1
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [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: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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2
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Linker S, Schellhaas C, Kamenik AS, Veldhuizen MM, Waibl F, Roth HJ, Fouché M, Rodde S, Riniker S. Lessons for Oral Bioavailability: How Conformationally Flexible Cyclic Peptides Enter and Cross Lipid Membranes. J Med Chem 2023; 66:2773-2788. [PMID: 36762908 PMCID: PMC9969412 DOI: 10.1021/acs.jmedchem.2c01837] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Indexed: 02/11/2023]
Abstract
Cyclic peptides extend the druggable target space due to their size, flexibility, and hydrogen-bonding capacity. However, these properties impact also their passive membrane permeability. As the "journey" through membranes cannot be monitored experimentally, little is known about the underlying process, which hinders rational design. Here, we use molecular simulations to uncover how cyclic peptides permeate a membrane. We show that side chains can act as "molecular anchors", establishing the first contact with the membrane and enabling insertion. Once inside, the peptides are positioned between headgroups and lipid tails─a unique polar/apolar interface. Only one of two distinct orientations at this interface allows for the formation of the permeable "closed" conformation. In the closed conformation, the peptide crosses to the lower leaflet via another "anchoring" and flipping mechanism. Our findings provide atomistic insights into the permeation process of flexible cyclic peptides and reveal design considerations for each step of the process.
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Affiliation(s)
- Stephanie
M. Linker
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Christian Schellhaas
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Anna S. Kamenik
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Mac M. Veldhuizen
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Franz Waibl
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Hans-Jörg Roth
- Novartis
Institutes for BioMedical Research, Novartis
Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Marianne Fouché
- Novartis
Institutes for BioMedical Research, Novartis
Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Stephane Rodde
- Novartis
Institutes for BioMedical Research, Novartis
Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Sereina Riniker
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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3
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Gary S, Bloom S. Peptide Carbocycles: From -SS- to -CC- via a Late-Stage "Snip-and-Stitch". ACS CENTRAL SCIENCE 2022; 8:1537-1547. [PMID: 36439308 PMCID: PMC9686213 DOI: 10.1021/acscentsci.2c00456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Indexed: 05/28/2023]
Abstract
One way to improve the therapeutic potential of peptides is through cyclization. This is commonly done using a disulfide bond between two cysteine residues in the peptide. However, disulfide bonds are susceptible to reductive cleavage, and this can deactivate the peptide and endanger endogenous proteins through covalent modification. Substituting disulfide bonds with more chemically robust carbon-based linkers has proven to be an effective strategy to better develop cyclic peptides as drugs, but finding the optimal carbon replacement is synthetically laborious. We report a new late-stage platform wherein a single disulfide bond in a cyclic peptide can serve as the progenitor for any number of new carbon-rich groups, derived from organodiiodides, using a Zn:Cu couple and a hydrosilane. We show that this platform can furnish entirely new carbocyclic scaffolds with enhanced permeability and structural integrity and that the stereochemistry of the new cycles can be biased by a judicious choice in silane.
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Affiliation(s)
- Samuel Gary
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas66045, United States
| | - Steven Bloom
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas66045, United States
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4
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Rzepiela AA, Viarengo-Baker LA, Tatarskii V, Kombarov R, Whitty A. Conformational Effects on the Passive Membrane Permeability of Synthetic Macrocycles. J Med Chem 2022; 65:10300-10317. [PMID: 35861996 DOI: 10.1021/acs.jmedchem.1c02090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Macrocyclic compounds (MCs) can have complex conformational properties that affect pharmacologically important behaviors such as membrane permeability. We measured the passive permeability of 3600 diverse nonpeptidic MCs and used machine learning to analyze the results. Incorporating selected properties based on the three-dimensional (3D) conformation gave models that predicted permeability with Q2 = 0.81. A biased spatial distribution of polar versus nonpolar regions was particularly important for good permeability, consistent with a mechanism in which the initial insertion of nonpolar portions of a MC helps facilitate the subsequent membrane entry of more polar parts. We also examined effects on permeability of 800 substructural elements by comparing matched molecular pairs. Some substitutions were invariably beneficial or invariably deleterious to permeability, while the influence of others was highly contextual. Overall, the work provides insights into how the permeability of MCs is influenced by their 3D conformational properties and suggests design hypotheses for achieving macrocycles with high membrane permeability.
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Affiliation(s)
- Anna A Rzepiela
- Pyxis Discovery, Delftechpark 26, 2628XH Delft, The Netherlands
| | - Lauren A Viarengo-Baker
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Victor Tatarskii
- Asinex Corporation, 101 N Chestnut St # 104, Winston-Salem, North Carolina 27101,United States
| | - Roman Kombarov
- Asinex Corporation, 101 N Chestnut St # 104, Winston-Salem, North Carolina 27101,United States
| | - Adrian Whitty
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.,Center for Molecular Discovery, Boston University, 24 Cummington Mall, Boston, Massachusetts 02215, United States
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5
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Abstract
Peptides have traditionally been perceived as poor drug candidates due to unfavorable characteristics mainly regarding their pharmacokinetic behavior, including plasma stability, membrane permeability and circulation half-life. Nonetheless, in recent years, general strategies to tackle those shortcomings have been established, and peptides are subsequently gaining increasing interest as drugs due to their unique ability to combine the advantages of antibodies and small molecules. Macrocyclic peptides are a special focus of drug development efforts due to their ability to address so called ‘undruggable’ targets characterized by large and flat protein surfaces lacking binding pockets. Here, the main strategies developed to date for adapting peptides for clinical use are summarized, which may soon help usher in an age highly shaped by peptide-based therapeutics. Nonetheless, limited membrane permeability is still to overcome before peptide therapeutics will be broadly accepted.
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6
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Taechalertpaisarn J, Ono S, Okada O, Johnstone TC, Scott Lokey R. A New Amino Acid for Improving Permeability and Solubility in Macrocyclic Peptides through Side Chain-to-Backbone Hydrogen Bonding. J Med Chem 2022; 65:5072-5084. [PMID: 35275623 PMCID: PMC10681114 DOI: 10.1021/acs.jmedchem.2c00010] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Despite the notoriously poor membrane permeability of peptides, many cyclic peptide natural products show high passive membrane permeability and potently inhibit a variety of "undruggable" intracellular targets. A major impediment to the design of cyclic peptides with good permeability is the high desolvation energy associated with the peptide backbone amide NH groups. While several strategies have been proposed to mitigate this deleterious effect, only few studies have used polar side chains to sequester backbone NH groups. We investigated the ability of N,N-pyrrolidinylglutamine (Pye), whose side chain contains a powerful hydrogen-bond-accepting C═O amide group but no hydrogen-bond donors, to sequester exposed backbone NH groups in a series of cyclic hexapeptide diastereomers. Analyses revealed that specific Leu-to-Pye substitutions conferred dramatic improvements in aqueous solubility and permeability in a scaffold- and position-dependent manner. Therefore, this approach offers a complementary tool for improving membrane permeability and solubility in cyclic peptides.
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Affiliation(s)
- Jaru Taechalertpaisarn
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Satoshi Ono
- Modality Laboratories, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshidacho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Okimasa Okada
- Modality Laboratories, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshidacho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Timothy C. Johnstone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - R. Scott Lokey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
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7
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Tamura T, Inoue M, Yoshimitsu Y, Hashimoto I, Ohashi N, Tsumura K, Suzuki K, Watanabe T, Hohsaka T. Chemical Synthesis and Cell-Free Expression of Thiazoline Ring-Bridged Cyclic Peptides and Their Properties on Biomembrane Permeability. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20210409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Takashi Tamura
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1211, Japan
- Synthetic Organic Chemistry Laboratories, FUJIFILM Corporation, 577 Ushijima, Kaisei-machi, Ashigarakami-gun, Kanagawa 258-8577, Japan
| | - Masaaki Inoue
- Synthetic Organic Chemistry Laboratories, FUJIFILM Corporation, 577 Ushijima, Kaisei-machi, Ashigarakami-gun, Kanagawa 258-8577, Japan
| | - Yuji Yoshimitsu
- Synthetic Organic Chemistry Laboratories, FUJIFILM Corporation, 577 Ushijima, Kaisei-machi, Ashigarakami-gun, Kanagawa 258-8577, Japan
| | - Ichihiko Hashimoto
- Analysis Technology Center, FUJIFILM Corporation, 210 Nakanuma, Minamiashigara, Kanagawa 258-0123, Japan
| | - Noriyuki Ohashi
- Analysis Technology Center, FUJIFILM Corporation, 210 Nakanuma, Minamiashigara, Kanagawa 258-0123, Japan
| | - Kyosuke Tsumura
- Analysis Technology Center, FUJIFILM Corporation, 210 Nakanuma, Minamiashigara, Kanagawa 258-0123, Japan
| | - Koo Suzuki
- Analysis Technology Center, FUJIFILM Corporation, 210 Nakanuma, Minamiashigara, Kanagawa 258-0123, Japan
| | - Takayoshi Watanabe
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1211, Japan
| | - Takahiro Hohsaka
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1211, Japan
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8
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Sun D. Recent Advances in Macrocyclic Drugs and Microwave-Assisted and/or Solid-Supported Synthesis of Macrocycles. Molecules 2022; 27:1012. [PMID: 35164274 PMCID: PMC8839925 DOI: 10.3390/molecules27031012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 11/19/2022] Open
Abstract
Macrocycles represent attractive candidates in organic synthesis and drug discovery. Since 2014, nineteen macrocyclic drugs, including three radiopharmaceuticals, have been approved by FDA for the treatment of bacterial and viral infections, cancer, obesity, immunosuppression, etc. As such, new synthetic methodologies and high throughput chemistry (e.g., microwave-assisted and/or solid-phase synthesis) to access various macrocycle entities have attracted great interest in this chemical space. This article serves as an update on our previous review related to macrocyclic drugs and new synthetic strategies toward macrocycles (Molecules, 2013, 18, 6230). In this work, I first reviewed recent FDA-approved macrocyclic drugs since 2014, followed by new advances in macrocycle synthesis using high throughput chemistry, including microwave-assisted and/or solid-supported macrocyclization strategies. Examples and highlights of macrocyclization include macrolactonization and macrolactamization, transition-metal catalyzed olefin ring-closure metathesis, intramolecular C-C and C-heteroatom cross-coupling, copper- or ruthenium-catalyzed azide-alkyne cycloaddition, intramolecular SNAr or SN2 nucleophilic substitution, condensation reaction, and multi-component reaction-mediated macrocyclization, and covering the literature since 2010.
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Affiliation(s)
- Dianqing Sun
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, HI 96720, USA
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9
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Klein VG, Bond AG, Craigon C, Lokey RS, Ciulli A. Amide-to-Ester Substitution as a Strategy for Optimizing PROTAC Permeability and Cellular Activity. J Med Chem 2021; 64:18082-18101. [PMID: 34881891 PMCID: PMC8713283 DOI: 10.1021/acs.jmedchem.1c01496] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Criteria for predicting the druglike properties of "beyond Rule of 5" Proteolysis Targeting Chimeras (PROTAC) degraders are underdeveloped. PROTAC components are often combined via amide couplings due to their reliability. Amides, however, can give rise to poor absorption, distribution, metabolism, and excretion (ADME) properties. We hypothesized that a bioisosteric amide-to-ester substitution could lead to improvements in both physicochemical properties and bioactivity. Using model compounds, bearing either amides or esters, we identify parameters for optimal lipophilicity and permeability. We applied these learnings to design a set of novel amide-to-ester-substituted, VHL-based BET degraders with the goal to increase permeability. Our ester PROTACs retained intracellular stability, were overall more potent degraders than their amide counterparts, and showed an earlier onset of the hook effect. These enhancements were driven by greater cell permeability rather than improvements in ternary complex formation. This largely unexplored amide-to-ester substitution provides a simple strategy to enhance PROTAC permeability and bioactivity and may prove beneficial to other beyond Ro5 molecules.
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Affiliation(s)
- Victoria G Klein
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Adam G Bond
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K
| | - Conner Craigon
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K
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10
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Brueckner AC, Deng Q, Cleves AE, Lesburg CA, Alvarez JC, Reibarkh MY, Sherer EC, Jain AN. Conformational Strain of Macrocyclic Peptides in Ligand-Receptor Complexes Based on Advanced Refinement of Bound-State Conformers. J Med Chem 2021; 64:3282-3298. [PMID: 33724820 DOI: 10.1021/acs.jmedchem.0c02159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Macrocyclic peptides are an important modality in drug discovery, but molecular design is limited due to the complexity of their conformational landscape. To better understand conformational propensities, global strain energies were estimated for 156 protein-macrocyclic peptide cocrystal structures. Unexpectedly large strain energies were observed when the bound-state conformations were modeled with positional restraints. Instead, low-energy conformer ensembles were generated using xGen that fit experimental X-ray electron density maps and gave reasonable strain energy estimates. The ensembles featured significant conformational adjustments while still fitting the electron density as well or better than the original coordinates. Strain estimates suggest the interaction energy in protein-ligand complexes can offset a greater amount of strain for macrocyclic peptides than for small molecules and non-peptidic macrocycles. Across all molecular classes, the approximate upper bound on global strain energies had the same relationship with molecular size, and bound-state ensembles from xGen yielded favorable binding energy estimates.
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Affiliation(s)
- Alexander C Brueckner
- Computational & Structural Chemistry, Merck & Co Inc, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Qiaolin Deng
- Computational & Structural Chemistry, Merck & Co Inc, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Ann E Cleves
- Bioengineering and Therapeutic Sciences, University of California San Francisco, Box 0128, San Francisco, California 94158, United States
| | - Charles A Lesburg
- Computational and Structural Chemistry, Merck and Co Inc, 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Juan C Alvarez
- Computational and Structural Chemistry, Merck and Co Inc, 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Mikhail Y Reibarkh
- Analytical Research and Development, Merck & Co Inc, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Edward C Sherer
- Analytical Research and Development, Merck & Co Inc, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Ajay N Jain
- Bioengineering and Therapeutic Sciences, University of California San Francisco, Box 0128, San Francisco, California 94158, United States
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11
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Hoang HN, Hill TA, Fairlie DP. Connecting Hydrophobic Surfaces in Cyclic Peptides Increases Membrane Permeability. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012643] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Huy N. Hoang
- Division of Chemistry and Structural Biology and ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Timothy A. Hill
- Division of Chemistry and Structural Biology and ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology and ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
- ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
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12
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Hoang HN, Hill TA, Fairlie DP. Connecting Hydrophobic Surfaces in Cyclic Peptides Increases Membrane Permeability. Angew Chem Int Ed Engl 2021; 60:8385-8390. [PMID: 33185961 DOI: 10.1002/anie.202012643] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/04/2020] [Indexed: 12/16/2022]
Abstract
N- or C-methylation in natural and synthetic cyclic peptides can increase membrane permeability, but it remains unclear why this happens in some cases but not others. Here we compare three-dimensional structures for cyclic peptides from six families, including isomers differing only in the location of an N- or Cα-methyl substituent. We show that a single methyl group only increases membrane permeability when it connects or expands hydrophobic surface patches. Positional isomers, with the same molecular weight, hydrogen bond donors/acceptors, rotatable bonds, calculated LogP, topological polar surface area, and total hydrophobic surface area, can have different membrane permeabilities that correlate with the size of the largest continuous hydrophobic surface patch. These results illuminate a key local molecular determinant of membrane permeability.
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Affiliation(s)
- Huy N Hoang
- Division of Chemistry and Structural Biology and ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Timothy A Hill
- Division of Chemistry and Structural Biology and ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David P Fairlie
- Division of Chemistry and Structural Biology and ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
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13
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Patterson JR, Terrell LR, Donatelli CA, Holt DA, Jolivette LJ, Rivero RA, Roethke TJ, Shu A, Stoy P, Ye G, Youngman M, Lawhorn BG. Design and Optimization of an Acyclic Amine Series of TRPV4 Antagonists by Electronic Modulation of Hydrogen Bond Interactions. J Med Chem 2020; 63:14867-14884. [PMID: 33201708 DOI: 10.1021/acs.jmedchem.0c01303] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Investigation of TRPV4 as a potential target for the treatment of pulmonary edema associated with heart failure generated a novel series of acyclic amine inhibitors displaying exceptional potency and PK properties. The series arose through a scaffold hopping approach, which relied on use of an internal H-bond to replace a saturated heterocyclic ring. Optimization of the lead through investigation of both aryl regions revealed approaches to increase potency through substituents believed to enhance separate intramolecular and intermolecular H-bond interactions. A proposed internal H-bond between the amine and neighboring benzenesulfonamide was stabilized by electronically modulating the benzenesulfonamide. In the aryl ether moiety, substituents para to the nitrile demonstrated an electronic effect on TRPV4 recognition. Finally, the acyclic amines inactivated CYP3A4 and this liability was addressed by modifications that sterically preclude formation of a putative metabolic intermediate complex to deliver advanced TRPV4 antagonists as leads for discovery of novel medicines.
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Affiliation(s)
- Jaclyn R Patterson
- Heart Failure Discovery Performance Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Lamont R Terrell
- Flexible Discovery Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Carla A Donatelli
- Heart Failure Discovery Performance Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Dennis A Holt
- Heart Failure Discovery Performance Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Larry J Jolivette
- Heart Failure Discovery Performance Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Ralph A Rivero
- Flexible Discovery Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Theresa J Roethke
- Heart Failure Discovery Performance Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Arthur Shu
- Flexible Discovery Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Patrick Stoy
- Heart Failure Discovery Performance Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Guosen Ye
- Heart Failure Discovery Performance Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Mark Youngman
- Flexible Discovery Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Brian G Lawhorn
- Heart Failure Discovery Performance Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
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14
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Pyridyl-Ala Modified Cyclic Hexapeptides: In-Vitro and In-Vivo Profiling for Oral Bioavailability. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-019-09935-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
We and others have been aiming at modifications to maintain or to enhance solubility while enabling permeability for cyclic hexapeptides. Especially, the 2-pyridyl-Ala modification was investigated, since in this case, the pyridyl-nitrogen is able to form an H-bond to the NH of the same residue. The hypothesis of a backbone side-chain interaction was demonstrated by NMR experiments, and further results obtained on a variety of pyridyl-Ala derivatives, studied systematically in the context of permeability, are presented in this contribution. Thus, this study sheds some more light on the pyridyl-Ala modification, which had been reported earlier. In addition to the in vitro profiling, the extent of oral bioavailability was assessed in rats. In principle, the pyridyl-Ala residue can be considered as an amino acid supporting oral uptake.
Graphic Abstract
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15
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Cai X, Jiang Y, Lin M, Zhang J, Guo H, Yang F, Leung W, Xu C. Ultrasound-Responsive Materials for Drug/Gene Delivery. Front Pharmacol 2020; 10:1650. [PMID: 32082157 PMCID: PMC7005489 DOI: 10.3389/fphar.2019.01650] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/16/2019] [Indexed: 12/15/2022] Open
Abstract
Ultrasound is one of the most commonly used methods in the diagnosis and therapy of diseases due to its safety, deep penetration into tissue, and non-invasive nature. In the drug/gene delivery systems, ultrasound shows many advantages in terms of site-specific delivery and spatial release control of drugs/genes and attracts increasing attention. Microbubbles are the most well-known ultrasound-responsive delivery materials. Recently, nanobubbles, droplets, micelles, and nanoliposomes have been developed as novel carriers in this field. Herein, we review advances of novel ultrasound-responsive materials (nanobubbles, droplets, micelles and nanoliposomes) and discuss the challenges of ultrasound-responsive materials in delivery systems to boost the development of ultrasound-responsive materials as delivery carriers.
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Affiliation(s)
- Xiaowen Cai
- Key Laboratory of Molecular Target and Clinical Pharmacology, State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yuan Jiang
- Key Laboratory of Molecular Target and Clinical Pharmacology, State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Mei Lin
- Key Laboratory of Molecular Target and Clinical Pharmacology, State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jiyong Zhang
- Department of Pediatrics, Shenzhen Maternity and Child Health Care Hospital, Shenzhen, China
| | - Huanhuan Guo
- Key Laboratory of Molecular Target and Clinical Pharmacology, State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Fanwen Yang
- Department of Biomedical Engineering, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Wingnang Leung
- Asia-Pacific Institute of Aging Studies, Lingnan University, Tuen Mun, Hong Kong, Hong Kong
| | - Chuanshan Xu
- Key Laboratory of Molecular Target and Clinical Pharmacology, State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
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16
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Chen Y. Advances in the Synthesis of Methylated Products through Indirect Approaches. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201901240] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yantao Chen
- Medicinal Chemistry, Research and Early DevelopmentCardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca 43183 Gothenburg Sweden
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17
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Alemán-Ponce de León D, Sánchez-Chávez AC, Polindara-García LA. Pd-Mediated γ-C(sp3)–H Bond Activation in Ammonia–Ugi 4-CR Adducts by Using Picolinamide as Directing Group. J Org Chem 2019; 84:12809-12834. [DOI: 10.1021/acs.joc.9b01436] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Diego Alemán-Ponce de León
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México 04510, México
| | - Anahí C. Sánchez-Chávez
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México 04510, México
| | - Luis A. Polindara-García
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México 04510, México
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18
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Yang MG, Xiao Z, Cherney RJ, Tebben AJ, Batt DG, Brown GD, Chen J, Cvijic ME, Dabros M, Duncia JV, Galella M, Gardner DS, Khandelwal P, Ko SS, Malley MF, Mo R, Pang J, Rose AV, Santella JB, Shi H, Srivastava A, Traeger SC, Wang B, Xu S, Zhao R, Barrish JC, Mandlekar S, Zhao Q, Carter PH. Use of a Conformational-Switching Mechanism to Modulate Exposed Polarity: Discovery of CCR2 Antagonist BMS-741672. ACS Med Chem Lett 2019; 10:300-305. [PMID: 30891130 DOI: 10.1021/acsmedchemlett.8b00439] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 01/16/2019] [Indexed: 12/21/2022] Open
Abstract
We encountered a dilemma in the course of studying a series of antagonists of the G-protein coupled receptor CC chemokine receptor-2 (CCR2): compounds with polar C3 side chains exhibited good ion channel selectivity but poor oral bioavailability, whereas compounds with lipophilic C3 side chains exhibited good oral bioavailability in preclinical species but poor ion channel selectivity. Attempts to solve this through the direct modulation of physicochemical properties failed. However, the installation of a protonation-dependent conformational switching mechanism resolved the problem because it enabled a highly selective and relatively polar molecule to access a small population of a conformer with lower polar surface area and higher membrane permeability. Optimization of the overall properties in this series yielded the CCR2 antagonist BMS-741672 (7), which embodied properties suitable for study in human clinical trials.
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Affiliation(s)
- Michael G. Yang
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Zili Xiao
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Robert J. Cherney
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Andrew J. Tebben
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Douglas G. Batt
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Gregory D. Brown
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Jing Chen
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Mary Ellen Cvijic
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Marta Dabros
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - John V. Duncia
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Michael Galella
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Daniel S. Gardner
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Purnima Khandelwal
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Soo S. Ko
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Mary F. Malley
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Ruowei Mo
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Jian Pang
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Anne V. Rose
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Joseph B. Santella
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Hong Shi
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Anurag Srivastava
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Sarah C. Traeger
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Bei Wang
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Songmei Xu
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Rulin Zhao
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Joel C. Barrish
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Sandhya Mandlekar
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Qihong Zhao
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Percy H. Carter
- Bristol-Myers Squibb Company, Research and Development, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
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Caron G, Kihlberg J, Ermondi G. Intramolecular hydrogen bonding: An opportunity for improved design in medicinal chemistry. Med Res Rev 2019; 39:1707-1729. [PMID: 30659634 DOI: 10.1002/med.21562] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/18/2018] [Accepted: 12/19/2019] [Indexed: 12/14/2022]
Abstract
Recent literature shows that intramolecular hydrogen bond (IMHB) formation can positively impact upon the triad of permeability, solubility, and potency of drugs and candidates. IMHB modulation can be applied to compounds in any chemical space as a means for discovering drug candidates with both acceptable potency and absorption, distribution, metabolism, and excretion-Tox profiles. Integrating IMHB formation in design of drugs is, therefore, an exciting and timely challenge for modern medicinal chemistry. In this review, we first provide some background about IMHBs from the medicinal chemist's point of view and highlight some IMHB-associated misconceptions. Second, we propose a classification of IMHBs for drug discovery purposes, review the most common in silico tactics to include IMHBs in lead optimization and list some experimental physicochemical descriptors, which quantify the propensity of compounds to form IMHBs. By focusing on the compounds size and the number of IMHBs that can potentially be formed, we also outline the major difficulties encountered when designing compounds based on the inclusion of IMHBs. Finally, we discuss recent case studies illustrating the application of IMHB to optimize cell permeability and physicochemical properties of small molecules, cyclic peptides and macrocycles.
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Affiliation(s)
- Giulia Caron
- Molecular Biotechnology and Health Sciences Department, University of Torino, Torino, Italy
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Department, University of Torino, Torino, Italy
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20
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Zhu Z, Shaginian A, Grady LSC, Davie CP, Lind K, Pal S, Thansandote P, Simpson GL. DNA-Encoded Macrocyclic Peptide Library. Methods Mol Biol 2019; 2001:273-284. [PMID: 31134575 DOI: 10.1007/978-1-4939-9504-2_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
DNA-encoded library technology (ELT) is a cutting-edge enabling technology platform for drug discovery. Here we describe how to design and synthesize a macrocyclic DNA-encoded library; how to perform selection, sequencing, and data analysis to identify potential active peptides; and how to synthesize off-DNA peptides to confirm activity. This approach provides an effective tool for pharmaceutical research based on peptides.
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21
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Chen Y. Recent Advances in Methylation: A Guide for Selecting Methylation Reagents. Chemistry 2018; 25:3405-3439. [DOI: 10.1002/chem.201803642] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Yantao Chen
- Medicinal Chemistry, Cardiovascular, Renal and Metabolism, IMED Biotech UnitAstraZeneca Gothenburg Sweden
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22
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Chopra G, Chopra N, Kaur D. Elucidating the intermolecular hydrogen bonding interaction of proline with amides—quantum chemical calculations. Struct Chem 2018. [DOI: 10.1007/s11224-018-1235-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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23
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Naylor MR, Ly AM, Handford MJ, Ramos DP, Pye CR, Furukawa A, Klein VG, Noland RP, Edmondson Q, Turmon AC, Hewitt WM, Schwochert J, Townsend CE, Kelly CN, Blanco MJ, Lokey RS. Lipophilic Permeability Efficiency Reconciles the Opposing Roles of Lipophilicity in Membrane Permeability and Aqueous Solubility. J Med Chem 2018; 61:11169-11182. [DOI: 10.1021/acs.jmedchem.8b01259] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Matthew R. Naylor
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Andrew M. Ly
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Mason J. Handford
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Daniel P. Ramos
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Cameron R. Pye
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Akihiro Furukawa
- Modality Research Laboratories, Daiichi Sankyo Company, Ltd., 1-2-58 Hiromachi, Shingawa-ku, Tokyo 140-8710, Japan
| | - Victoria G. Klein
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Ryan P. Noland
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Quinn Edmondson
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Alexandra C. Turmon
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - William M. Hewitt
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Joshua Schwochert
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Chad E. Townsend
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Colin N. Kelly
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Maria-Jesus Blanco
- Sage Therapeutics, 215 First Street, Suite 220, Cambridge, Massachusetts 02142, United States
| | - R. Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
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24
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Räder AFB, Weinmüller M, Reichart F, Schumacher-Klinger A, Merzbach S, Gilon C, Hoffman A, Kessler H. Orally Active Peptides: Is There a Magic Bullet? Angew Chem Int Ed Engl 2018; 57:14414-14438. [DOI: 10.1002/anie.201807298] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Andreas F. B. Räder
- Technische Universität München; Department Chemie; Institute for Advanced Study; Lichtenbergstrasse 4 85748 Garching Germany
| | - Michael Weinmüller
- Technische Universität München; Department Chemie; Institute for Advanced Study; Lichtenbergstrasse 4 85748 Garching Germany
| | - Florian Reichart
- Technische Universität München; Department Chemie; Institute for Advanced Study; Lichtenbergstrasse 4 85748 Garching Germany
| | | | - Shira Merzbach
- The Hebrew University of Jerusalem; Institutes of Chemistry and Drug Research; Israel
| | - Chaim Gilon
- The Hebrew University of Jerusalem; Institutes of Chemistry and Drug Research; Israel
| | - Amnon Hoffman
- The Hebrew University of Jerusalem; Institutes of Chemistry and Drug Research; Israel
| | - Horst Kessler
- Technische Universität München; Department Chemie; Institute for Advanced Study; Lichtenbergstrasse 4 85748 Garching Germany
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25
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Räder AFB, Weinmüller M, Reichart F, Schumacher-Klinger A, Merzbach S, Gilon C, Hoffman A, Kessler H. Oral aktive Peptide: Gibt es ein Patentrezept? Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807298] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Andreas F. B. Räder
- Technische Universität München; Department Chemie; Institute for Advanced Study; Lichtenbergstraße 4 85748 Garching Deutschland
| | - Michael Weinmüller
- Technische Universität München; Department Chemie; Institute for Advanced Study; Lichtenbergstraße 4 85748 Garching Deutschland
| | - Florian Reichart
- Technische Universität München; Department Chemie; Institute for Advanced Study; Lichtenbergstraße 4 85748 Garching Deutschland
| | | | - Shira Merzbach
- Hebrew University of Jerusalem; Institutes of Chemistry and Drug Research; Israel
| | - Chaim Gilon
- Hebrew University of Jerusalem; Institutes of Chemistry and Drug Research; Israel
| | - Amnon Hoffman
- Hebrew University of Jerusalem; Institutes of Chemistry and Drug Research; Israel
| | - Horst Kessler
- Technische Universität München; Department Chemie; Institute for Advanced Study; Lichtenbergstraße 4 85748 Garching Deutschland
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26
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27
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Peraro L, Kritzer JA. Emerging Methods and Design Principles for Cell-Penetrant Peptides. Angew Chem Int Ed Engl 2018; 57:11868-11881. [PMID: 29740917 PMCID: PMC7184558 DOI: 10.1002/anie.201801361] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/24/2018] [Indexed: 12/12/2022]
Abstract
Biomolecules such as antibodies, proteins, and peptides are important tools for chemical biology and leads for drug development. They have been used to inhibit a variety of extracellular proteins, but accessing intracellular proteins has been much more challenging. In this review, we discuss diverse chemical approaches that have yielded cell-penetrant peptides and identify three distinct strategies: masking backbone amides, guanidinium group patterning, and amphipathic patterning. We summarize a growing number of large data sets, which are starting to reveal more specific design guidelines for each strategy. We also discuss advantages and disadvantages of current methods for quantifying cell penetration. Finally, we provide an overview of best-odds approaches for applying these new methods and design principles to optimize cytosolic penetration for a given bioactive peptide.
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Affiliation(s)
- Leila Peraro
- Department of Chemistry, Tufts University, Medford, Massachusetts, 02155, USA
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts, 02155, USA
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28
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Ermondi G, Vallaro M, Camacho-Leal M, Potter T, Visentin S, Caron G. Charged cyclic hexapeptides: Updating molecular descriptors for permeability purposes. Eur J Pharm Sci 2018; 122:85-93. [DOI: 10.1016/j.ejps.2018.06.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 06/16/2018] [Accepted: 06/19/2018] [Indexed: 10/28/2022]
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29
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Peraro L, Kritzer JA. Neue Methoden und Designprinzipien für zellgängige Peptide. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801361] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Leila Peraro
- Department of Chemistry Tufts University Medford Massachusetts 02155 USA
| | - Joshua A. Kritzer
- Department of Chemistry Tufts University Medford Massachusetts 02155 USA
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30
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Improving oral bioavailability of cyclic peptides by N-methylation. Bioorg Med Chem 2018; 26:2766-2773. [DOI: 10.1016/j.bmc.2017.08.031] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/16/2017] [Accepted: 08/18/2017] [Indexed: 01/19/2023]
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31
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Rossi Sebastiano M, Doak BC, Backlund M, Poongavanam V, Over B, Ermondi G, Caron G, Matsson P, Kihlberg J. Impact of Dynamically Exposed Polarity on Permeability and Solubility of Chameleonic Drugs Beyond the Rule of 5. J Med Chem 2018; 61:4189-4202. [PMID: 29608068 DOI: 10.1021/acs.jmedchem.8b00347] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Conformational flexibility has been proposed to significantly affect drug properties outside rule-of-5 (Ro5) chemical space. Here, we investigated the influence of dynamically exposed polarity on cell permeability and aqueous solubility for a structurally diverse set of drugs and clinical candidates far beyond the Ro5, all of which populated multiple distinct conformations as revealed by X-ray crystallography. Efflux-inhibited (passive) Caco-2 cell permeability correlated strongly with the compounds' minimum solvent-accessible 3D polar surface areas (PSA), whereas aqueous solubility depended less on the specific 3D conformation. Inspection of the crystal structures highlighted flexibly linked aromatic side chains and dynamically forming intramolecular hydrogen bonds as particularly effective in providing "chameleonic" properties that allow compounds to display both high cell permeability and aqueous solubility. These structural features, in combination with permeability predictions based on the correlation to solvent-accessible 3D PSA, should inspire drug design in the challenging chemical space far beyond the Ro5.
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Affiliation(s)
| | - Bradley C Doak
- Department of Medicinal Chemistry, MIPS , Monash University , 381 Royal Parade , Parkville , Victoria 3052 , Australia
| | - Maria Backlund
- Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), a Node at the Chemical Biology Consortium Sweden, Science for Life Laboratory, Department of Pharmacy, BMC , Uppsala University , Box 580, SE-751 23 Uppsala , Sweden
| | | | - Björn Over
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit , AstraZeneca R&D Gothenburg , SE-431 83 Mölndal , Sweden
| | - Giuseppe Ermondi
- Department of Molecular Biotechnology and Health Sciences , University of Torino , Quarello 15 , 10135 Torino , Italy
| | - Giulia Caron
- Department of Molecular Biotechnology and Health Sciences , University of Torino , Quarello 15 , 10135 Torino , Italy
| | - Pär Matsson
- Department of Pharmacy, BMC , Uppsala University , Box 580, SE-751 23 Uppsala , Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC , Uppsala University , Box 576, SE-751 23 Uppsala , Sweden
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32
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Fine-tuning the physicochemical properties of peptide-based blood-brain barrier shuttles. Bioorg Med Chem 2018; 26:2099-2106. [PMID: 29567297 DOI: 10.1016/j.bmc.2018.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 02/26/2018] [Accepted: 03/07/2018] [Indexed: 01/12/2023]
Abstract
N-methylation is a powerful method to modify the physicochemical properties of peptides. We previously found that a fully N-methylated tetrapeptide, Ac-(N-MePhe)4-CONH2, was more lipophilic than its non-methylated analog Ac-(Phe)4-CONH2. In addition, the former crossed artificial and cell membranes while the latter did not. Here we sought to optimize the physicochemical properties of peptides and address how the number and position of N-methylated amino acids affect these properties. To this end, 15 analogs of Ac-(Phe)4-CONH2 were designed and synthesized in solid-phase. The solubility of the peptides in water and their lipophilicity, as measured by ultra performance liquid chromatography (UPLC) retention times, were determined. To study the permeability of the peptides, the Parallel Artificial Membrane Permeability Assay (PAMPA) was used as an in vitro model of the blood-brain barrier (BBB). Contrary to the parent peptide, the 15 analogs crossed the artificial membrane, thereby showing that N-methylation improved permeability. We also found that N-methylation enhanced lipophilicity but decreased the water solubility of peptides. Our results showed that both the number and position of N-methylated residues are important factors governing the physicochemical properties of peptides. There was no correlation between the number of N-methylated amide bonds and any of the properties measured. However, for the peptides consecutively N-methylated from the N-terminus to the C-terminus (p1, p5, p11, p12 and p16), lipophilicity correlated well with the number of N-methylated amide bonds and the permeability of the peptides. Moreover, the peptides were non-toxic to HEK293T cells, as determined by the 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay.
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33
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Zhu Z, Shaginian A, Grady LC, O’Keeffe T, Shi XE, Davie CP, Simpson GL, Messer JA, Evindar G, Bream RN, Thansandote PP, Prentice NR, Mason AM, Pal S. Design and Application of a DNA-Encoded Macrocyclic Peptide Library. ACS Chem Biol 2018; 13:53-59. [PMID: 29185700 DOI: 10.1021/acschembio.7b00852] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A DNA-encoded macrocyclic peptide library was designed and synthesized with 2.4 × 1012 members composed of 4-20 natural and non-natural amino acids. Affinity-based selection was performed against two therapeutic targets, VHL and RSV N protein. On the basis of selection data, some peptides were selected for resynthesis without a DNA tag, and their activity was confirmed.
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Affiliation(s)
- Zhengrong Zhu
- GlaxoSmithKline, 200 Cambridge Park Dr., Cambridge, Massachusetts 02140, United States
| | - Alex Shaginian
- GlaxoSmithKline, 200 Cambridge Park Dr., Cambridge, Massachusetts 02140, United States
| | - LaShadric C. Grady
- GlaxoSmithKline, 200 Cambridge Park Dr., Cambridge, Massachusetts 02140, United States
| | - Thomas O’Keeffe
- GlaxoSmithKline, 200 Cambridge Park Dr., Cambridge, Massachusetts 02140, United States
| | - Xiangguo E. Shi
- GlaxoSmithKline, 200 Cambridge Park Dr., Cambridge, Massachusetts 02140, United States
| | - Christopher P. Davie
- GlaxoSmithKline, 200 Cambridge Park Dr., Cambridge, Massachusetts 02140, United States
| | - Graham L. Simpson
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
| | - Jeffrey A. Messer
- GlaxoSmithKline, 200 Cambridge Park Dr., Cambridge, Massachusetts 02140, United States
| | - Ghotas Evindar
- GlaxoSmithKline, 200 Cambridge Park Dr., Cambridge, Massachusetts 02140, United States
| | - Robert N. Bream
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
| | | | - Naomi R. Prentice
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
| | - Andrew M. Mason
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
| | - Sandeep Pal
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
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34
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Alihodžić S, Bukvić M, Elenkov IJ, Hutinec A, Koštrun S, Pešić D, Saxty G, Tomašković L, Žiher D. Current Trends in Macrocyclic Drug Discovery and beyond -Ro5. PROGRESS IN MEDICINAL CHEMISTRY 2018; 57:113-233. [DOI: 10.1016/bs.pmch.2018.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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35
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Qian Z, Dougherty PG, Pei D. Targeting intracellular protein-protein interactions with cell-permeable cyclic peptides. Curr Opin Chem Biol 2017; 38:80-86. [PMID: 28388463 DOI: 10.1016/j.cbpa.2017.03.011] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/24/2017] [Accepted: 03/14/2017] [Indexed: 02/06/2023]
Abstract
Intracellular protein-protein interactions (PPIs) are challenging targets for conventional drug modalities, because small molecules generally do not bind to their large, flat binding sites with high affinity, whereas monoclonal antibodies cannot cross the cell membrane to reach the targets. Cyclic peptides in the 700-2000 molecular-weight range have the sufficient size and a balanced conformational flexibility/rigidity for binding to flat PPI interfaces with antibody-like affinity and specificity. Several powerful cyclic peptide library technologies were developed over the past decade to rapidly discover potent, specific cyclic peptide ligands against proteins of interest including those involved in PPIs. Methods are also being developed to enhance the membrane permeability of cyclic peptides through both passive diffusion and active transport mechanisms. Integration of the permeability-enhancing elements into cyclic peptide design has led to an increasing number of cell-permeable and biologically active cyclic peptides against intracellular PPIs. In this account, we review the recent developments in the design and synthesis of cell-permeable cyclic peptides.
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Affiliation(s)
- Ziqing Qian
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, United States
| | - Patrick G Dougherty
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, United States
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, United States.
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36
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Vorherr T, Lewis I, Berghausen J, Desrayaud S, Schaefer M. Modulation of Oral Bioavailability and Metabolism for Closely Related Cyclic Hexapeptides. Int J Pept Res Ther 2017. [PMID: 29527142 PMCID: PMC5838147 DOI: 10.1007/s10989-017-9590-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Abstract Recently, a variety of studies concerned with the permeability and oral bioavailability of cyclic peptides have been reported. In particular, strategies aiming at modifying peptides to maintain or to enhance solubility while enabling permeability constitute a significant challenge, but are of high interest to ensure a smooth drug discovery process. Current methodologies include N-methylation, matching of hydrogen bonding acceptors and donors across the macrocycle, and additional masking of polarity. In this study, we investigate further the pivotal effects of shielding on permeability and studied the metabolism of the corresponding peptides in more detail by comparing peptide concentrations in the portal versus the jugular vein in rats. Interestingly, minor changes in one particular side chain impacts both permeability and liver metabolism. Graphical Abstract ![]()
Electronic supplementary material The online version of this article (doi:10.1007/s10989-017-9590-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas Vorherr
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Ian Lewis
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Joerg Berghausen
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | | | - Michael Schaefer
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
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37
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Macrocycles as protein-protein interaction inhibitors. Biochem J 2017; 474:1109-1125. [PMID: 28298556 DOI: 10.1042/bcj20160619] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/12/2017] [Accepted: 01/18/2017] [Indexed: 12/13/2022]
Abstract
Macrocyclic compounds such as cyclic peptides have emerged as a new and exciting class of drug candidates for inhibition of intracellular protein-protein interactions, which are challenging targets for conventional drug modalities (i.e. small molecules and proteins). Over the past decade, several complementary technologies have been developed to synthesize macrocycle libraries and screen them for binding to therapeutically relevant targets. Two different approaches have also been explored to increase the membrane permeability of cyclic peptides. In this review, we discuss these methods and their applications in the discovery of macrocyclic compounds against protein-protein interactions.
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38
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Damalanka VC, Kim Y, Galasiti Kankanamalage AC, Lushington GH, Mehzabeen N, Battaile KP, Lovell S, Chang KO, Groutas WC. Design, synthesis, and evaluation of a novel series of macrocyclic inhibitors of norovirus 3CL protease. Eur J Med Chem 2017; 127:41-61. [PMID: 28038326 PMCID: PMC5296247 DOI: 10.1016/j.ejmech.2016.12.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/01/2016] [Accepted: 12/16/2016] [Indexed: 02/01/2023]
Abstract
Norovirus infections have a major impact on public health worldwide, yet there is a current dearth of norovirus-specific therapeutics and prophylactics. This report describes the discovery of a novel class of macrocyclic inhibitors of norovirus 3C-like protease, a cysteine protease that is essential for virus replication. SAR, structural, and biochemical studies were carried out to ascertain the effect of structure on pharmacological activity and permeability. Insights gained from these studies have laid a solid foundation for capitalizing on the therapeutic potential of the series of inhibitors described herein.
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Affiliation(s)
- Vishnu C Damalanka
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | | | | | - Nurjahan Mehzabeen
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, IL 60439, USA
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.
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39
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Francisco Hilário F, Traoré MDM, Zwick V, Berry L, Simões-Pires CA, Cuendet M, Fantozzi N, Pereira de Freitas R, Maynadier M, Wein S, Vial H, Wong YS. Synthesis of an Uncharged Tetra-cyclopeptide Acting as a Transmembrane Carrier: Enhanced Cellular and Nuclear Uptake. Org Lett 2017; 19:612-615. [DOI: 10.1021/acs.orglett.6b03776] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Flaviane Francisco Hilário
- Univ. Grenoble Alpes, Département de Pharmacochimie
Moléculaire, CNRS UMR 5063, ICMG FR 2607, 470 rue de la chimie, Grenoble 38041 Cedex 9, France
- Universidade Federal de Ouro Preto, Departamento de
Química, ICEB, Campus Universitário Morro do Cruzeiro, 35400-000 Ouro
Preto, Minas Gerais Brazil
- Universidade Federal de Minas Gerais, Depertamento de
Química, UFMG, Av Pres Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Mohamed Dit Mady Traoré
- Univ. Grenoble Alpes, Département de Pharmacochimie
Moléculaire, CNRS UMR 5063, ICMG FR 2607, 470 rue de la chimie, Grenoble 38041 Cedex 9, France
- Univ. Grenoble Alpes, Département de Chimie
Moléculaire, CNRS UMR 5250, ICMG FR 2607, 301 rue de la chimie, Grenoble 38041 Cedex 9, France
| | - Vincent Zwick
- School
of Pharmaceutical Sciences, University of Geneva, University of Lausanne, rue Michel Servet 1, 1211 Geneva, Switzerland
| | - Laurence Berry
- Laboratoire
Dynamique des Interactions Membranaires Normales et Pathologiques,
UMR5235, CNRS, University of Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
| | - Claudia A. Simões-Pires
- School
of Pharmaceutical Sciences, University of Geneva, University of Lausanne, rue Michel Servet 1, 1211 Geneva, Switzerland
| | - Muriel Cuendet
- School
of Pharmaceutical Sciences, University of Geneva, University of Lausanne, rue Michel Servet 1, 1211 Geneva, Switzerland
| | - Nicolas Fantozzi
- Univ. Grenoble Alpes, Département de Pharmacochimie
Moléculaire, CNRS UMR 5063, ICMG FR 2607, 470 rue de la chimie, Grenoble 38041 Cedex 9, France
| | - Rossimiriam Pereira de Freitas
- Universidade Federal de Minas Gerais, Depertamento de
Química, UFMG, Av Pres Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Marjorie Maynadier
- Laboratoire
Dynamique des Interactions Membranaires Normales et Pathologiques,
UMR5235, CNRS, University of Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
| | - Sharon Wein
- Laboratoire
Dynamique des Interactions Membranaires Normales et Pathologiques,
UMR5235, CNRS, University of Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
| | - Henri Vial
- Laboratoire
Dynamique des Interactions Membranaires Normales et Pathologiques,
UMR5235, CNRS, University of Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
| | - Yung-Sing Wong
- Univ. Grenoble Alpes, Département de Pharmacochimie
Moléculaire, CNRS UMR 5063, ICMG FR 2607, 470 rue de la chimie, Grenoble 38041 Cedex 9, France
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40
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CADD medicine: design is the potion that can cure my disease. J Comput Aided Mol Des 2017; 31:249-253. [PMID: 28070730 DOI: 10.1007/s10822-016-0004-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/19/2016] [Indexed: 01/24/2023]
Abstract
The acronym "CADD" is often used interchangeably to refer to "Computer Aided Drug Discovery" and "Computer Aided Drug Design". While the former definition implies the use of a computer to impact one or more aspects of discovering a drug, in this paper we contend that computational chemists are most effective when they enable teams to apply true design principles as they strive to create medicines to treat human disease. We argue that teams must bring to bear multiple sub-disciplines of computational chemistry in an integrated manner in order to utilize these principles to address the multi-objective nature of the drug discovery problem. Impact, resourcing principles, and future directions for the field are also discussed, including areas of future opportunity as well as a cautionary note about hype and hubris.
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41
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Structural and conformational determinants of macrocycle cell permeability. Nat Chem Biol 2016; 12:1065-1074. [DOI: 10.1038/nchembio.2203] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 08/04/2016] [Indexed: 12/31/2022]
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42
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Furukawa A, Townsend CE, Schwochert J, Pye CR, Bednarek MA, Lokey RS. Passive Membrane Permeability in Cyclic Peptomer Scaffolds Is Robust to Extensive Variation in Side Chain Functionality and Backbone Geometry. J Med Chem 2016; 59:9503-9512. [PMID: 27690434 DOI: 10.1021/acs.jmedchem.6b01246] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Synthetic and natural cyclic peptides provide a testing ground for studying membrane permeability in nontraditional drug scaffolds. Cyclic peptomers, which incorporate peptide and N-alkylglycine (peptoid) residues, combine the stereochemical and geometric complexity of peptides with the functional group diversity accessible to peptoids. We synthesized cyclic peptomer libraries by split-pool techniques, separately permuting side chain and backbone geometry, and analyzed their membrane permeabilities using the parallel artificial membrane permeability assay. Nearly half of the side chain permutations had permeability coefficients (Papp) > 1 × 10-6 cm/s. Some backbone geometries enhanced permeability due to their ability to form more stable intramolecular hydrogen bond networks compared with other scaffolds. These observations suggest that hexameric cyclic peptomers can have good passive permeability even in the context of extensive side chain and backbone variation, and that high permeability can generally be achieved within a relatively wide lipophilicity range.
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Affiliation(s)
- Akihiro Furukawa
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States.,Modality Research Laboratories, Daiichi Sankyo Co., Ltd. , 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Chad E Townsend
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States
| | - Joshua Schwochert
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States
| | - Cameron R Pye
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States
| | - Maria A Bednarek
- Department of Antibody Discovery & Protein Engineering, Medimmune Ltd. , Cambridge CB21 6GH, United Kingdom
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States
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43
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Sato H, Yoshida M, Murase H, Nakagawa H, Doi T. Combinatorial Solid-Phase Synthesis and Biological Evaluation of Cyclodepsipeptide Destruxin B as a Negative Regulator for Osteoclast Morphology. ACS COMBINATORIAL SCIENCE 2016; 18:590-5. [PMID: 27490097 DOI: 10.1021/acscombsci.6b00076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Combinatorial synthesis and biological evaluation of cyclodepsipeptide destruxin B have been achieved. The cyclization precursors were prepared by solid-phase peptide synthesis via a split and pool method utilizing SynPhase lanterns with colored tags and cogs, followed by cleavage from the polymer-support. Macrolactonization utilizing MNBA-DMAPO in solution-phase was successfully performed in parallel to afford the desired 64-member destruxin analogues in moderate to good yields. Biological evaluation of the synthesized analogues indicated that a MeAla residue for the building block A is required to induce the desired morphological changes in osteoclast-like multinuclear cells (OCLs), and introduction of the substituent at the R(4) position of a proline moiety is tolerated by the morphology and may enable the preparation of a molecular probe for the target identification in the osteoclasts.
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Affiliation(s)
- Hiroshi Sato
- Graduate
School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
- Mitsubishi Tanabe Pharma Corporation, 3-2-10, Dosho-machi, Chuo-ku, Osaka 541-8505, Japan
| | - Masahito Yoshida
- Graduate
School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Hayato Murase
- Department
of Applied Biological Chemistry, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Hiroshi Nakagawa
- Department
of Applied Biological Chemistry, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Takayuki Doi
- Graduate
School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
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44
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Matsson P, Doak BC, Over B, Kihlberg J. Cell permeability beyond the rule of 5. Adv Drug Deliv Rev 2016; 101:42-61. [PMID: 27067608 DOI: 10.1016/j.addr.2016.03.013] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/25/2016] [Accepted: 03/31/2016] [Indexed: 11/17/2022]
Abstract
Drug discovery for difficult targets that have large and flat binding sites is often better suited to compounds beyond the "rule of 5" (bRo5). However, such compounds carry higher pharmacokinetic risks, such as low solubility and permeability, and increased efflux and metabolism. Interestingly, recent drug approvals and studies suggest that cell permeable and orally bioavailable drugs can be discovered far into bRo5 space. Tactics such as reduction or shielding of polarity by N-methylation, bulky side chains and intramolecular hydrogen bonds may be used to increase cell permeability in this space, but often results in decreased solubility. Conformationally flexible compounds can, however, combine high permeability and solubility, properties that are keys for cell permeability and intestinal absorption. Recent developments in computational conformational analysis will aid design of such compounds and hence prediction of cell permeability. Transporter mediated efflux occurs for most investigated drugs in bRo5 space, however it is commonly overcome by high local intestinal concentrations on oral administration. In contrast, there is little data to support significant impact of transporter-mediated intestinal absorption in bRo5 space. Current knowledge of compound properties that govern transporter effects of bRo5 drugs is limited and requires further fundamental and comprehensive studies.
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Affiliation(s)
- Pär Matsson
- Department of Pharmacy, BMC, Uppsala University, Box 580, SE-751 23 Uppsala, Sweden
| | - Bradley C Doak
- Department of Medicinal Chemistry, MIPS, Monash University, 381 Royal Parade, Parkville, Victoria, Australia
| | - Björn Over
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden.
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45
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Hickey JL, Zaretsky S, St. Denis MA, Kumar Chakka S, Morshed MM, Scully CCG, Roughton AL, Yudin AK. Passive Membrane Permeability of Macrocycles Can Be Controlled by Exocyclic Amide Bonds. J Med Chem 2016; 59:5368-76. [DOI: 10.1021/acs.jmedchem.6b00222] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jennifer L. Hickey
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Encycle Therapeutics Inc., 101
College Street, Suite 314, Toronto, Ontario M5G 1L7, Canada
| | - Serge Zaretsky
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Megan A. St. Denis
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Encycle Therapeutics Inc., 101
College Street, Suite 314, Toronto, Ontario M5G 1L7, Canada
| | - Sai Kumar Chakka
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Encycle Therapeutics Inc., 101
College Street, Suite 314, Toronto, Ontario M5G 1L7, Canada
| | - M. Monzur Morshed
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Encycle Therapeutics Inc., 101
College Street, Suite 314, Toronto, Ontario M5G 1L7, Canada
| | - Conor C. G. Scully
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Andrew L. Roughton
- Encycle Therapeutics Inc., 101
College Street, Suite 314, Toronto, Ontario M5G 1L7, Canada
| | - Andrei K. Yudin
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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46
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Fouché M, Schäfer M, Berghausen J, Desrayaud S, Blatter M, Piéchon P, Dix I, Martin Garcia A, Roth HJ. Design and Development of a Cyclic Decapeptide Scaffold with Suitable Properties for Bioavailability and Oral Exposure. ChemMedChem 2016; 11:1048-59. [DOI: 10.1002/cmdc.201600082] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 03/09/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Marianne Fouché
- Global Discovery Chemistry/Macrocycles; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Michael Schäfer
- Global Discovery Chemistry/CADD; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Jörg Berghausen
- Metabolism and Pharmacokinetics; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Sandrine Desrayaud
- Metabolism and Pharmacokinetics; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Markus Blatter
- Global Discovery Chemistry/Analytics (NMR); Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Philippe Piéchon
- Global Discovery Chemistry/Analytics (Crystallography); Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Ina Dix
- Global Discovery Chemistry/Analytics (Crystallography); Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Aimar Martin Garcia
- The University of the Basque Country-Euskal Herriko Unibertsitatea; Campus de Leioa 48949 Leioa Spain
| | - Hans-Jörg Roth
- Global Discovery Chemistry/Macrocycles; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
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47
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Fouché M, Schäfer M, Blatter M, Berghausen J, Desrayaud S, Roth HJ. Pharmacokinetic Studies around the Mono- and Difunctionalization of a Bioavailable Cyclic Decapeptide Scaffold. ChemMedChem 2016; 11:1060-8. [DOI: 10.1002/cmdc.201600083] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Marianne Fouché
- Global Discovery Chemistry/Macrocycles; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Michael Schäfer
- Global Discovery Chemistry/CADD; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Markus Blatter
- Global Discovery Chemistry/Analytics (NMR); Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Jörg Berghausen
- Metabolism and Pharmacokinetics; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Sandrine Desrayaud
- Metabolism and Pharmacokinetics; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Hans-Jörg Roth
- Global Discovery Chemistry/Macrocycles; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
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48
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Bockus AT, Schwochert JA, Pye CR, Townsend CE, Sok V, Bednarek MA, Lokey RS. Going Out on a Limb: Delineating The Effects of β-Branching, N-Methylation, and Side Chain Size on the Passive Permeability, Solubility, and Flexibility of Sanguinamide A Analogues. J Med Chem 2015; 58:7409-18. [PMID: 26308180 DOI: 10.1021/acs.jmedchem.5b00919] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
It is well established that intramolecular hydrogen bonding and N-methylation play important roles in the passive permeability of cyclic peptides, but other structural features have been explored less intensively. Recent studies on the oral bioavailability of the cyclic heptapeptide sanguinamide A have raised the question of whether steric occlusion of polar groups via β-branching is an effective, yet untapped, tool in cyclic peptide permeability optimization. We report the structures of 17 sanguinamide A analogues designed to test the relative contributions of β-branching, N-methylation, and side chain size to passive membrane permeability and aqueous solubility. We demonstrate that β-branching has little effect on permeability compared to the effects of aliphatic carbon count and N-methylation of exposed NH groups. We highlight a new N-methylated analogue of sanguinamide A with a Leu substitution at position 2 that exhibits solvent-dependent flexibility and improved permeability over that of the natural product.
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Affiliation(s)
- Andrew T Bockus
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Joshua A Schwochert
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Cameron R Pye
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Chad E Townsend
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Vong Sok
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Maria A Bednarek
- Department of Antibody Discovery & Protein Engineering, Medimmune Ltd , Cambridge CB21 6GH, United Kingdom
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
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Schwochert J, Turner R, Thang M, Berkeley RF, Ponkey AR, Rodriguez KM, Leung SSF, Khunte B, Goetz G, Limberakis C, Kalgutkar AS, Eng H, Shapiro MJ, Mathiowetz AM, Price DA, Liras S, Jacobson MP, Lokey RS. Peptide to Peptoid Substitutions Increase Cell Permeability in Cyclic Hexapeptides. Org Lett 2015; 17:2928-31. [PMID: 26046483 DOI: 10.1021/acs.orglett.5b01162] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The effect of peptide-to-peptoid substitutions on the passive membrane permeability of an N-methylated cyclic hexapeptide is examined. In general, substitutions maintained permeability but increased conformational heterogeneity. Diversification with nonproteinogenic side chains increased permeability up to 3-fold. Additionally, the conformational impact of peptoid substitutions within a β-turn are explored. Based on these results, the strategic incorporation of peptoid residues into cyclic peptides can maintain or improve cell permeability, while increasing access to diverse side-chain functionality.
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Affiliation(s)
- Joshua Schwochert
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Rushia Turner
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Melissa Thang
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Ray F Berkeley
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Alexandra R Ponkey
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Kelsie M Rodriguez
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Siegfried S F Leung
- ‡Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Bhagyashree Khunte
- ∥World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Gilles Goetz
- ∥World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Chris Limberakis
- ∥World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Amit S Kalgutkar
- §Pharmacokinetics and Drug Metabolism, Cambridge Laboratories, Pfizer Inc. Cambridge, Massachusetts 02139, United States
| | - Heather Eng
- ⊥Pharmacokinetics and Drug Metabolism, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Michael J Shapiro
- ∥World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Alan M Mathiowetz
- ○World Wide Medicinal Chemistry, Cambridge Laboratories, Pfizer Inc. Cambridge, Massachusetts 02139, United States
| | - David A Price
- ○World Wide Medicinal Chemistry, Cambridge Laboratories, Pfizer Inc. Cambridge, Massachusetts 02139, United States
| | - Spiros Liras
- ○World Wide Medicinal Chemistry, Cambridge Laboratories, Pfizer Inc. Cambridge, Massachusetts 02139, United States
| | - Matthew P Jacobson
- ‡Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - R Scott Lokey
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
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Abstract
Recently, peptides have been validated to address intracellular targets and/or to be orally bioavailable. This review describes some of these scaffolds, offers insight in new cyclization methodologies thought to be beneficial to enhance permeability, and highlights modification on peptides thought to improve oral bioavailability. In this context, side chains and back-bone derivatization beneficial to encourage cellular uptake are presented. In addition, new methodologies supporting the assessment of permeability are discussed.
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