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Liu Y, Ma J, DesJarlais RL, Hagan R, Rech J, Liu C, Miller R, Schoellerman J, Luo J, Letavic M, Grasberger B, Maher MP. Molecular determinants of ASIC1 modulation by divalent cations. Sci Rep 2024; 14:2320. [PMID: 38282035 PMCID: PMC10822848 DOI: 10.1038/s41598-024-52845-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/24/2024] [Indexed: 01/30/2024] Open
Abstract
Acid-sensing ion channels (ASICs) are proton-gated cation channels widely expressed in the nervous system. ASIC gating is modulated by divalent cations as well as small molecules; however, the molecular determinants of gating modulation by divalent cations are not well understood. Previously, we identified two small molecules that bind to ASIC1a at a novel site in the acidic pocket and modulate ASIC1 gating in a manner broadly resembling divalent cations, raising the possibility that these small molecules may help to illuminate the molecular determinants of gating modulation by divalent cations. Here, we examined how these two groups of modulators might interact as well as mutational effects on ASIC1a gating and its modulation by divalent cations. Our results indicate that binding of divalent cations to an acidic pocket site plays a key role in gating modulation of the channel.
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2
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Xu G, Liu Z, Wang X, Lu T, DesJarlais RL, Thieu T, Zhang J, Devine ZH, Du F, Li Q, Milligan CM, Shaffer P, Cedervall PE, Spurlino JC, Stratton CF, Pietrak B, Szewczuk LM, Wong V, Steele RA, Bruinzeel W, Chintala M, Silva J, Gaul MD, Macielag MJ, Nargund R. Discovery of Potent and Orally Bioavailable Pyridine N-Oxide-Based Factor XIa Inhibitors through Exploiting Nonclassical Interactions. J Med Chem 2022; 65:10419-10440. [PMID: 35862732 DOI: 10.1021/acs.jmedchem.2c00442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Activated factor XI (FXIa) inhibitors are promising novel anticoagulants with low bleeding risk compared with current anticoagulants. The discovery of potent FXIa inhibitors with good oral bioavailability has been challenging. Herein, we describe our discovery effort, utilizing nonclassical interactions to improve potency, cellular permeability, and oral bioavailability by enhancing the binding while reducing polar atoms. Beginning with literature-inspired pyridine N-oxide-based FXIa inhibitor 1, the imidazole linker was first replaced with a pyrazole moiety to establish a polar C-H···water hydrogen-bonding interaction. Then, structure-based drug design was employed to modify lead molecule 2d in the P1' and P2' regions, with substituents interacting with key residues through various nonclassical interactions. As a result, a potent FXIa inhibitor 3f (Ki = 0.17 nM) was discovered. This compound demonstrated oral bioavailability in preclinical species (rat 36.4%, dog 80.5%, and monkey 43.0%) and displayed a dose-dependent antithrombotic effect in a rabbit arteriovenous shunt model of thrombosis.
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3
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Seierstad M, Tichenor MS, DesJarlais RL, Na J, Bacani GM, Chung DM, Mercado-Marin EV, Steffens HC, Mirzadegan T. Novel Reagent Space: Identifying Unorderable but Readily Synthesizable Building Blocks. ACS Med Chem Lett 2021; 12:1853-1860. [PMID: 34795876 DOI: 10.1021/acsmedchemlett.1c00340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/01/2021] [Indexed: 01/14/2023] Open
Abstract
Drug discovery building blocks available commercially or within an internal inventory cover a diverse range of chemical space and yet describe only a tiny fraction of all chemically feasible reagents. Vendors will eagerly provide tools to search the former; there is no straightforward method of mining the latter. We describe a procedure and use case in assembling chemical structures not available for purchase but that could likely be synthesized in one robust chemical transformation starting from readily available building blocks. Accessing this vast virtual chemical space dramatically increases our curated collection of reagents available for medicinal chemistry exploration and novel hit generation, almost tripling the number of those with 10 or fewer atoms.
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4
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Liu Y, Ma J, DesJarlais RL, Hagan R, Rech J, Lin D, Liu C, Miller R, Schoellerman J, Luo J, Letavic M, Grasberger B, Maher M. Molecular mechanism and structural basis of small-molecule modulation of the gating of acid-sensing ion channel 1. Commun Biol 2021; 4:174. [PMID: 33564124 PMCID: PMC7873226 DOI: 10.1038/s42003-021-01678-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 01/07/2021] [Indexed: 01/07/2023] Open
Abstract
Acid-sensing ion channels (ASICs) are proton-gated cation channels critical for neuronal functions. Studies of ASIC1, a major ASIC isoform and proton sensor, have identified acidic pocket, an extracellular region enriched in acidic residues, as a key participant in channel gating. While binding to this region by the venom peptide psalmotoxin modulates channel gating, molecular and structural mechanisms of ASIC gating modulation by small molecules are poorly understood. Here, combining functional, crystallographic, computational and mutational approaches, we show that two structurally distinct small molecules potently and allosterically inhibit channel activation and desensitization by binding at the acidic pocket and stabilizing the closed state of rat/chicken ASIC1. Our work identifies a previously unidentified binding site, elucidates a molecular mechanism of small molecule modulation of ASIC gating, and demonstrates directly the structural basis of such modulation, providing mechanistic and structural insight into ASIC gating, modulation and therapeutic targeting.
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Xu G, Gaul MD, Liu Z, DesJarlais RL, Qi J, Wang W, Krosky D, Petrounia I, Milligan CM, Hermans A, Lu HR, Huang DZ, Xu JZ, Spurlino JC. Hit-to-lead optimization and discovery of a potent, and orally bioavailable G protein coupled receptor kinase 2 (GRK2) inhibitor. Bioorg Med Chem Lett 2020; 30:127602. [PMID: 33038544 DOI: 10.1016/j.bmcl.2020.127602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/26/2020] [Accepted: 10/01/2020] [Indexed: 12/26/2022]
Abstract
G-protein coupled receptor kinase 2 (GRK2), which is upregulated in the failing heart, appears to play a critical role in heart failure (HF) progression in part because enhanced GRK2 activity promotes dysfunction of β-adrenergic signaling and myocyte death. An orally bioavailable GRK2 inhibitor could offer unique therapeutic outcomes that cannot be attained by current heart failure treatments that directly target GPCRs or angiotensin-converting enzyme. Herein, we describe the discovery of a potent, selective, and orally bioavailable GRK2 inhibitor, 8h, through high-throughput screening, hit-to-lead optimization, structure-based design, molecular modelling, synthesis, and biological evaluation. In the cellular target engagement assays, 8h enhances isoproterenol-mediated cyclic adenosine 3',5'-monophosphate (cAMP) production in HEK293 cells overexpressing GRK2. Compound 8h was further evaluated in a human stem cell-derived cardiomyocyte (HSC-CM) contractility assay and potentiated isoproterenol-induced beating rate in HSC-CMs.
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Struble T, Alvarez JC, Brown SP, Chytil M, Cisar J, DesJarlais RL, Engkvist O, Frank SA, Greve DR, Griffin DJ, Hou X, Johannes JW, Kreatsoulas C, Lahue B, Mathea M, Mogk G, Nicolaou CA, Palmer AD, Price DJ, Robinson RI, Salentin S, Xing L, Jaakkola T, Green WH, Barzilay R, Coley CW, Jensen KF. Current and Future Roles of Artificial Intelligence in Medicinal Chemistry Synthesis. J Med Chem 2020; 63:8667-8682. [PMID: 32243158 PMCID: PMC7457232 DOI: 10.1021/acs.jmedchem.9b02120] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Indexed: 12/20/2022]
Abstract
Artificial intelligence and machine learning have demonstrated their potential role in predictive chemistry and synthetic planning of small molecules; there are at least a few reports of companies employing in silico synthetic planning into their overall approach to accessing target molecules. A data-driven synthesis planning program is one component being developed and evaluated by the Machine Learning for Pharmaceutical Discovery and Synthesis (MLPDS) consortium, comprising MIT and 13 chemical and pharmaceutical company members. Together, we wrote this perspective to share how we think predictive models can be integrated into medicinal chemistry synthesis workflows, how they are currently used within MLPDS member companies, and the outlook for this field.
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DeRatt LG, Lawson EC, Kumar K, Hwang SS, DesJarlais RL, Kuduk SD. Tandem Suzuki Coupling/Intramolecular Oxetane Ring Opening to Form Polycyclic Ring Systems. Org Lett 2020; 22:5828-5832. [PMID: 32702238 DOI: 10.1021/acs.orglett.0c01899] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A tandem one-pot reaction featuring a cross-coupling followed by an intramolecular oxetane ring opening by mild nucleophiles is reported. The overall transformation comprises a carbon-carbon bond formation along with a carbon-heteroatom bond construction providing diverse multicyclic ring systems with a pendant hydroxymethyl handle for further elaboration. This approach constitutes a convergent method for rapid access to various scaffolds. Furthermore, a comparison of computed low-energy conformers is presented to rationalize instances in which cyclization was not observed.
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Damm-Ganamet KL, DesJarlais RL, Marrone T, Shih AY, Schiffer JM, Perez-Benito L, Mirzadegan T. Breaking the Glass Ceiling in Simulation and Modeling: Women in Pharmaceutical Discovery. J Med Chem 2020; 63:1929-1936. [PMID: 31913036 DOI: 10.1021/acs.jmedchem.9b01512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The topic of gender equality within the United States workforce is receiving a great deal of attention. The field of chemistry is no exception and is increasingly focused on taking steps to achieve gender diversity within the chemistry workforce. Over the past several years, many computational chemistry groups within large pharmaceutical companies have realized growth in the number of women, and here we discuss the key factors that we believe have played a role in attracting and retaining the authors of this review as computational chemists in pharma. Furthermore, we combine our professional experiences in the context of how computational methodology and technology have evolved over the past decades and how that evolution has facilitated the inclusion of more women into the field. Our hope is to be a part of a solution and provide insight that will allow the chemistry workforce to continue to make steps forward in attaining gender diversity in the workplace.
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Xu G, Gaul MD, Song F, Du F, Liang Y, DesJarlais RL, DiLoreto K, Shook B, Rentzeperis D, Santulli R, Eckardt A, Demarest K. Discovery of potent and orally bioavailable indazole-based glucagon receptor antagonists for the treatment of type 2 diabetes. Bioorg Med Chem Lett 2019; 29:126668. [DOI: 10.1016/j.bmcl.2019.126668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/30/2019] [Accepted: 09/03/2019] [Indexed: 12/27/2022]
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10
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Song F, Xu G, Gaul MD, Zhao B, Lu T, Zhang R, DesJarlais RL, DiLoreto K, Huebert N, Shook B, Rentzeperis D, Santulli R, Eckardt A, Demarest K. Design, synthesis and structure activity relationships of indazole and indole derivatives as potent glucagon receptor antagonists. Bioorg Med Chem Lett 2019; 29:1974-1980. [DOI: 10.1016/j.bmcl.2019.05.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 02/02/2023]
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11
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Zhang YM, Greco MN, Macielag MJ, Teleha CA, DesJarlais RL, Tang Y, Ho G, Hou C, Chen C, Zhao S, Kauffman J, Camacho R, Qi J, Murray W, Demarest K, Leonard J. 6-Benzhydryl-4-amino-quinolin-2-ones as Potent Cannabinoid Type 1 (CB 1) Receptor Inverse Agonists and Chemical Modifications for Peripheral Selectivity. J Med Chem 2018; 61:10276-10298. [PMID: 30339387 DOI: 10.1021/acs.jmedchem.8b01467] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A novel series of 6-benzhydryl-4-amino-quinolin-2-ones was discovered as cannabinoid type 1 receptor (CB1R) inverse agonists based on the high-throughput screening hit, compound 1a. Structure-activity relationships were studied to improve in vitro/in vivo pharmacology and restrict distribution to the peripheral circulation. We adopted several strategies such as increasing topological polar surface area, incorporating discrete polyethylene glycol side chains, and targeting P-glycoprotein (P-gp) to minimize access to the brain. Compound 6a is a P-gp substrate and a potent and highly selective CB1R inverse agonist, demonstrating excellent in vivo metabolic stability and a low brain to plasma ratio. However, brain receptor occupancy studies showed that compound 6a may accumulate in brain with repeat dosing. This was evidenced by compound 6a inhibiting food intake and inducing weight loss in diet-induced obese mice. Thus, a strategy based on P-gp efflux may not be adequate for peripheral restriction of the disclosed quinolinone series.
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Illig CR, Manthey CL, Meegalla SK, Wall MJ, Chen J, Wilson KJ, DesJarlais RL, Ballentine SK, Schubert C, Crysler CS, Chen Y, Molloy CJ, Chaikin MA, Donatelli RR, Yurkow E, Zhou Z, Player MR, Tomczuk BE. Enhancement of kinase selectivity in a potent class of arylamide FMS inhibitors. Bioorg Med Chem Lett 2013; 23:6363-9. [PMID: 24138939 DOI: 10.1016/j.bmcl.2013.09.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 09/20/2013] [Accepted: 09/23/2013] [Indexed: 11/18/2022]
Abstract
Structure-activity relationship (SAR) studies on a highly potent series of arylamide FMS inhibitors were carried out with the aim of improving FMS kinase selectivity, particularly over KIT. Potent compound 17r (FMS IC50 0.7 nM, FMS cell IC50 6.1 nM) was discovered that had good PK properties and a greater than fivefold improvement in selectivity for FMS over KIT kinase in a cellular assay relative to the previously reported clinical candidate 4. This improved selectivity was manifested in vivo by no observed decrease in circulating reticulocytes, a measure of bone safety, at the highest studied dose. Compound 17r was highly active in a mouse pharmacodynamic model and demonstrated disease-modifying effects in a dose-dependent manner in a strep cell wall-induced arthritis model of rheumatoid arthritis in rats.
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DesJarlais RL. Insights from structural analysis of cFMS/inhibitor complexes: common interactions via three structurally dissimilar scaffolds. Curr Top Med Chem 2012; 12:1271-81. [PMID: 22571789 DOI: 10.2174/156802612800672835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 02/14/2012] [Accepted: 02/16/2012] [Indexed: 11/22/2022]
Abstract
A small-molecule drug discovery effort can benefit from having several chemical series. Where multiple series are not available, it is often the goal of a project to find novel scaffolds. Structural studies of ligand/protein complexes provide important information on the interactions driving binding. By generalizing these, it is possible to find molecules lacking in similarity in their connectivity yet retaining the ability to interact with the same target protein. Our studies on inhibitors of the cFMS tyrosine kinase provide a dramatic example of three different chemical series that make the same key interactions with the target protein. Collectively, these structural data provide a striking example of the pharmacophore hypothesis at work. In addition, they should prompt one to employ a broad approach when attempting scaffold hopping or any search for a novel series. It is clear that molecules that bind with similar interactions to a target need not possess 2-dimensional molecular similarity.
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14
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Illig CR, Manthey CL, Wall MJ, Meegalla SK, Chen J, Wilson KJ, Ballentine SK, DesJarlais RL, Schubert C, Crysler CS, Chen Y, Molloy CJ, Chaikin MA, Donatelli RR, Yurkow E, Zhou Z, Player MR, Tomczuk BE. Optimization of a Potent Class of Arylamide Colony-Stimulating Factor-1 Receptor Inhibitors Leading to Anti-inflammatory Clinical Candidate 4-Cyano-N-[2-(1-cyclohexen-1-yl)-4-[1-[(dimethylamino)acetyl]-4-piperidinyl]phenyl]-1H-imidazole-2-carboxamide (JNJ-28312141). J Med Chem 2011; 54:7860-83. [DOI: 10.1021/jm200900q] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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15
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Schalk-Hihi C, Schubert C, Alexander R, Bayoumy S, Clemente JC, Deckman I, DesJarlais RL, Dzordzorme KC, Flores CM, Grasberger B, Kranz JK, Lewandowski F, Liu L, Ma H, Maguire D, Macielag MJ, McDonnell ME, Mezzasalma Haarlander T, Miller R, Milligan C, Reynolds C, Kuo LC. Crystal structure of a soluble form of human monoglyceride lipase in complex with an inhibitor at 1.35 Å resolution. Protein Sci 2011; 20:670-83. [PMID: 21308848 PMCID: PMC3081545 DOI: 10.1002/pro.596] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Accepted: 01/14/2011] [Indexed: 01/07/2023]
Abstract
A high-resolution structure of a ligand-bound, soluble form of human monoglyceride lipase (MGL) is presented. The structure highlights a novel conformation of the regulatory lid-domain present in the lipase family as well as the binding mode of a pharmaceutically relevant reversible inhibitor. Analysis of the structure lacking the inhibitor indicates that the closed conformation can accommodate the native substrate 2-arachidonoyl glycerol. A model is proposed in which MGL undergoes conformational and electrostatic changes during the catalytic cycle ultimately resulting in its dissociation from the membrane upon completion of the cycle. In addition, the study outlines a successful approach to transform membrane associated proteins, which tend to aggregate upon purification, into a monomeric and soluble form.
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17
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Van den Bulck K, Bailey GP, De Garavilla L, Smith R, D’Andrea M, Tegegne G, Duong T, DesJarlais RL. Variations on a theme of paracelsus: Bizarre developmental toxicity findings. Reprod Toxicol 2009. [DOI: 10.1016/j.reprotox.2009.05.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Huang H, Hutta DA, Rinker JM, Hu H, Parsons WH, Schubert C, DesJarlais RL, Crysler CS, Chaikin MA, Donatelli RR, Chen Y, Cheng D, Zhou Z, Yurkow E, Manthey CL, Player MR. Pyrido[2,3-d]pyrimidin-5-ones: A Novel Class of Antiinflammatory Macrophage Colony-Stimulating Factor-1 Receptor Inhibitors. J Med Chem 2009; 52:1081-99. [DOI: 10.1021/jm801406h] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Meegalla SK, Wall MJ, Chen J, Wilson KJ, Ballentine SK, DesJarlais RL, Schubert C, Crysler CS, Chen Y, Molloy CJ, Chaikin MA, Manthey CL, Player MR, Tomczuk BE, Illig CR. Structure-based optimization of a potent class of arylamide FMS inhibitors. Bioorg Med Chem Lett 2008; 18:3632-7. [DOI: 10.1016/j.bmcl.2008.04.059] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Accepted: 04/23/2008] [Indexed: 11/27/2022]
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20
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Huang H, Hutta DA, Hu H, DesJarlais RL, Schubert C, Petrounia IP, Chaikin MA, Manthey CL, Player MR. Design and synthesis of a pyrido[2,3-d]pyrimidin-5-one class of anti-inflammatory FMS inhibitors. Bioorg Med Chem Lett 2008; 18:2355-61. [DOI: 10.1016/j.bmcl.2008.02.070] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 02/26/2008] [Accepted: 02/27/2008] [Indexed: 11/24/2022]
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21
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Travins JM, Ali F, Huang H, Ballentine SK, Khalil E, Hufnagel HR, Pan W, Gushue J, Leonard K, Bone RF, Soll RM, DesJarlais RL, Crysler CS, Ninan N, Kirkpatrick J, Cummings MD, Huebert N, Molloy CJ, Gaul M, Tomczuk BE, Subasinghe NL. Biphenylsulfonyl-thiophene-carboxamidine inhibitors of the complement component C1s. Bioorg Med Chem Lett 2008; 18:1603-6. [PMID: 18242991 DOI: 10.1016/j.bmcl.2008.01.064] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2007] [Revised: 01/14/2008] [Accepted: 01/16/2008] [Indexed: 11/28/2022]
Abstract
Complement activation has been implicated in disease states such as hereditary angioedema, ischemia-reperfusion injury, acute respiratory distress syndrome, and acute transplant rejection. Even though the complement cascade provides several protein targets for potential therapeutic intervention only two complement inhibitors have been approved so far for clinical use including anti-C5 antibodies for the treatment of paroxysmal nocturnal hemoglobinuria and purified C1-esterase inhibitor replacement therapy for the control of hereditary angioedema flares. In the present study, optimization of potency and physicochemical properties of a series of thiophene amidine-based C1s inhibitors with potential utility as intravenous agents for the inhibition of the classical pathway of complement is described.
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Abstract
Virtual screening involves the mining of small molecule databases from various sources. The small molecule databases used in virtual screening are typically processed, from simple 2D representations, to maximize their information content and to optimize them for input to the particular virtual screening technology being used. Processing interprets or adds molecular information related to connectivity, stereochemistry, protonation, tautomers and conformation. For virtual screening with an automated docking protocol, a technique that relies on specific intermolecular atom-atom contacts for ranking molecules, it is expected that the pre-processing protocol can affect the results of the docking experiment. The possible effects of processing on docking results have not been extensively studied, and this topic has only recently emerged as a significant aspect of the docking-based virtual screening process. One recent report highlights significant effects of different processing procedures on docking enrichment, while another outlines a general ligand preparation strategy. Here we survey and comment on recent practice in the field.
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23
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Subasinghe NL, Travins JM, Ali F, Huang H, Ballentine SK, Marugán JJ, Khalil E, Hufnagel HR, Bone RF, DesJarlais RL, Crysler CS, Ninan N, Cummings MD, Molloy CJ, Tomczuk BE. A novel series of arylsulfonylthiophene-2-carboxamidine inhibitors of the complement component C1s. Bioorg Med Chem Lett 2006; 16:2200-4. [PMID: 16460935 DOI: 10.1016/j.bmcl.2006.01.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2005] [Revised: 01/10/2006] [Accepted: 01/11/2006] [Indexed: 11/23/2022]
Abstract
Inhibiting the classical pathway of complement activation by attenuating the proteolytic activity of the serine protease C1s is a potential strategy for the therapeutic intervention in disease states such as hereditary angioedema, ischemia-reperfusion injury, and acute transplant rejection. A series of arylsulfonylthiophene-2-carboxamidine inhibitors of C1s were synthesized and evaluated for C1s inhibitory activity. The most potent compound had a Ki of 10nM and >1000-fold selectivity over uPA, tPA, FX(a), thrombin, and plasmin.
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Abstract
The state of the art of various computational aspects of docking-based virtual screening of database of small molecules is presented. The review encompasses the different search algorithms and the scoring functions used in docking methods and their applications to protein and nucleic acid drug targets. Recent progress made in the development and application of methods to include target flexibility are summarized. The fundamental issues and challenges involved in comparing various docking methods are discussed. Limitations of current technologies as well as future prospects are presented.
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Leonard K, Pan W, Anaclerio B, Gushue JM, Guo Z, DesJarlais RL, Chaikin MA, Lattanze J, Crysler C, Manthey CL, Tomczuk BE, Marugan JJ. Non-peptidic αvβ3 antagonists containing indol-1-yl propionic acids. Bioorg Med Chem Lett 2005; 15:2679-84. [PMID: 15863341 DOI: 10.1016/j.bmcl.2005.01.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2004] [Revised: 01/11/2005] [Accepted: 01/13/2005] [Indexed: 10/25/2022]
Abstract
We describe the synthesis and structure/activity relationship of RGD mimetics that are potent inhibitors of the integrin alpha(v)beta3. Indol-1-yl propionic acids containing a variety of basic moieties at the 5-position, as well as substitutions alpha and beta to the carboxy terminus were synthesized and evaluated. Novel compounds with improved potency have been identified.
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