76 results on '"Ortwine DF"'
Search Results
2. Cryo-EM reveals an unprecedented binding site for Na V 1.7 inhibitors enabling rational design of potent hybrid inhibitors.
- Author
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Kschonsak M, Jao CC, Arthur CP, Rohou AL, Bergeron P, Ortwine DF, McKerrall SJ, Hackos DH, Deng L, Chen J, Li T, Dragovich PS, Volgraf M, Wright MR, Payandeh J, Ciferri C, and Tellis JC
- Subjects
- Humans, Ligands, Protein Domains, Binding Sites, Structure-Activity Relationship, Cryoelectron Microscopy
- Abstract
The voltage-gated sodium (Na
V ) channel NaV 1.7 has been identified as a potential novel analgesic target due to its involvement in human pain syndromes. However, clinically available NaV channel-blocking drugs are not selective among the nine NaV channel subtypes, NaV 1.1-NaV 1.9. Moreover, the two currently known classes of NaV 1.7 subtype-selective inhibitors (aryl- and acylsulfonamides) have undesirable characteristics that may limit their development. To this point understanding of the structure-activity relationships of the acylsulfonamide class of NaV 1.7 inhibitors, exemplified by the clinical development candidate GDC-0310 , has been based solely on a single co-crystal structure of an arylsulfonamide inhibitor bound to voltage-sensing domain 4 (VSD4). To advance inhibitor design targeting the NaV 1.7 channel, we pursued high-resolution ligand-bound NaV 1.7-VSD4 structures using cryogenic electron microscopy (cryo-EM). Here, we report that GDC-0310 engages the NaV 1.7-VSD4 through an unexpected binding mode orthogonal to the arylsulfonamide inhibitor class binding pose, which identifies a previously unknown ligand binding site in NaV channels. This finding enabled the design of a novel hybrid inhibitor series that bridges the aryl- and acylsulfonamide binding pockets and allows for the generation of molecules with substantially differentiated structures and properties. Overall, our study highlights the power of cryo-EM methods to pursue challenging drug targets using iterative and high-resolution structure-guided inhibitor design. This work also underscores an important role of the membrane bilayer in the optimization of selective NaV channel modulators targeting VSD4., Competing Interests: MK, CJ, CA, AR, PB, DO, SM, DH, LD, JC, TL, PD, MV, MW, JP, CC, JT are Genentech employees, (© 2023, Kschonsak, Jao et al.)- Published
- 2023
- Full Text
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3. Discovery of GNE-502 as an orally bioavailable and potent degrader for estrogen receptor positive breast cancer.
- Author
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Zbieg JR, Liang J, Li J, Blake RA, Chang J, Friedman L, Goodacre S, Hartman SJ, Rei Ingalla E, Kiefer JR, Kleinheinz T, Labadie S, Lai T, Liao J, McLean N, Metcalfe C, Mody V, Nannini M, Ortwine DF, Ran Y, Ray N, Roussel F, Sambrone A, Sampath D, Vinogradova M, Wai J, Wang T, Yeap K, Zhang B, Zheng X, Zhong Y, and Wang X
- Subjects
- Animals, Antineoplastic Agents administration & dosage, Antineoplastic Agents chemistry, Dose-Response Relationship, Drug, Female, Humans, MCF-7 Cells, Mice, Molecular Structure, Protein Conformation, Xenograft Model Antitumor Assays, Antineoplastic Agents pharmacokinetics, Antineoplastic Agents pharmacology, Breast Neoplasms drug therapy, Drug Discovery, Receptors, Estrogen metabolism
- Abstract
Fulvestrant is an FDA-approved drug with a dual mechanism of action (MOA), acting as a full antagonist and degrader of the estrogen receptor protein. A significant limitation of fulvestrant is the dosing regimen required for efficacy. Due to its high lipophilicity and poor pharmacokinetic profile, fulvestrant needs to be administered through intramuscular injections which leads to injection site soreness. This route of administration also limits the dose and target occupancy in patients. We envisioned a best-in-class molecule that would function with the same dual MOA as fulvestrant, but with improved physicochemical properties and would be orally bioavailable. Herein we report our progress toward that goal, resulting in a new lead GNE-502 which addressed some of the liabilities of our previously reported lead molecule GNE-149., (Copyright © 2021 Elsevier Ltd. All rights reserved.)
- Published
- 2021
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4. GDC-9545 (Giredestrant): A Potent and Orally Bioavailable Selective Estrogen Receptor Antagonist and Degrader with an Exceptional Preclinical Profile for ER+ Breast Cancer.
- Author
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Liang J, Zbieg JR, Blake RA, Chang JH, Daly S, DiPasquale AG, Friedman LS, Gelzleichter T, Gill M, Giltnane JM, Goodacre S, Guan J, Hartman SJ, Ingalla ER, Kategaya L, Kiefer JR, Kleinheinz T, Labadie SS, Lai T, Li J, Liao J, Liu Z, Mody V, McLean N, Metcalfe C, Nannini MA, Oeh J, O'Rourke MG, Ortwine DF, Ran Y, Ray NC, Roussel F, Sambrone A, Sampath D, Schutt LK, Vinogradova M, Wai J, Wang T, Wertz IE, White JR, Yeap SK, Young A, Zhang B, Zheng X, Zhou W, Zhong Y, and Wang X
- Subjects
- Animals, Antineoplastic Agents chemistry, Antineoplastic Agents pharmacokinetics, Carbolines chemistry, Carbolines pharmacokinetics, Dogs, Estrogen Receptor Antagonists chemistry, Estrogen Receptor Antagonists pharmacokinetics, Female, Humans, MCF-7 Cells, Macaca fascicularis, Mice, Molecular Structure, Rats, Structure-Activity Relationship, Xenograft Model Antitumor Assays, Antineoplastic Agents therapeutic use, Breast Neoplasms drug therapy, Carbolines therapeutic use, Estrogen Receptor Antagonists therapeutic use, Estrogen Receptor alpha metabolism
- Abstract
Breast cancer remains a leading cause of cancer death in women, representing a significant unmet medical need. Here, we disclose our discovery efforts culminating in a clinical candidate, 35 (GDC-9545 or giredestrant). 35 is an efficient and potent selective estrogen receptor degrader (SERD) and a full antagonist, which translates into better antiproliferation activity than known SERDs ( 1 , 6 , 7 , and 9 ) across multiple cell lines. Fine-tuning the physiochemical properties enabled once daily oral dosing of 35 in preclinical species and humans. 35 exhibits low drug-drug interaction liability and demonstrates excellent in vitro and in vivo safety profiles. At low doses, 35 induces tumor regressions either as a single agent or in combination with a CDK4/6 inhibitor in an ESR1
Y537S mutant PDX or a wild-type ERα tumor model. Currently, 35 is being evaluated in Phase III clinical trials.- Published
- 2021
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5. Discovery of Acyl-sulfonamide Na v 1.7 Inhibitors GDC-0276 and GDC-0310.
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Safina BS, McKerrall SJ, Sun S, Chen CA, Chowdhury S, Jia Q, Li J, Zenova AY, Andrez JC, Bankar G, Bergeron P, Chang JH, Chang E, Chen J, Dean R, Decker SM, DiPasquale A, Focken T, Hemeon I, Khakh K, Kim A, Kwan R, Lindgren A, Lin S, Maher J, Mezeyova J, Misner D, Nelkenbrecher K, Pang J, Reese R, Shields SD, Sojo L, Sheng T, Verschoof H, Waldbrook M, Wilson MS, Xie Z, Young C, Zabka TS, Hackos DH, Ortwine DF, White AD, Johnson JP Jr, Robinette CL, Dehnhardt CM, Cohen CJ, and Sutherlin DP
- Subjects
- Animals, Azetidines chemistry, Azetidines pharmacokinetics, Benzamides chemistry, Benzamides pharmacokinetics, Cells, Cultured, HEK293 Cells, Humans, Piperidines chemistry, Piperidines pharmacokinetics, Piperidines pharmacology, Rats, Sprague-Dawley, Sulfonamides chemistry, Sulfonamides pharmacokinetics, Voltage-Gated Sodium Channel Blockers chemistry, Voltage-Gated Sodium Channel Blockers pharmacokinetics, Rats, Azetidines pharmacology, Benzamides pharmacology, Drug Discovery, NAV1.7 Voltage-Gated Sodium Channel metabolism, Sulfonamides pharmacology, Voltage-Gated Sodium Channel Blockers pharmacology
- Abstract
Na
v 1.7 is an extensively investigated target for pain with a strong genetic link in humans, yet in spite of this effort, it remains challenging to identify efficacious, selective, and safe inhibitors. Here, we disclose the discovery and preclinical profile of GDC-0276 ( 1 ) and GDC-0310 ( 2 ), selective Nav 1.7 inhibitors that have completed Phase 1 trials. Our initial search focused on close-in analogues to early compound 3 . This resulted in the discovery of GDC-0276 ( 1 ), which possessed improved metabolic stability and an acceptable overall pharmacokinetics profile. To further derisk the predicted human pharmacokinetics and enable QD dosing, additional optimization of the scaffold was conducted, resulting in the discovery of a novel series of N-benzyl piperidine Nav 1.7 inhibitors. Improvement of the metabolic stability by blocking the labile benzylic position led to the discovery of GDC-0310 ( 2 ), which possesses improved Nav selectivity and pharmacokinetic profile over 1 .- Published
- 2021
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6. cis-Selective synthesis of 1,3-disubstituted tetrahydro-β-carbolines from N-sulfonyl N,S-acetals.
- Author
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Lennon Luo SX, Liu Y, Lambrecht MJ, Ortwine DF, DiPasquale AG, Liang J, Wang X, Zbieg JR, and Li J
- Abstract
Nucleophilic addition of Grignard reagents to tetrahydro-β-carboline (THC) N-sulfonyl N,S-acetal generates exclusively cis-1,3-disubstituted THCs with a unique 1,3-diaxial conformation. The stereochemical relationship of the 1,3-substituents was confirmed by 2-dimensional NMR spectroscopy and X-ray crystallography. The mechanism of the reaction is proposed based on crystal structures and molecular orbital calculations.
- Published
- 2019
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7. Discovery of a C-8 hydroxychromene as a potent degrader of estrogen receptor alpha with improved rat oral exposure over GDC-0927.
- Author
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Labadie SS, Li J, Blake RA, Chang JH, Goodacre S, Hartman SJ, Liang W, Kiefer JR, Kleinheinz T, Lai T, Liao J, Ortwine DF, Mody V, Ray NC, Roussel F, Vinogradova M, Yeap SK, Zhang B, Zheng X, Zbieg JR, Liang J, and Wang X
- Subjects
- Administration, Oral, Animals, Azetidines administration & dosage, Azetidines metabolism, Azetidines pharmacokinetics, Crystallography, X-Ray, Drug Discovery, Drug Stability, Flavonoids administration & dosage, Flavonoids metabolism, Flavonoids pharmacokinetics, Humans, MCF-7 Cells, Microsomes, Liver metabolism, Rats, Stereoisomerism, Structure-Activity Relationship, Azetidines pharmacology, Estrogen Receptor alpha metabolism, Flavonoids pharmacology
- Abstract
Phenolic groups are responsible for the high clearance and low oral bioavailability of the estrogen receptor alpha (ERα) clinical candidate GDC-0927. An exhaustive search for a backup molecule with improved pharmacokinetic (PK) properties identified several metabolically stable analogs, although in general at the expense of the desired potency and degradation efficiency. C-8 hydroxychromene 30 is the first example of a phenol-containing chromene that not only maintained excellent potency but also exhibited 10-fold higher oral exposure in rats. The improved in vivo clearance in rat was hypothesized to be the result of C-8 hydroxy group being sterically protected from glucuronide conjugation. The excellent potency underscores the possibility of replacing the presumed indispensable phenolic group at C-6 or C-7 of the chromene core. Co-crystal structures were obtained to highlight the change in key interactions and rationalize the retained potency., (Copyright © 2019 Elsevier Ltd. All rights reserved.)
- Published
- 2019
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8. Structure- and Ligand-Based Discovery of Chromane Arylsulfonamide Na v 1.7 Inhibitors for the Treatment of Chronic Pain.
- Author
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McKerrall SJ, Nguyen T, Lai KW, Bergeron P, Deng L, DiPasquale A, Chang JH, Chen J, Chernov-Rogan T, Hackos DH, Maher J, Ortwine DF, Pang J, Payandeh J, Proctor WR, Shields SD, Vogt J, Ji P, Liu W, Ballini E, Schumann L, Tarozzo G, Bankar G, Chowdhury S, Hasan A, Johnson JP Jr, Khakh K, Lin S, Cohen CJ, Dehnhardt CM, Safina BS, and Sutherlin DP
- Subjects
- Analgesics chemistry, Analgesics metabolism, Analgesics pharmacology, Analgesics therapeutic use, Animals, Binding Sites, Cell Line, Cell Survival drug effects, Chronic Pain drug therapy, Chronic Pain pathology, Dogs, Half-Life, Humans, Ligands, Male, Mice, Molecular Docking Simulation, Mutagenesis, Site-Directed, NAV1.7 Voltage-Gated Sodium Channel genetics, NAV1.7 Voltage-Gated Sodium Channel metabolism, Protein Isoforms antagonists & inhibitors, Protein Isoforms metabolism, Rats, Structure-Activity Relationship, Sulfonamides metabolism, Sulfonamides pharmacology, Sulfonamides therapeutic use, Voltage-Gated Sodium Channel Blockers metabolism, Voltage-Gated Sodium Channel Blockers pharmacology, Voltage-Gated Sodium Channel Blockers therapeutic use, NAV1.7 Voltage-Gated Sodium Channel chemistry, Sulfonamides chemistry, Voltage-Gated Sodium Channel Blockers chemistry
- Abstract
Using structure- and ligand-based design principles, a novel series of piperidyl chromane arylsulfonamide Na
v 1.7 inhibitors was discovered. Early optimization focused on improvement of potency through refinement of the low energy ligand conformation and mitigation of high in vivo clearance. An in vitro hepatotoxicity hazard was identified and resolved through optimization of lipophilicity and lipophilic ligand efficiency to arrive at GNE-616 (24), a highly potent, metabolically stable, subtype selective inhibitor of Nav 1.7. Compound 24 showed a robust PK/PD response in a Nav 1.7-dependent mouse model, and site-directed mutagenesis was used to identify residues critical for the isoform selectivity profile of 24.- Published
- 2019
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9. Unexpected equivalent potency of a constrained chromene enantiomeric pair rationalized by co-crystal structures in complex with estrogen receptor alpha.
- Author
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Zhang B, Kiefer JR, Blake RA, Chang JH, Hartman S, Ingalla ER, Kleinheinz T, Mody V, Nannini M, Ortwine DF, Ran Y, Sambrone A, Sampath D, Vinogradova M, Zhong Y, Nwachukwu JC, Nettles KW, Lai T, Liao J, Zheng X, Chen H, Wang X, and Liang J
- Subjects
- Antineoplastic Agents chemistry, Benzopyrans chemistry, Crystallization, Humans, MCF-7 Cells, Models, Molecular, Molecular Structure, Protein Conformation, Signal Transduction, Structure-Activity Relationship, Antineoplastic Agents pharmacology, Benzopyrans pharmacology, Estrogen Receptor alpha chemistry
- Abstract
Despite tremendous progress made in the understanding of the ERα signaling pathway and the approval of many therapeutic agents, ER+ breast cancer continues to be a leading cause of cancer death in women. We set out to discover compounds with a dual mechanism of action in which they not only compete with estradiol for binding with ERα, but also can induce the degradation of the ERα protein itself. We were attracted to the constrained chromenes containing a tetracyclic benzopyranobenzoxepine scaffold, which were reported as potent selective estrogen receptor modulators (SERMs). Incorporation of a fluoromethyl azetidine side chain yielded highly potent and efficacious selective estrogen receptor degraders (SERDs), such as 16aa and surprisingly, also its enantiomeric pair 16ab. Co-crystal structures of the enantiomeric pair 16aa and 16ab in complex with ERα revealed default (mimics the A-D rings of endogenous ligand estradiol) and core-flipped binding modes, rationalizing the equivalent potency observed for these enantiomers in the ERα degradation and MCF-7 anti-proliferation assays., (Copyright © 2019 Elsevier Ltd. All rights reserved.)
- Published
- 2019
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10. Water molecules in protein-ligand interfaces. Evaluation of software tools and SAR comparison.
- Author
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Nittinger E, Gibbons P, Eigenbrot C, Davies DR, Maurer B, Yu CL, Kiefer JR, Kuglstatter A, Murray J, Ortwine DF, Tang Y, and Tsui V
- Subjects
- Crystallography, X-Ray, Ligands, Protein Binding, Protein Domains, Software, Solvents chemistry, Structure-Activity Relationship, Thermodynamics, Agammaglobulinaemia Tyrosine Kinase chemistry, Computer Simulation, Models, Molecular, Protein Kinase Inhibitors chemistry, Water chemistry
- Abstract
Targeting the interaction with or displacement of the 'right' water molecule can significantly increase inhibitor potency in structure-guided drug design. Multiple computational approaches exist to predict which waters should be targeted for displacement to achieve the largest gain in potency. However, the relative success of different methods remains underexplored. Here, we present a comparison of the ability of five water prediction programs (3D-RISM, SZMAP, WaterFLAP, WaterRank, and WaterMap) to predict crystallographic water locations, calculate their binding free energies, and to relate differences in these energies to observed changes in potency. The structural cohort included nine Bruton's Tyrosine Kinase (BTK) structures, and nine bromodomain structures. Each program accurately predicted the locations of most crystallographic water molecules. However, the predicted binding free energies correlated poorly with the observed changes in inhibitor potency when solvent atoms were displaced by chemical changes in closely related compounds.
- Published
- 2019
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11. Identification of Selective Acyl Sulfonamide-Cycloalkylether Inhibitors of the Voltage-Gated Sodium Channel (Na V ) 1.7 with Potent Analgesic Activity.
- Author
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Sun S, Jia Q, Zenova AY, Wilson MS, Chowdhury S, Focken T, Li J, Decker S, Grimwood ME, Andrez JC, Hemeon I, Sheng T, Chen CA, White A, Hackos DH, Deng L, Bankar G, Khakh K, Chang E, Kwan R, Lin S, Nelkenbrecher K, Sellers BD, DiPasquale AG, Chang J, Pang J, Sojo L, Lindgren A, Waldbrook M, Xie Z, Young C, Johnson JP, Robinette CL, Cohen CJ, Safina BS, Sutherlin DP, Ortwine DF, and Dehnhardt CM
- Subjects
- Analgesics metabolism, Analgesics therapeutic use, Animals, Binding Sites, Drug Design, Half-Life, Humans, Male, Mice, Mice, Transgenic, Microsomes, Liver metabolism, Molecular Docking Simulation, NAV1.7 Voltage-Gated Sodium Channel metabolism, Pain chemically induced, Pain drug therapy, Pain pathology, Protein Structure, Tertiary, Rats, Rats, Sprague-Dawley, Structure-Activity Relationship, Sulfonamides metabolism, Sulfonamides therapeutic use, Voltage-Gated Sodium Channel Blockers metabolism, Voltage-Gated Sodium Channel Blockers therapeutic use, Analgesics chemistry, NAV1.7 Voltage-Gated Sodium Channel chemistry, Sulfonamides chemistry, Voltage-Gated Sodium Channel Blockers chemistry
- Abstract
Herein, we report the discovery and optimization of a series of orally bioavailable acyl sulfonamide Na
V 1.7 inhibitors that are selective for NaV 1.7 over NaV 1.5 and highly efficacious in in vivo models of pain and hNaV 1.7 target engagement. An analysis of the physicochemical properties of literature NaV 1.7 inhibitors suggested that acyl sulfonamides with high fsp3 could overcome some of the pharmacokinetic (PK) and efficacy challenges seen with existing series. Parallel library syntheses lead to the identification of analogue 7, which exhibited moderate potency against NaV 1.7 and an acceptable PK profile in rodents, but relatively poor stability in human liver microsomes. Further, design strategy then focused on the optimization of potency against hNaV 1.7 and improvement of human metabolic stability, utilizing induced fit docking in our previously disclosed X-ray cocrystal of the NaV 1.7 voltage sensing domain. These investigations culminated in the discovery of tool compound 33, one of the most potent and efficacious NaV 1.7 inhibitors reported to date.- Published
- 2019
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12. Design of Conformationally Constrained Acyl Sulfonamide Isosteres: Identification of N-([1,2,4]Triazolo[4,3- a]pyridin-3-yl)methane-sulfonamides as Potent and Selective hNa V 1.7 Inhibitors for the Treatment of Pain.
- Author
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Focken T, Chowdhury S, Zenova A, Grimwood ME, Chabot C, Sheng T, Hemeon I, Decker SM, Wilson M, Bichler P, Jia Q, Sun S, Young C, Lin S, Goodchild SJ, Shuart NG, Chang E, Xie Z, Li B, Khakh K, Bankar G, Waldbrook M, Kwan R, Nelkenbrecher K, Karimi Tari P, Chahal N, Sojo L, Robinette CL, White AD, Chen CA, Zhang Y, Pang J, Chang JH, Hackos DH, Johnson JP Jr, Cohen CJ, Ortwine DF, Sutherlin DP, Dehnhardt CM, and Safina BS
- Subjects
- Amino Acid Sequence, Animals, Dogs, Drug Stability, Humans, Kinetics, Mice, Molecular Conformation, Pain metabolism, Rats, Sulfonamides pharmacokinetics, Sulfonamides therapeutic use, Voltage-Gated Sodium Channel Blockers pharmacokinetics, Voltage-Gated Sodium Channel Blockers therapeutic use, Drug Design, NAV1.7 Voltage-Gated Sodium Channel metabolism, Pain drug therapy, Sulfonamides chemistry, Sulfonamides pharmacology, Voltage-Gated Sodium Channel Blockers chemistry, Voltage-Gated Sodium Channel Blockers pharmacology
- Abstract
The sodium channel Na
V 1.7 has emerged as a promising target for the treatment of pain based on strong genetic validation of its role in nociception. In recent years, a number of aryl and acyl sulfonamides have been reported as potent inhibitors of NaV 1.7, with high selectivity over the cardiac isoform NaV 1.5. Herein, we report on the discovery of a novel series of N-([1,2,4]triazolo[4,3- a]pyridin-3-yl)methanesulfonamides as selective NaV 1.7 inhibitors. Starting with the crystal structure of an acyl sulfonamide, we rationalized that cyclization to form a fused heterocycle would improve physicochemical properties, in particular lipophilicity. Our design strategy focused on optimization of potency for block of NaV 1.7 and human metabolic stability. Lead compounds 10, 13 (GNE-131), and 25 showed excellent potency, good in vitro metabolic stability, and low in vivo clearance in mouse, rat, and dog. Compound 13 also displayed excellent efficacy in a transgenic mouse model of induced pain.- Published
- 2018
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13. Discovery of GDC-0853: A Potent, Selective, and Noncovalent Bruton's Tyrosine Kinase Inhibitor in Early Clinical Development.
- Author
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Crawford JJ, Johnson AR, Misner DL, Belmont LD, Castanedo G, Choy R, Coraggio M, Dong L, Eigenbrot C, Erickson R, Ghilardi N, Hau J, Katewa A, Kohli PB, Lee W, Lubach JW, McKenzie BS, Ortwine DF, Schutt L, Tay S, Wei B, Reif K, Liu L, Wong H, and Young WB
- Subjects
- Agammaglobulinaemia Tyrosine Kinase drug effects, Agammaglobulinaemia Tyrosine Kinase genetics, Animals, Anti-Inflammatory Agents pharmacokinetics, Anti-Inflammatory Agents toxicity, Arthritis, Experimental drug therapy, Arthritis, Rheumatoid drug therapy, Dogs, Drug Discovery, Humans, Lupus Erythematosus, Systemic drug therapy, Madin Darby Canine Kidney Cells, Models, Molecular, Molecular Structure, Piperazines pharmacokinetics, Piperazines toxicity, Protein Kinase Inhibitors pharmacokinetics, Protein Kinase Inhibitors toxicity, Pyridones pharmacokinetics, Pyridones toxicity, Rats, Rats, Inbred Lew, Rats, Sprague-Dawley, Agammaglobulinaemia Tyrosine Kinase antagonists & inhibitors, Anti-Inflammatory Agents pharmacology, Piperazines pharmacology, Protein Kinase Inhibitors pharmacology, Pyridones pharmacology
- Abstract
Bruton's tyrosine kinase (Btk) is a nonreceptor cytoplasmic tyrosine kinase involved in B-cell and myeloid cell activation, downstream of B-cell and Fcγ receptors, respectively. Preclinical studies have indicated that inhibition of Btk activity might offer a potential therapy in autoimmune diseases such as rheumatoid arthritis and systemic lupus erythematosus. Here we disclose the discovery and preclinical characterization of a potent, selective, and noncovalent Btk inhibitor currently in clinical development. GDC-0853 (29) suppresses B cell- and myeloid cell-mediated components of disease and demonstrates dose-dependent activity in an in vivo rat model of inflammatory arthritis. It demonstrates highly favorable safety, pharmacokinetic (PK), and pharmacodynamic (PD) profiles in preclinical and Phase 2 studies ongoing in patients with rheumatoid arthritis, lupus, and chronic spontaneous urticaria. On the basis of its potency, selectivity, long target residence time, and noncovalent mode of inhibition, 29 has the potential to be a best-in-class Btk inhibitor for a wide range of immunological indications.
- Published
- 2018
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14. Mechanism-specific assay design facilitates the discovery of Nav1.7-selective inhibitors.
- Author
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Chernov-Rogan T, Li T, Lu G, Verschoof H, Khakh K, Jones SW, Beresini MH, Liu C, Ortwine DF, McKerrall SJ, Hackos DH, Sutherlin D, Cohen CJ, and Chen J
- Subjects
- Animals, High-Throughput Screening Assays, Humans, Insect Proteins, Membrane Potentials, NAV1.7 Voltage-Gated Sodium Channel drug effects, NAV1.7 Voltage-Gated Sodium Channel genetics, Rats, Veratridine, Wasp Venoms, Drug Discovery methods, Molecular Targeted Therapy, Voltage-Gated Sodium Channel Blockers analysis
- Abstract
Many ion channels, including Nav1.7, Cav1.3, and Kv1.3, are linked to human pathologies and are important therapeutic targets. To develop efficacious and safe drugs, subtype-selective modulation is essential, but has been extremely difficult to achieve. We postulate that this challenge is caused by the poor assay design, and investigate the Nav1.7 membrane potential assay, one of the most extensively employed screening assays in modern drug discovery. The assay uses veratridine to activate channels, and compounds are identified based on the inhibition of veratridine-evoked activities. We show that this assay is biased toward nonselective pore blockers and fails to detect the most potent, selective voltage-sensing domain 4 (VSD4) blockers, including PF-05089771 (PF-771) and GX-936. By eliminating a key binding site for pore blockers and replacing veratridine with a VSD-4 binding activator, we directed the assay toward non-pore-blocking mechanisms and discovered Nav1.7-selective chemical scaffolds. Hence, we address a major hurdle in Nav1.7 drug discovery, and this mechanistic approach to assay design is applicable to Cav3.1, Kv1.3, and many other ion channels to facilitate drug discovery., Competing Interests: Conflict of interest statement: H.V., K.K., and C.J.C. are employees of Xenon Pharmaceuticals; and T.C.-R., T.L., G.L., S.W.J., M.H.B., C.L., D.F.O., S.J.M., D.H.H., D.S., and J.C. are employees of Genentech., (Copyright © 2018 the Author(s). Published by PNAS.)
- Published
- 2018
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15. Computational Support of Medicinal Chemistry in Industrial Settings.
- Author
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Ortwine DF
- Subjects
- Biotechnology, Drug Industry, Humans, Chemistry, Pharmaceutical methods, Computational Biology methods, Drug Discovery methods
- Abstract
The practice of computational chemistry in an industrial setting poses unique opportunities and challenges. Industrial computational chemists must manage large amounts of data, master modeling software, write scripts to perform custom calculations, and stay abreast of scientific advances in the field. Just as importantly, because computational chemists are full partners in the drug discovery effort at companies, in order to influence and streamline the drug discovery process, they must communicate effectively with medicinal chemists and other scientists to deliver results of their calculations in a timely fashion. The skills necessary to play this role require education that emphasizes a combination of chemistry, programming, and communication skills. Professors are encouraged to incorporate such training in their curriculum.
- Published
- 2018
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16. From a novel HTS hit to potent, selective, and orally bioavailable KDM5 inhibitors.
- Author
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Liang J, Labadie S, Zhang B, Ortwine DF, Patel S, Vinogradova M, Kiefer JR, Mauer T, Gehling VS, Harmange JC, Cummings R, Lai T, Liao J, Zheng X, Liu Y, Gustafson A, Van der Porten E, Mao W, Liederer BM, Deshmukh G, An L, Ran Y, Classon M, Trojer P, Dragovich PS, and Murray L
- Subjects
- Administration, Oral, Animals, Biological Availability, Dose-Response Relationship, Drug, Enzyme Inhibitors administration & dosage, Enzyme Inhibitors chemistry, Humans, Mice, Microsomes, Liver chemistry, Microsomes, Liver metabolism, Molecular Docking Simulation, Molecular Structure, Pyrazoles administration & dosage, Pyrazoles chemistry, Rats, Retinoblastoma-Binding Protein 2 metabolism, Structure-Activity Relationship, Enzyme Inhibitors pharmacology, High-Throughput Screening Assays, Pyrazoles pharmacology, Retinoblastoma-Binding Protein 2 antagonists & inhibitors
- Abstract
A high-throughput screening (HTS) of the Genentech/Roche library identified a novel, uncharged scaffold as a KDM5A inhibitor. Lacking insight into the binding mode, initial attempts to improve inhibitor potency failed to improve potency, and synthesis of analogs was further hampered by the presence of a C-C bond between the pyrrolidine and pyridine. Replacing this with a C-N bond significantly simplified synthesis, yielding pyrazole analog 35, of which we obtained a co-crystal structure with KDM5A. Using structure-based design approach, we identified 50 with improved biochemical, cell potency and reduced MW and lower lipophilicity (LogD) compared with the original hit. Furthermore, 50 showed lower clearance than 9 in mice. In combination with its remarkably low plasma protein binding (PPB) in mice (40%), oral dosing of 50 at 5mg/kg resulted in unbound C
max ∼2-fold of its cell potency (PC9 H3K4Me3 0.96μM), meeting our criteria for an in vivo tool compound from a new scaffold., (Copyright © 2017 Elsevier Ltd. All rights reserved.)- Published
- 2017
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17. Discovery of Potent and Selective Tricyclic Inhibitors of Bruton's Tyrosine Kinase with Improved Druglike Properties.
- Author
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Wang X, Barbosa J, Blomgren P, Bremer MC, Chen J, Crawford JJ, Deng W, Dong L, Eigenbrot C, Gallion S, Hau J, Hu H, Johnson AR, Katewa A, Kropf JE, Lee SH, Liu L, Lubach JW, Macaluso J, Maciejewski P, Mitchell SA, Ortwine DF, DiPaolo J, Reif K, Scheerens H, Schmitt A, Wong H, Xiong JM, Xu J, Zhao Z, Zhou F, Currie KS, and Young WB
- Abstract
In our continued effort to discover and develop best-in-class Bruton's tyrosine kinase (Btk) inhibitors for the treatment of B-cell lymphomas, rheumatoid arthritis, and systemic lupus erythematosus, we devised a series of novel tricyclic compounds that improved upon the druglike properties of our previous chemical matter. Compounds exemplified by G-744 are highly potent, selective for Btk, metabolically stable, well tolerated, and efficacious in an animal model of arthritis.
- Published
- 2017
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18. Enabling drug discovery project decisions with integrated computational chemistry and informatics.
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Tsui V, Ortwine DF, and Blaney JM
- Subjects
- Chemistry, Pharmaceutical, Computational Biology, Drug Discovery, Molecular Dynamics Simulation, Software, Computer-Aided Design, Drug Design, Models, Molecular
- Abstract
Computational chemistry/informatics scientists and software engineers in Genentech Small Molecule Drug Discovery collaborate with experimental scientists in a therapeutic project-centric environment. Our mission is to enable and improve pre-clinical drug discovery design and decisions. Our goal is to deliver timely data, analysis, and modeling to our therapeutic project teams using best-in-class software tools. We describe our strategy, the organization of our group, and our approaches to reach this goal. We conclude with a summary of the interdisciplinary skills required for computational scientists and recommendations for their training.
- Published
- 2017
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19. Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge.
- Author
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Rustenburg AS, Dancer J, Lin B, Feng JA, Ortwine DF, Mobley DL, and Chodera JD
- Subjects
- Chromatography, Liquid, Computer Simulation, Hydrogen-Ion Concentration, Models, Chemical, Solubility, Tandem Mass Spectrometry, Thermodynamics, Cyclohexanes chemistry, Pharmaceutical Preparations chemistry, Solvents chemistry, Water chemistry
- Abstract
Small molecule distribution coefficients between immiscible nonaqueuous and aqueous phases-such as cyclohexane and water-measure the degree to which small molecules prefer one phase over another at a given pH. As distribution coefficients capture both thermodynamic effects (the free energy of transfer between phases) and chemical effects (protonation state and tautomer effects in aqueous solution), they provide an exacting test of the thermodynamic and chemical accuracy of physical models without the long correlation times inherent to the prediction of more complex properties of relevance to drug discovery, such as protein-ligand binding affinities. For the SAMPL5 challenge, we carried out a blind prediction exercise in which participants were tasked with the prediction of distribution coefficients to assess its potential as a new route for the evaluation and systematic improvement of predictive physical models. These measurements are typically performed for octanol-water, but we opted to utilize cyclohexane for the nonpolar phase. Cyclohexane was suggested to avoid issues with the high water content and persistent heterogeneous structure of water-saturated octanol phases, since it has greatly reduced water content and a homogeneous liquid structure. Using a modified shake-flask LC-MS/MS protocol, we collected cyclohexane/water distribution coefficients for a set of 53 druglike compounds at pH 7.4. These measurements were used as the basis for the SAMPL5 Distribution Coefficient Challenge, where 18 research groups predicted these measurements before the experimental values reported here were released. In this work, we describe the experimental protocol we utilized for measurement of cyclohexane-water distribution coefficients, report the measured data, propose a new bootstrap-based data analysis procedure to incorporate multiple sources of experimental error, and provide insights to help guide future iterations of this valuable exercise in predictive modeling., Competing Interests: VIII. CONFLICT OF INTEREST STATEMENTDLM and JDC are members of the Scientific Advisory Board for Schrödinger, LLC.
- Published
- 2016
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20. Battling Btk Mutants With Noncovalent Inhibitors That Overcome Cys481 and Thr474 Mutations.
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Johnson AR, Kohli PB, Katewa A, Gogol E, Belmont LD, Choy R, Penuel E, Burton L, Eigenbrot C, Yu C, Ortwine DF, Bowman K, Franke Y, Tam C, Estevez A, Mortara K, Wu J, Li H, Lin M, Bergeron P, Crawford JJ, and Young WB
- Subjects
- Adenine analogs & derivatives, Agammaglobulinaemia Tyrosine Kinase, Antineoplastic Agents pharmacology, Antineoplastic Agents therapeutic use, Humans, Kinetics, Leukemia, Lymphocytic, Chronic, B-Cell drug therapy, Piperidines, Protein Kinase Inhibitors pharmacology, Protein Kinase Inhibitors therapeutic use, Protein-Tyrosine Kinases metabolism, Pyrazoles therapeutic use, Pyrimidines therapeutic use, Cysteine genetics, Mutation, Protein-Tyrosine Kinases antagonists & inhibitors, Protein-Tyrosine Kinases genetics, Threonine genetics
- Abstract
The Bruton's tyrosine kinase (Btk) inhibitor ibrutinib has shown impressive clinical efficacy in a range of B-cell malignancies. However, acquired resistance has emerged, and second generation therapies are now being sought. Ibrutinib is a covalent, irreversible inhibitor that modifies Cys481 in the ATP binding site of Btk and renders the enzyme inactive, thereby blocking B-cell receptor signal transduction. Not surprisingly, Cys481 is the most commonly mutated Btk residue in cases of acquired resistance to ibrutinib. Mutations at other sites, including Thr474, a gatekeeper residue, have also been detected. Herein, we describe noncovalent Btk inhibitors that differ from covalent inhibitors like ibrutinib in that they do not interact with Cys481, they potently inhibit the ibrutinib-resistant Btk C481S mutant in vitro and in cells, and they are exquisitely selective for Btk. Noncovalent inhibitors such as GNE-431 also show excellent potency against the C481R, T474I, and T474M mutants. X-ray crystallographic analysis of Btk provides insight into the unique mode of binding of these inhibitors that explains their high selectivity for Btk and their retained activity against mutant forms of Btk. This class of noncovalent Btk inhibitors may provide a treatment option to patients, especially those who have acquired resistance to ibrutinib by mutation of Cys481 or Thr474.
- Published
- 2016
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21. Design and evaluation of 1,7-naphthyridones as novel KDM5 inhibitors.
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Labadie SS, Dragovich PS, Cummings RT, Deshmukh G, Gustafson A, Han N, Harmange JC, Kiefer JR, Li Y, Liang J, Liederer BM, Liu Y, Manieri W, Mao W, Murray L, Ortwine DF, Trojer P, VanderPorten E, Vinogradova M, and Wen L
- Subjects
- Animals, Crystallography, X-Ray, Dogs, Drug Design, Humans, Madin Darby Canine Kidney Cells, Naphthyridines chemistry, Structure-Activity Relationship, Jumonji Domain-Containing Histone Demethylases antagonists & inhibitors, Naphthyridines pharmacology, Nuclear Proteins antagonists & inhibitors, Repressor Proteins antagonists & inhibitors, Retinoblastoma-Binding Protein 2 antagonists & inhibitors
- Abstract
Features from a high throughput screening (HTS) hit and a previously reported scaffold were combined to generate 1,7-naphthyridones as novel KDM5 enzyme inhibitors with nanomolar potencies. These molecules exhibited high selectivity over the related KDM4C and KDM2B isoforms. An X-ray co-crystal structure of a representative molecule bound to KDM5A showed that these inhibitors are competitive with the co-substrate (2-oxoglutarate or 2-OG)., (Copyright © 2016 Elsevier Ltd. All rights reserved.)
- Published
- 2016
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22. Lead optimization of a pyrazolo[1,5-a]pyrimidin-7(4H)-one scaffold to identify potent, selective and orally bioavailable KDM5 inhibitors suitable for in vivo biological studies.
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Liang J, Zhang B, Labadie S, Ortwine DF, Vinogradova M, Kiefer JR, Gehling VS, Harmange JC, Cummings R, Lai T, Liao J, Zheng X, Liu Y, Gustafson A, Van der Porten E, Mao W, Liederer BM, Deshmukh G, Classon M, Trojer P, Dragovich PS, and Murray L
- Subjects
- Administration, Oral, Animals, Binding Sites, Crystallography, X-Ray, Female, Half-Life, Histones metabolism, Humans, Liver metabolism, Mice, Microsomes, Liver metabolism, Molecular Dynamics Simulation, Pyrazoles chemical synthesis, Pyrazoles pharmacokinetics, Pyrimidinones blood, Pyrimidinones chemical synthesis, Pyrimidinones pharmacokinetics, Rats, Retinoblastoma-Binding Protein 2 metabolism, Structure-Activity Relationship, Pyrazoles chemistry, Pyrimidinones chemistry, Retinoblastoma-Binding Protein 2 antagonists & inhibitors
- Abstract
Starting with a lead [1,5-a]pyrimidin-7(4H)-one-containing molecule (1), we generated potent, selective and orally bioavailable KDM5 inhibitors. Using structure- and property-based approaches, we designed 48 with improved cell potency (PC9 H3K4Me3 EC50=0.34μM). Furthermore, 48 maintained suitable physiochemical properties and displayed an excellent pharmacokinetic (PK) profile in mice. When dosed orally in mice at 50mg/kg twice a day (BID), 48 showed an unbound maximal plasma concentration (Cmax) >15-fold over its cell EC50, thereby providing a robust chemical probe for studying KDM5 biological functions in vivo., (Copyright © 2016 Elsevier Ltd. All rights reserved.)
- Published
- 2016
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23. Fragment Molecular Orbital Method Applied to Lead Optimization of Novel Interleukin-2 Inducible T-Cell Kinase (ITK) Inhibitors.
- Author
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Heifetz A, Trani G, Aldeghi M, MacKinnon CH, McEwan PA, Brookfield FA, Chudyk EI, Bodkin M, Pei Z, Burch JD, and Ortwine DF
- Subjects
- Benzothiazoles chemistry, Crystallography, X-Ray, Drug Design, Enzyme Induction, Indazoles chemistry, Models, Molecular, Protein Kinase Inhibitors chemistry, Protein-Tyrosine Kinases biosynthesis, Pyridines chemistry, Quantum Theory, Interleukin-2 physiology, Protein Kinase Inhibitors pharmacology, Protein-Tyrosine Kinases antagonists & inhibitors
- Abstract
Inhibition of inducible T-cell kinase (ITK), a nonreceptor tyrosine kinase, may represent a novel treatment for allergic asthma. In our previous reports, we described the discovery of sulfonylpyridine (SAP), benzothiazole (BZT), indazole (IND), and tetrahydroindazole (THI) series as novel ITK inhibitors and how computational tools such as dihedral scans and docking were used to support this process. X-ray crystallography and modeling were applied to provide essential insight into ITK-ligand interactions. However, "visual inspection" traditionally used for the rationalization of protein-ligand affinity cannot always explain the full complexity of the molecular interactions. The fragment molecular orbital (FMO) quantum-mechanical (QM) method provides a complete list of the interactions formed between the ligand and protein that are often omitted from traditional structure-based descriptions. FMO methodology was successfully used as part of a rational structure-based drug design effort to improve the ITK potency of high-throughput screening hits, ultimately delivering ligands with potency in the subnanomolar range.
- Published
- 2016
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24. Discovery of highly potent and selective Bruton's tyrosine kinase inhibitors: Pyridazinone analogs with improved metabolic stability.
- Author
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Young WB, Barbosa J, Blomgren P, Bremer MC, Crawford JJ, Dambach D, Eigenbrot C, Gallion S, Johnson AR, Kropf JE, Lee SH, Liu L, Lubach JW, Macaluso J, Maciejewski P, Mitchell SA, Ortwine DF, Di Paolo J, Reif K, Scheerens H, Schmitt A, Wang X, Wong H, Xiong JM, Xu J, Yu C, Zhao Z, and Currie KS
- Subjects
- Agammaglobulinaemia Tyrosine Kinase, Animals, Dogs, Humans, Mice, Microsomes, Liver metabolism, Models, Molecular, Protein Kinase Inhibitors metabolism, Protein Kinase Inhibitors pharmacokinetics, Protein-Tyrosine Kinases metabolism, Pyridazines metabolism, Pyridazines pharmacokinetics, Pyrimidinones metabolism, Pyrimidinones pharmacokinetics, Rats, Thiophenes metabolism, Thiophenes pharmacokinetics, Protein Kinase Inhibitors chemistry, Protein Kinase Inhibitors pharmacology, Protein-Tyrosine Kinases antagonists & inhibitors, Pyridazines chemistry, Pyridazines pharmacology, Pyrimidinones chemistry, Pyrimidinones pharmacology, Thiophenes chemistry, Thiophenes pharmacology
- Abstract
BTK inhibitor GDC-0834 (1) was found to be rapidly metabolized in human studies, resulting in a suspension of clinical trials. The primary route of metabolism was through cleavage of the acyclic amide bond connecting the terminal tetrahydrobenzothiophene with the central linker aryl ring. SAR studies were focused on reducing metabolic cleavage of this amide, and resulted in the identification of several central aryl linker substituents that conferred improved stability. The most promising substituted aryl linkers were then incorporated into an optimized pyridazinone scaffold, resulting in the identification of lead analog 23, possessing improved potency, metabolic stability and preclinical properties., (Copyright © 2015 Elsevier Ltd. All rights reserved.)
- Published
- 2016
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25. Structural basis of Nav1.7 inhibition by an isoform-selective small-molecule antagonist.
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Ahuja S, Mukund S, Deng L, Khakh K, Chang E, Ho H, Shriver S, Young C, Lin S, Johnson JP Jr, Wu P, Li J, Coons M, Tam C, Brillantes B, Sampang H, Mortara K, Bowman KK, Clark KR, Estevez A, Xie Z, Verschoof H, Grimwood M, Dehnhardt C, Andrez JC, Focken T, Sutherlin DP, Safina BS, Starovasnik MA, Ortwine DF, Franke Y, Cohen CJ, Hackos DH, Koth CM, and Payandeh J
- Subjects
- Amino Acid Sequence, Cell Membrane chemistry, Crystallization methods, Crystallography, X-Ray, DNA Mutational Analysis, Humans, Models, Molecular, Molecular Sequence Data, NAV1.7 Voltage-Gated Sodium Channel genetics, Pain Perception drug effects, Protein Engineering, Protein Isoforms antagonists & inhibitors, Protein Isoforms chemistry, Protein Structure, Secondary, Protein Structure, Tertiary, NAV1.7 Voltage-Gated Sodium Channel chemistry, Sodium Channel Blockers chemistry, Sodium Channel Blockers pharmacology, Sulfonamides chemistry, Sulfonamides pharmacology, Thiadiazoles chemistry, Thiadiazoles pharmacology
- Abstract
Voltage-gated sodium (Nav) channels propagate action potentials in excitable cells. Accordingly, Nav channels are therapeutic targets for many cardiovascular and neurological disorders. Selective inhibitors have been challenging to design because the nine mammalian Nav channel isoforms share high sequence identity and remain recalcitrant to high-resolution structural studies. Targeting the human Nav1.7 channel involved in pain perception, we present a protein-engineering strategy that has allowed us to determine crystal structures of a novel receptor site in complex with isoform-selective antagonists. GX-936 and related inhibitors bind to the activated state of voltage-sensor domain IV (VSD4), where their anionic aryl sulfonamide warhead engages the fourth arginine gating charge on the S4 helix. By opposing VSD4 deactivation, these compounds inhibit Nav1.7 through a voltage-sensor trapping mechanism, likely by stabilizing inactivated states of the channel. Residues from the S2 and S3 helices are key determinants of isoform selectivity, and bound phospholipids implicate the membrane as a modulator of channel function and pharmacology. Our results help to elucidate the molecular basis of voltage sensing and establish structural blueprints to design selective Nav channel antagonists., (Copyright © 2015, American Association for the Advancement of Science.)
- Published
- 2015
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26. An integrated suite of modeling tools that empower scientists in structure- and property-based drug design.
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Feng JA, Aliagas I, Bergeron P, Blaney JM, Bradley EK, Koehler MF, Lee ML, Ortwine DF, Tsui V, Wu J, and Gobbi A
- Subjects
- Computer-Aided Design, Molecular Conformation, TYK2 Kinase antagonists & inhibitors, TYK2 Kinase chemistry, Drug Design, Molecular Docking Simulation, Quantitative Structure-Activity Relationship, Software
- Abstract
Structure- and property-based drug design is an integral part of modern drug discovery, enabling the design of compounds aimed at improving potency and selectivity. However, building molecules using desktop modeling tools can easily lead to poor designs that appear to form many favorable interactions with the protein's active site. Although a proposed molecule looks good on screen and appears to fit into the protein site X-ray crystal structure or pharmacophore model, doing so might require a high-energy small molecule conformation, which would likely be inactive. To help scientists make better design decisions, we have built integrated, easy-to-use, interactive software tools to perform docking experiments, de novo design, shape and pharmacophore based database searches, small molecule conformational analysis and molecular property calculations. Using a combination of these tools helps scientists in assessing the likelihood that a designed molecule will be active and have desirable drug metabolism and pharmacokinetic properties. Small molecule discovery success requires project teams to rapidly design and synthesize potent molecules with good ADME properties. Empowering scientists to evaluate ideas quickly and make better design decisions with easy-to-access and easy-to-understand software on their desktop is now a key part of our discovery process.
- Published
- 2015
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27. Tetrahydroindazoles as Interleukin-2 Inducible T-Cell Kinase Inhibitors. Part II. Second-Generation Analogues with Enhanced Potency, Selectivity, and Pharmacodynamic Modulation in Vivo.
- Author
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Burch JD, Barrett K, Chen Y, DeVoss J, Eigenbrot C, Goldsmith R, Ismaili MH, Lau K, Lin Z, Ortwine DF, Zarrin AA, McEwan PA, Barker JJ, Ellebrandt C, Kordt D, Stein DB, Wang X, Chen Y, Hu B, Xu X, Yuen PW, Zhang Y, and Pei Z
- Subjects
- Animals, Cell Proliferation drug effects, Crystallography, X-Ray, Cytotoxins chemistry, Cytotoxins pharmacology, Cytotoxins toxicity, Female, Humans, Indazoles pharmacology, Indazoles toxicity, Interleukin-13 biosynthesis, Interleukin-2 biosynthesis, Jurkat Cells, Mice, Inbred C57BL, Models, Molecular, Molecular Structure, Phosphorylation, Receptors, Antigen, T-Cell metabolism, Stereoisomerism, Structure-Activity Relationship, Sulfones chemistry, Sulfones pharmacology, Sulfones toxicity, Sulfoxides chemistry, Sulfoxides pharmacology, Sulfoxides toxicity, Indazoles chemistry, Protein-Tyrosine Kinases antagonists & inhibitors
- Abstract
The medicinal chemistry community has directed considerable efforts toward the discovery of selective inhibitors of interleukin-2 inducible T-cell kinase (ITK), given its role in T-cell signaling downstream of the T-cell receptor (TCR) and the implications of this target for inflammatory disorders such as asthma. We have previously disclosed a structure- and property-guided lead optimization effort which resulted in the discovery of a new series of tetrahydroindazole-containing selective ITK inhibitors. Herein we disclose further optimization of this series that resulted in further potency improvements, reduced off-target receptor binding liabilities, and reduced cytotoxicity. Specifically, we have identified a correlation between the basicity of solubilizing elements in the ITK inhibitors and off-target antiproliferative effects, which was exploited to reduce cytotoxicity while maintaining kinase selectivity. Optimized analogues were shown to reduce IL-2 and IL-13 production in vivo following oral or intraperitoneal dosing in mice.
- Published
- 2015
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28. A probabilistic method to report predictions from a human liver microsomes stability QSAR model: a practical tool for drug discovery.
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Aliagas I, Gobbi A, Heffron T, Lee ML, Ortwine DF, Zak M, and Khojasteh SC
- Subjects
- Humans, Models, Biological, Probability, Quantitative Structure-Activity Relationship, Support Vector Machine, Drug Discovery methods, Microsomes, Liver metabolism, Pharmaceutical Preparations metabolism
- Abstract
Using data from the in vitro liver microsomes metabolic stability assay, we have developed QSAR models to predict in vitro human clearance. Models were trained using in house high-throughput assay data reported as the predicted human hepatic clearance by liver microsomes or pCLh. Machine learning regression methods were used to generate the models. Model output for a given molecule was reported as its probability of being metabolically stable, thus allowing for synthesis prioritization based on this prediction. Use of probability, instead of the regression value or categories, has been found to be an efficient way for both reporting and assessing predictions. Model performance is evaluated using prospective validation. These models have been integrated into a number of desktop tools, and the models are routinely used to prioritize the synthesis of compounds. We discuss two therapeutic projects at Genentech that exemplify the benefits of a probabilistic approach in applying the models. A three-year retrospective analysis of measured liver microsomes stability data on all registered compounds at Genentech reveals that the use of these models has resulted in an improved metabolic stability profile of synthesized compounds.
- Published
- 2015
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29. Potent and selective Bruton's tyrosine kinase inhibitors: discovery of GDC-0834.
- Author
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Young WB, Barbosa J, Blomgren P, Bremer MC, Crawford JJ, Dambach D, Gallion S, Hymowitz SG, Kropf JE, Lee SH, Liu L, Lubach JW, Macaluso J, Maciejewski P, Maurer B, Mitchell SA, Ortwine DF, Di Paolo J, Reif K, Scheerens H, Schmitt A, Sowell CG, Wang X, Wong H, Xiong JM, Xu J, Zhao Z, and Currie KS
- Subjects
- Agammaglobulinaemia Tyrosine Kinase, Animals, Benzamides chemistry, Benzamides metabolism, Binding Sites, Bridged Bicyclo Compounds, Heterocyclic chemistry, Bridged Bicyclo Compounds, Heterocyclic metabolism, Crystallography, X-Ray, Dogs, Half-Life, Humans, Mice, Microsomes, Liver metabolism, Molecular Dynamics Simulation, Protein Binding, Protein Kinase Inhibitors chemical synthesis, Protein Kinase Inhibitors pharmacokinetics, Protein Structure, Tertiary, Protein-Tyrosine Kinases metabolism, Pyrimidinones chemical synthesis, Pyrimidinones pharmacokinetics, Rats, Structure-Activity Relationship, Thiophenes chemical synthesis, Thiophenes pharmacokinetics, Protein Kinase Inhibitors chemistry, Protein-Tyrosine Kinases antagonists & inhibitors, Pyrimidinones chemistry, Thiophenes chemistry
- Abstract
SAR studies focused on improving the pharmacokinetic (PK) properties of the previously reported potent and selective Btk inhibitor CGI-1746 (1) resulted in the clinical candidate GDC-0834 (2), which retained the potency and selectivity of CGI-1746, but with much improved PK in preclinical animal models. Structure based design efforts drove this work as modifications to 1 were investigated at both the solvent exposed region as well as 'H3 binding pocket'. However, in vitro metabolic evaluation of 2 revealed a non CYP-mediated metabolic process that was more prevalent in human than preclinical species (mouse, rat, dog, cyno), leading to a high-level of uncertainly in predicting human pharmacokinetics. Due to its promising potency, selectivity, and preclinical efficacy, a single dose IND was filed and 2 was taken in to a single dose phase I trial in healthy volunteers to quickly evaluate the human pharmacokinetics. In human, 2 was found to be highly labile at the exo-cyclic amide bond that links the tetrahydrobenzothiophene moiety to the central aniline ring, resulting in insufficient parent drug exposure. This information informed the back-up program and discovery of improved inhibitors., (Copyright © 2015 Elsevier Ltd. All rights reserved.)
- Published
- 2015
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30. Design, synthesis and structure-activity relationships of a novel class of sulfonylpyridine inhibitors of Interleukin-2 inducible T-cell kinase (ITK).
- Author
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Trani G, Barker JJ, Bromidge SM, Brookfield FA, Burch JD, Chen Y, Eigenbrot C, Heifetz A, Ismaili MHA, Johnson A, Krülle TM, MacKinnon CH, Maghames R, McEwan PA, Montalbetti CAGN, Ortwine DF, Pérez-Fuertes Y, Vaidya DG, Wang X, Zarrin AA, and Pei Z
- Subjects
- Binding Sites, Crystallography, X-Ray, Kinetics, Molecular Dynamics Simulation, Protein Binding, Protein Kinase Inhibitors chemistry, Protein Kinase Inhibitors metabolism, Protein Structure, Tertiary, Protein-Tyrosine Kinases metabolism, Pyrazoles chemistry, Pyridines chemical synthesis, Pyridines metabolism, Structure-Activity Relationship, Sulfones chemistry, Drug Design, Protein Kinase Inhibitors chemical synthesis, Protein-Tyrosine Kinases antagonists & inhibitors, Pyridines chemistry
- Abstract
Starting from benzylpyrimidine 2, molecular modeling and X-ray crystallography were used to design highly potent inhibitors of Interleukin-2 inducible T-cell kinase (ITK). Sulfonylpyridine 4i showed sub-nanomolar affinity against ITK, was selective versus Lck and its activity in the Jurkat cell-based assay was greatly improved over 2., (Copyright © 2014 Elsevier Ltd. All rights reserved.)
- Published
- 2014
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31. Property- and structure-guided discovery of a tetrahydroindazole series of interleukin-2 inducible T-cell kinase inhibitors.
- Author
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Burch JD, Lau K, Barker JJ, Brookfield F, Chen Y, Chen Y, Eigenbrot C, Ellebrandt C, Ismaili MH, Johnson A, Kordt D, MacKinnon CH, McEwan PA, Ortwine DF, Stein DB, Wang X, Winkler D, Yuen PW, Zhang Y, Zarrin AA, and Pei Z
- Subjects
- Animals, Crystallography, X-Ray, Dogs, Drug Design, Humans, Indazoles pharmacokinetics, Indazoles pharmacology, Jurkat Cells, Kinetics, Mice, Models, Molecular, Protein Kinase Inhibitors pharmacokinetics, Protein Kinase Inhibitors pharmacology, Rats, Solubility, Structure-Activity Relationship, Indazoles chemical synthesis, Protein Kinase Inhibitors chemical synthesis, Protein-Tyrosine Kinases antagonists & inhibitors
- Abstract
Interleukin-2 inducible T-cell kinase (ITK), a member of the Tec family of tyrosine kinases, plays a major role in T-cell signaling downstream of the T-cell receptor (TCR), and considerable efforts have been directed toward discovery of ITK-selective inhibitors as potential treatments of inflammatory disorders such as asthma. Using a previously disclosed indazole series of inhibitors as a starting point, and using X-ray crystallography and solubility forecast index (SFI) as guides, we evolved a series of tetrahydroindazole inhibitors with improved potency, selectivity, and pharmaceutical properties. Highlights include identification of a selectivity pocket above the ligand plane, and identification of appropriate lipophilic substituents to occupy this space. This effort culminated in identification of a potent and selective ITK inhibitor (GNE-9822) with good ADME properties in preclinical species.
- Published
- 2014
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32. Discovery and optimization of indazoles as potent and selective interleukin-2 inducible T cell kinase (ITK) inhibitors.
- Author
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Pastor RM, Burch JD, Magnuson S, Ortwine DF, Chen Y, De La Torre K, Ding X, Eigenbrot C, Johnson A, Liimatta M, Liu Y, Shia S, Wang X, Wu LC, and Pei Z
- Subjects
- Crystallography, X-Ray, Dose-Response Relationship, Drug, Humans, Indazoles chemical synthesis, Indazoles chemistry, Jurkat Cells, Models, Molecular, Molecular Structure, Protein Kinase Inhibitors chemical synthesis, Protein Kinase Inhibitors chemistry, Protein-Tyrosine Kinases metabolism, Structure-Activity Relationship, Drug Discovery, Indazoles pharmacology, Protein Kinase Inhibitors pharmacology, Protein-Tyrosine Kinases antagonists & inhibitors
- Abstract
There is evidence that small molecule inhibitors of the non-receptor tyrosine kinase ITK, a component of the T-cell receptor signaling cascade, could represent a novel asthma therapeutic class. Moreover, given the expected chronic dosing regimen of any asthma treatment, highly selective as well as potent inhibitors would be strongly preferred in any potential therapeutic. Here we report hit-to-lead optimization of a series of indazoles that demonstrate sub-nanomolar inhibitory potency against ITK with strong cellular activity and good kinase selectivity. We also elucidate the binding mode of these inhibitors by solving the X-ray crystal structures of the complexes., (Copyright © 2014 Elsevier Ltd. All rights reserved.)
- Published
- 2014
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33. Structure-based design and synthesis of potent benzothiazole inhibitors of interleukin-2 inducible T cell kinase (ITK).
- Author
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MacKinnon CH, Lau K, Burch JD, Chen Y, Dines J, Ding X, Eigenbrot C, Heifetz A, Jaochico A, Johnson A, Kraemer J, Kruger S, Krülle TM, Liimatta M, Ly J, Maghames R, Montalbetti CA, Ortwine DF, Pérez-Fuertes Y, Shia S, Stein DB, Trani G, Vaidya DG, Wang X, Bromidge SM, Wu LC, and Pei Z
- Subjects
- Animals, Benzothiazoles chemical synthesis, Crystallography, X-Ray, Drug Design, Humans, Mice, Models, Molecular, Protein-Tyrosine Kinases chemistry, Signal Transduction, Structure-Activity Relationship, Benzothiazoles chemistry, Benzothiazoles pharmacology, Protein-Tyrosine Kinases antagonists & inhibitors
- Abstract
Inhibition of the non-receptor tyrosine kinase ITK, a component of the T-cell receptor signalling cascade, may represent a novel treatment for allergic asthma. Here we report the structure-based optimization of a series of benzothiazole amides that demonstrate sub-nanomolar inhibitory potency against ITK with good cellular activity and kinase selectivity. We also elucidate the binding mode of these inhibitors by solving the X-ray crystal structures of several inhibitor-ITK complexes., (Copyright © 2013 Elsevier Ltd. All rights reserved.)
- Published
- 2013
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34. A hit to lead discovery of novel N-methylated imidazolo-, pyrrolo-, and pyrazolo-pyrimidines as potent and selective mTOR inhibitors.
- Author
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Lee W, Ortwine DF, Bergeron P, Lau K, Lin L, Malek S, Nonomiya J, Pei Z, Robarge KD, Schmidt S, Sideris S, and Lyssikatos JP
- Subjects
- Dose-Response Relationship, Drug, Humans, Models, Molecular, Molecular Structure, Protein Kinase Inhibitors chemical synthesis, Protein Kinase Inhibitors chemistry, Pyrimidines chemical synthesis, Pyrimidines chemistry, Structure-Activity Relationship, TOR Serine-Threonine Kinases metabolism, Drug Discovery, Protein Kinase Inhibitors pharmacology, Pyrimidines pharmacology, TOR Serine-Threonine Kinases antagonists & inhibitors
- Abstract
A series of N-7-methyl-imidazolopyrimidine inhibitors of the mTOR kinase have been designed and prepared, based on the hypothesis that the N-7-methyl substituent on imidazolopyrimidine would impart selectivity for mTOR over the related PI3Kα and δ kinases. The corresponding N-Me substituted pyrrolo[3,2-d]pyrimidines and pyrazolo[4,3-d]pyrimidines also show potent mTOR inhibition with selectivity toward both PI3α and δ kinases. The most potent compound synthesized is pyrazolo[4,3-d]pyrimidine 21c. Compound 21c shows a Ki of 2 nM against mTOR inhibition, remarkable selectivity (>2900×) over PI3 kinases, and excellent potency in cell-based assays., (Copyright © 2013 Elsevier Ltd. All rights reserved.)
- Published
- 2013
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35. Histone deacetylase (HDAC) inhibitor kinetic rate constants correlate with cellular histone acetylation but not transcription and cell viability.
- Author
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Lauffer BE, Mintzer R, Fong R, Mukund S, Tam C, Zilberleyb I, Flicke B, Ritscher A, Fedorowicz G, Vallero R, Ortwine DF, Gunzner J, Modrusan Z, Neumann L, Koth CM, Lupardus PJ, Kaminker JS, Heise CE, and Steiner P
- Subjects
- Acetylation, Benzamides chemistry, Binding, Competitive, Cell Line, Tumor, Cell Survival drug effects, Humans, Hydroxamic Acids chemistry, Inhibitory Concentration 50, Kinetics, Oligonucleotide Array Sequence Analysis, Protein Binding, Pyridines chemistry, Transcription, Genetic, Vorinostat, Gene Expression Regulation, Enzymologic, Gene Expression Regulation, Neoplastic, Histone Deacetylase Inhibitors chemistry, Histones chemistry
- Abstract
Histone deacetylases (HDACs) are critical in the control of gene expression, and dysregulation of their activity has been implicated in a broad range of diseases, including cancer, cardiovascular, and neurological diseases. HDAC inhibitors (HDACi) employing different zinc chelating functionalities such as hydroxamic acids and benzamides have shown promising results in cancer therapy. Although it has also been suggested that HDACi with increased isozyme selectivity and potency may broaden their clinical utility and minimize side effects, the translation of this idea to the clinic remains to be investigated. Moreover, a detailed understanding of how HDACi with different pharmacological properties affect biological functions in vitro and in vivo is still missing. Here, we show that a panel of benzamide-containing HDACi are slow tight-binding inhibitors with long residence times unlike the hydroxamate-containing HDACi vorinostat and trichostatin-A. Characterization of changes in H2BK5 and H4K14 acetylation following HDACi treatment in the neuroblastoma cell line SH-SY5Y revealed that the timing and magnitude of histone acetylation mirrored both the association and dissociation kinetic rates of the inhibitors. In contrast, cell viability and microarray gene expression analysis indicated that cell death induction and changes in transcriptional regulation do not correlate with the dissociation kinetic rates of the HDACi. Therefore, our study suggests that determining how the selective and kinetic inhibition properties of HDACi affect cell function will help to evaluate their therapeutic utility.
- Published
- 2013
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36. The evaluation of 25 chiral stationary phases and the utilization of sub-2.0μm coated polysaccharide chiral stationary phases via supercritical fluid chromatography.
- Author
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Hamman C, Wong M, Aliagas I, Ortwine DF, Pease J, Schmidt DE Jr, and Victorino J
- Subjects
- Chromatography, Supercritical Fluid methods, Solvents, Chromatography, Supercritical Fluid instrumentation, Polysaccharides chemistry
- Abstract
A rapid screening method to identify the best conditions for chiral separations is described. We analyzed a representative set of 80 racemic compounds against 25 different chiral stationary phases with three different mobile phases to identify the combination of columns and mobile phases that will separate the most compounds on the initial screen. While the OD separated the largest number of compounds, we found the best combination of six columns to be the AD, AS, AY, CC4, ID and Whelk-O1. The second team included the CCC, Cellulose-1, Cellulose-3 or OJ, IA, IE and IF. All 80 compounds were separated with a resolution range of 0.65-15.36. Screening the covalently bonded phases provided separation for 79 of the 80 compounds. We also found ethanol (0.1% NH4OH) separated more compounds than methanol (0.1% NH4OH) or isopropanol (0.1% NH4OH). As part of this study, we also compared the effectiveness of stationary phases that have the same chiral selector. Finally, we demonstrated the effectiveness of using a fast, 1.5-min screening method that utilizes a 1.7μm coated polysaccharide chiral stationary phase., (Copyright © 2013 Elsevier B.V. All rights reserved.)
- Published
- 2013
- Full Text
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37. Pyrimidoaminotropanes as potent, selective, and efficacious small molecule kinase inhibitors of the mammalian target of rapamycin (mTOR).
- Author
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Estrada AA, Shore DG, Blackwood E, Chen YH, Deshmukh G, Ding X, Dipasquale AG, Epler JA, Friedman LS, Koehler MF, Liu L, Malek S, Nonomiya J, Ortwine DF, Pei Z, Sideris S, St-Jean F, Trinh L, Truong T, and Lyssikatos JP
- Subjects
- Chromatography, Liquid, Enzyme Inhibitors chemistry, Humans, Magnetic Resonance Spectroscopy, Mass Spectrometry, Tropanes chemistry, Enzyme Inhibitors pharmacology, TOR Serine-Threonine Kinases antagonists & inhibitors, Tropanes pharmacology
- Abstract
We have recently reported a series of tetrahydroquinazoline (THQ) mTOR inhibitors that produced a clinical candidate 1 (GDC-0349). Through insightful design, we hoped to discover and synthesize a new series of small molecule inhibitors that could attenuate CYP3A4 time-dependent inhibition commonly observed with the THQ scaffold, maintain or improve aqueous solubility and oral absorption, reduce free drug clearance, and selectively increase mTOR potency. Through key in vitro and in vivo studies, we demonstrate that a pyrimidoaminotropane based core was able to address each of these goals. This effort culminated in the discovery of 20 (GNE-555), a highly potent, selective, metabolically stable, and efficacious mTOR inhibitor.
- Published
- 2013
- Full Text
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38. Physicochemical and DMPK in silico models: facilitating their use by medicinal chemists.
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Ortwine DF and Aliagas I
- Subjects
- Computer Simulation, Humans, Models, Theoretical, Structure-Activity Relationship, Substrate Specificity, Drug Design, Software, Technology, Pharmaceutical methods
- Abstract
It is known that the developability of drugs is related to their physicochemical and DMPK properties. Given the time and expense involved in discovering and developing new drugs, maximizing the chance of success by calculating properties ahead of chemical synthesis and testing, and only acting on those candidates whose properties fall into a desired range, would seem to make sense. This paper provides an overview of calculable physicochemical and DMPK properties, an assessment of their relative difficulty of their calculation and accuracy, and available software. Methods companies have employed to communicate results will be discussed, including the use of composite scoring functions and ranking schemes. Calculations do no good if chemists will not use them to prioritize synthesis decisions. Strategies are presented for facilitating model usage. An approach adopted at Genentech for presenting results that involves the close coupling of property calculations with 3D structure based drug design is described.
- Published
- 2013
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39. Potent, selective, and orally bioavailable inhibitors of the mammalian target of rapamycin kinase domain exhibiting single agent antiproliferative activity.
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Koehler MF, Bergeron P, Blackwood E, Bowman KK, Chen YH, Deshmukh G, Ding X, Epler J, Lau K, Lee L, Liu L, Ly C, Malek S, Nonomiya J, Oeh J, Ortwine DF, Sampath D, Sideris S, Trinh L, Truong T, Wu J, Pei Z, and Lyssikatos JP
- Subjects
- Administration, Oral, Animals, Antineoplastic Agents chemistry, Antineoplastic Agents pharmacology, Biological Availability, Cell Line, Tumor, Drug Screening Assays, Antitumor, Female, Humans, Male, Mechanistic Target of Rapamycin Complex 1, Mechanistic Target of Rapamycin Complex 2, Mice, Mice, Nude, Molecular Docking Simulation, Neoplasm Transplantation, Phosphoinositide-3 Kinase Inhibitors, Phosphorylation, Prostatic Neoplasms, Pyrimidines chemistry, Pyrimidines pharmacology, Pyrroles chemistry, Pyrroles pharmacology, Quinazolines chemistry, Quinazolines pharmacology, Structure-Activity Relationship, Transplantation, Heterologous, Antineoplastic Agents chemical synthesis, Multiprotein Complexes antagonists & inhibitors, Pyrimidines chemical synthesis, Pyrroles chemical synthesis, Quinazolines chemical synthesis, TOR Serine-Threonine Kinases antagonists & inhibitors
- Abstract
Selective inhibitors of mammalian target of rapamycin (mTOR) kinase based upon saturated heterocycles fused to a pyrimidine core were designed and synthesized. Each series produced compounds with K(i) < 10 nM for the mTOR kinase and >500-fold selectivity over closely related PI3 kinases. This potency translated into strong pathway inhibition, as measured by phosphorylation of mTOR substrate proteins and antiproliferative activity in cell lines with a constitutively active PI3K pathway. Two compounds exhibiting suitable mouse PK were profiled in in vivo tumor models and were shown to suppress mTORC1 and mTORC2 signaling for over 12 h when dosed orally. Both compounds were additionally shown to suppress tumor growth in vivo in a PC3 prostate cancer model over a 14 day study.
- Published
- 2012
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40. Discovery and Biological Profiling of Potent and Selective mTOR Inhibitor GDC-0349.
- Author
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Pei Z, Blackwood E, Liu L, Malek S, Belvin M, Koehler MF, Ortwine DF, Chen H, Cohen F, Kenny JR, Bergeron P, Lau K, Ly C, Zhao X, Estrada AA, Truong T, Epler JA, Nonomiya J, Trinh L, Sideris S, Lesnick J, Bao L, Vijapurkar U, Mukadam S, Tay S, Deshmukh G, Chen YH, Ding X, Friedman LS, and Lyssikatos JP
- Abstract
Aberrant activation of the PI3K-Akt-mTOR signaling pathway has been observed in human tumors and tumor cell lines, indicating that these protein kinases may be attractive therapeutic targets for treating cancer. Optimization of advanced lead 1 culminated in the discovery of clinical development candidate 8h, GDC-0349, a potent and selective ATP-competitive inhibitor of mTOR. GDC-0349 demonstrates pathway modulation and dose-dependent efficacy in mouse xenograft cancer models.
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- 2012
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41. Potent, selective, and orally bioavailable inhibitors of mammalian target of rapamycin (mTOR) kinase based on a quaternary substituted dihydrofuropyrimidine.
- Author
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Cohen F, Bergeron P, Blackwood E, Bowman KK, Chen H, Dipasquale AG, Epler JA, Koehler MF, Lau K, Lewis C, Liu L, Ly CQ, Malek S, Nonomiya J, Ortwine DF, Pei Z, Robarge KD, Sideris S, Trinh L, Truong T, Wu J, Zhao X, and Lyssikatos JP
- Subjects
- Administration, Oral, Animals, Antineoplastic Agents pharmacokinetics, Antineoplastic Agents pharmacology, Biological Availability, Cell Line, Tumor, Drug Screening Assays, Antitumor, Drug Stability, Furans pharmacokinetics, Furans pharmacology, Humans, Mice, Mice, Nude, Models, Molecular, Neoplasm Transplantation, Phosphoinositide-3 Kinase Inhibitors, Pyrimidines pharmacokinetics, Pyrimidines pharmacology, Rats, Species Specificity, Stereoisomerism, Structure-Activity Relationship, Transplantation, Heterologous, Antineoplastic Agents chemical synthesis, Furans chemical synthesis, Pyrimidines chemical synthesis, TOR Serine-Threonine Kinases antagonists & inhibitors
- Abstract
A series of inhibitors of mTOR kinase based on a quaternary-substituted dihydrofuropyrimidine was designed and synthesized. The most potent compounds in this series inhibited mTOR kinase with K(i) < 1.0 nM and were highly (>100×) selective for mTOR over the closely related PI3 kinases. Compounds in this series showed inhibition of the pathway and antiproliferative activity in cell-based assays. Furthermore, these compounds had excellent mouse PK, and showed a robust PK-PD relationship in a mouse model of cancer.
- Published
- 2011
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42. Identification, characterization, and implications of species-dependent plasma protein binding for the oral Hedgehog pathway inhibitor vismodegib (GDC-0449).
- Author
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Giannetti AM, Wong H, Dijkgraaf GJ, Dueber EC, Ortwine DF, Bravo BJ, Gould SE, Plise EG, Lum BL, Malhi V, and Graham RA
- Subjects
- Anilides administration & dosage, Anilides pharmacokinetics, Animals, Biophysics, Cell Line, Half-Life, Hedgehog Proteins metabolism, Humans, Protein Binding, Pyridines administration & dosage, Pyridines pharmacokinetics, Rats, Signal Transduction drug effects, Species Specificity, Thermodynamics, Anilides metabolism, Hedgehog Proteins antagonists & inhibitors, Pyridines metabolism
- Abstract
Vismodegib (GDC-0449) is is an orally available selective Hedgehog pathway inhibitor in development for cancer treatment. The drug is ≥95% protein bound in plasma at clinically relevant concentrations and has an approximately 200-fold longer single dose half-life in humans than rats. We have identified a strong linear relationship between plasma drug concentrations and α-1-acid glycoprotein (AAG) in a phase I study. Biophysical and cellular techniques have been used to reveal that vismodegib strongly binds to human AAG (K(D) = 13 μM) and binds albumin with lower affinity (K(D) = 120 μM). Additionally, binding to rat AAG is reduced ∼20-fold relative to human, whereas the binding affinity to rat and human albumin was similar. Molecular docking studies reveal the reason for the signficiant species dependence on binding. These data highlight the utility of biophysical techniques in creating a comprehensive picture of protein binding across species.
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- 2011
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43. Design, synthesis, and pharmacological evaluation of phenoxy pyridyl derivatives as dual norepinephrine reuptake inhibitors and 5-HT1A partial agonists.
- Author
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Dounay AB, Barta NS, Campbell BM, Coleman C, Collantes EM, Denny L, Dutta S, Gray DL, Hou D, Iyer R, Maiti SN, Ortwine DF, Probert A, Stratman NC, Subedi R, Whisman T, Xu W, and Zoski K
- Subjects
- Adrenergic Uptake Inhibitors metabolism, Adrenergic Uptake Inhibitors pharmacology, Cell Line, Crystallography, X-Ray, Drug Evaluation, Preclinical methods, Humans, Microsomes, Liver drug effects, Microsomes, Liver metabolism, Norepinephrine Plasma Membrane Transport Proteins metabolism, Phenols chemical synthesis, Phenols metabolism, Phenols pharmacology, Pyridines metabolism, Pyridines pharmacology, Receptor, Serotonin, 5-HT1A metabolism, Serotonin Receptor Agonists metabolism, Serotonin Receptor Agonists pharmacology, Adrenergic Uptake Inhibitors chemical synthesis, Drug Design, Norepinephrine Plasma Membrane Transport Proteins antagonists & inhibitors, Pyridines chemical synthesis, Serotonin 5-HT1 Receptor Agonists, Serotonin Receptor Agonists chemical synthesis
- Abstract
Preclinical studies suggest that compounds with dual norepinephrine reuptake inhibitor (NRI) and 5-HT(1A) partial agonist properties may provide an important new therapeutic approach to ADHD, depression, and anxiety. Reported herein is the discovery of a novel chemical series with a favorable NRI and 5-HT(1A) partial agonist pharmacological profile as well as excellent selectivity for the norepinephrine transporter over the dopamine transporter., (Copyright (c) 2009 Elsevier Ltd. All rights reserved.)
- Published
- 2010
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- View/download PDF
44. Synthesis and structure-activity relationships of N-6 substituted analogues of 9-hydroxy-4-phenylpyrrolo[3,4-c]carbazole-1,3(2H,6H)-diones as inhibitors of Wee1 and Chk1 checkpoint kinases.
- Author
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Smaill JB, Baker EN, Booth RJ, Bridges AJ, Dickson JM, Dobrusin EM, Ivanovic I, Kraker AJ, Lee HH, Lunney EA, Ortwine DF, Palmer BD, Quin J 3rd, Squire CJ, Thompson AM, and Denny WA
- Subjects
- Carbazoles chemistry, HT29 Cells, Humans, Magnetic Resonance Spectroscopy, Models, Molecular, Protein Kinase Inhibitors chemistry, Structure-Activity Relationship, Carbazoles chemical synthesis, Carbazoles pharmacology, Cell Cycle Proteins antagonists & inhibitors, Nuclear Proteins antagonists & inhibitors, Protein Kinase Inhibitors chemical synthesis, Protein Kinase Inhibitors pharmacology, Protein-Tyrosine Kinases antagonists & inhibitors
- Abstract
A series of N-6 substituted 9-hydroxy-4-phenylpyrrolo[3,4-c]carbazole-1,3(2H,6H)-diones were prepared from N-substituted (5-methoxyphenyl)ethenylindoles. The target compounds were tested for their ability to inhibit the G2/M cell cycle checkpoint kinases, Wee1 and Chk1. Analogues with neutral or cationic N-6 side chains were potent dual inhibitors. Acidic side chains provided potent (average IC(50) 0.057 microM) and selective (average ratio 223-fold) Wee1 inhibition. Co-crystal structures of inhibitors bound to Wee1 show that the pyrrolo[3,4-c]carbazole scaffold binds in the ATP-binding site, with N-6 substituents involved in H-bonding to conserved water molecules. HT-29 cells treated with doxorubicin and then target compounds demonstrate an active Cdc2/cyclin B complex, inhibition of the doxorubicin-induced phosphorylation of tyrosine 15 of Cdc2 and abrogation of the G2 checkpoint.
- Published
- 2008
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45. Quinazolinones and pyrido[3,4-d]pyrimidin-4-ones as orally active and specific matrix metalloproteinase-13 inhibitors for the treatment of osteoarthritis.
- Author
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Li JJ, Nahra J, Johnson AR, Bunker A, O'Brien P, Yue WS, Ortwine DF, Man CF, Baragi V, Kilgore K, Dyer RD, and Han HK
- Subjects
- Administration, Oral, Animals, Biological Availability, Male, Pyridines pharmacokinetics, Pyridines pharmacology, Pyrimidines pharmacokinetics, Pyrimidines pharmacology, Quinazolinones pharmacokinetics, Quinazolinones pharmacology, Rabbits, Rats, Rats, Sprague-Dawley, Structure-Activity Relationship, Matrix Metalloproteinase Inhibitors, Osteoarthritis drug therapy, Pyridines chemical synthesis, Pyrimidines chemical synthesis, Quinazolinones chemical synthesis
- Abstract
Quinazolinones 8 and pyrido[3,4-d]pyrimidin-4-ones 9 as orally active and specific matrix metalloproteinase-13 inhibitors were discovered for the treatment of osteoarthritis. Starting from a high-through-put screening (HTS) hit thizolopyrimidin-dione 7, we obtained two chemotypes, 8 and 9, using computer-aided drug design (CADD) and methodical structure-activity relationship (SAR) studies. They occupy the unique S 1'-specificity pocket and do not bind to the Zn(2+) ion. Some pyrido[3,4-d]pyrimidin-4-ones, such as 10a, possess favorable absorption, distribution, metabolism, and elimination (ADME) and safety profiles. 10a effectively prevents cartilage damage in rabbit animal models of osteoarthritis without inducing musculoskeletal side effects when given at extremely high doses to rats.
- Published
- 2008
- Full Text
- View/download PDF
46. 4-anilino-5-carboxamido-2-pyridone derivatives as noncompetitive inhibitors of mitogen-activated protein kinase kinase.
- Author
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Spicer JA, Rewcastle GW, Kaufman MD, Black SL, Plummer MS, Denny WA, Quin J 3rd, Shahripour AB, Barrett SD, Whitehead CE, Milbank JB, Ohren JF, Gowan RC, Omer C, Camp HS, Esmaeil N, Moore K, Sebolt-Leopold JS, Pryzbranowski S, Merriman RL, Ortwine DF, Warmus JS, Flamme CM, Pavlovsky AG, and Tecle H
- Subjects
- Amides chemistry, Amides pharmacology, Aniline Compounds chemistry, Aniline Compounds pharmacology, Animals, Antineoplastic Agents chemistry, Antineoplastic Agents pharmacology, Benzamides pharmacology, Cell Line, Tumor, Drug Screening Assays, Antitumor, Extracellular Signal-Regulated MAP Kinases metabolism, MAP Kinase Kinase 1 chemistry, MAP Kinase Kinase 2 chemistry, Male, Mice, Models, Molecular, Neoplasm Transplantation, Phosphorylation, Pyridones chemistry, Pyridones pharmacology, Rats, Structure-Activity Relationship, Amides chemical synthesis, Aniline Compounds chemical synthesis, Antineoplastic Agents chemical synthesis, MAP Kinase Kinase 1 antagonists & inhibitors, MAP Kinase Kinase 2 antagonists & inhibitors, Pyridones chemical synthesis
- Abstract
A new series of MEK1 inhibitors, the 4-anilino-5-carboxamido-2-pyridones, were designed and synthesized using a combination of medicinal chemistry, computational chemistry, and structural elucidation. The effect of variation in the carboxamide side chain, substitution on the pyridone nitrogen, and replacement of the 4'-iodide were all investigated. This study afforded several compounds which were either equipotent or more potent than the clinical candidate CI-1040 (1) in an isolated enzyme assay, as well as murine colon carcinoma (C26) cells, as measured by suppression of phosphorylated ERK substrate. Most notably, pyridone 27 was found to be more potent than 1 in vitro and produced a 100% response rate at a lower dose than 1, when tested for in vivo efficacy in animals bearing C26 tumors.
- Published
- 2007
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47. Discovery and characterization of a novel inhibitor of matrix metalloprotease-13 that reduces cartilage damage in vivo without joint fibroplasia side effects.
- Author
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Johnson AR, Pavlovsky AG, Ortwine DF, Prior F, Man CF, Bornemeier DA, Banotai CA, Mueller WT, McConnell P, Yan C, Baragi V, Lesch C, Roark WH, Wilson M, Datta K, Guzman R, Han HK, and Dyer RD
- Subjects
- Animals, Collagen chemistry, Collagen metabolism, Crystallography, X-Ray, Enzyme Inhibitors pharmacology, Humans, Ions, Matrix Metalloproteinase 13 chemistry, Matrix Metalloproteinase 13 metabolism, Models, Biological, Models, Chemical, Models, Molecular, Rabbits, Rats, Zinc chemistry, Cartilage metabolism, Joint Diseases metabolism, Matrix Metalloproteinase 13 physiology
- Abstract
Matrix metalloproteinase-13 (MMP13) is a Zn(2+)-dependent protease that catalyzes the cleavage of type II collagen, the main structural protein in articular cartilage. Excess MMP13 activity causes cartilage degradation in osteoarthritis, making this protease an attractive therapeutic target. However, clinically tested MMP inhibitors have been associated with a painful, joint-stiffening musculoskeletal side effect that may be due to their lack of selectivity. In our efforts to develop a disease-modifying osteoarthritis drug, we have discovered MMP13 inhibitors that differ greatly from previous MMP inhibitors; they do not bind to the catalytic zinc ion, they are noncompetitive with respect to substrate binding, and they show extreme selectivity for inhibiting MMP13. By structure-based drug design, we generated an orally active MMP13 inhibitor that effectively reduces cartilage damage in vivo and does not induce joint fibroplasias in a rat model of musculoskeletal syndrome side effects. Thus, highly selective inhibition of MMP13 in patients may overcome the major safety and efficacy challenges that have limited previously tested non-selective MMP inhibitors. MMP13 inhibitors such as the ones described here will help further define the role of this protease in arthritis and other diseases and may soon lead to drugs that safely halt cartilage damage in patients.
- Published
- 2007
- Full Text
- View/download PDF
48. 4-Phenylpyrrolo[3,4-c]carbazole-1,3(2H,6H)-dione inhibitors of the checkpoint kinase Wee1. Structure-activity relationships for chromophore modification and phenyl ring substitution.
- Author
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Palmer BD, Thompson AM, Booth RJ, Dobrusin EM, Kraker AJ, Lee HH, Lunney EA, Mitchell LH, Ortwine DF, Smaill JB, Swan LM, and Denny WA
- Subjects
- Benzene Derivatives chemistry, Carbazoles chemistry, Checkpoint Kinase 1, Crystallography, X-Ray, Humans, Models, Molecular, Protein Binding, Protein Kinases chemistry, Pyrroles chemistry, Structure-Activity Relationship, Benzene Derivatives chemical synthesis, Carbazoles chemical synthesis, Cell Cycle Proteins antagonists & inhibitors, Cell Cycle Proteins chemistry, Nuclear Proteins antagonists & inhibitors, Nuclear Proteins chemistry, Protein-Tyrosine Kinases antagonists & inhibitors, Protein-Tyrosine Kinases chemistry, Pyrroles chemical synthesis
- Abstract
High-throughput screening has identified a novel class of inhibitors of the checkpoint kinase Wee1, which have potential for use in cancer chemotherapy. These inhibitors are based on a 4-phenylpyrrolo[3,4-c]carbazole-1,3(2H,6H)-dione template and have been shown by X-ray crystallography to bind at the ATP site of the enzyme. An extensive study of the effects of substitution around this template has been carried out, which has identified substituents which lead to improvements in potency and selectivity for Wee1. While retention of the maleimide ring and pendant 4-phenyl group is necessary for potency, replacement of the carbazole nitrogen by oxygen is well tolerated and results in improved Wee1 selectivity against the related checkpoint kinase Chk1. Wee1 potency and selectivity are also enhanced by the incorporation of lipophilic functionality at the 2'-position of the 4-phenyl ring, and Wee1 selectivity against Chk1 is favored by C3-C5 alkyl substitution of the carbazole nitrogen. These studies provide a basis for the design of active analogues of the pyrrolocarbazole lead with improved physical properties.
- Published
- 2006
- Full Text
- View/download PDF
49. Stereoselective binding of an enantiomeric pair of stromelysin-1 inhibitors caused by conformational entropy factors.
- Author
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Parker MH, Ortwine DF, O'Brien PM, Lunney EA, Banotai CA, Mueller WT, McConnell P, and Brouillette CG
- Subjects
- Calorimetry methods, Catalytic Domain, Humans, Matrix Metalloproteinase 3 metabolism, Molecular Conformation, Molecular Structure, Protein Binding, Stereoisomerism, Thermodynamics, Hydroxamic Acids chemistry, Hydroxamic Acids metabolism, Matrix Metalloproteinase Inhibitors, Oligopeptides chemistry, Oligopeptides metabolism, Protease Inhibitors chemistry, Protease Inhibitors metabolism
- Abstract
Isothermal titration calorimetry was used to analyze the binding of an enantiomeric pair of inhibitors to the stromelysin-1 catalytic domain. Differences in binding affinity are attributable to different conformational entropy penalties suffered upon binding. Two possible explanations for these differences are proposed.
- Published
- 2000
- Full Text
- View/download PDF
50. A rationalization of the acidic pH dependence for stromelysin-1 (Matrix metalloproteinase-3) catalysis and inhibition.
- Author
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Johnson LL, Pavlovsky AG, Johnson AR, Janowicz JA, Man CF, Ortwine DF, Purchase CF 2nd, White AD, and Hupe DJ
- Subjects
- Binding Sites, Catalytic Domain, Humans, Hydrogen-Ion Concentration, Matrix Metalloproteinase 3 chemistry, Matrix Metalloproteinase Inhibitors, Protein Structure, Secondary, Matrix Metalloproteinase 3 metabolism
- Abstract
The pH dependence of matrix metalloproteinase (MMP) catalysis is described by a broad bell-shaped curve, indicating the involvement of two unspecified ionizable groups in proteolysis. Stromelysin-1 has a third pK(a) near 6, resulting in a uniquely sharp acidic catalytic optimum, which has recently been attributed to His(224). This suggests the presence of a critical, but unidentified, S1' substructure. Integrating biochemical characterizations of inhibitor-enzyme interactions with active site topography from corresponding crystal structures, we isolated contributions to the pH dependence of catalysis and inhibition of active site residues Glu(202) and His(224). The acidic pK(a) 5.6 is attributed to the Glu(202).zinc.H(2)O complex, consistent with a role for the invariant active site Glu as a general base in MMP catalysis. The His(224)-dependent substructure is identified as a tripeptide (Pro(221)-Leu(222)-Tyr(223)) that forms the substrate cleft lower wall. Substrate binding induces a beta-conformation in this sequence, which extends and anchors the larger beta-sheet of the enzyme. substrate complex and appears to be essential for productive substrate binding. Because the PXY tripeptide is strictly conserved among MMPs, this "beta-anchor" may represent a common motif required for macromolecular substrate hydrolysis. The striking acidic profile of stromelysin-1 defined by the combined ionization of Glu(202) and His(224) allows the design of highly selective inhibitors.
- Published
- 2000
- Full Text
- View/download PDF
Catalog
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