4). 5-LOX must traffic to the nuclear membrane to interact with its partner and undergo a conformational change so that AA can enter the active site. Additionally, the enzyme must retain the hydroperoxy-reaction intermediate for its final transformation to LTA4. Each of these steps provide a unique target for inhibition. Next, we describe the recent structures of GPCRs that recognize metabolites of the 5-LOX pathway and thus provide target alternatives. We also highlight the role of 5-LOX in the biosynthesis of anti-inflammatory lipid mediators (LM), the so-called specialized pro-resolving mediators (SPM). The involvement of 5-LOX in the biosynthesis of LM with opposing functions undoubtedly complicates the continuing search for 5-LOX inhibitors as therapeutic leads. Finally, we address the recent discovery of how some allosteric 5-LOX inhibitors promote oxygenation at the 12/15 carbon on AA to generate mediators that resolve, rather than promote, inflammation.
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Affiliation(s)
- Nathaniel C Gilbert
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.
| | - Marcia E Newcomer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, 07743 Jena, Germany
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Shamovsky I, Ripa L, Narjes F, Bonn B, Schiesser S, Terstiege I, Tyrchan C. Mechanism-Based Insights into Removing the Mutagenicity of Aromatic Amines by Small Structural Alterations. J Med Chem 2021; 64:8545-8563. [PMID: 34110134 DOI: 10.1021/acs.jmedchem.1c00514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aromatic and heteroaromatic amines (ArNH2) are activated by cytochrome P450 monooxygenases, primarily CYP1A2, into reactive N-arylhydroxylamines that can lead to covalent adducts with DNA nucleobases. Hereby, we give hands-on mechanism-based guidelines to design mutagenicity-free ArNH2. The mechanism of N-hydroxylation of ArNH2 by CYP1A2 is investigated by density functional theory (DFT) calculations. Two putative pathways are considered, the radicaloid route that goes via the classical ferryl-oxo oxidant and an alternative anionic pathway through Fenton-like oxidation by ferriheme-bound H2O2. Results suggest that bioactivation of ArNH2 follows the anionic pathway. We demonstrate that H-bonding and/or geometric fit of ArNH2 to CYP1A2 as well as feasibility of both proton abstraction by the ferriheme-peroxo base and heterolytic cleavage of arylhydroxylamines render molecules mutagenic. Mutagenicity of ArNH2 can be removed by structural alterations that disrupt geometric and/or electrostatic fit to CYP1A2, decrease the acidity of the NH2 group, destabilize arylnitrenium ions, or disrupt their pre-covalent transition states with guanine.
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Saier L, Peyruchaud O. Emerging role of cysteinyl LTs in cancer. Br J Pharmacol 2021; 179:5036-5055. [PMID: 33527344 DOI: 10.1111/bph.15402] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/28/2020] [Accepted: 01/23/2021] [Indexed: 01/31/2023] Open
Abstract
Cysteinyl leukotrienes (CysLTs) are inflammatory lipid mediators that play a central role in the pathophysiology of several inflammatory diseases. Recently, there has been an increased interest in determining how these lipid mediators orchestrate tumour development and metastasis through promoting a pro-tumour micro-environment. Up-regulation of CysLTs receptors and CysLTs production is found in a number of cancers and has been associated with increased tumorigenesis. Understanding the molecular mechanisms underlying the role of CysLTs and their receptors in cancer progression will help investigate the potential of targeting CysLTs signalling for anti-cancer therapy. This review gives an overview of the biological effects of CysLTs and their receptors, along with current knowledge of their regulation and expression. It also provides a recent update on the molecular mechanisms that have been postulated to explain their role in tumorigenesis and on the potential of anti-CysLTs in the treatment of cancer.
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Affiliation(s)
- Lou Saier
- INSERM, Unit 1033, LYOS, Lyon, France.,Université Claude Bernard Lyon 1, Lyon, France
| | - Olivier Peyruchaud
- INSERM, Unit 1033, LYOS, Lyon, France.,Université Claude Bernard Lyon 1, Lyon, France
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Talele TT. Opportunities for Tapping into Three-Dimensional Chemical Space through a Quaternary Carbon. J Med Chem 2020; 63:13291-13315. [PMID: 32805118 DOI: 10.1021/acs.jmedchem.0c00829] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A quaternary carbon bears four other carbon substituents or combination of four non-hydrogen substituents at four vertices of a tetrahedron. The spirocyclic quaternary carbon positioned at the center of a bioactive molecule offers conformational rigidity, which in turn reduces the penalty for conformational entropy. The quaternary carbon is a predominant feature of natural product structures and has been associated with more effective and selective binding to target proteins compared to planar compounds with a high sp2 count. The presence of a quaternary carbon stereocenter allows the exploration of novel chemical space to obtain new molecules with enhanced three-dimensionality. These characteristics, coupled to an increasing awareness to develop sp3-rich molecules, boosted utility of quaternary carbon stereocenters in bioactive compounds. It is hoped that this Perspective will inspire the chemist to utilize quaternary carbon stereocenters to enhance potency, selectivity, and other drug-like properties.
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Affiliation(s)
- Tanaji T Talele
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York 11439, United States
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Thulasingam M, Haeggström JZ. Integral Membrane Enzymes in Eicosanoid Metabolism: Structures, Mechanisms and Inhibitor Design. J Mol Biol 2020; 432:4999-5022. [PMID: 32745470 DOI: 10.1016/j.jmb.2020.07.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 12/14/2022]
Abstract
Eicosanoids are potent lipid mediators involved in central physiological processes such as hemostasis, renal function and parturition. When formed in excess, eicosanoids become critical players in a range of pathological conditions, in particular pain, fever, arthritis, asthma, cardiovascular disease and cancer. Eicosanoids are generated via oxidative metabolism of arachidonic acid along the cyclooxygenase (COX) and lipoxygenase (LOX) pathways. Specific lipid species are formed downstream of COX and LOX by specialized synthases, some of which reside on the nuclear and endoplasmic reticulum, including mPGES-1, FLAP, LTC4 synthase, and MGST2. These integral membrane proteins are members of the family "membrane-associated proteins in eicosanoid and glutathione metabolism" (MAPEG). Here we focus on this enzyme family, which encompasses six human members typically catalyzing glutathione dependent transformations of lipophilic substrates. Enzymes of this family have evolved to combat the topographical challenge and unfavorable energetics of bringing together two chemically different substrates, from cytosol and lipid bilayer, for catalysis within a membrane environment. Thus, structural understanding of these enzymes are of utmost importance to unravel their molecular mechanisms, mode of substrate entry and product release, in order to facilitate novel drug design against severe human diseases.
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Affiliation(s)
- Madhuranayaki Thulasingam
- Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | - Jesper Z Haeggström
- Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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Bergare J, Kingston L, Guly DJ, Dolan J, Lewis RJ, Elmore CS. The synthesis of one H-2 labeled and two H-3 labeled leukotriene C4 synthase inhibitors. J Labelled Comp Radiopharm 2020; 63:434-441. [PMID: 32441366 DOI: 10.1002/jlcr.3862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 11/06/2022]
Abstract
As part of a medicinal chemistry program aimed at developing a leukotriene C4 synthase inhibitor for the treatment of asthma, two tritium-labeled and one stable isotope-labeled compounds were required. The synthesis of the tritium-labeled compounds used a standard bromination-tritiodehalogentation approach. One of the tritium-labeled compounds was observed to exchange its tritium label slowly with the solvent. The stable isotope-labeled compound was prepared in seven steps (3% overall yield) from [2 H6 ]acetone in a modification of the route used by medicinal chemistry.
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Affiliation(s)
- Jonas Bergare
- Isotope Chemistry, Pharmaceutical Science, R&D, AstraZeneca, Gothenberg, Sweden
| | - Lee Kingston
- Isotope Chemistry, Pharmaceutical Science, R&D, AstraZeneca, Gothenberg, Sweden
| | - Dominic J Guly
- Key Organics Ltd, Highfield Road Industrial Estate, Camelford, PL32 9RA, UK
| | - James Dolan
- Key Organics Ltd, Highfield Road Industrial Estate, Camelford, PL32 9RA, UK
| | - Richard J Lewis
- Medicinal Chemistry, Research and Early Development, Respiratory, Inflammation and Autoimmune, BioPharmaceuticals R&D, AstraZeneca, Gothenberg, Sweden
| | - Charles S Elmore
- Isotope Chemistry, Pharmaceutical Science, R&D, AstraZeneca, Gothenberg, Sweden
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Affiliation(s)
- Matthew D. Lloyd
- Drug & Target Development, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, U.K
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Pettersen A, Putra OD, Light ME, Namatame Y. A peculiar dehydration and solid–solid phase transition of the active pharmaceutical ingredient AZD9898 based on in situ single crystal-to-single crystal transformations. CrystEngComm 2020. [DOI: 10.1039/d0ce00276c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Isostructural dehydration from form A hydrate to form B, and solid–solid phase transition from form B to C of AZD9898 were revealed by in situ single crystal-to-single crystal transformations.
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Affiliation(s)
- Anna Pettersen
- Early Product Development and Manufacturing
- Pharmaceutical Sciences
- BioPharmaceuticals R&D
- AstraZeneca Gothenburg
- Mölndal SE-431 83
| | - Okky Dwichandra Putra
- New Modality and Parenteral Development
- Pharmaceutical Technology and Development
- AstraZeneca Gothenburg
- Mölndal SE-431 83
- Sweden
| | - Mark E. Light
- UK National Crystallography Service
- School of Chemistry
- Faculty of Engineering and Physical Sciences
- University of Southampton
- SO17 1BJ Southampton
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