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Chan BWGL, Lynch NB, Tran W, Joyce JM, Savage GP, Meutermans W, Montgomery AP, Kassiou M. Fragment-based drug discovery for disorders of the central nervous system: designing better drugs piece by piece. Front Chem 2024; 12:1379518. [PMID: 38698940 PMCID: PMC11063241 DOI: 10.3389/fchem.2024.1379518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/12/2024] [Indexed: 05/05/2024] Open
Abstract
Fragment-based drug discovery (FBDD) has emerged as a powerful strategy to confront the challenges faced by conventional drug development approaches, particularly in the context of central nervous system (CNS) disorders. FBDD involves the screening of libraries that comprise thousands of small molecular fragments, each no greater than 300 Da in size. Unlike the generally larger molecules from high-throughput screening that limit customisation, fragments offer a more strategic starting point. These fragments are inherently compact, providing a strong foundation with good binding affinity for the development of drug candidates. The minimal elaboration required to transition the hit into a drug-like molecule is not only accelerated, but also it allows for precise modifications to enhance both their activity and pharmacokinetic properties. This shift towards a fragment-centric approach has seen commercial success and holds considerable promise in the continued streamlining of the drug discovery and development process. In this review, we highlight how FBDD can be integrated into the CNS drug discovery process to enhance the exploration of a target. Furthermore, we provide recent examples where FBDD has been an integral component in CNS drug discovery programs, enabling the improvement of pharmacokinetic properties that have previously proven challenging. The FBDD optimisation process provides a systematic approach to explore this vast chemical space, facilitating the discovery and design of compounds piece by piece that are capable of modulating crucial CNS targets.
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Affiliation(s)
| | - Nicholas B. Lynch
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
| | - Wendy Tran
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
| | - Jack M. Joyce
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
| | | | | | | | - Michael Kassiou
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
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2
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Alekseeva AS, Boldyrev IA. Alternative Targets for sPLA2 Activity: Role of Membrane-Enzyme Interactions. MEMBRANES 2023; 13:618. [PMID: 37504984 PMCID: PMC10384401 DOI: 10.3390/membranes13070618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/29/2023]
Abstract
The secreted phospholipases A2 (sPLA2s) play important roles both physiologically and pathologically, with their expression increasing significantly in diseases such as sepsis, inflammation, different cancers, glaucoma, obesity, Alzheimer's disease and even COVID-19. The fact has led to a large-scale search for inhibitors of these enzymes. In total, several dozen promising molecules have been proposed, but not a single one has successfully passed clinical trials. The failures in clinical studies motivated in-depth fundamental studies of PLA2s. Here we review alternative ways to control sPLA2 activity, outside its catalytic site. The concept can be realized by preventing sPLA2 from attaching to the membrane surface; by binding to an external protein which blocks sPLA2 hydrolytic activity; by preventing sPLA2 from orienting properly on the membrane surface; and by preventing substrate binding to the enzyme, keeping the catalytic site unaltered. Evidence in the literature is summarized in the review with the aim to serve as a starting point for new types of sPLA2 inhibitors.
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Affiliation(s)
- Anna S Alekseeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Ivan A Boldyrev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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3
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Biological Properties and Clinical Significance of Lipoprotein-Associated Phospholipase A2 in Ischemic Stroke. Cardiovasc Ther 2022; 2022:3328574. [PMID: 36313479 PMCID: PMC9586817 DOI: 10.1155/2022/3328574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/19/2022] [Accepted: 09/29/2022] [Indexed: 11/27/2022] Open
Abstract
Ischemic stroke, which occurs following blockage of the blood supply to the brain, is a leading cause of death worldwide. Its main cause is atherosclerosis, a disease of the arteries characterized by the deposition of plaques of fatty material on the inner artery walls. Multiple proteins involved in the inflammation response have been identified as diagnosing biomarkers of ischemic stroke. One of these is lipoprotein-associated phospholipase A2 (Lp-PLA2), an enzyme that can hydrolyze circulating oxidized phospholipids, generating proinflammatory lysophosphatidylcholine and promoting the development of atherosclerosis. In the last two decades, a number of studies have revealed that both the concentration and the activity of Lp-PLA2 are independent biomarkers of ischemic stroke. The US Food and Drug Administration (FDA) has approved two tests to determine Lp-PLA2 mass and activity for predicting stroke. In this review, we summarize the biological properties of Lp-PLA2, the detection sensitivity and limitations of Lp-PLA2 measurement, the clinical significance and association of Lp-PLA2 in ischemic stroke, and the prospects of therapeutic inhibition of Lp-PLA2 as an intervention and treatment.
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4
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Lal Gupta P, Carlson HA. Cosolvent Simulations with Fragment-Bound Proteins Identify Hot Spots to Direct Lead Growth. J Chem Theory Comput 2022; 18:3829-3844. [PMID: 35533286 DOI: 10.1021/acs.jctc.1c01054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In drug design, chemical groups are sequentially added to improve a weak-binding fragment into a tight-binding lead molecule. Often, the direction to make these additions is unclear, and there are numerous chemical modifications to choose. Lead development can be guided by crystal structures of the fragment-bound protein, but this alone is unable to capture structural changes like closing or opening of the binding site and any side-chain movements. Accounting for adaptation of the site requires a dynamic approach. Here, we use molecular dynamics calculations of small organic solvents with protein-fragment pairs to reveal the nearest "hot spots". These close hot spots show the direction to make appropriate additions and suggest types of chemical modifications that could improve binding affinity. Mixed-solvent molecular dynamics (MixMD) is a cosolvent simulation technique that is well established for finding binding "hot spots" in active sites and allosteric sites of proteins. We simulated 20 fragment-bound and apo forms of key pharmaceutical targets to map out hot spots for potential lead space. Furthermore, we analyzed whether the presence of a fragment facilitates the probes' binding in the lead space, a type of binding cooperativity. To the best of our knowledge, this is the first use of cosolvent MD conducted with bound inhibitors in the simulation. Our work provides a general framework to extract molecular features of binding sites to choose chemical groups for growing lead molecules. Of the 20 systems, 17 systems were well mapped by MixMD. For the three not-mapped systems, two had lead growth out into solution away from the protein, and the third had very small modifications which indicated no nearby hot spots. Therefore, our lack of mapping in three systems was appropriate given the experimental data (true-negative cases). The simulations are run for very short time scales, making this method tractable for use in the pharmaceutical industry.
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Affiliation(s)
- Pancham Lal Gupta
- Department of Medicinal Chemistry, College of Pharmacy, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Heather A Carlson
- Department of Medicinal Chemistry, College of Pharmacy, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
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5
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Bhukya G, Kaki SS. Design and Synthesis of Sebacic Acid from Castor Oil by New Alternate Route. EUR J LIPID SCI TECH 2022. [DOI: 10.1002/ejlt.202100244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Gandhi Bhukya
- Centre for Lipid Science & Technology CSIR‐Indian Institute of Chemical Technology Uppal Road, Tarnaka Hyderabad 500007 India
- Academy of Scientific and Innovative Research CSIR Ghaziabad 201002 India
| | - Shiva Shanker Kaki
- Centre for Lipid Science & Technology CSIR‐Indian Institute of Chemical Technology Uppal Road, Tarnaka Hyderabad 500007 India
- Academy of Scientific and Innovative Research CSIR Ghaziabad 201002 India
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6
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Fragment-to-lead tailored in silico design. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 40:44-57. [PMID: 34916022 DOI: 10.1016/j.ddtec.2021.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 06/25/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023]
Abstract
Fragment-based drug discovery (FBDD) emerged as a disruptive technology and became established during the last two decades. Its rationality and low entry costs make it appealing, and the numerous examples of approved drugs discovered through FBDD validate the approach. However, FBDD still faces numerous challenges. Perhaps the most important one is the transformation of the initial fragment hits into viable leads. Fragment-to-lead (F2L) optimization is resource-intensive and is therefore limited in the possibilities that can be actively pursued. In silico strategies play an important role in F2L, as they can perform a deeper exploration of chemical space, prioritize molecules with high probabilities of being active and generate non-obvious ideas. Here we provide a critical overview of current in silico strategies in F2L optimization and highlight their remarkable impact. While very effective, most solutions are target- or fragment- specific. We propose that fully integrated in silico strategies, capable of automatically and systematically exploring the fast-growing available chemical space can have a significant impact on accelerating the release of fragment originated drugs.
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Batsika CS, Gerogiannopoulou ADD, Mantzourani C, Vasilakaki S, Kokotos G. The design and discovery of phospholipase A 2 inhibitors for the treatment of inflammatory diseases. Expert Opin Drug Discov 2021; 16:1287-1305. [PMID: 34143707 DOI: 10.1080/17460441.2021.1942835] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AREAS COVERED This review article summarizes the most important synthetic PLA2 inhibitors developed to target each one of the four major types of human PLA2 (cytosolic cPLA2, calcium-independent iPLA2, secreted sPLA2, and lipoprotein-associated Lp-PLA2), discussing their in vitro and in vivo activities as well as their recent applications and therapeutic properties. Recent findings on the role of PLA2 in the pathobiology of COVID-19 are also discussed. EXPERT OPINION Although a number of PLA2 inhibitors have entered clinical trials, none has reached the market yet. Lipoprotein-associated PLA2 is now considered a biomarker of vascular inflammation rather than a therapeutic target for inhibitors like darapladib. Inhibitors of cytosolic PLA2 may find topical applications for diseases like atopic dermatitis and psoriasis. Inhibitors of secreted PLA2, varespladib and varespladib methyl, are under investigation for repositioning in snakebite envenoming. A deeper understanding of PLA2 enzymes is needed for the development of novel selective inhibitors. Lipidomic technologies combined with medicinal chemistry approaches may be useful tools toward this goal.
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Affiliation(s)
| | | | - Christiana Mantzourani
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Greece
| | - Sofia Vasilakaki
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Greece
| | - George Kokotos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Greece
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Dong L, Li Y, Wu H. Platelet activating-factor acetylhydrolase II: A member of phospholipase A2 family that hydrolyzes oxidized phospholipids. Chem Phys Lipids 2021; 239:105103. [PMID: 34116047 DOI: 10.1016/j.chemphyslip.2021.105103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/09/2021] [Accepted: 06/05/2021] [Indexed: 10/21/2022]
Abstract
Intracellular platelet activating-factor acetylhydrolase type II (PAF-AH II) is a 40-kDa monomeric enzyme. It was originally identified as an enzyme that hydrolyzes the acetyl group of PAF (1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine). As a member of phospholipase A2 super family, PAF-AH II has broad substrate specificity. It can hydrolyze phospholipids with relatively short-length or oxidatively modified sn-2 chains which endows it with various functions such as protection against oxidative stress, transacetylase activity and producing lipid mediators. PAF-AH II has been proven to be involved in several diseases such as allergic diseases, oxidative stress-induced injury and ischemia injury, thus it has drawn more attention from researchers. In this paper, we outline an entire summary of PAF-AH II, including its structure, substrate specificity, activity assay, inhibitors and biological activities.
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Affiliation(s)
- Linyue Dong
- Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yiming Li
- Department of TCM Chemistry, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Huali Wu
- Department of TCM Chemistry, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
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9
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Kumar SP, Patel CN, Rawal RM, Pandya HA. Energetic contributions of amino acid residues and its cross‐talk to delineate ligand‐binding mechanism. Proteins 2020; 88:1207-1225. [DOI: 10.1002/prot.25894] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/20/2020] [Accepted: 04/03/2020] [Indexed: 02/02/2023]
Affiliation(s)
| | - Chirag N. Patel
- Department of Botany, Bioinformatics, and Climate Change Impacts ManagementUniversity School of Sciences, Gujarat University Ahmedabad India
| | - Rakesh M. Rawal
- Department of Life SciencesUniversity School of Sciences, Gujarat University Ahmedabad India
| | - Himanshu A. Pandya
- Department of Life SciencesUniversity School of Sciences, Gujarat University Ahmedabad India
- Department of Botany, Bioinformatics, and Climate Change Impacts ManagementUniversity School of Sciences, Gujarat University Ahmedabad India
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Nikolaou A, Kokotou MG, Vasilakaki S, Kokotos G. Small-molecule inhibitors as potential therapeutics and as tools to understand the role of phospholipases A 2. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:941-956. [PMID: 30905350 PMCID: PMC7106526 DOI: 10.1016/j.bbalip.2018.08.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/10/2018] [Accepted: 08/16/2018] [Indexed: 11/20/2022]
Abstract
Phospholipase A2 (PLA2) enzymes are involved in various inflammatory pathological conditions including arthritis, cardiovascular and autoimmune diseases. The regulation of their catalytic activity is of high importance and a great effort has been devoted in developing synthetic inhibitors. We summarize the most important small-molecule synthetic PLA2 inhibitors developed to target each one of the four major types of human PLA2 (cytosolic cPLA2, calcium-independent iPLA2, secreted sPLA2, and lipoprotein-associated LpPLA2). We discuss recent applications of inhibitors to understand the role of each PLA2 type and their therapeutic potential. Potent and selective PLA2 inhibitors have been developed. Although some of them have been evaluated in clinical trials, none reached the market yet. Apart from their importance as potential medicinal agents, PLA2 inhibitors are excellent tools to unveil the role that each PLA2 type plays in cells and in vivo. Modern medicinal chemistry approaches are expected to generate improved PLA2 inhibitors as new agents to treat inflammatory diseases.
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Affiliation(s)
- Aikaterini Nikolaou
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Maroula G Kokotou
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Sofia Vasilakaki
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - George Kokotos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece.
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11
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Huang F, Wang K, Shen J. Lipoprotein-associated phospholipase A2: The story continues. Med Res Rev 2019; 40:79-134. [PMID: 31140638 PMCID: PMC6973114 DOI: 10.1002/med.21597] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 04/20/2019] [Accepted: 04/30/2019] [Indexed: 12/15/2022]
Abstract
Inflammation is thought to play an important role in the pathogenesis of vascular diseases. Lipoprotein-associated phospholipase A2 (Lp-PLA2) mediates vascular inflammation through the regulation of lipid metabolism in blood, thus, it has been extensively investigated to identify its role in vascular inflammation-related diseases, mainly atherosclerosis. Although darapladib, the most advanced Lp-PLA2 inhibitor, failed to meet the primary endpoints of two large phase III trials in atherosclerosis patients cotreated with standard medical care, the research on Lp-PLA2 has not been terminated. Novel pathogenic, epidemiologic, genetic, and crystallographic studies regarding Lp-PLA2 have been reported recently, while novel inhibitors were identified through a fragment-based lead discovery strategy. More strikingly, recent clinical and preclinical studies revealed that Lp-PLA2 inhibition showed promising therapeutic effects in diabetic macular edema and Alzheimer's disease. In this review, we not only summarized the knowledge of Lp-PLA2 established in the past decades but also emphasized new findings in recent years. We hope this review could be valuable for helping researchers acquire a much deeper insight into the nature of Lp-PLA2, identify more potent and selective Lp-PLA2 inhibitors, and discover the potential indications of Lp-PLA2 inhibitors.
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Affiliation(s)
- Fubao Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Kai Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China
| | - Jianhua Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China
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12
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Guibbal F, Meneyrol V, Ait-Arsa I, Diotel N, Patché J, Veeren B, Bénard S, Gimié F, Yong-Sang J, Khantalin I, Veerapen R, Jestin E, Meilhac O. Synthesis and Automated Labeling of [ 18F]Darapladib, a Lp-PLA 2 Ligand, as Potential PET Imaging Tool of Atherosclerosis. ACS Med Chem Lett 2019; 10:743-748. [PMID: 31097993 DOI: 10.1021/acsmedchemlett.8b00643] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/04/2019] [Indexed: 11/30/2022] Open
Abstract
Atherosclerosis and its associated clinical complications are major health issues in industrialized countries. Lipoprotein-associated phospholipase A2 (Lp-PLA2) was demonstrated to play an important role in atherogenesis and to be a potential risk prediction factor of plaque rupture. Darapladib is one of the most potent Lp-PLA2 inhibitors with an IC50 of 0.25 nM. Using its affinity for Lp-PLA2, we describe herein the total synthesis of darapladib radiolabeling precursor and the automated radiolabeling process for positron emission tomography (PET) imaging via an arylboronate moiety. The tracer thus obtained was tested in a mouse model of atherosclerosis (ApoE KO) and compared with the widely used [18F]fluorodeoxyglucose ([18F]FDG) PET tracer, known to label metabolically active cells. [18F]Darapladib showed a significant accumulation within mice aortic atheromatous plaques dissected out ex vivo compared to [18F]FDG. Incubation of the radiotracer with human carotid samples showed a strong accumulation within the atherosclerotic plaques and supports its potential for use in PET imaging.
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Affiliation(s)
- Florian Guibbal
- Université de La Réunion, INSERM, UMR 1188 Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Saint-Denis de La Réunion, France
| | - Vincent Meneyrol
- CYclotron Réunion Océan Indien CYROI, 2 rue Maxime Rivière, 97490 Sainte-Clotilde, France
| | - Imade Ait-Arsa
- CYclotron Réunion Océan Indien CYROI, 2 rue Maxime Rivière, 97490 Sainte-Clotilde, France
| | - Nicolas Diotel
- Université de La Réunion, INSERM, UMR 1188 Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Saint-Denis de La Réunion, France
| | - Jessica Patché
- Université de La Réunion, INSERM, UMR 1188 Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Saint-Denis de La Réunion, France
| | - Bryan Veeren
- Université de La Réunion, INSERM, UMR 1188 Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Saint-Denis de La Réunion, France
| | - Sébastien Bénard
- CYclotron Réunion Océan Indien CYROI, 2 rue Maxime Rivière, 97490 Sainte-Clotilde, France
| | - Fanny Gimié
- CYclotron Réunion Océan Indien CYROI, 2 rue Maxime Rivière, 97490 Sainte-Clotilde, France
| | - Jennyfer Yong-Sang
- Université de La Réunion, INSERM, UMR 1188 Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Saint-Denis de La Réunion, France
| | | | - Reuben Veerapen
- Clinique de Sainte-Clotilde, 127, Route de Bois de Nèfles, Sainte-Clotilde, Réunion, France
| | - Emmanuelle Jestin
- Université de La Réunion, INSERM, UMR 1188 Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Saint-Denis de La Réunion, France
- CYclotron Réunion Océan Indien CYROI, 2 rue Maxime Rivière, 97490 Sainte-Clotilde, France
| | - Olivier Meilhac
- Université de La Réunion, INSERM, UMR 1188 Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Saint-Denis de La Réunion, France
- CHU de La Réunion, Saint-Denis de La Réunion, France
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13
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van Zundert GCP, Hudson BM, de Oliveira SHP, Keedy DA, Fonseca R, Heliou A, Suresh P, Borrelli K, Day T, Fraser JS, van den Bedem H. qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps. J Med Chem 2018; 61:11183-11198. [PMID: 30457858 DOI: 10.1021/acs.jmedchem.8b01292] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Proteins and ligands sample a conformational ensemble that governs molecular recognition, activity, and dissociation. In structure-based drug design, access to this conformational ensemble is critical to understand the balance between entropy and enthalpy in lead optimization. However, ligand conformational heterogeneity is currently severely underreported in crystal structures in the Protein Data Bank, owing in part to a lack of automated and unbiased procedures to model an ensemble of protein-ligand states into X-ray data. Here, we designed a computational method, qFit-ligand, to automatically resolve conformationally averaged ligand heterogeneity in crystal structures, and applied it to a large set of protein receptor-ligand complexes. In an analysis of the cancer related BRD4 domain, we found that up to 29% of protein crystal structures bound with drug-like molecules present evidence of unmodeled, averaged, relatively isoenergetic conformations in ligand-receptor interactions. In many retrospective cases, these alternate conformations were adventitiously exploited to guide compound design, resulting in improved potency or selectivity. Combining qFit-ligand with high-throughput screening or multitemperature crystallography could therefore augment the structure-based drug design toolbox.
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Affiliation(s)
| | - Brandi M Hudson
- Department of Bioengineering and Therapeutic Sciences , UCSF , San Francisco , California 94158 , United States
| | - Saulo H P de Oliveira
- SLAC National Accelerator Laboratory , Stanford University , Menlo Park , California 94025 United States
| | - Daniel A Keedy
- Department of Bioengineering and Therapeutic Sciences , UCSF , San Francisco , California 94158 , United States
| | - Rasmus Fonseca
- Department of Molecular and Cellular Physiology , Stanford University , Stanford , California 94305 , United States
| | - Amelie Heliou
- LIX, Ecole Polytechnique, CNRS, Inria , Université Paris-Saclay , 91128 Palaiseau , France
| | - Pooja Suresh
- Department of Bioengineering and Therapeutic Sciences , UCSF , San Francisco , California 94158 , United States
| | | | - Tyler Day
- Schrödinger , New York , New York 10036 , United States
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences , UCSF , San Francisco , California 94158 , United States
| | - Henry van den Bedem
- Department of Bioengineering and Therapeutic Sciences , UCSF , San Francisco , California 94158 , United States.,SLAC National Accelerator Laboratory , Stanford University , Menlo Park , California 94025 United States
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14
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Guibbal F, Bénard S, Patché J, Meneyrol V, Couprie J, Yong-Sang J, Meilhac O, Jestin E. Regioselectivity of thiouracil alkylation: Application to optimization of Darapladib synthesis. Bioorg Med Chem Lett 2017; 28:787-792. [PMID: 29336874 DOI: 10.1016/j.bmcl.2017.12.052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/22/2017] [Accepted: 12/23/2017] [Indexed: 01/26/2023]
Abstract
Darapladib is one of the most potent Lp-PLA2 (Lipoprotein-associated phospholipase A2) inhibitor with an IC50 of 0.25 nM. We demonstrate that a crucial step of Darapladib synthesis was not correctly described in the literature, leading to the production of wrong regioisomers. Moreover we show that the inhibitory activity is directly linked to the position on N1 since compounds bearing alkylation on different sites have potentially less interaction within the active site of Lp-PLA2.
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Affiliation(s)
- Florian Guibbal
- Université de La Réunion, INSERM, UMR 1188 Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Saint-Denis de La Réunion, France
| | - Sébastien Bénard
- Radiochimie et imagerie du petit animal (RIPA), CYclotron Réunion Océan Indien CYROI, 2 rue Maxime Rivière, 97490 Sainte-Clotilde, France
| | - Jessica Patché
- Université de La Réunion, INSERM, UMR 1188 Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Saint-Denis de La Réunion, France
| | - Vincent Meneyrol
- Radiochimie et imagerie du petit animal (RIPA), CYclotron Réunion Océan Indien CYROI, 2 rue Maxime Rivière, 97490 Sainte-Clotilde, France
| | - Joël Couprie
- Université de La Réunion, INSERM, UMR 1188 Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Saint-Denis de La Réunion, France
| | - Jennyfer Yong-Sang
- Université de La Réunion, INSERM, UMR 1188 Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Saint-Denis de La Réunion, France
| | - Olivier Meilhac
- Université de La Réunion, INSERM, UMR 1188 Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Saint-Denis de La Réunion, France; CHU de La Réunion, Saint-Denis de La Réunion, France.
| | - Emmanuelle Jestin
- Université de La Réunion, INSERM, UMR 1188 Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Saint-Denis de La Réunion, France; Radiochimie et imagerie du petit animal (RIPA), CYclotron Réunion Océan Indien CYROI, 2 rue Maxime Rivière, 97490 Sainte-Clotilde, France
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15
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Liu Q, Huang F, Yuan X, Wang K, Zou Y, Shen J, Xu Y. Structure-Guided Discovery of Novel, Potent, and Orally Bioavailable Inhibitors of Lipoprotein-Associated Phospholipase A2. J Med Chem 2017; 60:10231-10244. [PMID: 29193967 DOI: 10.1021/acs.jmedchem.7b01530] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Lipoprotein-associated phospholipase A2 (Lp-PLA2) is a promising therapeutic target for atherosclerosis, Alzheimer's disease, and diabetic macular edema. Here we report the identification of novel sulfonamide scaffold Lp-PLA2 inhibitors derived from a relatively weak fragment. Similarity searching on this fragment followed by molecular docking leads to the discovery of a micromolar inhibitor with a 300-fold potency improvement. Subsequently, by the application of a structure-guided design strategy, a successful hit-to-lead optimization was achieved and a number of Lp-PLA2 inhibitors with single-digit nanomolar potency were obtained. After preliminary evaluation of the properties of drug-likeness in vitro and in vivo, compound 37 stands out from this congeneric series of inhibitors for good inhibitory activity and favorable oral bioavailability in male Sprague-Dawley rats, providing a quality candidate for further development. The present study thus clearly demonstrates the power and advantage of integrally employing fragment screening, crystal structures determination, virtual screening, and medicinal chemistry in an efficient lead discovery project, providing a good example for structure-based drug design.
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Affiliation(s)
- Qiufeng Liu
- School of Life Science and Technology, ShanghaiTech University , Shanghai 200031, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Fubao Huang
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Xiaojing Yuan
- University of Chinese Academy of Sciences , Beijing 100049, China
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16
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Johnson CN, Erlanson DA, Jahnke W, Mortenson PN, Rees DC. Fragment-to-Lead Medicinal Chemistry Publications in 2016. J Med Chem 2017; 61:1774-1784. [PMID: 29087197 DOI: 10.1021/acs.jmedchem.7b01298] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The popularity of fragment-based drug discovery (FBDD) is demonstrated by the number of recent successful fragment-to-lead (F2L) publications. This Miniperspective provides a tabulated summary of the F2L literature published in the year 2016, along with discussion of general trends. It uses the same format as our summary of the 2015 literature and is intended to be a resource for both FBDD practitioners and medicinal chemists in general.
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Affiliation(s)
- Christopher N Johnson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
| | - Daniel A Erlanson
- Carmot Therapeutics Inc. , 740 Heinz Avenue , Berkeley , California 94710 , United States
| | - Wolfgang Jahnke
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics , 4002 Basel , Switzerland
| | - Paul N Mortenson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
| | - David C Rees
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
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17
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CADD medicine: design is the potion that can cure my disease. J Comput Aided Mol Des 2017; 31:249-253. [PMID: 28070730 DOI: 10.1007/s10822-016-0004-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/19/2016] [Indexed: 01/24/2023]
Abstract
The acronym "CADD" is often used interchangeably to refer to "Computer Aided Drug Discovery" and "Computer Aided Drug Design". While the former definition implies the use of a computer to impact one or more aspects of discovering a drug, in this paper we contend that computational chemists are most effective when they enable teams to apply true design principles as they strive to create medicines to treat human disease. We argue that teams must bring to bear multiple sub-disciplines of computational chemistry in an integrated manner in order to utilize these principles to address the multi-objective nature of the drug discovery problem. Impact, resourcing principles, and future directions for the field are also discussed, including areas of future opportunity as well as a cautionary note about hype and hubris.
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18
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Woolford AJA, Day PJ, Bénéton V, Berdini V, Coyle JE, Dudit Y, Grondin P, Huet P, Lee LYW, Manas ES, McMenamin RL, Murray CW, Page LW, Patel VK, Potvain F, Rich SJ, Sang Y, Somers DO, Trottet L, Wan Z, Zhang X. Fragment-Based Approach to the Development of an Orally Bioavailable Lactam Inhibitor of Lipoprotein-Associated Phospholipase A2 (Lp-PLA2). J Med Chem 2016; 59:10738-10749. [DOI: 10.1021/acs.jmedchem.6b01427] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Alison J.-A. Woolford
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Philip J. Day
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Véronique Bénéton
- Centre
de Recherches Francois Hyafil, GlaxoSmithKline, 25−27 Avenue du Québec, Les Ulis, France
| | - Valerio Berdini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Joseph E. Coyle
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Yann Dudit
- Centre
de Recherches Francois Hyafil, GlaxoSmithKline, 25−27 Avenue du Québec, Les Ulis, France
| | - Pascal Grondin
- Centre
de Recherches Francois Hyafil, GlaxoSmithKline, 25−27 Avenue du Québec, Les Ulis, France
| | - Pascal Huet
- Centre
de Recherches Francois Hyafil, GlaxoSmithKline, 25−27 Avenue du Québec, Les Ulis, France
| | - Lydia Y. W. Lee
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Eric S. Manas
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Rachel L. McMenamin
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Christopher W. Murray
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Lee W. Page
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | | | - Florent Potvain
- Centre
de Recherches Francois Hyafil, GlaxoSmithKline, 25−27 Avenue du Québec, Les Ulis, France
| | - Sharna J. Rich
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Yingxia Sang
- Neurodegeneration
DPU, GlaxoSmithKline, 898 Halei Road, Zhangjiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Don O. Somers
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, United Kingdom
| | - Lionel Trottet
- Centre
de Recherches Francois Hyafil, GlaxoSmithKline, 25−27 Avenue du Québec, Les Ulis, France
| | - Zehong Wan
- Neurodegeneration
DPU, GlaxoSmithKline, 898 Halei Road, Zhangjiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Xiaomin Zhang
- Neurodegeneration
DPU, GlaxoSmithKline, 898 Halei Road, Zhangjiang Hi-Tech
Park, Pudong, Shanghai 201203, China
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19
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Kokotou MG, Limnios D, Nikolaou A, Psarra A, Kokotos G. Inhibitors of phospholipase A2 and their therapeutic potential: an update on patents (2012-2016). Expert Opin Ther Pat 2016; 27:217-225. [DOI: 10.1080/13543776.2017.1246540] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Maroula G. Kokotou
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitris Limnios
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Aikaterini Nikolaou
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Anastasia Psarra
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - George Kokotos
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
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