51
|
Liverton NJ. Evolution of HCV NS3/4a Protease Inhibitors. TOPICS IN MEDICINAL CHEMISTRY 2019. [DOI: 10.1007/7355_2018_39] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
52
|
Affiliation(s)
- Bradley C. Doak
- Department of Medicinal Chemistry, MIPS, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| |
Collapse
|
53
|
Tevs OA, Veremeychik YV, Lodochnikova OA, Plemenkov VV, Litvinov IA. Synthesis of Hybrid Pharmacophores Based on Adducts of N-Sulfinylaniline and Norbornadiene. RUSS J GEN CHEM+ 2018. [DOI: 10.1134/s1070363218110300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
54
|
Chung PY, Lam PL, Zhou YY, Gasparello J, Finotti A, Chilin A, Marzaro G, Gambari R, Bian ZX, Kwok WM, Wong WY, Wang X, Lam AKY, Chan ASC, Li X, Ma JYW, Chui CH, Lam KH, Tang JCO. Targeting DNA Binding for NF-κB as an Anticancer Approach in Hepatocellular Carcinoma. Cells 2018; 7:cells7100177. [PMID: 30360426 PMCID: PMC6209864 DOI: 10.3390/cells7100177] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 12/14/2022] Open
Abstract
Quinoline core has been shown to possess a promising role in the development of anticancer agents. However, the correlation between its broad spectrum of bioactivity and the underlying mechanism of actions is poorly understood. The present study, with the use of bioinformatics approaches, reported a series of designed molecules which integrated quinoline core and sulfonyl moiety, with the objective of evaluating the substituent and linker effects on anticancer activities and associated mechanistic targets. We identified potent compounds (1h, 2h, 5 and 8) exhibiting significant anticancer effects towards liver cancer cells (Hep3B) with the 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) relative values of cytotoxicity below 0.40, a value in the range of doxorubicin positive control with the value of 0.12. Bulky substituents and the presence of bromine atom, as well as the presence of sulfonamide linkage, are likely the favorable structural components for molecules exerting a strong anticancer effect. To the best of our knowledge, our findings obtained from chemical synthesis, in vitro cytotoxicity, bioinformatics-based molecular docking analysis (similarity ensemble approach, SEA),and electrophoretic mobility shift assay provided the first evidence in correlation to the anticancer activities of the selected compound 5 with the modulation on the binding of transcription factor NF-κB to its target DNA. Accordingly, compound 5 represented a lead structure for the development of quinoline-based NF-κB inhibitors and this work added novel information on the understanding of the mechanism of action for bioactive sulfonyl-containing quinoline compounds against hepatocellular carcinoma.
Collapse
Affiliation(s)
- Po-Yee Chung
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.
| | - Pik-Ling Lam
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.
| | - Yuan-Yuan Zhou
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.
| | - Jessica Gasparello
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
| | - Alessia Finotti
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
| | - Adriana Chilin
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35122 Padova, Italy.
| | - Giovanni Marzaro
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35122 Padova, Italy.
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
| | - Zhao-Xiang Bian
- Clinical Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
| | - Wai-Ming Kwok
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.
| | - Wai-Yeung Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.
| | - Xi Wang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.
| | - Alfred King-Yin Lam
- Griffith Medical School, Griffith University, Gold Coast, QLD 4222, Australia.
| | - Albert Sun-Chi Chan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
| | - Xingshu Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
| | | | - Chung-Hin Chui
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.
| | - Kim-Hung Lam
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.
| | - Johnny Cheuk-On Tang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.
| |
Collapse
|
55
|
Ernouf G, Brayer JL, Folléas B, Demoute JP, Meyer C, Cossy J. [3,3]-Sigmatropic Rearrangement of Cyclopropenylcarbinyl Cyanates: Access to Alkylidene(aminocyclopropane) Derivatives. Chemistry 2018; 24:15104-15111. [PMID: 30021051 DOI: 10.1002/chem.201803231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Indexed: 12/21/2022]
Abstract
Cyclopropenylcarbinyl cyanates, generated in situ by dehydration of the corresponding carbamates, underwent an efficient and stereoselective [3,3]-sigmatropic rearrangement leading to the corresponding alkylidene(isocyanatocyclopropanes), which could be converted into various alkylidene(aminocyclopropane) derivatives in a one-pot manner. This transformation complements the repertoire of sigmatropic rearrangements involving cyclopropenylcarbinol derivatives and in particular, the previously reported Overman rearrangement of cyclopropenylcarbinyl trichloroacetimidates.
Collapse
Affiliation(s)
- Guillaume Ernouf
- Laboratory of Organic Chemistry, Institute of Chemistry, Biology, and Innovation (CBI) ESPCI Paris, CNRS (UMR 8231), PSL Research University, 10 rue Vauquelin, 75231, Paris Cedex 05, France
| | | | - Benoît Folléas
- Diverchim, 6 rue du Noyer, ZAC du Moulin, 95734, Roissy CDG, France
| | | | - Christophe Meyer
- Laboratory of Organic Chemistry, Institute of Chemistry, Biology, and Innovation (CBI) ESPCI Paris, CNRS (UMR 8231), PSL Research University, 10 rue Vauquelin, 75231, Paris Cedex 05, France
| | - Janine Cossy
- Laboratory of Organic Chemistry, Institute of Chemistry, Biology, and Innovation (CBI) ESPCI Paris, CNRS (UMR 8231), PSL Research University, 10 rue Vauquelin, 75231, Paris Cedex 05, France
| |
Collapse
|
56
|
Karlsson S, Gardelli C, Lindhagen M, Nikitidis G, Svensson T. Route Optimization and Manufacture of Multihundred Grams of a Ghrelin Receptor Agonist. Org Process Res Dev 2018. [DOI: 10.1021/acs.oprd.8b00179] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Staffan Karlsson
- Early Chemical Development, Pharmaceutical Sciences, IMED Biotech Unit, AstraZeneca Gothenburg, SE-431 83 Mölndal, Sweden
| | - Cristina Gardelli
- Medicinal Chemistry, Respiratory, Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca Gothenburg, SE-431 83 Mölndal, Sweden
| | - Marika Lindhagen
- Early Chemical Development, Pharmaceutical Sciences, IMED Biotech Unit, AstraZeneca Gothenburg, SE-431 83 Mölndal, Sweden
| | - Grigorios Nikitidis
- Early Chemical Development, Pharmaceutical Sciences, IMED Biotech Unit, AstraZeneca Gothenburg, SE-431 83 Mölndal, Sweden
| | - Tor Svensson
- Medicinal Chemistry, Respiratory, Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca Gothenburg, SE-431 83 Mölndal, Sweden
| |
Collapse
|
57
|
Matthew AN, Leidner F, Newton A, Petropoulos CJ, Huang W, Ali A, KurtYilmaz N, Schiffer CA. Molecular Mechanism of Resistance in a Clinically Significant Double-Mutant Variant of HCV NS3/4A Protease. Structure 2018; 26:1360-1372.e5. [PMID: 30146168 DOI: 10.1016/j.str.2018.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/01/2018] [Accepted: 07/21/2018] [Indexed: 12/22/2022]
Abstract
Despite significant progress in hepatitis C virus (HCV) protease inhibitor (PI) drug design, resistance remains a problem causing treatment failure. Double-substitution variants, notably Y56H/D168A, have emerged in patients who fail therapy with a PI-containing regimen. The resistance conferred by Asp168 substitutions has been well characterized and avoided in newer inhibitors. However, an additional mutation at Tyr56 confers resistance to even the most robust inhibitors. Here, we elucidate the molecular mechanisms of resistance for the Y56H/D168A variant against grazoprevir (and four analogs), paritaprevir, and danoprevir through inhibition assays, co-crystal structures, and molecular dynamics simulations. The PIs' susceptibility to Y56H/D168A varies, with those stacking on the catalytic His57 losing the most potency. For such inhibitors, the Y56H substitution disrupts favorable stacking interactions with the neighboring catalytic His57. This indirect mechanism of resistance threatens to cause multi-PI failure as all HCV PIs in clinical development rely on interactions with the catalytic triad.
Collapse
Affiliation(s)
- Ashley N Matthew
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Florian Leidner
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Alicia Newton
- Monogram Biosciences, South San Francisco, CA 94080, USA
| | | | - Wei Huang
- Monogram Biosciences, South San Francisco, CA 94080, USA
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nese KurtYilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| |
Collapse
|
58
|
Yu M, Lou S, Gonzalez-Bobes F. Ring-Closing Metathesis in Pharmaceutical Development: Fundamentals, Applications, and Future Directions. Org Process Res Dev 2018. [DOI: 10.1021/acs.oprd.8b00093] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Miao Yu
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - Sha Lou
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - Francisco Gonzalez-Bobes
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| |
Collapse
|
59
|
Young RJ, Leeson PD. Mapping the Efficiency and Physicochemical Trajectories of Successful Optimizations. J Med Chem 2018; 61:6421-6467. [DOI: 10.1021/acs.jmedchem.8b00180] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Robert J. Young
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Paul D. Leeson
- Paul Leeson Consulting Ltd., The Malt House, Main Street, Congerstone, Nuneaton, Warwickshire CV13 6LZ, U.K
| |
Collapse
|
60
|
Belfrage AK, Abdurakhmanov E, Åkerblom E, Brandt P, Alogheli H, Neyts J, Danielson UH, Sandström A. Pan-NS3 protease inhibitors of hepatitis C virus based on an R3-elongated pyrazinone scaffold. Eur J Med Chem 2018; 148:453-464. [DOI: 10.1016/j.ejmech.2018.02.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 01/20/2018] [Accepted: 02/10/2018] [Indexed: 02/07/2023]
|
61
|
Namoto K, Sirockin F, Sellner H, Wiesmann C, Villard F, Moreau RJ, Valeur E, Paulding SC, Schleeger S, Schipp K, Loup J, Andrews L, Swale R, Robinson M, Farady CJ. Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease inhibitors. Bioorg Med Chem Lett 2018; 28:906-909. [PMID: 29433930 DOI: 10.1016/j.bmcl.2018.01.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 01/28/2018] [Accepted: 01/30/2018] [Indexed: 01/09/2023]
Abstract
The design and synthesis of macrocyclic inhibitors of human rhinovirus 3C protease is described. A macrocyclic linkage of the P1 and P3 residues, and the subsequent structure-based optimization of the macrocycle conformation and size led to the identification of a potent biochemical inhibitor 10 with sub-micromolar antiviral activity.
Collapse
Affiliation(s)
- Kenji Namoto
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland.
| | - Finton Sirockin
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Holger Sellner
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Christian Wiesmann
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Frederic Villard
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Robert J Moreau
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA 94608-2916, USA
| | - Eric Valeur
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Stephanie C Paulding
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Simone Schleeger
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Kathrin Schipp
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Joachim Loup
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Lori Andrews
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA 94608-2916, USA
| | - Ryann Swale
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA 94608-2916, USA
| | - Michael Robinson
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA 94608-2916, USA
| | - Christopher J Farady
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland.
| |
Collapse
|
62
|
Brandenberg OF, Prier CK, Chen K, Knight AM, Wu Z, Arnold FH. Stereoselective Enzymatic Synthesis of Heteroatom-Substituted Cyclopropanes. ACS Catal 2018. [DOI: 10.1021/acscatal.7b04423] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Oliver F. Brandenberg
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Christopher K. Prier
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Kai Chen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Anders M. Knight
- Division of Biology and Bioengineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Zachary Wu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| |
Collapse
|
63
|
Design, synthesis and identification of silicon-containing HCV NS5A inhibitors with pan-genotype activity. Eur J Med Chem 2018; 148:95-105. [PMID: 29454920 DOI: 10.1016/j.ejmech.2018.02.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/30/2018] [Accepted: 02/09/2018] [Indexed: 01/26/2023]
Abstract
Modification of a HCV NS5A inhibitor, ombitasvir, led to the identification of 10d with improved pan-genotype NS5A inhibition and better pharmacokinetic properties. The key structural changes to ombitasvir include bioisosteric replacement of carbon with silicon atom. Compared with ombitasvir, the activity of anti-HCV genotypes (GT 1 to 6) of 10d is increased to some extent, especially the inhibitory activity against genotype 3a and 6a is increased by more than seven times, and the dog's in vivo pharmacokinetics properties were also superior to ombitasvir. Further drug evaluation showed that 10d was similar to ombitasvir on plasma protein binding and liver distribution profiles, with no cytotoxicity and no inhibitory effect on both CYP 450 and hERG ligand binding. However, permeability assay results indicated that 10d was not the substrate of P-gp or BCRP transporter, which is different from that of ombitasvir. The results of a 14-day repeat-dose toxicity study identified no toxicity with 10d. Our findings in preclinical tests suggest that the silicon-containing compound 10d could be worthy of continued study as a potential drug candidate.
Collapse
|
64
|
Attia KAM, El-Abasawi NM, El-Olemy A, Serag A. Different spectrophotometric methods applied for the analysis of simeprevir in the presence of its oxidative degradation product: Acomparative study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 190:1-9. [PMID: 28889051 DOI: 10.1016/j.saa.2017.08.066] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 08/05/2017] [Accepted: 08/31/2017] [Indexed: 06/07/2023]
Abstract
Five simple spectrophotometric methods were developed for the determination of simeprevir in the presence of its oxidative degradation product namely, ratio difference, mean centering, derivative ratio using the Savitsky-Golay filters, second derivative and continuous wavelet transform. These methods are linear in the range of 2.5-40μg/mL and validated according to the ICH guidelines. The obtained results of accuracy, repeatability and precision were found to be within the acceptable limits. The specificity of the proposed methods was tested using laboratory prepared mixtures and assessed by applying the standard addition technique. Furthermore, these methods were statistically comparable to RP-HPLC method and good results were obtained. So, they can be used for the routine analysis of simeprevir in quality-control laboratories.
Collapse
Affiliation(s)
- Khalid A M Attia
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Al-Azhar University, 11751 Nasr City, Cairo, Egypt
| | - Nasr M El-Abasawi
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Al-Azhar University, 11751 Nasr City, Cairo, Egypt
| | - Ahmed El-Olemy
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Al-Azhar University, 11751 Nasr City, Cairo, Egypt
| | - Ahmed Serag
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Al-Azhar University, 11751 Nasr City, Cairo, Egypt.
| |
Collapse
|
65
|
Zhong M, Peng E, Huang N, Huang Q, Huq A, Lau M, Colonno R, Li L. Discovery of novel potent HCV NS5B polymerase non-nucleoside inhibitors bearing a fused benzofuran scaffold. Bioorg Med Chem Lett 2018; 28:963-968. [PMID: 29422387 DOI: 10.1016/j.bmcl.2018.01.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 01/12/2018] [Accepted: 01/17/2018] [Indexed: 12/20/2022]
Abstract
This letter describes the discovery of a fused benzofuran scaffold viable for preparing a series of novel potent HCV NS5B polymerase non-nucleoside inhibitors. Designed on the basis of the functionalized benzofuran derivative nesbuvir (HCV-796), these compounds presumably bind similarly to the allosteric binding site in the "palm" domain of HCV NS5B protein. SAR of each potential hydrogen-bonding interaction site of this novel scaffold is discussed along with some preliminary genotypic profile and PK data of several advanced compounds.
Collapse
Affiliation(s)
- Min Zhong
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 184, San Francisco, CA 94158, USA.
| | - Eric Peng
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 184, San Francisco, CA 94158, USA
| | - Ningwu Huang
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 184, San Francisco, CA 94158, USA
| | - Qi Huang
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 184, San Francisco, CA 94158, USA
| | - Anja Huq
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 184, San Francisco, CA 94158, USA
| | - Meiyen Lau
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 184, San Francisco, CA 94158, USA
| | - Richard Colonno
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 184, San Francisco, CA 94158, USA
| | - Leping Li
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 184, San Francisco, CA 94158, USA.
| |
Collapse
|
66
|
Lin Y, Wang Q, Wu Y, Wang C, Jia H, Zhang C, Huang J, Guo H. Pd-catalyzed [3 + 2] cycloaddition of vinylcyclopropanes with 1-azadienes: synthesis of 4-cyclopentylbenzo[e][1,2,3]oxathiazine 2,2-dioxides. RSC Adv 2018; 8:40798-40803. [PMID: 35557890 PMCID: PMC9091363 DOI: 10.1039/c8ra08881k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/29/2018] [Indexed: 12/24/2022] Open
Abstract
The palladium-catalyzed [3 + 2] cycloaddition of vinylcyclopropanes and 1-azadienes has been developed under mild reaction conditions, giving the multisubstituted cyclopentane derivatives in good to excellent yields with moderate to good diastereoselectivities. The relative configuration of both diastereomers of the products have been determined through X-ray crystallographic diffraction. Pd-catalyzed [3 + 2] cycloaddition of vinylcyclopropanes with 1-azadienes gave highly functionalized cyclopentane derivatives in high yields.![]()
Collapse
Affiliation(s)
- Yan Lin
- Department of Applied Chemistry
- China Agricultural University
- Beijing 100193
- China
| | - Qijun Wang
- Department of Applied Chemistry
- China Agricultural University
- Beijing 100193
- China
| | - Yang Wu
- Department of Applied Chemistry
- China Agricultural University
- Beijing 100193
- China
| | - Chang Wang
- Department of Applied Chemistry
- China Agricultural University
- Beijing 100193
- China
| | - Hao Jia
- Department of Applied Chemistry
- China Agricultural University
- Beijing 100193
- China
| | - Cheng Zhang
- Department of Applied Chemistry
- China Agricultural University
- Beijing 100193
- China
| | - Jiaxing Huang
- Department of Applied Chemistry
- China Agricultural University
- Beijing 100193
- China
| | - Hongchao Guo
- Department of Applied Chemistry
- China Agricultural University
- Beijing 100193
- China
| |
Collapse
|
67
|
Alihodžić S, Bukvić M, Elenkov IJ, Hutinec A, Koštrun S, Pešić D, Saxty G, Tomašković L, Žiher D. Current Trends in Macrocyclic Drug Discovery and beyond -Ro5. PROGRESS IN MEDICINAL CHEMISTRY 2018; 57:113-233. [DOI: 10.1016/bs.pmch.2018.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
68
|
Agbowuro AA, Huston WM, Gamble AB, Tyndall JDA. Proteases and protease inhibitors in infectious diseases. Med Res Rev 2017; 38:1295-1331. [PMID: 29149530 DOI: 10.1002/med.21475] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/10/2017] [Accepted: 10/17/2017] [Indexed: 12/31/2022]
Abstract
There are numerous proteases of pathogenic organisms that are currently targeted for therapeutic intervention along with many that are seen as potential drug targets. This review discusses the chemical and biological makeup of some key druggable proteases expressed by the five major classes of disease causing agents, namely bacteria, viruses, fungi, eukaryotes, and prions. While a few of these enzymes including HIV protease and HCV NS3-4A protease have been targeted to a clinically useful level, a number are yet to yield any clinical outcomes in terms of antimicrobial therapy. A significant aspect of this review discusses the chemical and pharmacological characteristics of inhibitors of the various proteases discussed. A total of 25 inhibitors have been considered potent and safe enough to be trialed in humans and are at different levels of clinical application. We assess the mechanism of action and clinical performance of the protease inhibitors against infectious agents with their developmental strategies and look to the next frontiers in the use of protease inhibitors as anti-infective agents.
Collapse
Affiliation(s)
| | - Wilhelmina M Huston
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Allan B Gamble
- School of Pharmacy, University of Otago, Dunedin, New Zealand
| | | |
Collapse
|
69
|
Attia KAM, El-Abasawi NM, El-Olemy A, Serag A. Simeprevir oxidative degradation product: Molecular modeling,in silicotoxicity and resolution by synchronous spectrofluorimetry. LUMINESCENCE 2017; 33:382-390. [DOI: 10.1002/bio.3425] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/24/2017] [Accepted: 10/01/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Khalid A. M. Attia
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy; Al-Azhar University; Cairo Egypt
| | - Nasr M. El-Abasawi
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy; Al-Azhar University; Cairo Egypt
| | - Ahmed El-Olemy
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy; Al-Azhar University; Cairo Egypt
| | - Ahmed Serag
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy; Al-Azhar University; Cairo Egypt
| |
Collapse
|
70
|
Jin G, Lee J, Lee K. Chemical genetics-based development of small molecules targeting hepatitis C virus. Arch Pharm Res 2017; 40:1021-1036. [PMID: 28856597 DOI: 10.1007/s12272-017-0949-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 08/20/2017] [Indexed: 12/21/2022]
Abstract
Hepatitis C virus (HCV) infection is a major worldwide problem that has emerged as one of the most significant diseases affecting humans. There are currently no vaccines or efficient therapies without side effects, despite today's advanced medical technology. Currently, the common therapy for most patients (i.e. genotype 1) is combination of HCV-specific direct-acting antivirals (DAAs). Up to 2011, the standard of care (SOC) was a combination of peg-IFNα with ribavirin (RBV). After approval of NS3/4A protease inhibitor, SOC was peg-IFNα and RBV with either the first-generation DAAs boceprevir or telaprevir. In the past several years, various novel small molecules have been discovered and some of them (i.e., HCV polymerase, protease, helicase and entry inhibitors) have undergone clinical trials. Between 2013 and 2016, the second-generation DAA drugs simeprevir, asunaprevir, daclatasvir, dasabuvir, sofosbuvir, and elbasvir were approved, as well as the combinational drugs Harvoni®, Zepatier®, Technivie®, and Epclusa®. A number of reviews have been recently published describing the structure-activity relationship (SAR) in the development of HCV inhibitors and outlining current therapeutic approaches to hepatitis C infection. Target identification involves studying a drug's mechanism of action (MOA), and a variety of target identification methods have been developed in the past few years. Chemical biology has emerged as a powerful tool for studying biological processes using small molecules. The use of chemical genetic methods is a valuable strategy for studying the molecular mechanisms of the viral lifecycle and screening for anti-viral agents. Two general screening approaches have been employed: forward and reverse chemical genetics. This review reveals information on the small molecules in HCV drug discovery by using chemical genetics for targeting the HCV protein and describes successful examples of targets identified with these methods.
Collapse
Affiliation(s)
- Guanghai Jin
- College of Pharmacy, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Jisu Lee
- College of Pharmacy, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Kyeong Lee
- College of Pharmacy, Dongguk University-Seoul, Goyang, 10326, Republic of Korea.
| |
Collapse
|
71
|
Novel peptidyl α-aminoalkylphosphonates as inhibitors of hepatitis C virus NS3/4A protease. Antiviral Res 2017; 144:286-298. [DOI: 10.1016/j.antiviral.2017.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 05/10/2017] [Accepted: 06/20/2017] [Indexed: 12/13/2022]
|
72
|
Isosorbide-based peptidomimetics as inhibitors of hepatitis C virus serine protease. Bioorg Med Chem Lett 2017; 27:3661-3665. [DOI: 10.1016/j.bmcl.2017.07.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 11/21/2022]
|
73
|
Biocatalytic Asymmetric Synthesis of (1R, 2S)-N-Boc-vinyl-ACCA Ethyl Ester with a Newly Isolated Sphingomonas aquatilis. Appl Biochem Biotechnol 2017; 184:500-512. [DOI: 10.1007/s12010-017-2567-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/21/2017] [Indexed: 01/17/2023]
|
74
|
Gawin R, Tracz A, Chwalba M, Kozakiewicz A, Trzaskowski B, Skowerski K. Cyclic Alkyl Amino Ruthenium Complexes—Efficient Catalysts for Macrocyclization and Acrylonitrile Cross Metathesis. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00597] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rafał Gawin
- Apeiron Synthesis
SA ul., Duńska 9, 54-427 Wrocław, Poland
| | - Andrzej Tracz
- Apeiron Synthesis
SA ul., Duńska 9, 54-427 Wrocław, Poland
| | - Michał Chwalba
- Apeiron Synthesis
SA ul., Duńska 9, 54-427 Wrocław, Poland
| | - Anna Kozakiewicz
- Faculty
of Chemistry, University of Nicolaus Copernicus, Gagarina 7, 87-100 Toruń, Poland
| | - Bartosz Trzaskowski
- Centre
of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warszawa, Poland
| | | |
Collapse
|
75
|
Cp*Rh(III)-Catalyzed Directed C−H Methylation and Arylation of Quinoline N
-Oxides at the C-8 Position. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700484] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
76
|
Campos GRF, Bittar C, Jardim ACG, Shimizu JF, Batista MN, Paganini ER, Ribeiro de Assis L, Bartlett C, Harris M, da Silva Bolzani V, Regasini LO, Rahal P. Hepatitis C virus in vitro replication is efficiently inhibited by acridone Fac4. J Gen Virol 2017; 98:1693-1701. [PMID: 28699869 PMCID: PMC7615702 DOI: 10.1099/jgv.0.000808] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hepatitis C virus (HCV) affects about 170 million people worldwide. The current treatment has a high cost and variable response rates according to the virus genotype. Acridones, a group of compounds extracted from natural sources, showed potential antiviral actions against HCV. Thus, this study aimed to evaluate the effect of a panel of 14 synthetic acridones on the HCV life cycle. The compounds were screened using an Huh7.5 cell line stably harbouring the HCV genotype 2a subgenomic replicon SGR-Feo-JFH-1. Cells were incubated in the presence or absence of compounds for 72 h and cell viability and replication levels were assessed by MTT and luciferase assays, respectively. At a concentration of 5 µM the acridone Fac4 exhibited a >90 % inhibition of HCV replication with no effect on cell viability. The effects of Fac4 on virus replication, entry and release steps were evaluated in Huh7.5 cells infected with the JFH-1 isolate of HCV (HCVcc). Fac4 inhibited JFH-1 replication to approximately 70 %, while no effect was observed on virus entry. The antiviral activity of Fac4 was also observed on viral release, with almost 80 % of inhibition. No inhibitory effect was observed against genotype 3 replication. Fac4 was able to intercalate into dsRNA, however did not inhibit NS5B polymerase activity or translation driven by the HCV IRES. Although its mode of action is partly understood, Fac4 presents significant inhibition of HCV replication and can therefore be considered as a candidate for the development of a future anti-HCV treatment.
Collapse
Affiliation(s)
| | - Cíntia Bittar
- Institute of Bioscience, Language and Exact Science, IBILCE, UNESP – São Paulo State University, São José do Rio Preto, SP, Brazil
| | - Ana Carolina Gomes Jardim
- Institute of Biomedical Science, ICBIM, UFU – Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Jacqueline Farinha Shimizu
- Institute of Bioscience, Language and Exact Science, IBILCE, UNESP – São Paulo State University, São José do Rio Preto, SP, Brazil
| | - Mariana Nogueira Batista
- Institute of Bioscience, Language and Exact Science, IBILCE, UNESP – São Paulo State University, São José do Rio Preto, SP, Brazil
| | - Eder Ramos Paganini
- Institute of Bioscience, Language and Exact Science, IBILCE, UNESP – São Paulo State University, São José do Rio Preto, SP, Brazil
| | - Letícia Ribeiro de Assis
- Institute of Bioscience, Language and Exact Science, IBILCE, UNESP – São Paulo State University, São José do Rio Preto, SP, Brazil
| | - Christopher Bartlett
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | | | - Luis Octavio Regasini
- Institute of Bioscience, Language and Exact Science, IBILCE, UNESP – São Paulo State University, São José do Rio Preto, SP, Brazil
- Institute of Chemistry, São Paulo State University, Araraquara, SP, Brazil
| | - Paula Rahal
- Institute of Bioscience, Language and Exact Science, IBILCE, UNESP – São Paulo State University, São José do Rio Preto, SP, Brazil
| |
Collapse
|
77
|
Matthew AN, Zephyr J, Hill CJ, Jahangir M, Newton A, Petropoulos CJ, Huang W, Kurt-Yilmaz N, Schiffer CA, Ali A. Hepatitis C Virus NS3/4A Protease Inhibitors Incorporating Flexible P2 Quinoxalines Target Drug Resistant Viral Variants. J Med Chem 2017; 60:5699-5716. [PMID: 28594175 DOI: 10.1021/acs.jmedchem.7b00426] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A substrate envelope-guided design strategy is reported for improving the resistance profile of HCV NS3/4A protease inhibitors. Analogues of 5172-mcP1P3 were designed by incorporating diverse quinoxalines at the P2 position that predominantly interact with the invariant catalytic triad of the protease. Exploration of structure-activity relationships showed that inhibitors with small hydrophobic substituents at the 3-position of P2 quinoxaline maintain better potency against drug resistant variants, likely due to reduced interactions with residues in the S2 subsite. In contrast, inhibitors with larger groups at this position were highly susceptible to mutations at Arg155, Ala156, and Asp168. Excitingly, several inhibitors exhibited exceptional potency profiles with EC50 values ≤5 nM against major drug resistant HCV variants. These findings support that inhibitors designed to interact with evolutionarily constrained regions of the protease, while avoiding interactions with residues not essential for substrate recognition, are less likely to be susceptible to drug resistance.
Collapse
Affiliation(s)
- Ashley N Matthew
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
| | - Jacqueto Zephyr
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
| | - Caitlin J Hill
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
| | - Muhammad Jahangir
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
| | - Alicia Newton
- Monogram Biosciences , South San Francisco, California 94080, United States
| | | | - Wei Huang
- Monogram Biosciences , South San Francisco, California 94080, United States
| | - Nese Kurt-Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
| |
Collapse
|
78
|
QSAR studies of the bioactivity of hepatitis C virus (HCV) NS3/4A protease inhibitors by multiple linear regression (MLR) and support vector machine (SVM). Bioorg Med Chem Lett 2017; 27:2931-2938. [PMID: 28501513 DOI: 10.1016/j.bmcl.2017.05.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/14/2017] [Accepted: 05/01/2017] [Indexed: 12/23/2022]
Abstract
In this study, quantitative structure-activity relationship (QSAR) models using various descriptor sets and training/test set selection methods were explored to predict the bioactivity of hepatitis C virus (HCV) NS3/4A protease inhibitors by using a multiple linear regression (MLR) and a support vector machine (SVM) method. 512 HCV NS3/4A protease inhibitors and their IC50 values which were determined by the same FRET assay were collected from the reported literature to build a dataset. All the inhibitors were represented with selected nine global and 12 2D property-weighted autocorrelation descriptors calculated from the program CORINA Symphony. The dataset was divided into a training set and a test set by a random and a Kohonen's self-organizing map (SOM) method. The correlation coefficients (r2) of training sets and test sets were 0.75 and 0.72 for the best MLR model, 0.87 and 0.85 for the best SVM model, respectively. In addition, a series of sub-dataset models were also developed. The performances of all the best sub-dataset models were better than those of the whole dataset models. We believe that the combination of the best sub- and whole dataset SVM models can be used as reliable lead designing tools for new NS3/4A protease inhibitors scaffolds in a drug discovery pipeline.
Collapse
|
79
|
Attia KA, El-Abasawi NM, El-Olemy A, Serag A. Stability-indicating HPLC-DAD Method for the Determination of Simeprevir. ACTA ACUST UNITED AC 2017. [DOI: 10.1080/22297928.2017.1287004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
80
|
Current therapy for chronic hepatitis C: The role of direct-acting antivirals. Antiviral Res 2017; 142:83-122. [PMID: 28238877 PMCID: PMC7172984 DOI: 10.1016/j.antiviral.2017.02.014] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/07/2017] [Accepted: 02/22/2017] [Indexed: 12/12/2022]
Abstract
One of the most exciting developments in antiviral research has been the discovery of the direct-acting antivirals (DAAs) that effectively cure chronic hepatitis C virus (HCV) infections. Based on more than 100 clinical trials and real-world studies, we provide a comprehensive overview of FDA-approved therapies and newly discovered anti-HCV agents with a special focus on drug efficacy, mechanisms of action, and safety. We show that HCV drug development has advanced in multiple aspects: (i) interferon-based regimens were replaced by interferon-free regimens; (ii) genotype-specific drugs evolved to drugs for all HCV genotypes; (iii) therapies based upon multiple pills per day were simplified to a single pill per day; (iv) drug potency increased from moderate (∼60%) to high (>90%) levels of sustained virologic responses; (v) treatment durations were shortened from 48 to 12 or 8 weeks; and (vi) therapies could be administered orally regardless of prior treatment history and cirrhotic status. However, despite these remarkable achievements made in HCV drug discovery, challenges remain in the management of difficult-to-treat patients. HCV genotype-specific drugs evolve to pan-genotypic drugs. Drug potency increases from moderate (∼60%) to high (>90%) levels of sustained virologic response. Treatment durations are shortened from a 48-week to 12-week or 8-week period. HCV therapies based upon multiple pills per day are simplified to a single pill per day. HCV therapies are administered orally regardless of prior treatment history and cirrhotic status.
Collapse
|
81
|
Guo Z, Black S, Hu Y, McMonagle P, Ingravallo P, Chase R, Curry S, Asante-Appiah E. Unraveling the structural basis of grazoprevir potency against clinically relevant substitutions in hepatitis C virus NS3/4A protease from genotype 1a. J Biol Chem 2017; 292:6202-6212. [PMID: 28228479 DOI: 10.1074/jbc.m116.772996] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/03/2017] [Indexed: 12/14/2022] Open
Abstract
Grazoprevir is a potent pan-genotype and macrocyclic inhibitor of hepatitis C virus (HCV) NS3/4A protease and was developed for treating chronic HCV infection. In HCV genotype (GT) 1a, grazoprevir maintains potent activity against a majority of NS3 resistance-associated amino acid substitutions, including the highly prevalent and naturally occurring Q80K polymorphism that impacts simeprevir, another NS3/4A protease inhibitor. The basis for an unexpected difference in the clinical impact of some NS3 substitutions was investigated. Phenotypic analysis of resistance-associated substitutions identified in NS3 from GT1a-infected patients who failed therapy with grazoprevir (in combination with elbasvir, an inhibitor of HCV NS5A protein) showed that positions 56, 156, and 168 in NS3 were most impactful because they diminished protein-inhibitor interactions. Although an amino acid substitution from aspartic acid to alanine at position 168 (D168A) reduced the potency of grazoprevir, its combination with R155K unexpectedly nullified this effect. Molecular dynamics and free-energy surface studies indicated that Asp-168 is important in anchoring Arg-155 for ligand binding but is not critical for Lys-155 because of the inherent flexibility of its side chain. Moreover, modeling studies supported a strong direct cation-heterocycle interaction between the Lys-155 side chain of the double substitution, R155K/D168A, and the lone pair on the quinoxaline in grazoprevir. This unique interaction provides a structural basis for grazoprevir's higher potency than simeprevir, an inhibitor to which the double substitution confers a significant reduction in potency. Our findings are consistent with the detection of R155K/D168A in NS3 from virologic failures treated with simeprevir but not grazoprevir.
Collapse
Affiliation(s)
- Zhuyan Guo
- From the Departments of Chemistry, Modeling and Informatics and
| | - Stuart Black
- Infectious Diseases, Merck Research Laboratories, Kenilworth, New Jersey 07033
| | - Yuan Hu
- From the Departments of Chemistry, Modeling and Informatics and
| | - Patricia McMonagle
- Infectious Diseases, Merck Research Laboratories, Kenilworth, New Jersey 07033
| | - Paul Ingravallo
- Infectious Diseases, Merck Research Laboratories, Kenilworth, New Jersey 07033
| | - Robert Chase
- Infectious Diseases, Merck Research Laboratories, Kenilworth, New Jersey 07033
| | - Stephanie Curry
- Infectious Diseases, Merck Research Laboratories, Kenilworth, New Jersey 07033
| | | |
Collapse
|
82
|
Marshall NC, Finlay BB, Overall CM. Sharpening Host Defenses during Infection: Proteases Cut to the Chase. Mol Cell Proteomics 2017; 16:S161-S171. [PMID: 28179412 PMCID: PMC5393396 DOI: 10.1074/mcp.o116.066456] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/03/2017] [Indexed: 01/14/2023] Open
Abstract
The human immune system consists of an intricate network of tightly controlled pathways, where proteases are essential instigators and executioners at multiple levels. Invading microbial pathogens also encode proteases that have evolved to manipulate and dysregulate host proteins, including host proteases during the course of disease. The identification of pathogen proteases as well as their substrates and mechanisms of action have empowered significant developments in therapeutics for infectious diseases. Yet for many pathogens, there remains a great deal to be discovered. Recently, proteomic techniques have been developed that can identify proteolytically processed proteins across the proteome. These “degradomics” approaches can identify human substrates of microbial proteases during infection in vivo and expose the molecular-level changes that occur in the human proteome during infection as an operational network to develop hypotheses for further research as well as new therapeutics. This Perspective Article reviews how proteases are utilized during infection by both the human host and invading bacterial pathogens, including archetypal virulence-associated microbial proteases, such as the Clostridia spp. botulinum and tetanus neurotoxins. We highlight the potential knowledge that degradomics studies of host–pathogen interactions would uncover, as well as how degradomics has been successfully applied in similar contexts, including use with a viral protease. We review how microbial proteases have been targeted in current therapeutic approaches and how microbial proteases have shaped and even contributed to human therapeutics beyond infectious disease. Finally, we discuss how, moving forward, degradomics research can greatly contribute to our understanding of how microbial pathogens cause disease in vivo and lead to the identification of novel substrates in vivo, and the development of improved therapeutics to counter these pathogens.
Collapse
Affiliation(s)
- Natalie C Marshall
- From the ‡Department of Microbiology & Immunology.,§Michael Smith Laboratories
| | - B Brett Finlay
- From the ‡Department of Microbiology & Immunology.,§Michael Smith Laboratories.,¶Department of Biochemistry & Molecular Biology
| | - Christopher M Overall
- ¶Department of Biochemistry & Molecular Biology, .,**Department of Oral Biological & Medical Sciences, Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
83
|
McIver AL, Zhang W, Liu Q, Jiang X, Stashko MA, Nichols J, Miley MJ, Norris-Drouin J, Machius M, DeRyckere D, Wood E, Graham DK, Earp HS, Kireev D, Frye SV, Wang X. Discovery of Macrocyclic Pyrimidines as MerTK-Specific Inhibitors. ChemMedChem 2017; 12:207-213. [PMID: 28032464 PMCID: PMC5336325 DOI: 10.1002/cmdc.201600589] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 12/22/2016] [Indexed: 11/08/2022]
Abstract
Macrocycles have attracted significant attention in drug discovery recently. In fact, a few de novo designed macrocyclic kinase inhibitors are currently in clinical trials with good potency and selectivity for their intended target. In this study, we successfully engaged a structure-based drug design approach to discover macrocyclic pyrimidines as potent Mer tyrosine kinase (MerTK)-specific inhibitors. An enzyme-linked immunosorbent assay (ELISA) in 384-well format was employed to evaluate the inhibitory activity of macrocycles in a cell-based assay assessing tyrosine phosphorylation of MerTK. Through structure-activity relationship (SAR) studies, analogue 11 [UNC2541; (S)-7-amino-N-(4-fluorobenzyl)-8-oxo-2,9,16-triaza-1(2,4)-pyrimidinacyclohexadecaphane-1-carboxamide] was identified as a potent and MerTK-specific inhibitor that exhibits sub-micromolar inhibitory activity in the cell-based ELISA. In addition, an X-ray structure of MerTK protein in complex with 11 was resolved to show that these macrocycles bind in the MerTK ATP pocket.
Collapse
Affiliation(s)
- Andrew L. McIver
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy
| | - Weihe Zhang
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy
| | - Qingyang Liu
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy
| | - Xinpeng Jiang
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy
| | - Michael A. Stashko
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy
| | | | - Michael J Miley
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jacqueline Norris-Drouin
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy
| | - Mischa Machius
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Deborah DeRyckere
- Aflac Cancer and Blood Disorders Center of Children's Healthcare of Atlanta, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | | | - Douglas K. Graham
- Meryx, Inc., USA
- Aflac Cancer and Blood Disorders Center of Children's Healthcare of Atlanta, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - H Shelton Earp
- Meryx, Inc., USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy
| | - Stephen V. Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy
- Meryx, Inc., USA
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xiaodong Wang
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy
| |
Collapse
|
84
|
Kajetanowicz A, Milewski M, Rogińska J, Gajda R, Woźniak K. Hoveyda-Type Quinone-Containing Complexes - Catalysts to Prevent Migration of the Double Bond under Metathesis Conditions. European J Org Chem 2017. [DOI: 10.1002/ejoc.201601344] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Anna Kajetanowicz
- Institute of Organic Chemistry; Polish Academy of Sciences; Kasprzaka 44/52 01-224 Warsaw Poland
| | - Mariusz Milewski
- Institute of Organic Chemistry; Polish Academy of Sciences; Kasprzaka 44/52 01-224 Warsaw Poland
| | - Joanna Rogińska
- Institute of Organic Chemistry; Polish Academy of Sciences; Kasprzaka 44/52 01-224 Warsaw Poland
| | - Roman Gajda
- Department of Chemistry; Warsaw University; Żwirki i Wigury Street 101 02-089 Warsaw Poland
| | - Krzysztof Woźniak
- Department of Chemistry; Warsaw University; Żwirki i Wigury Street 101 02-089 Warsaw Poland
| |
Collapse
|
85
|
Preclinical Characterization and Human Microdose Pharmacokinetics of ITMN-8187, a Nonmacrocyclic Inhibitor of the Hepatitis C Virus NS3 Protease. Antimicrob Agents Chemother 2016; 61:AAC.01569-16. [PMID: 27795376 DOI: 10.1128/aac.01569-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/09/2016] [Indexed: 12/11/2022] Open
Abstract
The current paradigm for the treatment of chronic hepatitis C virus (HCV) infection involves combinations of agents that act directly on steps of the HCV life cycle. Here we report the preclinical characteristics of ITMN-8187, a nonmacrocyclic inhibitor of the NS3/4A HCV protease. X-ray crystallographic studies of ITMN-8187 and simeprevir binding to NS3/4A protease demonstrated good agreement between structures. Low nanomolar biochemical potency was maintained against NS3/4A derived from HCV genotypes 1, 2b, 4, 5, and 6. In cell-based potency assays, half-maximal reduction of genotype 1a and 1b HCV replicon RNA was afforded by 11 and 4 nM doses of ITMN-8187, respectively. Combinations of ITMN-8187 with other directly acting antiviral agents in vitro displayed additive antiviral efficacy. A 30-mg/kg of body weight dose of ITMN-8187 administered for 4 days yielded significant viral load reductions through day 5 in a chimeric mouse model of HCV. A 3-mg/kg oral dose administered to rats, dogs, or monkeys yielded concentrations in plasma 16 h after dosing that exceeded the half-maximal effective concentration of ITMN-8187. Human microdose pharmacokinetics showed low intersubject variability and prolonged oral absorption with first-order elimination kinetics compatible with once-daily dosing. These preclinical characteristics compare favorably with those of other NS3/4A inhibitors approved for the treatment of chronic HCV infection.
Collapse
|
86
|
Grychowska K, Kubica B, Drop M, Colacino E, Bantreil X, Pawłowski M, Martinez J, Subra G, Zajdel P, Lamaty F. Application of the ring-closing metathesis to the formation of 2-aryl-1H-pyrrole-3-carboxylates as building blocks for biologically active compounds. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.09.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
87
|
Ekins S, Liebler J, Neves BJ, Lewis WG, Coffee M, Bienstock R, Southan C, Andrade CH. Illustrating and homology modeling the proteins of the Zika virus. F1000Res 2016; 5:275. [PMID: 27746901 DOI: 10.12688/f1000research.8213.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/29/2016] [Indexed: 12/28/2022] Open
Abstract
The Zika virus (ZIKV) is a flavivirus of the family Flaviviridae, which is similar to dengue virus, yellow fever and West Nile virus. Recent outbreaks in South America, Latin America, the Caribbean and in particular Brazil have led to concern for the spread of the disease and potential to cause Guillain-Barré syndrome and microcephaly. Although ZIKV has been known of for over 60 years there is very little in the way of knowledge of the virus with few publications and no crystal structures. No antivirals have been tested against it either in vitro or in vivo. ZIKV therefore epitomizes a neglected disease. Several suggested steps have been proposed which could be taken to initiate ZIKV antiviral drug discovery using both high throughput screens as well as structure-based design based on homology models for the key proteins. We now describe preliminary homology models created for NS5, FtsJ, NS4B, NS4A, HELICc, DEXDc, peptidase S7, NS2B, NS2A, NS1, E stem, glycoprotein M, propeptide, capsid and glycoprotein E using SWISS-MODEL. Eleven out of 15 models pass our model quality criteria for their further use. While a ZIKV glycoprotein E homology model was initially described in the immature conformation as a trimer, we now describe the mature dimer conformer which allowed the construction of an illustration of the complete virion. By comparing illustrations of ZIKV based on this new homology model and the dengue virus crystal structure we propose potential differences that could be exploited for antiviral and vaccine design. The prediction of sites for glycosylation on this protein may also be useful in this regard. While we await a cryo-EM structure of ZIKV and eventual crystal structures of the individual proteins, these homology models provide the community with a starting point for structure-based design of drugs and vaccines as well as a for computational virtual screening.
Collapse
Affiliation(s)
- Sean Ekins
- Collaborations in Chemistry, Fuquay-Varina, NC, USA; Collaborations Pharmaceuticals Inc., Fuquay-Varina, NC, USA; Collaborative Drug Discovery Inc, Burlingame, CA, USA
| | | | - Bruno J Neves
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, GO, Brazil
| | - Warren G Lewis
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Megan Coffee
- The International Rescue Committee, New York, NY, USA
| | | | | | - Carolina H Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, GO, Brazil
| |
Collapse
|
88
|
Structural and conformational determinants of macrocycle cell permeability. Nat Chem Biol 2016; 12:1065-1074. [DOI: 10.1038/nchembio.2203] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 08/04/2016] [Indexed: 12/31/2022]
|
89
|
McCauley JA, Rudd MT. Hepatitis C virus NS3/4a protease inhibitors. Curr Opin Pharmacol 2016; 30:84-92. [DOI: 10.1016/j.coph.2016.07.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/20/2016] [Accepted: 07/25/2016] [Indexed: 02/04/2023]
|
90
|
Abstract
Unusual amino acids are fundamental building blocks of modern medicinal chemistry. The combination of readily functionalized amine and carboxyl groups attached to a chiral central core along with one or two potentially diverse side chains provides a unique three-dimensional structure with a high degree of functionality. This makes them invaluable as starting materials for syntheses of complex molecules, highly diverse elements for SAR campaigns, integral components of peptidomimetic drugs, and potential drugs on their own. This Perspective highlights the diversity of unnatural amino acid structures found in hit-to-lead and lead optimization campaigns and clinical stage and approved drugs, reflecting their increasingly important role in medicinal chemistry.
Collapse
Affiliation(s)
- Mark A T Blaskovich
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland Australia 4072
| |
Collapse
|
91
|
Soumana DI, Yilmaz NK, Ali A, Prachanronarong KL, Schiffer CA. Molecular and Dynamic Mechanism Underlying Drug Resistance in Genotype 3 Hepatitis C NS3/4A Protease. J Am Chem Soc 2016; 138:11850-9. [PMID: 27512818 PMCID: PMC5221612 DOI: 10.1021/jacs.6b06454] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV), affecting an estimated 150 million people worldwide, is the leading cause of viral hepatitis, cirrhosis and hepatocellular carcinoma. HCV is genetically diverse with six genotypes (GTs) and multiple subtypes of different global distribution and prevalence. Recent development of direct-acting antivirals against HCV including NS3/4A protease inhibitors (PIs) has greatly improved treatment outcomes for GT-1. However, all current PIs exhibit significantly lower potency against GT-3. Lack of structural data on GT-3 protease has limited our ability to understand PI failure in GT-3. In this study the molecular basis for reduced potency of current inhibitors against GT-3 NS3/4A protease is elucidated with structure determination, molecular dynamics simulations and inhibition assays. A chimeric GT-1a3a NS3/4A protease amenable to crystallization was engineered to recapitulate decreased sensitivity of GT-3 protease to PIs. High-resolution crystal structures of this GT-1a3a bound to 3 PIs, asunaprevir, danoprevir and vaniprevir, had only subtle differences relative to GT-1 despite orders of magnitude loss in affinity. In contrast, hydrogen-bonding interactions within and with the protease active site and dynamic fluctuations of the PIs were drastically altered. The correlation between loss of intermolecular dynamics and inhibitor potency suggests a mechanism where polymorphisms between genotypes (or selected mutations) in the drug target confer resistance through altering the intermolecular dynamics of the protein-inhibitor complex.
Collapse
Affiliation(s)
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Kristina L. Prachanronarong
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| |
Collapse
|
92
|
Discovery of ravidasvir (PPI-668) as a potent pan-genotypic HCV NS5A inhibitor. Bioorg Med Chem Lett 2016; 26:4508-4512. [DOI: 10.1016/j.bmcl.2016.07.066] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/25/2016] [Accepted: 07/27/2016] [Indexed: 12/17/2022]
|
93
|
Sun LQ, Mull E, Zheng B, D'Andrea S, Zhao Q, Wang AX, Sin N, Venables BL, Sit SY, Chen Y, Chen J, Cocuzza A, Bilder DM, Mathur A, Rampulla R, Chen BC, Palani T, Ganesan S, Arunachalam PN, Falk P, Levine S, Chen C, Friborg J, Yu F, Hernandez D, Sheaffer AK, Knipe JO, Han YH, Schartman R, Donoso M, Mosure K, Sinz MW, Zvyaga T, Rajamani R, Kish K, Tredup J, Klei HE, Gao Q, Ng A, Mueller L, Grasela DM, Adams S, Loy J, Levesque PC, Sun H, Shi H, Sun L, Warner W, Li D, Zhu J, Wang YK, Fang H, Cockett MI, Meanwell NA, McPhee F, Scola PM. Discovery of a Potent Acyclic, Tripeptidic, Acyl Sulfonamide Inhibitor of Hepatitis C Virus NS3 Protease as a Back-up to Asunaprevir with the Potential for Once-Daily Dosing. J Med Chem 2016; 59:8042-60. [PMID: 27564532 DOI: 10.1021/acs.jmedchem.6b00821] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The discovery of a back-up to the hepatitis C virus NS3 protease inhibitor asunaprevir (2) is described. The objective of this work was the identification of a drug with antiviral properties and toxicology parameters similar to 2, but with a preclinical pharmacokinetic (PK) profile that was predictive of once-daily dosing. Critical to this discovery process was the employment of an ex vivo cardiovascular (CV) model which served to identify compounds that, like 2, were free of the CV liabilities that resulted in the discontinuation of BMS-605339 (1) from clinical trials. Structure-activity relationships (SARs) at each of the structural subsites in 2 were explored with substantial improvement in PK through modifications at the P1 site, while potency gains were found with small, but rationally designed structural changes to P4. Additional modifications at P3 were required to optimize the CV profile, and these combined SARs led to the discovery of BMS-890068 (29).
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Arvind Mathur
- Department of Discovery Synthesis, Bristol-Myers Squibb Research and Development , Route 206 and Provinceline Road, Princeton, New Jersey 08543, United States
| | - Richard Rampulla
- Department of Discovery Synthesis, Bristol-Myers Squibb Research and Development , Route 206 and Provinceline Road, Princeton, New Jersey 08543, United States
| | - Bang-Chi Chen
- Department of Discovery Synthesis, Bristol-Myers Squibb Research and Development , Route 206 and Provinceline Road, Princeton, New Jersey 08543, United States
| | - Theerthagiri Palani
- Biocon Bristol-Myers Squibb R&D Center , Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore 560099, India
| | - Sivakumar Ganesan
- Biocon Bristol-Myers Squibb R&D Center , Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore 560099, India
| | - Pirama Nayagam Arunachalam
- Biocon Bristol-Myers Squibb R&D Center , Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore 560099, India
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Qi Gao
- Department of Pharmaceutical Development, Bristol-Myers Squibb Research and Development , 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Alicia Ng
- Department of Pharmaceutical Development, Bristol-Myers Squibb Research and Development , 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | | | | | - Stephen Adams
- Department of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534, United States
| | | | - Paul C Levesque
- Department of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Huabin Sun
- Department of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Hong Shi
- Department of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Lucy Sun
- Department of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - William Warner
- Department of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Danshi Li
- Department of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Jialong Zhu
- Department of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534, United States
| | | | | | | | | | | | | |
Collapse
|
94
|
Identification of Peptide Leads to Inhibit Hepatitis C Virus: Inhibitory Effect of Plectasin Peptide Against Hepatitis C Serine Protease. Int J Pept Res Ther 2016. [DOI: 10.1007/s10989-016-9544-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
95
|
Tevs OA, Veremeichik YV, Shurpik DN, Lodochnikova OA, Plemenkov VV. Acylated benzothiazinesulfoneamides: Synthesis and molecular structure. RUSS J GEN CHEM+ 2016. [DOI: 10.1134/s1070363216080120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
96
|
Court JJ, Poisson C, Ardzinski A, Bilimoria D, Chan L, Chandupatla K, Chauret N, Collier PN, Das SK, Denis F, Dorsch W, Iyer G, Lauffer D, L'Heureux L, Li P, Luisi BS, Mani N, Nanthakumar S, Nicolas O, Rao BG, Ronkin S, Selliah S, Shawgo RS, Tang Q, Waal ND, Yannopoulos CG, Green J. Discovery of Novel Thiophene-Based, Thumb Pocket 2 Allosteric Inhibitors of the Hepatitis C NS5B Polymerase with Improved Potency and Physicochemical Profiles. J Med Chem 2016; 59:6293-302. [PMID: 27366941 DOI: 10.1021/acs.jmedchem.6b00541] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The hepatitis C viral proteins NS3/4A protease, NS5B polymerase, and NS5A are clinically validated targets for direct-acting antiviral therapies. The NS5B polymerase may be inhibited directly through the action of nucleosides or nucleotide analogues or allosterically at a number of well-defined sites. Herein we describe the further development of a series of thiophene carboxylate allosteric inhibitors of NS5B polymerase that act at the thumb pocket 2 site. Lomibuvir (1) is an allosteric HCV NS5B inhibitor that has demonstrated excellent antiviral activity and potential clinical utility in combination with other direct acting antiviral agents. Efforts to further explore and develop this series led to compound 23, a compound with comparable potency and improved physicochemical properties.
Collapse
Affiliation(s)
- John J Court
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Carl Poisson
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Andrzej Ardzinski
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Darius Bilimoria
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Laval Chan
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Kishan Chandupatla
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Nathalie Chauret
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Philip N Collier
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Sanjoy Kumar Das
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Francois Denis
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Warren Dorsch
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Ganesh Iyer
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - David Lauffer
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Lucille L'Heureux
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Pan Li
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Brian S Luisi
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Nagraj Mani
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Suganthi Nanthakumar
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Olivier Nicolas
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - B Govinda Rao
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Steven Ronkin
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Subajini Selliah
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Rebecca S Shawgo
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Qing Tang
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Nathan D Waal
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Constantin G Yannopoulos
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Jeremy Green
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| |
Collapse
|
97
|
Talele TT. The "Cyclopropyl Fragment" is a Versatile Player that Frequently Appears in Preclinical/Clinical Drug Molecules. J Med Chem 2016; 59:8712-8756. [PMID: 27299736 DOI: 10.1021/acs.jmedchem.6b00472] [Citation(s) in RCA: 554] [Impact Index Per Article: 69.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Recently, there has been an increasing use of the cyclopropyl ring in drug development to transition drug candidates from the preclinical to clinical stage. Important features of the cyclopropane ring are, the (1) coplanarity of the three carbon atoms, (2) relatively shorter (1.51 Å) C-C bonds, (3) enhanced π-character of C-C bonds, and (4) C-H bonds are shorter and stronger than those in alkanes. The present review will focus on the contributions that a cyclopropyl ring makes to the properties of drugs containing it. Consequently, the cyclopropyl ring addresses multiple roadblocks that can occur during drug discovery such as (a) enhancing potency, (b) reducing off-target effects,
Collapse
Affiliation(s)
- Tanaji T Talele
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University , 8000 Utopia Parkway, Queens, New York 11439, United States
| |
Collapse
|
98
|
Wheeler P, Phillips JH, Pederson RL. Scalable Methods for the Removal of Ruthenium Impurities from Metathesis Reaction Mixtures. Org Process Res Dev 2016. [DOI: 10.1021/acs.oprd.6b00138] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Philip Wheeler
- Materia, Inc., 60 N San Gabriel Blvd., Pasadena, California 91107, United States
| | - John H. Phillips
- Materia, Inc., 60 N San Gabriel Blvd., Pasadena, California 91107, United States
| | - Richard L. Pederson
- Materia, Inc., 60 N San Gabriel Blvd., Pasadena, California 91107, United States
| |
Collapse
|
99
|
Pettersson M, Hou X, Kuhn M, Wager TT, Kauffman GW, Verhoest PR. Quantitative Assessment of the Impact of Fluorine Substitution on P-Glycoprotein (P-gp) Mediated Efflux, Permeability, Lipophilicity, and Metabolic Stability. J Med Chem 2016; 59:5284-96. [DOI: 10.1021/acs.jmedchem.6b00027] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Martin Pettersson
- Worldwide
Medicinal Chemistry, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Xinjun Hou
- Worldwide
Medicinal Chemistry, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Max Kuhn
- Research
Statistics, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Travis T. Wager
- Worldwide
Medicinal Chemistry, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Gregory W. Kauffman
- Computational
ADME Group, Department of Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Patrick R. Verhoest
- Worldwide
Medicinal Chemistry, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
100
|
Ren S, Jin Y, Huang Y, Ma L, Liu Y, Meng C, Guan S, Xie L, Chen X. HCV NS3Ag: a reliable and clinically useful predictor of antiviral outcomes in genotype 1b hepatitis C virus-infected patients. Eur J Clin Microbiol Infect Dis 2016; 35:1195-203. [PMID: 27173787 DOI: 10.1007/s10096-016-2653-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 04/18/2016] [Indexed: 11/25/2022]
Abstract
Since hepatitis C virus (HCV) non-structural 3 (NS3) protease inhibitor (PI) combined with pegylated interferon/ribavirin (PR) has been approved for chronic HCV genotype (GT) 1b infection, a reliable and clinically useful predictor combining with serum HCV RNA to predict early virologic response, breakthrough, and relapse is important during HCV antiviral treatment. We evaluated the role of HCV NS3 antigen (HCV NS3Ag) on the prediction of virologic response in patients with HCV GT1b during PR or PR/simeprevir (triple) therapy. Three hundred patients were recruited, and HCV RNA and HCV NS3Ag were tested at baseline and weeks 2, 4, 12, 24, 48, and 72. NS3Ag and HCV RNA were significantly related (r(2) = 0.67) in the whole patient selection. The kinetic pattern of HCV RNA and HCV NS3Ag during triple treatment was similar. HCV NS3Ag levels in the triple group closely followed those of HCV RNA; the r(2) values were 0.756 (baseline), 0.837 (2 weeks), 0.989 (4 weeks), and 0.993 (12 weeks), respectively. For patients treated with PR, the positive and negative predictive values (PPVs and NPVs) for viral response were 96.31 % and 67.19 %, respectively, at week 4 by using the decrease of NS3Ag (dHCV NS3Ag) combined with HCV RNA. At week 12, the PPV was similar at 94.16 %, while the NPV reached 87.26 %. The PPV and NPV for the prediction of relapse and breakthrough were 90.6 % and 76.7 %, respectively. HCV NS3Ag is a valuable marker and could be a supplementary predictor of HCV RNA for the prediction of antiviral response, breakthrough, or relapse during HCV antiviral treatment.
Collapse
Affiliation(s)
- S Ren
- Beijing You'an Hospital, Capital Medical University, No. 8 Xitoutiao, You'anmenwai, Fengtai District, Beijing, 100069, People's Republic of China
| | - Y Jin
- Beijing You'an Hospital, Capital Medical University, No. 8 Xitoutiao, You'anmenwai, Fengtai District, Beijing, 100069, People's Republic of China
| | - Y Huang
- Beijing Municipal Liver Diseases Institute, No. 8 Xitoutiao, You'anmenwai, Fengtai District, Beijing, 100069, People's Republic of China
| | - L Ma
- Beijing You'an Hospital, Capital Medical University, No. 8 Xitoutiao, You'anmenwai, Fengtai District, Beijing, 100069, People's Republic of China
| | - Y Liu
- Beijing You'an Hospital, Capital Medical University, No. 8 Xitoutiao, You'anmenwai, Fengtai District, Beijing, 100069, People's Republic of China
| | - C Meng
- Beijing Municipal Liver Diseases Institute, No. 8 Xitoutiao, You'anmenwai, Fengtai District, Beijing, 100069, People's Republic of China
| | - S Guan
- Beijing Municipal Liver Diseases Institute, No. 8 Xitoutiao, You'anmenwai, Fengtai District, Beijing, 100069, People's Republic of China
| | - L Xie
- Beijing Municipal Liver Diseases Institute, No. 8 Xitoutiao, You'anmenwai, Fengtai District, Beijing, 100069, People's Republic of China.
| | - X Chen
- Beijing You'an Hospital, Capital Medical University, No. 8 Xitoutiao, You'anmenwai, Fengtai District, Beijing, 100069, People's Republic of China.
| |
Collapse
|