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da Rocha MN, de Sousa DS, da Silva Mendes FR, Dos Santos HS, Marinho GS, Marinho MM, Marinho ES. Ligand and structure-based virtual screening approaches in drug discovery: minireview. Mol Divers 2024:10.1007/s11030-024-10979-6. [PMID: 39223358 DOI: 10.1007/s11030-024-10979-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024]
Abstract
The compilation of ligand and structure-based molecular modeling methods has become an important practice in virtual screening applied to drug discovery. This systematic review addresses and ranks various virtual screening strategies to drive the selection of the optimal method for studies that have as their starting point a multi-ligand investigation and investigation based on the protein structure of a therapeutic target. This study shows examples of applications and an evaluation based on the objective and problematic of a series of virtual screening studies present in the ScienceDirect® database. The results showed that the molecular docking technique is widely used in scientific production, indicating that approaches that use protein structure as a starting point are the most promising strategy for drug discovery that relies on virtual screening-based research.
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Affiliation(s)
- Matheus Nunes da Rocha
- Postgraduate Program in Natural Sciences, Sciences and Technology Center, State University of Ceará, Fortaleza, CE, Brazil.
| | - Damião Sampaio de Sousa
- Postgraduate Program in Natural Sciences, Sciences and Technology Center, State University of Ceará, Fortaleza, CE, Brazil
| | | | - Helcio Silva Dos Santos
- Postgraduate Program in Natural Sciences, Sciences and Technology Center, State University of Ceará, Fortaleza, CE, Brazil
- Chemistry Department, State University of Acaraú Valley, Sobral, CE, Brazil
| | - Gabrielle Silva Marinho
- Faculdade de Educação, Ciências e Letras de Iguatu, State University of Ceará, Fortaleza, CE, Brazil
| | | | - Emmanuel Silva Marinho
- Postgraduate Program in Natural Sciences, Sciences and Technology Center, State University of Ceará, Fortaleza, CE, Brazil
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2
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Benselama W, Benchouk W. In silico design based on quantum chemical, molecular docking studies and ADMET predictions of ciprofloxacin derivatives as novel potential antibacterial and antimycrobacterium agents. J Biomol Struct Dyn 2024; 42:7650-7666. [PMID: 37551116 DOI: 10.1080/07391102.2023.2240906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/20/2023] [Indexed: 08/09/2023]
Abstract
Drug designing and development is an important area of research for pharmaceutical companies and chemical scientists. In this paper, we report the prediction of new ciprofloxacin derivatives by quantum chemical, molecular docking studies and pharmacokinetic properties. Theoretical studies were performed by geometry optimization computation using B3LYP level at 6-311 G (d,p) basis set. The absorption, distribution, metabolism, excretion and toxicity (ADMET) parameters were predicted and the result show that all compounds have a great ADMET profile. To study the antibacterial, anti-Mycobacterium tuberculosis activities, ciprofloxacin and its derivatives were interacted with the proteins: Thymidylate Kinase (PDB: 4QGG), Biotin carboxylase (PDB: 3JZF) and β-lactamase BlaC (PDB: 3N7W). The results of the docking studies indicate that one pharmacophore designed presents a great inhibition behavior against gram-positive organism (4QGG) and significant interactions observed between the compound and ARG48, GLN101, ARG105 and GLU37 residues of 4QGG. Also, another derivative designed present the best inhibition against gram-negative organism (3JZF) several interactions were noticed between the compound and GLY165, ILE287, LEU278, HIS236, HIS209, MET169 and LYS159 residues of (3JZF). As well as, one designed candidate is good inhibitors for β-lactamase (3N7W) multiple no bonded interactions were observed between the compound and SER84, ILE117, ASN186, LYS87, ARG187, ASN186 and THR251 residues of(3N7W). Molecular dynamics (MD) simulation study was also performed for 100 ns to confirm the stability behaviour of the main protein and inhibitor complexes. The MD simulation study validated the stability of three compounds in the protein binding pocket as potent binders. Natural bonding orbital analysis, reactivity indices and molecular electrostatic potential were carried out. The research finding of this study can be helpful to design a new potent antibacterial, antimycrobacterium candidate's drugs that will serve as the basis for future in vitro and in vivo research.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wafa Benselama
- Laboratory of Applied Thermodynamics and Molecular Modeling, Department of Chemistry, Faculty of Science, University of Tlemcen, Tlemcen, Algeria
| | - Wafaa Benchouk
- Laboratory of Applied Thermodynamics and Molecular Modeling, Department of Chemistry, Faculty of Science, University of Tlemcen, Tlemcen, Algeria
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3
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Pettersson M, Johnson DS, Humphrey JM, Am Ende CW, Butler TW, Dorff PH, Efremov IV, Evrard E, Green ME, Helal CJ, Kauffman GW, Mullins PB, Navaratnam T, O'Donnell CJ, O'Sullivan TJ, Patel NC, Stepan AF, Stiff CM, Subramanyam C, Trapa P, Tran TP, Vetelino BC, Yang E, Xie L, Pustilnik LR, Steyn SJ, Wood KM, Bales KR, Hajos-Korcsok E, Verhoest PR. Discovery of Clinical Candidate PF-06648671: A Potent γ-Secretase Modulator for the Treatment of Alzheimer's Disease. J Med Chem 2024; 67:10248-10262. [PMID: 38848667 DOI: 10.1021/acs.jmedchem.4c00580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
Herein, we describe the design and synthesis of γ-secretase modulator (GSM) clinical candidate PF-06648671 (22) for the treatment of Alzheimer's disease. A key component of the design involved a 2,5-cis-tetrahydrofuran (THF) linker to impart conformational rigidity and lock the compound into a putative bioactive conformation. This effort was guided using a pharmacophore model since crystallographic information was not available for the membrane-bound γ-secretase protein complex at the time of this work. PF-06648671 achieved excellent alignment of whole cell in vitro potency (Aβ42 IC50 = 9.8 nM) and absorption, distribution, metabolism, and excretion (ADME) parameters. This resulted in favorable in vivo pharmacokinetic (PK) profile in preclinical species, and PF-06648671 achieved a human PK profile suitable for once-a-day dosing. Furthermore, PF-06648671 was found to have favorable brain availability in rodent, which translated into excellent central exposure in human and robust reduction of amyloid β (Aβ) 42 in cerebrospinal fluid (CSF).
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Affiliation(s)
- Martin Pettersson
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Douglas S Johnson
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - John M Humphrey
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | | | - Todd W Butler
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Peter H Dorff
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Ivan V Efremov
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Edelweiss Evrard
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Michael E Green
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Christopher J Helal
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Gregory W Kauffman
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Patrick B Mullins
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Thayalan Navaratnam
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | | | - Theresa J O'Sullivan
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Nandini C Patel
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Antonia F Stepan
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Cory M Stiff
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | | | - Patrick Trapa
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Tuan P Tran
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Beth Cooper Vetelino
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Eddie Yang
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Longfei Xie
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Leslie R Pustilnik
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Stefanus J Steyn
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Kathleen M Wood
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Kelly R Bales
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Eva Hajos-Korcsok
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Patrick R Verhoest
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
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4
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Tarui A, Shimomura H, Yasuno Y, Karuo Y, Sato K, Kawai K, Omote M. Decarboxylative Aldol Reaction of α,α-Difluoro-β-keto Esters: Easy Access to Difluoroenolate. ACS OMEGA 2024; 9:26275-26284. [PMID: 38911753 PMCID: PMC11190933 DOI: 10.1021/acsomega.4c02105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/26/2024] [Accepted: 05/23/2024] [Indexed: 06/25/2024]
Abstract
Yb(OTf)3 promoted the Krapcho decarboxylation of 2,2-difluoro-3-oxopropanoate, and a subsequent aldol reaction was achieved. This process is the first example of generating difluoroenolates through a decarboxylation-type process, and a large number of carbonyl compounds are applicable to the aldol reaction. The protocol is a complete one-pot reaction that uses the bench-stable and nonhygroscopic 2,2-difluoro-3-oxopropanoate to generate the difluoroenolate. This strategy has been applied for the synthesis of CF2-containing bioactive GABAB agonists, contributing to drug design.
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Affiliation(s)
- Atsushi Tarui
- Faculty of Pharmaceutical
Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Hiroshi Shimomura
- Faculty of Pharmaceutical
Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Yohei Yasuno
- Faculty of Pharmaceutical
Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Yukiko Karuo
- Faculty of Pharmaceutical
Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Kazuyuki Sato
- Faculty of Pharmaceutical
Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Kentaro Kawai
- Faculty of Pharmaceutical
Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Masaaki Omote
- Faculty of Pharmaceutical
Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
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5
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Mammoliti O, Martina S, Claes P, Coti G, Blanque R, Jagerschmidt C, Shoji K, Borgonovi M, De Vos S, Marsais F, Oste L, Quinton E, López-Ramos M, Amantini D, Brys R, Jimenez JM, Galien R, van der Plas S. Discovery of GLPG3667, a Selective ATP Competitive Tyrosine Kinase 2 Inhibitor for the Treatment of Autoimmune Diseases. J Med Chem 2024; 67:8545-8568. [PMID: 38805213 PMCID: PMC11181332 DOI: 10.1021/acs.jmedchem.4c00769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024]
Abstract
Tyrosine kinase 2 (TYK2) mediates cytokine signaling through type 1 interferon, interleukin (IL)-12/IL-23, and the IL-10 family. There appears to be an association between TYK2 genetic variants and inflammatory conditions, and clinical evidence suggests that selective inhibition of TYK2 could produce a unique therapeutic profile. Here, we describe the discovery of compound 9 (GLPG3667), a reversible and selective TYK2 adenosine triphosphate competitive inhibitor in development for the treatment of inflammatory and autoimmune diseases. The preclinical pharmacokinetic profile was favorable, and TYK2 selectivity was confirmed in peripheral blood mononuclear cells and whole blood assays. Dermal ear inflammation was reduced in an IL-23-induced in vivo mouse model of psoriasis. GLPG3667 also completed a phase 1b study (NCT04594928) in patients with moderate-to-severe psoriasis where clinical effect was shown within the 4 weeks of treatment and it is now in phase 2 trials for the treatment of dermatomyositis (NCT05695950) and systemic lupus erythematosus (NCT05856448).
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Affiliation(s)
- Oscar Mammoliti
- Galapagos
NV, Generaal De Wittelaan
L11, A3, 2800 Mechelen, Belgium
| | | | - Pieter Claes
- Galapagos
NV, Generaal De Wittelaan
L11, A3, 2800 Mechelen, Belgium
| | - Ghjuvanni Coti
- Galapagos
NV, Generaal De Wittelaan
L11, A3, 2800 Mechelen, Belgium
| | - Roland Blanque
- Galapagos
SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France
| | | | - Kenji Shoji
- Galapagos
SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France
| | - Monica Borgonovi
- Galapagos
SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France
| | - Steve De Vos
- Galapagos
NV, Generaal De Wittelaan
L11, A3, 2800 Mechelen, Belgium
| | - Florence Marsais
- Galapagos
SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France
| | - Line Oste
- Galapagos
NV, Generaal De Wittelaan
L11, A3, 2800 Mechelen, Belgium
| | - Evelyne Quinton
- Galapagos
SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France
| | | | - David Amantini
- Galapagos
SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France
| | - Reginald Brys
- Galapagos
NV, Generaal De Wittelaan
L11, A3, 2800 Mechelen, Belgium
| | | | - René Galien
- Galapagos
SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France
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6
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Pereira AMG, de Oliveira VM, da Rocha MN, Roberto CHA, Cajazeiras FFM, Guedes JM, Marinho MM, Teixeira AMR, Marinho ES, de Lima-Neto P, Dos Santos HS. Structure and Ligand Based Virtual Screening and MPO Topological Analysis of Triazolo Thiadiazepine-fused Coumarin Derivatives as Anti-Parkinson Drug Candidates. Mol Biotechnol 2024:10.1007/s12033-024-01200-y. [PMID: 38834896 DOI: 10.1007/s12033-024-01200-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 05/10/2024] [Indexed: 06/06/2024]
Abstract
Parkinson's disease (PD) is a debilitating condition that can cause locomotor problems in affected patients, such as tremors and body rigidity. PD therapy often includes the use of monoamine oxidase B (MAOB) inhibitors, particularly phenylhalogen compounds and coumarin-based semi-synthetic compounds. The objective of this study was to analyze the structural, pharmacokinetic, and pharmacodynamic profile of a series of Triazolo Thiadiazepine-fused Coumarin Derivatives (TDCDs) against MAOB, in comparison with the inhibitor safinamide. To achieve this goal, we utilized structure-based virtual screening techniques, including target prediction and absorption, distribution, metabolism, and excretion (ADME) prediction based on multi-parameter optimization (MPO) topological analysis, as well as ligand-based virtual screening techniques, such as docking and molecular dynamics. The findings indicate that the TDCDs exhibit structural similarity to other bioactive compounds containing coumarin and MAOB-binding azoles, which are present in the ChEMBL database. The topological analyses suggest that TDCD3 has the best ADME profile, particularly due to the alignment between low lipophilicity and high polarity. The coumarin and triazole portions make a strong contribution to this profile, resulting in a permeability with Papp estimated at 2.15 × 10-5 cm/s, indicating high cell viability. The substance is predicted to be metabolically stable. It is important to note that this is an objective evaluation based on the available data. Molecular docking simulations showed that the ligand has an affinity energy of - 8.075 kcal/mol with MAOB and interacts with biological substrate residues such as Pro102 and Phe103. The results suggest that the compound has a safe profile in relation to the MAOB model, making it a promising active ingredient for the treatment of PD.
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Affiliation(s)
- Antônio Mateus Gomes Pereira
- Doctoral Program in Biotechnology, Northeast Biotechnology Network, State University of Ceará, Fortaleza, CE, Brazil
- Center of Molecular Bioprospecting and Applied Experimentation, University Center INTA - UNINTA, Sobral, CE, Brazil
| | | | - Matheus Nunes da Rocha
- Postgraduate Program in Natural Sciences, State University of Ceará, Fortaleza, CE, Brazil
| | | | | | - Jesyka Macêdo Guedes
- Center of Exact Sciences and Technology, State University Vale Do Acaraú, Sobral, CE, Brazil
| | - Márcia Machado Marinho
- Center of Exact Sciences and Technology, State University Vale Do Acaraú, Sobral, CE, Brazil
| | | | - Emmanuel Silva Marinho
- Postgraduate Program in Natural Sciences, State University of Ceará, Fortaleza, CE, Brazil
| | - Pedro de Lima-Neto
- Department of Analytical Chemistry and Phisicochemistry, Federal University of Ceará, Campus Do Pici, Fortaleza, CE, Brazil
| | - Hélcio Silva Dos Santos
- Center of Exact Sciences and Technology, State University Vale Do Acaraú, Sobral, CE, Brazil.
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7
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Hoshikawa T, Kurokawa T, Yoshimura H, Shibuguchi T. α-Fluorination of tropane compounds and its impact on physicochemical and ADME properties. Bioorg Med Chem Lett 2024; 108:129798. [PMID: 38754562 DOI: 10.1016/j.bmcl.2024.129798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Using an electrochemical C(sp3)-H fluorination reaction, a series of α-fluorinated tropane compounds were synthesized and their druglikeness parameters were assessed to compare with the parent compounds. Improvements were observed in membrane permeability, P-gp liability, and inhibitory effects on hERG and Nav1.5 channels, accompanied with a trend of decreased aqueous solubility and microsomal stability. It was also revealed that α-fluorination reduced the basicity of tropane nitrogen atom for about 1000-fold.
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8
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Lin D, Lechermann LM, Huestis MP, Marik J, Sap JBI. Light-Driven Radiochemistry with Fluorine-18, Carbon-11 and Zirconium-89. Angew Chem Int Ed Engl 2024; 63:e202317136. [PMID: 38135665 DOI: 10.1002/anie.202317136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 12/24/2023]
Abstract
This review discusses recent advances in light-driven radiochemistry for three key isotopes: fluorine-18, carbon-11, and zirconium-89, and their applications in positron emission tomography (PET). In the case of fluorine-18, the predominant approach involves the use of cyclotron-produced [18F]fluoride or reagents derived thereof. Light serves to activate either the substrate or the fluorine-18 labeled reagent. Advancements in carbon-11 photo-mediated radiochemistry have been leveraged for the radiolabeling of small molecules, achieving various transformations, including 11C-methylation, 11C-carboxylation, 11C-carbonylation, and 11C-cyanation. Contrastingly, zirconium-89 photo-mediated radiochemistry differs from fluorine-18 and carbon-11 approaches. In these cases, light facilitates a postlabeling click reaction, which has proven valuable for the labeling of large biomolecules such as monoclonal antibodies (mAbs). New technological developments, such as the incorporation of photoreactors in commercial radiosynthesizers, illustrate the commitment the field is making in embracing photochemistry. Taken together, these advances in photo-mediated radiochemistry enable radiochemists to apply new retrosynthetic strategies in accessing novel PET radiotracers.
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Affiliation(s)
- Daniel Lin
- Department of Translational Imaging, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
- Current address: University of Southern California Department of Chemistry, Loker Hydrocarbon Research Institute, 837 Bloom Walk, Los Angeles, CA 90089, USA
| | - Laura M Lechermann
- Department of Translational Imaging, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Malcolm P Huestis
- Discovery Chemistry, Genentech, Inc., DNA Way, South San Francisco, CA 94080, USA
| | - Jan Marik
- Department of Translational Imaging, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
- Discovery Chemistry, Genentech, Inc., DNA Way, South San Francisco, CA 94080, USA
| | - Jeroen B I Sap
- Department of Translational Imaging, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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9
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Rodrigues Dos Santos Barbosa C, Macêdo NS, de Sousa Silveira Z, Rocha JE, Freitas TS, Muniz DF, Araújo IM, Datiane de Morais Oliveira-Tintino C, Marinho ES, Nunes da Rocha M, Marinho MM, Bezerra AH, Ribeiro de Sousa G, Barbosa-Filho JM, de Souza-Ferrari J, Melo Coutinho HD, Silva Dos Santos H, Bezerra da Cunha FA. Evaluation of the antibacterial and inhibitory activity of the MepA efflux pump of Staphylococcus aureus by riparins I, II, III, and IV. Arch Biochem Biophys 2023; 748:109782. [PMID: 37839789 DOI: 10.1016/j.abb.2023.109782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/26/2023] [Accepted: 10/03/2023] [Indexed: 10/17/2023]
Abstract
The efflux pump mechanism contributes to the antibiotic resistance of widely distributed strains of Staphylococcus aureus. Therefore, in the present work, the ability of the riparins N-(4-methoxyphenethyl)benzamide (I), 2-hydroxy-N-[2-(4-methoxyphenyl)ethyl]benzamide (II), 2, 6-dihydroxy-N-[ 2-(4-methoxyphenyl)ethyl]benzamide (III), and 3,4,5-trimethoxy-N-[2-(4-methoxyphenethyl)benzamide (IV) as potential inhibitors of the MepA efflux pump in S. aureus K2068 (fluoroquinolone-resistant). In addition, we performed checkerboard assays to obtain more information about the activity of riparins as potential inhibitors of MepA efflux and also analyzed the ability of riparins to act on the permeability of the bacterial membrane of S. aureus by the fluorescence method with SYTOX Green. A molecular coupling assay was performed to characterize the interaction between riparins and MepA, and ADMET (absorption, distribution, metabolism, and excretion) properties were analyzed. We observed that I-IV riparins did not show direct antibacterial activity against S. aureus. However, combination assays with substrates of MepA, ciprofloxacin, and ethidium bromide (EtBr) revealed a potentiation of the efficacy of these substrates by reducing the minimum inhibitory concentration (MIC). Furthermore, increased EtBr fluorescence emission was observed for all riparins. The checkerboard assay showed synergism between riparins I, II, and III, ciprofloxacin, and EtBr. Furthermore, riparins III and IV exhibited permeability in the S. aureus membrane at a concentration of 200 μg/mL. Molecular docking showed that riparins I, II, and III bound in a different region from the binding site of chlorpromazine (standard pump inhibitor), indicating a possible synergistic effect with the reference inhibitor. In contrast, riparin IV binds in the same region as the chlorpromazine binding site. From the in silico ADMET prediction based on MPO, it could be concluded that the molecules of riparin I-IV present their physicochemical properties within the ideal pharmacological spectrum allowing their preparation as an oral drug. Furthermore, the prediction of cytotoxicity in liver cell lines showed a low cytotoxic effect for riparins I-IV.
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Affiliation(s)
| | - Nair Silva Macêdo
- Biological Chemistry, Department of Biological Chemistry, Cariri Regional University (URCA), Crato, CE, Brazil.
| | - Zildene de Sousa Silveira
- Biological Chemistry, Department of Biological Chemistry, Cariri Regional University (URCA), Crato, CE, Brazil.
| | - Janaína Esmeraldo Rocha
- Biological Chemistry, Department of Biological Chemistry, Cariri Regional University (URCA), Crato, CE, Brazil.
| | - Thiago Sampaio Freitas
- Biological Chemistry, Department of Biological Chemistry, Cariri Regional University (URCA), Crato, CE, Brazil.
| | - Débora Feitosa Muniz
- Biological Chemistry, Department of Biological Chemistry, Cariri Regional University (URCA), Crato, CE, Brazil.
| | - Isaac Moura Araújo
- Biological Chemistry, Department of Biological Chemistry, Cariri Regional University (URCA), Crato, CE, Brazil.
| | | | - Emmanuel Silva Marinho
- State University of Ceará, Graduate Program in Natural Sciences, Laboratory of Natural Products Chemistry, Fortaleza, Ceará, Brazil.
| | - Matheus Nunes da Rocha
- State University of Ceará, Graduate Program in Natural Sciences, Laboratory of Natural Products Chemistry, Fortaleza, Ceará, Brazil.
| | - Marcia Machado Marinho
- Center of Exact Sciences and Technology, State University of Ceará, Fortaleza, CE, Brazil.
| | | | - Gabriela Ribeiro de Sousa
- Natural and Synthetic Bioactive Products, Federal University of Paraiba (UFPB), João Pessoa, PB, Brazil.
| | - José Maria Barbosa-Filho
- Natural and Synthetic Bioactive Products, Federal University of Paraiba (UFPB), João Pessoa, PB, Brazil.
| | | | | | - Hélcio Silva Dos Santos
- Rede Nordeste de Biotecnologia (RENORBIO-Nucleadora UECE), Universidade Estadual Vale do Acaraú (UVA), Sobral, CE, Brazil.
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10
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Chandrasekharan SP, Dhami A, Mohanan K. Ag-Catalyzed Annulation of o-Alkynylaryl Aldehydes, Amines, and Diazo Compounds: Construction of Trifluoromethyl- and Cyano-Functionalized Benzo[ d]azepines. Org Lett 2023; 25:5806-5811. [PMID: 37530707 DOI: 10.1021/acs.orglett.3c02053] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
A Ag-catalyzed three-component annulation protocol, which uses o-alkynylaryl aldehydes, amines, and trifluorodiazoethane or diazoacetonitrile, to forge a new class of trifluoromethyl- and cyano-functionalized benzo[d]azepine is presented in this Letter. The key transformations involved in this reaction are the transient formation of the isoquinolinium intermediate and the subsequent ring-expansive addition of in situ-formed silver trifluorodiazoethylide to this intermediate. The practicality of this protocol is illustrated by realizing access to a wide range of densely functionalized benzo[d]azepines.
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Affiliation(s)
- Sanoop P Chandrasekharan
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow 226031, India
| | - Anamika Dhami
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow 226031, India
| | - Kishor Mohanan
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow 226031, India
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
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11
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Romanov-Michailidis F, Hsiao CC, Urner LM, Jerhaoui S, Surkyn M, Miller B, Vos A, Dominguez Blanco M, Bueters R, Vinken P, Bekkers M, Walker D, Pietrak B, Eyckmans W, Dores-Sousa JL, Joo Koo S, Lento W, Bauser M, Philippar U, Rombouts FJR. Discovery of an Oral, Beyond-Rule-of-Five Mcl-1 Protein-Protein Interaction Modulator with the Potential of Treating Hematological Malignancies. J Med Chem 2023; 66:6122-6148. [PMID: 37114951 DOI: 10.1021/acs.jmedchem.2c01953] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Avoidance of apoptosis is critical for the development and sustained growth of tumors. The pro-survival protein myeloid cell leukemia 1 (Mcl-1) is an anti-apoptotic member of the Bcl-2 family of proteins which is overexpressed in many cancers. Upregulation of Mcl-1 in human cancers is associated with high tumor grade, poor survival, and resistance to chemotherapy. Therefore, pharmacological inhibition of Mcl-1 is regarded as an attractive approach to treating relapsed or refractory malignancies. Herein, we disclose the design, synthesis, optimization, and early preclinical evaluation of a potent and selective small-molecule inhibitor of Mcl-1. Our exploratory design tactics focused on structural modifications which improve the potency and physicochemical properties of the inhibitor while minimizing the risk of functional cardiotoxicity. Despite being in the "non-Lipinski" beyond-Rule-of-Five property space, the developed compound benefits from exquisite oral bioavailability in vivo and induces potent pharmacodynamic inhibition of Mcl-1 in a mouse xenograft model.
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Affiliation(s)
| | - Chien-Chi Hsiao
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Lorenz M Urner
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Soufyan Jerhaoui
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Michel Surkyn
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Bradley Miller
- Janssen Research & Development LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Ann Vos
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | | | - Ruud Bueters
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Petra Vinken
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Mariette Bekkers
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - David Walker
- Janssen Research & Development LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Beth Pietrak
- Janssen Research & Development LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Werner Eyckmans
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | | | - Seong Joo Koo
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - William Lento
- Janssen Research & Development LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Marcus Bauser
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Ulrike Philippar
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
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12
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Pasqua AE, Sharp SY, Chessum NEA, Hayes A, Pellegrino L, Tucker MJ, Miah A, Wilding B, Evans LE, Rye CS, Mok NY, Liu M, Henley AT, Gowan S, De Billy E, te Poele R, Powers M, Eccles SA, Clarke PA, Raynaud FI, Workman P, Jones K, Cheeseman MD. HSF1 Pathway Inhibitor Clinical Candidate (CCT361814/NXP800) Developed from a Phenotypic Screen as a Potential Treatment for Refractory Ovarian Cancer and Other Malignancies. J Med Chem 2023; 66:5907-5936. [PMID: 37017629 PMCID: PMC10150365 DOI: 10.1021/acs.jmedchem.3c00156] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Indexed: 04/06/2023]
Abstract
CCT251236 1, a potent chemical probe, was previously developed from a cell-based phenotypic high-throughput screen (HTS) to discover inhibitors of transcription mediated by HSF1, a transcription factor that supports malignancy. Owing to its activity against models of refractory human ovarian cancer, 1 was progressed into lead optimization. The reduction of P-glycoprotein efflux became a focus of early compound optimization; central ring halogen substitution was demonstrated by matched molecular pair analysis to be an effective strategy to mitigate this liability. Further multiparameter optimization led to the design of the clinical candidate, CCT361814/NXP800 22, a potent and orally bioavailable fluorobisamide, which caused tumor regression in a human ovarian adenocarcinoma xenograft model with on-pathway biomarker modulation and a clean in vitro safety profile. Following its favorable dose prediction to human, 22 has now progressed to phase 1 clinical trial as a potential future treatment for refractory ovarian cancer and other malignancies.
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Affiliation(s)
- A. Elisa Pasqua
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Swee Y. Sharp
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Nicola E. A. Chessum
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Angela Hayes
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Loredana Pellegrino
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Michael J. Tucker
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Asadh Miah
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Birgit Wilding
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Lindsay E. Evans
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Carl S. Rye
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - N. Yi Mok
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Manjuan Liu
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Alan T. Henley
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Sharon Gowan
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Emmanuel De Billy
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Robert te Poele
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Marissa Powers
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Suzanne A. Eccles
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Paul A. Clarke
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Florence I. Raynaud
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Paul Workman
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Keith Jones
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Matthew D. Cheeseman
- Centre for Cancer Drug Discovery
and Division of Cancer Therapeutics at The Institute of Cancer Research, London SW7 3RP, United Kingdom
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13
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Development of new spiro[1,3]dithiine-4,11'-indeno[1,2-b]quinoxaline derivatives as S. aureus Sortase A inhibitors and radiosterilization with molecular modeling simulation. Bioorg Chem 2023; 131:106307. [PMID: 36481380 DOI: 10.1016/j.bioorg.2022.106307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/14/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022]
Abstract
Multi-drug resistant microbes have become a severe threat to human health and arise a worldwide concern. A total of fifteen spiro-1,3-dithiinoindenoquinoxaline derivatives 2-7 were synthesized and evaluated for their biological activities against five standard and MDRB pathogens. The MIC and MBC/MFC for the most active derivatives were determined in vitro via broth microdilution assay. These derivatives showed significant activity against the tested strains with microbicidal behavior, with compound 4b as the most active compound (MIC range between 0.06 and 0.25 µg/mL for bacteria strains and MIC = 0.25 µg/mL for C. albicans). The most active spiro-1,3-dithiinoindenoquinoxaline derivatives were able to inhibit the activity of SrtA with IC50 values ranging from 22.15 ± 0.4 µM to 37.12 ± 1.4 µM. In addition, the active spiro-1,3-dithiinoindenoquinoxaline attenuated the in vitro virulence-related phenotype of SrtA by weakening the adherence of S. aureus to fibrinogen and reducing the biofilm formation. Surprisingly, compound 4b revealed potent SrtA inhibitory activity with IC50 = 22.15 µM, inhibiting the adhesion of S. aureus with 39.22 ± 0.15 % compared with untreated 9.43 ± 1.52 %, and showed a reduction in the biofilm biomass of S. aureus with 32.27 ± 0.52 %. We further investigated the effect of gamma radiation as a sterilization method on the microbial load and found that a dose of 5 kGy was sufficient to eradicate the microbial load. The quantum chemical studies exhibited that the tested derivatives have a small energy band gap (ΔE = -2.95 to -3.61 eV) and therefore exert potent bioactivity by interacting with receptors more stabilizing.
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14
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Cecere G, Guasch L, Olivares-Morales AM, Umehara K, Stepan AF. LipMetE (Lipophilic Metabolism Efficiency) as a Simple Guide for Half-Life and Dosing Regimen Prediction of Oral Drugs. ACS Med Chem Lett 2022; 13:1444-1451. [PMID: 36105329 PMCID: PMC9465707 DOI: 10.1021/acsmedchemlett.2c00183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/19/2022] [Indexed: 11/28/2022] Open
Abstract
The in vivo half-life is a key property of every drug molecule, as it determines dosing regimens, peak-to-trough ratios and often dose. However, half-life optimization can be challenging due to its multifactorial nature, with in vitro metabolic turnover, plasma protein binding and volume of distribution all impacting half-life. We here propose that the medicinal chemistry design parameter Lipophilic Metabolism Efficiency (LipMetE) can greatly simplify half-life optimization of neutral and basic compounds. Using mathematical transformations, examples from preclinical GABAA projects and clinical compounds with human pharmacokinetic data, we show that LipMetE is directly proportional to the logarithm of half-life. As the design parameter LipMetE can be swiftly calculated using the readily available parameters LogD, intrinsic clearance and fraction unbound in human liver microsomes or hepatocytes, this approach enables rational half-life optimization from the early stages of drug discovery projects.
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Affiliation(s)
- Giuseppe Cecere
- Roche
Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland
| | - Laura Guasch
- Roche
Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland
| | - Andres M. Olivares-Morales
- Roche
Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland
| | - Kenichi Umehara
- Roche
Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland
| | - Antonia F. Stepan
- Roche
Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland
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15
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Hawryluk N, Robinson D, Shen Y, Kyne G, Bedore M, Menon S, Canan S, von Geldern T, Townson S, Gokool S, Ehrens A, Koschel M, Lhermitte-Vallarino N, Martin C, Hoerauf A, Hernandez G, Dalvie D, Specht S, Hübner MP, Scandale I. Discovery of Substituted Di(pyridin-2-yl)-1,2,4-thiadiazol-5-amines as Novel Macrofilaricidal Compounds for the Treatment of Human Filarial Infections. J Med Chem 2022; 65:11388-11403. [PMID: 35972896 PMCID: PMC9421654 DOI: 10.1021/acs.jmedchem.2c00960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Filarial diseases, including lymphatic filariasis and onchocerciasis, are considered among the most devastating of all tropical diseases, affecting about 145 million people worldwide. Efforts to control and eliminate onchocerciasis are impeded by a lack of effective treatments that target the adult filarial stage. Herein, we describe the discovery of a series of substituted di(pyridin-2-yl)-1,2,4-thiadiazol-5-amines as novel macrofilaricides for the treatment of human filarial infections.
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Affiliation(s)
- Natalie Hawryluk
- Bristol Myers Squibb, San Diego, California 92121, United States
| | - Dale Robinson
- Bristol Myers Squibb, San Diego, California 92121, United States
| | - Yixing Shen
- Bristol Myers Squibb, San Diego, California 92121, United States
| | - Graham Kyne
- Zoetis, Kalamazoo, Michigan 49001, United States
| | | | - Sanjay Menon
- Zoetis, Kalamazoo, Michigan 49001, United States
| | - Stacie Canan
- Bristol Myers Squibb, San Diego, California 92121, United States
| | | | - Simon Townson
- Northwick Park Institute for Medical Research, London HA1 3UJ, UK
| | - Suzanne Gokool
- Northwick Park Institute for Medical Research, London HA1 3UJ, UK
| | - Alexandra Ehrens
- Institute for Medical Microbiology, Immunology & Parasitology, University Hospital Bonn, 53127 Bonn, Germany.,German Center for Infection Research (DZIF), partner site Bonn-Cologne, 53127 Bonn, Germany
| | - Marianne Koschel
- Institute for Medical Microbiology, Immunology & Parasitology, University Hospital Bonn, 53127 Bonn, Germany
| | - Nathaly Lhermitte-Vallarino
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245), Muséum national d'Histoire Naturelle, Paris 75005, France
| | - Coralie Martin
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245), Muséum national d'Histoire Naturelle, Paris 75005, France
| | - Achim Hoerauf
- Institute for Medical Microbiology, Immunology & Parasitology, University Hospital Bonn, 53127 Bonn, Germany.,German Center for Infection Research (DZIF), partner site Bonn-Cologne, 53127 Bonn, Germany
| | | | - Deepak Dalvie
- Bristol Myers Squibb, San Diego, California 92121, United States
| | - Sabine Specht
- Institute for Medical Microbiology, Immunology & Parasitology, University Hospital Bonn, 53127 Bonn, Germany.,Drugs for Neglected Diseases Initiative, Geneva 1204, Switzerland
| | - Marc Peter Hübner
- Institute for Medical Microbiology, Immunology & Parasitology, University Hospital Bonn, 53127 Bonn, Germany.,German Center for Infection Research (DZIF), partner site Bonn-Cologne, 53127 Bonn, Germany
| | - Ivan Scandale
- Drugs for Neglected Diseases Initiative, Geneva 1204, Switzerland
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16
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Kelly AM, Berry MR, Tasker SZ, McKee SA, Fan TM, Hergenrother PJ. Target-Agnostic P-Glycoprotein Assessment Yields Strategies to Evade Efflux, Leading to a BRAF Inhibitor with Intracranial Efficacy. J Am Chem Soc 2022; 144:12367-12380. [PMID: 35759775 DOI: 10.1021/jacs.2c03944] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The blood-brain barrier (BBB) presents a major hurdle in the development of central nervous system (CNS) active therapeutics, and expression of the P-glycoprotein (P-gp) efflux transporter at the blood-brain interface further impedes BBB penetrance of most small molecules. Designing efflux liabilities out of compounds can be laborious, and there is currently no generalizable approach to directly transform periphery-limited agents to ones active in the CNS. Here, we describe a target-agnostic, prospective assessment of P-gp efflux using diverse compounds. Our results demonstrate that reducing the molecular size or appending a carboxylic acid in many cases enables evasion of P-gp efflux in cell-based experiments and in mice. These strategies were then applied to transform a periphery-limited V600EBRAF inhibitor, dabrafenib, into versions that possess potent and selective anti-cancer activity but now also evade P-gp-mediated efflux. When compared to dabrafenib, the compound developed herein (everafenib) has superior BBB penetrance and superior efficacy in an intracranial mouse model of metastatic melanoma, suggesting it as a lead candidate for the treatment of melanoma metastases to the brain and gliomas with BRAF mutation. More generally, the results described herein suggest the actionability of the trends observed in these target-agnostic efflux studies and provide guidance for the conversion of non-BBB-penetrant drugs into versions that are BBB-penetrant and efficacious.
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Affiliation(s)
- Aya M Kelly
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Matthew R Berry
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Sarah Z Tasker
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Sydney A McKee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Timothy M Fan
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Paul J Hergenrother
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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17
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Lackner RM, O’Connell W, Zhang H, Chenoweth DM. A general strategy for the design and evaluation of heterobifunctional tools: applications to protein localization and phase separation. Chembiochem 2022; 23:e202200209. [DOI: 10.1002/cbic.202200209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/18/2022] [Indexed: 11/12/2022]
Affiliation(s)
| | - Will O’Connell
- Carnegie Mellon University Biological Sciences UNITED STATES
| | - Huaiying Zhang
- Carnegie Mellon University Biological Sciences UNITED STATES
| | - David M. Chenoweth
- University of Pennsylvania Chemistry 231 South 34th Street 19104-6323 Philadelphia UNITED STATES
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18
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Zheng X, Shen Q, Yin C, Li L, Zhong T, Yu C. Photoinduced Three‐Component Difluoroamidosulfonylation/Bicyclization: Regioselectivity Synthesis of Seven‐Membered Dibenzosultams. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202200292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Xiangyun Zheng
- College of Pharmaceutical Sciences Zhejiang University of Technology Hangzhou 310014 People's Republic of China
| | - Qitao Shen
- College of Pharmaceutical Sciences Zhejiang University of Technology Hangzhou 310014 People's Republic of China
| | - Chuanliu Yin
- College of Pharmaceutical Sciences Zhejiang University of Technology Hangzhou 310014 People's Republic of China
| | - Lianghao Li
- College of Pharmaceutical Sciences Zhejiang University of Technology Hangzhou 310014 People's Republic of China
| | - Tianshuo Zhong
- College of Pharmaceutical Sciences Zhejiang University of Technology Hangzhou 310014 People's Republic of China
| | - Chuanming Yu
- College of Pharmaceutical Sciences Zhejiang University of Technology Hangzhou 310014 People's Republic of China
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19
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Wang J, Takahashi K, Shoup TM, Gong L, Li Y, El Fakhri G, Zhang Z, Brownell AL. Organomediated Cleavage of Benzoyl Group Enables an Efficient Synthesis of 1- (6-Nitropyridin-2-yl)thiourea and its application for developing 18F-labeled PET Tracers. Bioorg Chem 2022; 124:105804. [DOI: 10.1016/j.bioorg.2022.105804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/08/2022] [Accepted: 04/08/2022] [Indexed: 11/24/2022]
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20
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Wang X, Lin Z, Bustin KA, McKnight NR, Parsons WH, Matthews ML. Discovery of Potent and Selective Inhibitors against Protein-Derived Electrophilic Cofactors. J Am Chem Soc 2022; 144:5377-5388. [PMID: 35235319 PMCID: PMC10159212 DOI: 10.1021/jacs.1c12748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Electrophilic cofactors are widely distributed in nature and play important roles in many physiological and disease processes, yet they have remained blind spots in traditional activity-based protein profiling (ABPP) approaches that target nucleophiles. More recently, reverse-polarity (RP)-ABPP using hydrazine probes identified an electrophilic N-terminal glyoxylyl (Glox) group for the first time in secernin-3 (SCRN3). The biological function(s) of both the protein and Glox as a cofactor has not yet been pharmacologically validated because of the lack of selective inhibitors that could disrupt and therefore identify its activity. Here, we present the first platform for analyzing the reactivity and selectivity of an expanded nucleophilic probe library toward main-chain carbonyl cofactors such as Glox and pyruvoyl (Pyvl) groups. We first applied the library proteome-wide to profile and confirm engagement with various electrophilic protein targets, including secernin-2 (SCRN2), shown here also to possess a Glox group. A broadly reactive indole ethylhydrazine probe was used for a competitive in vitro RP-ABPP assay to screen for selective inhibitors against such cofactors from a set of commercially available nucleophilic fragments. Using Glox-containing SCRN proteins as a case study, naphthyl hydrazine was identified as a potent and selective SCRN3 inhibitor, showing complete inhibition in cell lysates with no significant cross-reactivity detected for other enzymes. Moving forward, this platform provides the fundamental basis for the development of selective Glox inhibitors and represents a starting point to advance small molecules that modulate electrophile-dependent function.
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Affiliation(s)
- Xie Wang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zongtao Lin
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Katelyn A Bustin
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Nate R McKnight
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - William H Parsons
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
| | - Megan L Matthews
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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21
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Taoka BM, Wu WL, Hao J, Dolmaski M, Wang H, Levorse D, Orth P, Hyde LA, Smith B, Michener MS, Kennedy ME, Parker EM, Cumming JN. Design and discovery of C2-fluoroalkyl iminothiazine dioxides as BACE inhibitors. Bioorg Med Chem Lett 2022; 56:128463. [PMID: 34838652 DOI: 10.1016/j.bmcl.2021.128463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 11/25/2022]
Abstract
This paper describes the structure-activity-relationships of novel fluoroalkyl substituents at the C2 position of iminothiazine dioxide beta secretase inhibitors. Key discoveries include reduced amidine basicity and its effect on Pgp, cell potency, and efficacy in various preclinical in vivo efficacy animal models. Findings from these structure-activity-relationships are discussed.
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Affiliation(s)
- Brandon M Taoka
- Department of Discovery Chemistry, MRL, Merck & Co. Inc., 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Wen-Lian Wu
- Department of Discovery Chemistry, MRL, Merck & Co. Inc., 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Jinsong Hao
- Department of Discovery Chemistry, MRL, Merck & Co. Inc., 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Martin Dolmaski
- Department of Discovery Chemistry, MRL, Merck & Co. Inc., 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Hongwu Wang
- Department of Computational and Structural Chemistry, MRL, Merck & Co. Inc., 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Dorthy Levorse
- Department of Preclinical Development, MRL, Merck & Co. Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Peter Orth
- Department of Computational and Structural Chemistry, MRL, Merck & Co. Inc., 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Lynn A Hyde
- Department of Neuroscience, Safety and Laboratory Animal Research, MRL, Merck & Co. Inc., 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Brad Smith
- Department of Safety and Laboratory Animal Research MRL, Merck & Co. Inc., 770 Sumneytown Pike, West Point, PA 19486, USA
| | - Maria S Michener
- Department of Safety and Laboratory Animal Research MRL, Merck & Co. Inc., 770 Sumneytown Pike, West Point, PA 19486, USA
| | - Matthew E Kennedy
- Department of Neuroscience, Safety and Laboratory Animal Research, MRL, Merck & Co. Inc., 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Eric M Parker
- Department of Neuroscience, Safety and Laboratory Animal Research, MRL, Merck & Co. Inc., 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Jared N Cumming
- Department of Discovery Chemistry, MRL, Merck & Co. Inc., 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
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22
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Alexandrino DAM, Almeida CMR, Mucha AP, Carvalho MF. Revisiting pesticide pollution: The case of fluorinated pesticides. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 292:118315. [PMID: 34634397 DOI: 10.1016/j.envpol.2021.118315] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/11/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Fluorinated pesticides acquired a significant market share in the agrochemical sector due to the surge of new fluoroorganic ingredients approved in the last two decades. This growing trend has not been accompanied by a comprehensive scientific and regulatory framework entailing all their potential negative impacts for the environment, especially when considering the hazardous properties that may result from the incorporation of fluorine into organic molecules. This review aims to address the safe/hazardous dichotomy associated with fluorinated pesticides by providing an updated outlook on their relevancy in the agrochemical sector and how it leads to their role as environmental pollutants. Specifically, the environmental fate and distribution of these pesticides in the ecosystems is discussed, while also analysing their potential to act as toxic substances for non-target organisms.
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Affiliation(s)
- Diogo A M Alexandrino
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal; School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal.
| | - C Marisa R Almeida
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - Ana P Mucha
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal; Faculty of Sciences, University of Porto, Rua do Campo Alegre 790, 4150-171, Porto, Portugal
| | - Maria F Carvalho
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal; School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
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23
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Chen Z, Sun J, Ke Z, Huang X, Li Z. Silver-catalyzed stereoselective C-4 arylthiodifluoromethylation of coumarin-3-carboxylic acids via a double decarboxylative strategy. Org Chem Front 2022. [DOI: 10.1039/d1qo01609a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A facile silver-catalyzed dual decarboxylation of arylthio-difluoroacetic acid with coumarin-3-carboxylic acids/chromone-3-carboxylic acids was developed.
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Affiliation(s)
- Zhiwei Chen
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Jie Sun
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Zhiwei Ke
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Xiaoxiao Huang
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Ziwei Li
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P. R. China
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24
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Casimiro-Garcia A, Allais C, Brennan A, Choi C, Dower G, Farley KA, Fleming M, Flick A, Frisbie RK, Hall J, Hepworth D, Jones H, Knafels JD, Kortum S, Lovering FE, Mathias JP, Mohan S, Morgan PM, Parng C, Parris K, Pullen N, Schlerman F, Stansfield J, Strohbach JW, Vajdos FF, Vincent F, Wang H, Wang X, Webster R, Wright SW. Discovery of a Series of Pyrimidine Carboxamides as Inhibitors of Vanin-1. J Med Chem 2021; 65:757-784. [PMID: 34967602 DOI: 10.1021/acs.jmedchem.1c01849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A diaryl ketone series was identified as vanin-1 inhibitors from a high-throughput screening campaign. While this novel scaffold provided valuable probe 2 that was used to build target confidence, concerns over the ketone moiety led to the replacement of this group. The successful replacement of this moiety was achieved with pyrimidine carboxamides derived from cyclic secondary amines that were extensively characterized using biophysical and crystallographic methods as competitive inhibitors of vanin-1. Through optimization of potency and physicochemical and ADME properties, and guided by co-crystal structures with vanin-1, 3 was identified with a suitable profile for advancement into preclinical development.
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Affiliation(s)
- Agustin Casimiro-Garcia
- Medicine Design, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Christophe Allais
- Medicine Design, Pfizer Inc., 445 Eastern Point Rd, Groton, Connecticut 06340, United States
| | - Agnes Brennan
- Inflammation and Immunology Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Chulho Choi
- Medicine Design, Pfizer Inc., 445 Eastern Point Rd, Groton, Connecticut 06340, United States
| | - Gabriela Dower
- Inflammation and Immunology Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Kathleen A Farley
- Medicine Design, Pfizer Inc., 445 Eastern Point Rd, Groton, Connecticut 06340, United States
| | - Margaret Fleming
- Inflammation and Immunology Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Andrew Flick
- Medicine Design, Pfizer Inc., 445 Eastern Point Rd, Groton, Connecticut 06340, United States
| | - Richard K Frisbie
- Medicine Design, Pfizer Inc., 445 Eastern Point Rd, Groton, Connecticut 06340, United States
| | - Justin Hall
- Medicine Design, Pfizer Inc., 445 Eastern Point Rd, Groton, Connecticut 06340, United States
| | - David Hepworth
- Medicine Design, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Hannah Jones
- Medicine Design, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - John D Knafels
- Medicine Design, Pfizer Inc., 445 Eastern Point Rd, Groton, Connecticut 06340, United States
| | - Steve Kortum
- Medicine Design, Pfizer Inc., 445 Eastern Point Rd, Groton, Connecticut 06340, United States
| | - Frank E Lovering
- Medicine Design, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - John P Mathias
- Medicine Design, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Sashi Mohan
- Inflammation and Immunology Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Paul M Morgan
- Inflammation and Immunology Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Chuenlei Parng
- Medicine Design, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Kevin Parris
- Medicine Design, Pfizer Inc., 445 Eastern Point Rd, Groton, Connecticut 06340, United States
| | - Nick Pullen
- Inflammation and Immunology Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Franklin Schlerman
- Inflammation and Immunology Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - John Stansfield
- Early Clinical Development Non-Clinical Statistics, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Joseph W Strohbach
- Medicine Design, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Felix F Vajdos
- Medicine Design, Pfizer Inc., 445 Eastern Point Rd, Groton, Connecticut 06340, United States
| | - Fabien Vincent
- Medicine Design, Pfizer Inc., 445 Eastern Point Rd, Groton, Connecticut 06340, United States
| | - Hong Wang
- Medicine Design, Pfizer Inc., 445 Eastern Point Rd, Groton, Connecticut 06340, United States
| | - Xiaolun Wang
- Medicine Design, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Robert Webster
- Medicine Design, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Stephen W Wright
- Medicine Design, Pfizer Inc., 445 Eastern Point Rd, Groton, Connecticut 06340, United States
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25
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Huang X, Lv M, Ma Q, Zhang Y, Xu H. High Value-Added Application of Natural Products in Crop Protection: Semisynthesis and Acaricidal Activity of Limonoid-Type Derivatives and Investigation of Their Biocompatible O/W Nanoemulsions as Agronanopesticide Candidates. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:14488-14500. [PMID: 34842424 DOI: 10.1021/acs.jafc.1c05450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The increasingly serious resistance of Tetranychus cinnabarinus Boisduval to a wide range of insecticides/acaricides poses a major challenge to their control. The citrus processing industry generates a huge quantity of various wastes that contain many limonoids. To effectively utilize these byproducts and discover more potent green acaricidal molecules as sustainable alternatives for traditional resistant pesticides, various limonoid-type derivatives (halogenated/seven-membered lactam derivatives of obacunone and halogenated/oxime esters/oxime ethers/seven-membered lactam derivatives of limonin) were synthesized based on a diversity-oriented synthetic strategy. The key steric configurations of 10 derivatives were further confirmed by X-ray crystallography. Compound 9m, which displayed greater than 9.7-fold potent acaricidal activity of limonin, was of preeminence. In addition, some interesting structure-activity relationships were observed. Moreover, a biocompatible O/W nanoemulsion delivery system was used to prepare the limonin-based agronanoacaricide, which exhibited pronounced control efficiency against T. cinnabarinus Boisduval in the greenhouse. This systematic investigation will provide valuable information and guidance for future value-added applications of novel eco-friendly natural product-based nanopesticides.
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Affiliation(s)
- Xiaobo Huang
- College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Min Lv
- College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Qianjun Ma
- College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yuanyuan Zhang
- College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hui Xu
- College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
- School of Marine Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
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26
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Nanotherapeutics approaches to overcome P-glycoprotein-mediated multi-drug resistance in cancer. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2021; 40:102494. [PMID: 34775061 DOI: 10.1016/j.nano.2021.102494] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/08/2021] [Accepted: 10/27/2021] [Indexed: 12/19/2022]
Abstract
Multidrug resistance (MDR) in cancer chemotherapy is a growing concern for medical practitioners. P-glycoprotein (P-gp) overexpression is one of the major reasons for multidrug resistance in cancer chemotherapy. The P-gp overexpression in cancer cells depends on several factors like adenosine triphosphate (ATP) hydrolysis, hypoxia-inducible factor 1 alpha (HIF-1α), and drug physicochemical properties such as lipophilicity, molecular weight, and molecular size. Further multiple exposures of anticancer drugs to the P-gp efflux protein cause acquired P-gp overexpression. Unique structural and functional characteristics of nanotechnology-based drug delivery systems provide opportunities to circumvent P-gp mediated MDR. The primary mechanism behind the nanocarrier systems in P-gp inhibition includes: bypassing or inhibiting the P-gp efflux pump to combat MDR. In this review, we discuss the role of P-gp in MDR and highlight the recent progress in different nanocarriers to overcome P-gp mediated MDR in terms of their limitations and potentials.
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27
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Mata G, Miles DH, Drew SL, Fournier J, Lawson KV, Mailyan AK, Sharif EU, Yan X, Beatty JW, Banuelos J, Chen J, Ginn E, Chen A, Gerrick KY, Pham AT, Wong K, Soni D, Dhanota P, Shaqfeh SG, Meleza C, Narasappa N, Singh H, Zhao X, Jin L, Schindler U, Walters MJ, Young SW, Walker NP, Leleti MR, Powers JP, Jeffrey JL. Design, Synthesis, and Structure-Activity Relationship Optimization of Pyrazolopyrimidine Amide Inhibitors of Phosphoinositide 3-Kinase γ (PI3Kγ). J Med Chem 2021; 65:1418-1444. [PMID: 34672584 DOI: 10.1021/acs.jmedchem.1c01153] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phosphoinositide-3-kinase γ (PI3Kγ) is highly expressed in immune cells and promotes the production and migration of inflammatory mediators. The inhibition of PI3Kγ has been shown to repolarize the tumor immune microenvironment to a more inflammatory phenotype, thereby controlling immune suppression in cancer. Herein, we report the structure-based optimization of an early lead series of pyrazolopyrimidine isoindolinones, which culminated in the discovery of highly potent and isoform-selective PI3Kγ inhibitors with favorable drug-like properties. X-ray cocrystal structure analysis, molecular docking studies, and detailed structure-activity relationship investigations resulted in the identification of the optimal amide and isoindolinone substituents to achieve a desirable combination of potency, selectivity, and metabolic stability. Preliminary in vitro studies indicate that inhibition of PI3Kγ with compound 56 results in a significant immune response by increasing pro-inflammatory cytokine gene expression in M1 macrophages.
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Affiliation(s)
- Guillaume Mata
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Dillon H Miles
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Samuel L Drew
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Jeremy Fournier
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Kenneth V Lawson
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Artur K Mailyan
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Ehesan U Sharif
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Xuelei Yan
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Joel W Beatty
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Jesus Banuelos
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Jie Chen
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Elaine Ginn
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Ada Chen
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Kimberline Y Gerrick
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Amber T Pham
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Kent Wong
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Divyank Soni
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Puja Dhanota
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Stefan G Shaqfeh
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Cesar Meleza
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Nell Narasappa
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Hema Singh
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Xiaoning Zhao
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Lixia Jin
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Ulrike Schindler
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Matthew J Walters
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Stephen W Young
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Nigel P Walker
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Manmohan Reddy Leleti
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Jay P Powers
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Jenna L Jeffrey
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
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28
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Xiong B, Wang Y, Chen Y, Xing S, Liao Q, Chen Y, Li Q, Li W, Sun H. Strategies for Structural Modification of Small Molecules to Improve Blood-Brain Barrier Penetration: A Recent Perspective. J Med Chem 2021; 64:13152-13173. [PMID: 34505508 DOI: 10.1021/acs.jmedchem.1c00910] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the development of central nervous system (CNS) drugs, the blood-brain barrier (BBB) restricts many drugs from entering the brain to exert therapeutic effects. Although many novel delivery methods of large molecule drugs have been designed to assist transport, small molecule drugs account for the vast majority of the CNS drugs used clinically. From this perspective, we review studies from the past five years that have sought to modify small molecules to increase brain exposure. Medicinal chemists make it easier for small molecules to cross the BBB by improving diffusion, reducing efflux, and activating carrier transporters. On the basis of their excellent work, we summarize strategies for structural modification of small molecules to improve BBB penetration. These strategies are expected to provide a reference for the future development of small molecule CNS drugs.
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Affiliation(s)
- Baichen Xiong
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Yuanyuan Wang
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Ying Chen
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Shuaishuai Xing
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Qinghong Liao
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Yao Chen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People's Republic of China
| | - Qi Li
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China.,School of Basic Medicine, Qingdao University, Qingdao 266071, People's Republic of China
| | - Wei Li
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Haopeng Sun
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
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29
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Wang C, Wang L, Meng QG, Huang ZX, Ma NN, Wang CH. Crystal structure of (E)-2-((3-fluoropyridin-4-yl)methylene)-7-methoxy-3,4-dihydronaphthalen-1(2H)-one, C17H14FNO2. Z KRIST-NEW CRYST ST 2021. [DOI: 10.1515/ncrs-2021-0223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
C17H14FNO2, monoclinic, P21/n (no. 14), a = 8.0937(8) Å, b = 7.1326(6) Å, c = 22.367(2) Å, β = 90.863(9)°, V = 1291.1(2) Å3, Z = 4, R
gt
(F) = 0.0404, wR
ref
(F
2) = 0.0974, T = 99.97(16) K.
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Affiliation(s)
- Chen Wang
- School of Pharmacy, The Key Laboratory of Prescription Effect and Clinical Evaluation of State Administration of Traditional Chinese Medicine of China, Binzhou Medical University , Yantai , 264003 , P. R. China
| | - Lei Wang
- School of Pharmacy, The Key Laboratory of Prescription Effect and Clinical Evaluation of State Administration of Traditional Chinese Medicine of China, Binzhou Medical University , Yantai , 264003 , P. R. China
| | - Qing-Guo Meng
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University , Yantai , 264005 , P. R. China
| | - Zhi-Xin Huang
- School of Pharmacy, The Key Laboratory of Prescription Effect and Clinical Evaluation of State Administration of Traditional Chinese Medicine of China, Binzhou Medical University , Yantai , 264003 , P. R. China
| | - Nuan-Nuan Ma
- School of Pharmacy, The Key Laboratory of Prescription Effect and Clinical Evaluation of State Administration of Traditional Chinese Medicine of China, Binzhou Medical University , Yantai , 264003 , P. R. China
| | - Chun-Hua Wang
- School of Pharmacy, The Key Laboratory of Prescription Effect and Clinical Evaluation of State Administration of Traditional Chinese Medicine of China, Binzhou Medical University , Yantai , 264003 , P. R. China
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30
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Lee WC, Kang SM, Lee BC, Kim SE, Kim DW. Multifunctional Crown-5-calix[4]arene-based Phase-Transfer Catalysts for Aromatic 18F-Fluorination. Org Lett 2020; 22:9551-9555. [PMID: 33270463 DOI: 10.1021/acs.orglett.0c03604] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methylated bis-triethylene glycolic crown-5-calix[4]arene (M-BTC5A) as a phase-transfer catalyst showed the best performance among other analogues and even conventional Kryptofix 222 in the nucleophilic aromatic 18F-fluorination of diaryliodonium tosylate precursors owing to (i) the efficient release of reactive "naked" [18F]fluoride, (ii) the high stabilization of the precursor in the reaction, and, presumably, (iii) the ease of access between the precursor and the K18F/M-BTC5A complex facilitated by π-π interactions. [18F]Flumazenil was produced in high radiochemical yield using M-BTC5A.
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Affiliation(s)
- Won Chang Lee
- Department of Nuclear Medicine, Seoul National University Hospital, Seongnam 13620, Republic of Korea.,Department of Transdisciplinary Studies, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea
| | - Seok Min Kang
- Department of Chemistry and Chemical Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Byung Chul Lee
- Department of Nuclear Medicine, Seoul National University Hospital, Seongnam 13620, Republic of Korea.,Center for Nanomolecular Imaging and Innovative Drug Development, Advanced institutes of Convergence Technology, Suwon 16229, Republic of Korea
| | - Sang Eun Kim
- Department of Nuclear Medicine, Seoul National University Hospital, Seongnam 13620, Republic of Korea.,Center for Nanomolecular Imaging and Innovative Drug Development, Advanced institutes of Convergence Technology, Suwon 16229, Republic of Korea.,Department of Molecular and Biophamaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong Wook Kim
- Department of Chemistry and Chemical Engineering, Inha University, Incheon 22212, Republic of Korea
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31
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Abula A, Xu Z, Zhu Z, Peng C, Chen Z, Zhu W, Aisa HA. Substitution Effect of the Trifluoromethyl Group on the Bioactivity in Medicinal Chemistry: Statistical Analysis and Energy Calculations. J Chem Inf Model 2020; 60:6242-6250. [DOI: 10.1021/acs.jcim.0c00898] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Amina Abula
- The Key Laboratory of Plant Resources and Chemistry in Arid Regions and Key Laboratory of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, South Beijing Road 40-1, Urumqi, Xinjiang 830011, People’s Republic of China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People’s Republic of China
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhijian Xu
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People’s Republic of China
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhengdan Zhu
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People’s Republic of China
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Cheng Peng
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People’s Republic of China
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhaoqiang Chen
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People’s Republic of China
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Weiliang Zhu
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People’s Republic of China
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Haji Akber Aisa
- The Key Laboratory of Plant Resources and Chemistry in Arid Regions and Key Laboratory of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, South Beijing Road 40-1, Urumqi, Xinjiang 830011, People’s Republic of China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People’s Republic of China
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32
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Esposito C, Wang S, Lange UEW, Oellien F, Riniker S. Combining Machine Learning and Molecular Dynamics to Predict P-Glycoprotein Substrates. J Chem Inf Model 2020; 60:4730-4749. [DOI: 10.1021/acs.jcim.0c00525] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Carmen Esposito
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Shuzhe Wang
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Udo E. W. Lange
- Neuroscience Discovery, Medicinal Chemistry, AbbVie Deutschland GmbH & Co KG, Knollstrasse, 67061 Ludwigshafen, Germany
| | - Frank Oellien
- Neuroscience Discovery, Medicinal Chemistry, AbbVie Deutschland GmbH & Co KG, Knollstrasse, 67061 Ludwigshafen, Germany
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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33
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Hudson AR, Santora VJ, Petroski RE, Almos TA, Anderson G, Barido R, Basinger J, Bellows CL, Bookser BC, Broadbent NJ, Cabebe C, Chai CK, Chen M, Chow S, Chung DM, Heger L, Danks AM, Freestone GC, Gitnick D, Gupta V, Hoffmaster C, Kaplan AP, Kennedy MR, Lee D, Limberis J, Ly K, Mak CC, Masatsugu B, Morse AC, Na J, Neul D, Nikpur J, Renick J, Sebring K, Sevidal S, Tabatabaei A, Wen J, Xia S, Yan Y, Yoder ZW, Zook D, Peters M, Breitenbucher JG. Azetidine-based selective glycine transporter-1 (GlyT1) inhibitors with memory enhancing properties. Bioorg Med Chem Lett 2020; 30:127214. [PMID: 32527538 DOI: 10.1016/j.bmcl.2020.127214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 11/24/2022]
Abstract
A strategy to conformationally restrain a series of GlyT1 inhibitors identified potent analogs that exhibited slowly interconverting rotational isomers. Further studies to address this concern led to a series of azetidine-based inhibitors. Compound 26 was able to elevate CSF glycine levels in vivo and demonstrated potency comparable to Bitopertin in an in vivo rat receptor occupancy study. Compound 26 was subsequently shown to enhance memory in a Novel Object Recognition (NOR) behavioral study after a single dose of 0.03 mg/kg, and in a contextual fear conditioning (cFC) study after four QD doses of 0.01-0.03 mg/kg.
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Affiliation(s)
- Andrew R Hudson
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States.
| | - Vincent J Santora
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Robert E Petroski
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Theresa A Almos
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Gary Anderson
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Richard Barido
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Jillian Basinger
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Chris L Bellows
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Brett C Bookser
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Nicola J Broadbent
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Clifford Cabebe
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Chih-Kun Chai
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Mi Chen
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Stephine Chow
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - De Michael Chung
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Lindsay Heger
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Anne M Danks
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Graeme C Freestone
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Dany Gitnick
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Varsha Gupta
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | | | - Alan P Kaplan
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Michael R Kennedy
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Dong Lee
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - James Limberis
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Kiev Ly
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Chi Ching Mak
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Brittany Masatsugu
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Andrew C Morse
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Jim Na
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - David Neul
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - John Nikpur
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Joel Renick
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Kristen Sebring
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Samantha Sevidal
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Ali Tabatabaei
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Jenny Wen
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Shouzhen Xia
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Yingzhuo Yan
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Zachary W Yoder
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Douglas Zook
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - Marco Peters
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
| | - J Guy Breitenbucher
- Dart Neuroscience, 12278 Scripps Summit Dr, San Diego, CA 92131, United States
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34
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Mugnaini C, Kostrzewa M, Bryk M, Mahmoud AM, Brizzi A, Lamponi S, Giorgi G, Ferlenghi F, Vacondio F, Maccioni P, Colombo G, Mor M, Starowicz K, Di Marzo V, Ligresti A, Corelli F. Design, Synthesis, and Physicochemical and Pharmacological Profiling of 7-Hydroxy-5-oxopyrazolo[4,3- b]pyridine-6-carboxamide Derivatives with Antiosteoarthritic Activity In Vivo. J Med Chem 2020; 63:7369-7391. [PMID: 32515588 DOI: 10.1021/acs.jmedchem.0c00595] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The hallmark of joint diseases, such as osteoarthritis (OA), is pain, originating from both inflammatory and neuropathic components, and compounds able to modulate the signal transduction pathways of the cannabinoid type-2 receptor (CB2R) can represent a helpful option in the treatment of OA. In this perspective, a set of 18 cannabinoid type-2 receptor (CB2R) ligands was developed based on an unprecedented structure. With the aim of improving the physicochemical properties of previously reported 4-hydroxy-2-quinolone-3-carboxamides, a structural optimization program led to the discovery of isosteric 7-hydroxy-5-oxopyrazolo[4,3-b]pyridine-6-carboxamide derivatives. These new compounds are endowed with high affinity for the CB2R and moderate to good selectivity over the cannabinoid type-1 receptor (CB1R), associated with good physicochemical characteristics. As to the functional activity at the CB2R, compounds able to act either as agonists or as inverse agonists/antagonists were discovered. Among them, compound 51 emerged as a potent CB2R agonist able to reduce pain in rats carrying OA induced by injection of monoiodoacetic acid (MIA).
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Affiliation(s)
- Claudia Mugnaini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Magdalena Kostrzewa
- Endocannabinoid Research Group, Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.,Institute of Genetics and Biophysics, National Research Council of Italy, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Marta Bryk
- Institute of Genetics and Biophysics, National Research Council of Italy, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Ali Mokhtar Mahmoud
- Endocannabinoid Research Group, Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Antonella Brizzi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Stefania Lamponi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Gianluca Giorgi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Francesca Ferlenghi
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Federica Vacondio
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Paola Maccioni
- Institute of Neuroscience, National Research Council of Italy, S.S. 554, km 4,500, 09042 Monserrato, Cagliari, Italy
| | - Giancarlo Colombo
- Institute of Neuroscience, National Research Council of Italy, S.S. 554, km 4,500, 09042 Monserrato, Cagliari, Italy
| | - Marco Mor
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Katarzyna Starowicz
- Department of Neurochemistry, Institute of Pharmacology, Polish Academy of Sciences, ul. Smetna 12, 31-343 Cracow, Poland
| | - Vincenzo Di Marzo
- Endocannabinoid Research Group, Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Alessia Ligresti
- Endocannabinoid Research Group, Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Federico Corelli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
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35
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Chen Z, Bai X, Sun J, Xu Y. Fe(III)-Catalyzed Decarboxylative C3-Difluoroarylmethylation of Coumarins with α,α-Difluoroarylacetic Acids. J Org Chem 2020; 85:7674-7682. [PMID: 32436381 DOI: 10.1021/acs.joc.0c00113] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A facile Fe(III)-catalyzed oxidative decarboxylative radical coupling reaction of α,α-difluoroarylacetic acids with coumarins has been developed. This transformation, which provides a series of C-3 difluoroarylmethylated coumarins containing various functional groups in moderate-to-good yields, features easily accessible starting materials and operational simplicity.
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Affiliation(s)
- Zhiwei Chen
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou310014, P. R. China
| | - Xiang Bai
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou310014, P. R. China
| | - Jie Sun
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou310014, P. R. China
| | - Yicheng Xu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou310014, P. R. China
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36
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Synthesis of (R) and (S)-3-Chloro-5-(3-methylmorpholino)-4H-1,2,6-thiadiazin-4-ones. MOLBANK 2020. [DOI: 10.3390/m1128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Reaction of 3,5-dichloro-4H-1,2,6-thiadiazin-4-one with (R) and (S)-3-methylmorpholines (2 equiv), in THF, at ca. 20 °C gave (R) and (S)-3-chloro-5-(3-methylmorpholino)-4H-1,2,6-thiadiazin-4-ones in 95 and 97% yields, respectively. The new compounds were fully characterized.
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37
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Liu Z, Chen H, Wang P, Li Y, Wold EA, Leonard PG, Joseph S, Brasier AR, Tian B, Zhou J. Discovery of Orally Bioavailable Chromone Derivatives as Potent and Selective BRD4 Inhibitors: Scaffold Hopping, Optimization, and Pharmacological Evaluation. J Med Chem 2020; 63:5242-5256. [PMID: 32255647 DOI: 10.1021/acs.jmedchem.0c00035] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bromodomain-containing protein 4 (BRD4) represents a promising drug target for anti-inflammatory therapeutics. Herein, we report the design, synthesis, and pharmacological evaluation of novel chromone derivatives via scaffold hopping to discover a new class of orally bioavailable BRD4-selective inhibitors. Two potent BRD4 bromodomain 1 (BD1)-selective inhibitors 44 (ZL0513) and 45 (ZL0516) have been discovered with high binding affinity (IC50 values of 67-84 nM) and good selectivity over other BRD family proteins and distant BD-containing proteins. Both compounds significantly inhibited the expression of Toll-like receptor-induced inflammatory genes in vitro and airway inflammation in murine models. The cocrystal structure of 45 in complex with human BRD4 BD1 at a high resolution of 2.0 Å has been solved, offering a solid structural basis for its binding validation and further structure-based optimization. These BRD4 BD1 inhibitors demonstrated impressive in vivo efficacy and overall promising pharmacokinetic properties, indicating their therapeutic potential for the treatment of inflammatory diseases.
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Affiliation(s)
- Zhiqing Liu
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Haiying Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Pingyuan Wang
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Yi Li
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Eric A Wold
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Paul G Leonard
- Core for Biomolecular Structure and Function, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Sarah Joseph
- Core for Biomolecular Structure and Function, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Allan R Brasier
- Institute for Clinical and Translational Research (ICTR), University of Wisconsin-Madison School of Medicine and Public Health, 4248 Health Sciences Learning Center, Madison, Wisconsin 53705, United States
| | - Bing Tian
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas 77555, United States.,Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States.,Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas 77555, United States.,Institute for Translational Sciences, University of Texas Medical Branch, Galveston, Texas 77555, United States
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38
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Johnson BM, Shu YZ, Zhuo X, Meanwell NA. Metabolic and Pharmaceutical Aspects of Fluorinated Compounds. J Med Chem 2020; 63:6315-6386. [PMID: 32182061 DOI: 10.1021/acs.jmedchem.9b01877] [Citation(s) in RCA: 310] [Impact Index Per Article: 77.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The applications of fluorine in drug design continue to expand, facilitated by an improved understanding of its effects on physicochemical properties and the development of synthetic methodologies that are providing access to new fluorinated motifs. In turn, studies of fluorinated molecules are providing deeper insights into the effects of fluorine on metabolic pathways, distribution, and disposition. Despite the high strength of the C-F bond, the departure of fluoride from metabolic intermediates can be facile. This reactivity has been leveraged in the design of mechanism-based enzyme inhibitors and has influenced the metabolic fate of fluorinated compounds. In this Perspective, we summarize the literature associated with the metabolism of fluorinated molecules, focusing on examples where the presence of fluorine influences the metabolic profile. These studies have revealed potentially problematic outcomes with some fluorinated motifs and are enhancing our understanding of how fluorine should be deployed.
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Affiliation(s)
- Benjamin M Johnson
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Yue-Zhong Shu
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb Company, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Xiaoliang Zhuo
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Nicholas A Meanwell
- Discovery Chemistry Platforms, Small Molecule Drug Discovery, Bristol Myers Squibb Company, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
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39
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Kiani Y, Jabeen I. Lipophilic Metabolic Efficiency (LipMetE) and Drug Efficiency Indices to Explore the Metabolic Properties of the Substrates of Selected Cytochrome P450 Isoforms. ACS OMEGA 2020; 5:179-188. [PMID: 31956764 PMCID: PMC6963890 DOI: 10.1021/acsomega.9b02344] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/10/2019] [Indexed: 06/10/2023]
Abstract
Cytochrome P450 (CYP450) enzymes belong to a superfamily of heme-containing proteins that are involved in the metabolism of structurally diverse endogenous and exogenous compounds. Various proof-of-concept studies indicate that metabolic stability and intrinsic clearance of CYP450 substrates are linked with the respective lipophilicity (log P or log D). This necessitates the normalization of lipophilicity (log P or log D) of a given CYP450 substrate with respect to its metabolic stability (LipMetE) and intrinsic clearance (log10CLint,u). Therefore, in this article, the LipMetE values of already known substrates of CYP1A2, CYP2C9, CYP2C19, CYP2D6, and CYP3A4, including some marketed drugs, have been calculated to elucidate the relationship between lipophilicity (log D 7.4) and in vitro clearance. Moreover, various drug efficiency metrics including lipophilic efficiency (LipE) and ligand efficiency (LE) have been evaluated, and the thresholds of these parameters have been defined for the CYP450 substrates exhibiting normalized LipMetE. Our results indicate that for a given range of LipMetE, greater the log D value of the substrate the more avidly it binds to a given CYP450 enzyme and shows more intrinsic clearance (log10CLint,u). Overall, the majority of the model substrates of CYP450 isoforms and already marketed drugs in our datasets exhibit log D 7.4 values of ∼2.5 with LipMetE values in the range of 0-2.5 and LipE values of ≤3. Overall, consideration of these parameters in ADME profiling could aid in reducing the drug failure rate in the later stages of clinical investigations.
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40
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Amrine CSM, Long JL, Raja HA, Kurina SJ, Burdette JE, Pearce CJ, Oberlies NH. Engineering Fluorine into Verticillins (Epipolythiodioxopiperazine Alkaloids) via Precursor-Directed Biosynthesis. JOURNAL OF NATURAL PRODUCTS 2019; 82:3104-3110. [PMID: 31633350 PMCID: PMC6996222 DOI: 10.1021/acs.jnatprod.9b00711] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Precursor-directed biosynthesis was used to generate a series of fluorinated verticillins. The biosynthesis of these epipolythiodioxopiperazine alkaloids was monitored in situ via the droplet liquid microjunction surface sampling probe (droplet probe), and a suite of NMR and mass spectrometry data were used for their characterization. All analogues demonstrated nanomolar IC50 values vs a panel of cancer cell lines. This approach yielded new compounds that would be difficult to generate via synthesis.
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Affiliation(s)
- Chiraz Soumia M Amrine
- Department of Chemistry and Biochemistry , University of North Carolina at Greensboro , Greensboro , North Carolina 27402 , United States
| | - Jessica L Long
- Department of Chemistry and Biochemistry , University of North Carolina at Greensboro , Greensboro , North Carolina 27402 , United States
| | - Huzefa A Raja
- Department of Chemistry and Biochemistry , University of North Carolina at Greensboro , Greensboro , North Carolina 27402 , United States
| | - Steven J Kurina
- Department of Pharmaceutical Sciences , University of Illinois at Chicago , Chicago , Illinois 60612 , United States
| | - Joanna E Burdette
- Department of Pharmaceutical Sciences , University of Illinois at Chicago , Chicago , Illinois 60612 , United States
| | - Cedric J Pearce
- Mycosynthetix Inc. , 505 Meadowlands Drive, Suite 103 , Hillsborough , North Carolina 27278 , United States
| | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry , University of North Carolina at Greensboro , Greensboro , North Carolina 27402 , United States
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41
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Cavalluzzi MM, Imbrici P, Gualdani R, Stefanachi A, Mangiatordi GF, Lentini G, Nicolotti O. Human ether-à-go-go-related potassium channel: exploring SAR to improve drug design. Drug Discov Today 2019; 25:344-366. [PMID: 31756511 DOI: 10.1016/j.drudis.2019.11.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/22/2019] [Accepted: 11/12/2019] [Indexed: 12/12/2022]
Abstract
hERG is best known as a primary anti-target, the inhibition of which is responsible for serious side effects. A renewed interest in hERG as a desired target, especially in oncology, was sparked because of its role in cellular proliferation and apoptosis. In this study, we survey the most recent advances regarding hERG by focusing on SAR in the attempt to elucidate, at a molecular level, off-target and on-target actions of potential hERG binders, which are highly promiscuous and largely varying in structure. Understanding the rationale behind hERG interactions and the molecular determinants of hERG activity is a real challenge and comprehension of this is of the utmost importance to prioritize compounds in early stages of drug discovery and to minimize cardiotoxicity attrition in preclinical and clinical studies.
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Affiliation(s)
- Maria Maddalena Cavalluzzi
- Dipartimento di Farmacia - Scienze del Farmaco, Università degli Studi di Bari 'Aldo Moro', Via E. Orabona, 4, 70126 Bari, Italy
| | - Paola Imbrici
- Dipartimento di Farmacia - Scienze del Farmaco, Università degli Studi di Bari 'Aldo Moro', Via E. Orabona, 4, 70126 Bari, Italy
| | - Roberta Gualdani
- Laboratory of Cell Physiology, Institute of Neuroscience, Université Catholique de Louvain, Brussels 1200, Belgium
| | - Angela Stefanachi
- Dipartimento di Farmacia - Scienze del Farmaco, Università degli Studi di Bari 'Aldo Moro', Via E. Orabona, 4, 70126 Bari, Italy
| | | | - Giovanni Lentini
- Dipartimento di Farmacia - Scienze del Farmaco, Università degli Studi di Bari 'Aldo Moro', Via E. Orabona, 4, 70126 Bari, Italy
| | - Orazio Nicolotti
- Dipartimento di Farmacia - Scienze del Farmaco, Università degli Studi di Bari 'Aldo Moro', Via E. Orabona, 4, 70126 Bari, Italy.
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42
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Han C, Alabanza LM, Kelly SM, Orsi DL, Gosselin F, Altman RA. BBDFA: A Practical Reagent for Trifluoromethylation of Allylic and Benzylic Alcohols on Preparative Scale. Org Process Res Dev 2019. [DOI: 10.1021/acs.oprd.9b00201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Chong Han
- Department of Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Lady Mae Alabanza
- Department of Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Sean M. Kelly
- Department of Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Douglas L. Orsi
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Francis Gosselin
- Department of Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Ryan A. Altman
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
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43
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Shirahashi H, Toriihara E, Suenaga Y, Yoshida H, Akaogi K, Endou Y, Wakabayashi M, Takashima M. The discovery of novel 3-aryl-indazole derivatives as peripherally restricted pan-Trk inhibitors for the treatment of pain. Bioorg Med Chem Lett 2019; 29:2320-2326. [PMID: 31235262 DOI: 10.1016/j.bmcl.2019.06.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/24/2019] [Accepted: 06/15/2019] [Indexed: 10/26/2022]
Abstract
The design, synthesis, and biological evaluation of novel 3-aryl-indazole derivatives as peripherally selective pan-Trk inhibitors are described. Three strategies were used to obtain a potent compound exhibiting low central nervous system (CNS) penetration and high plasma exposure: 1) a structure-based drug design (SBDD) approach was used to improve potency; 2) a substrate for an efflux transporter for lowering brain penetration was explored; and 3) the most basic pKa (pKa-MB) value was used as an indicator to identify compounds with good membrane permeability. This enabled the identification of the peripherally targeted 17c with the potency, kinase-selectivity, and plasma exposure required to demonstrate in vivo efficacy in a Complete Freund's adjuvant (CFA)-induced thermal hypersensitivity model.
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Affiliation(s)
- Hiromitsu Shirahashi
- Pharmaceuticals Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan.
| | - Eisuke Toriihara
- Pharmaceuticals Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
| | - Yoshihito Suenaga
- Pharmaceuticals Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
| | - Hideyuki Yoshida
- Pharmaceuticals Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
| | - Kensuke Akaogi
- Pharmaceuticals Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
| | - Yukiko Endou
- Pharmaceuticals Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
| | - Makoto Wakabayashi
- Pharmaceuticals Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
| | - Misato Takashima
- Pharmaceuticals Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan.
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44
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von Rudorff GF, Watermann T, Guo XY, Sebastiani D. Conformational Space of a Polyphilic Molecule with a Fluorophilic Side Chain Integrated in a DPPC Bilayer. J Comput Chem 2019; 38:576-583. [PMID: 28211109 DOI: 10.1002/jcc.24711] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 11/17/2016] [Accepted: 11/18/2016] [Indexed: 12/21/2022]
Abstract
We investigate the conformational space of a polyphilic molecule with hydrophilic, lipophilic and fluorophilic parts inserted as a transmembrane agent into a dipalmitoylphosphatidylcholine bilayer by means of all-atom molecular dynamics simulations. Special focus is put on the competing structural driving forces arising from the hydrophilic, lipophilic and fluorophilic side chains and the aromatic backbone of the polyphile. We observe a significant difference between the lipophilic and the fluorophilic side chains regarding their intramembrane distribution. While the lipophilic groups remain membrane-centered, the fluorophilic parts tend to orient toward the phosphate headgroups. This trend is important for understanding the influence of polyphile agents on the properties of phospholipid membranes. From a fundamental point of view, our computed distribution functions of the side chains are related to the interplay of sterical, enthalpic and entropic driving forces. Our findings illustrate the potential of rationally designed membrane additives which can be exploited to tune the properties of phospholipid membranes. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Guido F von Rudorff
- Department of Physics and Astronomy, University College London, Gower Street, London, United Kingdom.,Institute of Chemistry, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz 4, Halle, 06120, Germany
| | - Tobias Watermann
- Institute of Chemistry, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz 4, Halle, 06120, Germany
| | - Xiang-Yang Guo
- Institute of Chemistry, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz 4, Halle, 06120, Germany
| | - Daniel Sebastiani
- Institute of Chemistry, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz 4, Halle, 06120, Germany
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45
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Boström J, Brown DG, Young RJ, Keserü GM. Expanding the medicinal chemistry synthetic toolbox. Nat Rev Drug Discov 2018; 17:709-727. [DOI: 10.1038/nrd.2018.116] [Citation(s) in RCA: 267] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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46
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Schnute ME, Wennerstål M, Alley J, Bengtsson M, Blinn JR, Bolten CW, Braden T, Bonn T, Carlsson B, Caspers N, Chen M, Choi C, Collis LP, Crouse K, Färnegårdh M, Fennell KF, Fish S, Flick AC, Goos-Nilsson A, Gullberg H, Harris PK, Heasley SE, Hegen M, Hromockyj AE, Hu X, Husman B, Janosik T, Jones P, Kaila N, Kallin E, Kauppi B, Kiefer JR, Knafels J, Koehler K, Kruger L, Kurumbail RG, Kyne RE, Li W, Löfstedt J, Long SA, Menard CA, Mente S, Messing D, Meyers MJ, Napierata L, Nöteberg D, Nuhant P, Pelc MJ, Prinsen MJ, Rhönnstad P, Backström-Rydin E, Sandberg J, Sandström M, Shah F, Sjöberg M, Sundell A, Taylor AP, Thorarensen A, Trujillo JI, Trzupek JD, Unwalla R, Vajdos FF, Weinberg RA, Wood DC, Xing L, Zamaratski E, Zapf CW, Zhao Y, Wilhelmsson A, Berstein G. Discovery of 3-Cyano-N-(3-(1-isobutyrylpiperidin-4-yl)-1-methyl-4-(trifluoromethyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)benzamide: A Potent, Selective, and Orally Bioavailable Retinoic Acid Receptor-Related Orphan Receptor C2 Inverse Agonist. J Med Chem 2018; 61:10415-10439. [DOI: 10.1021/acs.jmedchem.8b00392] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Tomas Bonn
- Karo Bio AB (now Karo Pharma AB), 111 48 Stockholm, Sweden
| | - Bo Carlsson
- Karo Bio AB (now Karo Pharma AB), 111 48 Stockholm, Sweden
| | - Nicole Caspers
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Ming Chen
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Chulho Choi
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | | | | | | | | | | | - Andrew C. Flick
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | | | | | | | - Steven E. Heasley
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | | | | | | | - Bolette Husman
- Karo Bio AB (now Karo Pharma AB), 111 48 Stockholm, Sweden
| | - Tomasz Janosik
- Karo Bio AB (now Karo Pharma AB), 111 48 Stockholm, Sweden
| | | | | | | | - Björn Kauppi
- Karo Bio AB (now Karo Pharma AB), 111 48 Stockholm, Sweden
| | | | - John Knafels
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Konrad Koehler
- Karo Bio AB (now Karo Pharma AB), 111 48 Stockholm, Sweden
| | - Lars Kruger
- Karo Bio AB (now Karo Pharma AB), 111 48 Stockholm, Sweden
| | - Ravi G. Kurumbail
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Robert E. Kyne
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | | | | | | | - Carol A. Menard
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | | | | | | | | | | | - Philippe Nuhant
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | | | | | | | | | | | | | | | - Maria Sjöberg
- Karo Bio AB (now Karo Pharma AB), 111 48 Stockholm, Sweden
| | - Aron Sundell
- Karo Bio AB (now Karo Pharma AB), 111 48 Stockholm, Sweden
| | | | | | - John I. Trujillo
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | | | | | - Felix F. Vajdos
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
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Helal CJ, Bartolozzi A, Goble SD, Mani NS, Guzman-Perez A, Ohri AK, Shi ZC, Subramanyam C. Increased building block access through collaboration. Drug Discov Today 2018; 23:1458-1462. [DOI: 10.1016/j.drudis.2018.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/15/2018] [Accepted: 03/06/2018] [Indexed: 12/12/2022]
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48
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Chen C, Lee MH, Weng CF, Leong MK. Theoretical Prediction of the Complex P-Glycoprotein Substrate Efflux Based on the Novel Hierarchical Support Vector Regression Scheme. Molecules 2018; 23:E1820. [PMID: 30037151 PMCID: PMC6100076 DOI: 10.3390/molecules23071820] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/13/2022] Open
Abstract
P-glycoprotein (P-gp), a membrane-bound transporter, can eliminate xenobiotics by transporting them out of the cells or blood⁻brain barrier (BBB) at the expense of ATP hydrolysis. Thus, P-gp mediated efflux plays a pivotal role in altering the absorption and disposition of a wide range of substrates. Nevertheless, the mechanism of P-gp substrate efflux is rather complex since it can take place through active transport and passive permeability in addition to multiple P-gp substrate binding sites. A nonlinear quantitative structure⁻activity relationship (QSAR) model was developed in this study using the novel machine learning-based hierarchical support vector regression (HSVR) scheme to explore the perplexing relationships between descriptors and efflux ratio. The predictions by HSVR were found to be in good agreement with the observed values for the molecules in the training set (n = 50, r² = 0.96, qCV2 = 0.94, RMSE = 0.10, s = 0.10) and test set (n = 13, q² = 0.80⁻0.87, RMSE = 0.21, s = 0.22). When subjected to a variety of statistical validations, the developed HSVR model consistently met the most stringent criteria. A mock test also asserted the predictivity of HSVR. Consequently, this HSVR model can be adopted to facilitate drug discovery and development.
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Affiliation(s)
- Chun Chen
- Department of Chemistry, National Dong Hwa University, Shoufeng, Hualien 97401, Taiwan.
| | - Ming-Han Lee
- Department of Chemistry, National Dong Hwa University, Shoufeng, Hualien 97401, Taiwan.
| | - Ching-Feng Weng
- Department of Life Science and Institute of Biotechnology, National Dong Hwa University, Shoufeng, Hualien 97401, Taiwan.
| | - Max K Leong
- Department of Chemistry, National Dong Hwa University, Shoufeng, Hualien 97401, Taiwan.
- Department of Life Science and Institute of Biotechnology, National Dong Hwa University, Shoufeng, Hualien 97401, Taiwan.
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49
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Altman RA, Sharma KK, Rajewski LG, Toren PC, Baltezor MJ, Pal M, Karad SN. Tyr 1-ψ[( Z)CF═CH]-Gly 2 Fluorinated Peptidomimetic Improves Distribution and Metabolism Properties of Leu-Enkephalin. ACS Chem Neurosci 2018; 9:1735-1742. [PMID: 29648788 DOI: 10.1021/acschemneuro.8b00085] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Opioid peptides are key regulators in cellular and intercellular physiological responses, and could be therapeutically useful for modulating several pathological conditions. Unfortunately, the use of peptide-based agonists to target centrally located opioid receptors is limited by poor physicochemical (PC), distribution, metabolic, and pharmacokinetic (DMPK) properties that restrict penetration across the blood-brain barrier via passive diffusion. To address these problems, the present paper exploits fluorinated peptidomimetics to simultaneously modify PC and DMPK properties, thus facilitating entry into the central nervous system. As an initial example, the present paper exploited the Tyr1-ψ[( Z)CF═CH]-Gly2 peptidomimetic to improve PC druglike characteristics (computational), plasma and microsomal degradation, and systemic and CNS distribution of Leu-enkephalin (Tyr-Gly-Gly-Phe-Leu). Thus, the fluoroalkene replacement transformed an instable in vitro tool compound into a stable and centrally distributed in vivo probe. In contrast, the Tyr1-ψ[CF3CH2-NH]-Gly2 peptidomimetic decreased stability by accelerating proteolysis at the Gly3-Phe4 position.
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Affiliation(s)
- Ryan A. Altman
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Krishna K. Sharma
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Lian G. Rajewski
- Biotechnology Innovation and Optimization Center, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Paul C. Toren
- Biotechnology Innovation and Optimization Center, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Michael J. Baltezor
- Biotechnology Innovation and Optimization Center, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Mohan Pal
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Somnath N. Karad
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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50
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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
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