1
|
Faris J, Adaligil E, Popovych N, Ono S, Takahashi M, Nguyen H, Plise E, Taechalertpaisarn J, Lee HW, Koehler MFT, Cunningham CN, Lokey RS. Membrane Permeability in a Large Macrocyclic Peptide Driven by a Saddle-Shaped Conformation. J Am Chem Soc 2024; 146:4582-4591. [PMID: 38330910 PMCID: PMC10885153 DOI: 10.1021/jacs.3c10949] [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: 10/17/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 02/10/2024]
Abstract
The effort to modulate challenging protein targets has stimulated interest in ligands that are larger and more complex than typical small-molecule drugs. While combinatorial techniques such as mRNA display routinely produce high-affinity macrocyclic peptides against classically undruggable targets, poor membrane permeability has limited their use toward primarily extracellular targets. Understanding the passive membrane permeability of macrocyclic peptides would, in principle, improve our ability to design libraries whose leads can be more readily optimized against intracellular targets. Here, we investigate the permeabilities of over 200 macrocyclic 10-mers using the thioether cyclization motif commonly found in mRNA display macrocycle libraries. We identified the optimal lipophilicity range for achieving permeability in thioether-cyclized 10-mer cyclic peptide-peptoid hybrid scaffolds and showed that permeability could be maintained upon extensive permutation in the backbone. In one case, changing a single amino acid from d-Pro to d-NMe-Ala, representing the loss of a single methylene group in the side chain, resulted in a highly permeable scaffold in which the low-dielectric conformation shifted from the canonical cross-beta geometry of the parent compounds into a novel saddle-shaped fold in which all four backbone NH groups were sequestered from the solvent. This work provides an example by which pre-existing physicochemical knowledge of a scaffold can benefit the design of macrocyclic peptide mRNA display libraries, pointing toward an approach for biasing libraries toward permeability by design. Moreover, the compounds described herein are a further demonstration that geometrically diverse, highly permeable scaffolds exist well beyond conventional drug-like chemical space.
Collapse
Affiliation(s)
- Justin
H. Faris
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
| | - Emel Adaligil
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Nataliya Popovych
- Department
of Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, United States
| | - Satoshi Ono
- Innovative
Research Division, Mitsubishi Tanabe Pharma
Corporation, Kanagawa 227-0033, Japan
| | - Mifune Takahashi
- Department
of Drug Metabolism and Pharmacokinetics, Genentech, South
San Francisco, California 94080, United States
| | - Huy Nguyen
- Department
of Analytical Research, Genentech, South San Francisco, California 94080, United States
| | - Emile Plise
- Department
of Drug Metabolism and Pharmacokinetics, Genentech, South
San Francisco, California 94080, United States
| | - Jaru Taechalertpaisarn
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
| | - Hsiau-Wei Lee
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
| | - Michael F. T. Koehler
- Department
of Medicinal Chemistry, Genentech, South San Francisco, California 94080, United States
| | - Christian N. Cunningham
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - R. Scott Lokey
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
| |
Collapse
|
2
|
Asano D, Takakusa H, Nakai D. Oral Absorption of Middle-to-Large Molecules and Its Improvement, with a Focus on New Modality Drugs. Pharmaceutics 2023; 16:47. [PMID: 38258058 PMCID: PMC10820198 DOI: 10.3390/pharmaceutics16010047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/11/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
To meet unmet medical needs, middle-to-large molecules, including peptides and oligonucleotides, have emerged as new therapeutic modalities. Owing to their middle-to-large molecular sizes, middle-to-large molecules are not suitable for oral absorption, but there are high expectations around orally bioavailable macromolecular drugs, since oral administration is the most convenient dosing route. Therefore, extensive efforts have been made to create bioavailable middle-to-large molecules or develop absorption enhancement technology, from which some successes have recently been reported. For example, Rybelsus® tablets and Mycapssa® capsules, both of which contain absorption enhancers, were approved as oral medications for type 2 diabetes and acromegaly, respectively. The oral administration of Rybelsus and Mycapssa exposes their pharmacologically active peptides with molecular weights greater than 1000, namely, semaglutide and octreotide, respectively, into systemic circulation. Although these two medications represent major achievements in the development of orally absorbable peptide formulations, the oral bioavailability of peptides after taking Rybelsus and Mycapssa is still only around 1%. In this article, we review the approaches and recent advances of orally bioavailable middle-to-large molecules and discuss challenges for improving their oral absorption.
Collapse
Affiliation(s)
- Daigo Asano
- Drug Metabolism and Pharmacokinetics Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan; (H.T.); (D.N.)
| | | | | |
Collapse
|
3
|
Ghosh P, Raj N, Verma H, Patel M, Chakraborti S, Khatri B, Doreswamy CM, Anandakumar SR, Seekallu S, Dinesh MB, Jadhav G, Yadav PN, Chatterjee J. An amide to thioamide substitution improves the permeability and bioavailability of macrocyclic peptides. Nat Commun 2023; 14:6050. [PMID: 37770425 PMCID: PMC10539501 DOI: 10.1038/s41467-023-41748-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 09/06/2023] [Indexed: 09/30/2023] Open
Abstract
Solvent shielding of the amide hydrogen bond donor (NH groups) through chemical modification or conformational control has been successfully utilized to impart membrane permeability to macrocyclic peptides. We demonstrate that passive membrane permeability can also be conferred by masking the amide hydrogen bond acceptor (>C = O) through a thioamide substitution (>C = S). The membrane permeability is a consequence of the lower desolvation penalty of the macrocycle resulting from a concerted effect of conformational restriction, local desolvation of the thioamide bond, and solvent shielding of the amide NH groups. The enhanced permeability and metabolic stability on thioamidation improve the bioavailability of a macrocyclic peptide composed of hydrophobic amino acids when administered through the oral route in rats. Thioamidation of a bioactive macrocyclic peptide composed of polar amino acids results in analogs with longer duration of action in rats when delivered subcutaneously. These results highlight the potential of O to S substitution as a stable backbone modification in improving the pharmacological properties of peptide macrocycles.
Collapse
Affiliation(s)
- Pritha Ghosh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Nishant Raj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Hitesh Verma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Monika Patel
- Neuroscience & Ageing Biology, CSIR-CDRI, Lucknow, 226031, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sohini Chakraborti
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Chandrashekar M Doreswamy
- Department of Pre-clinical Research, Anthem Biosciences Pvt. Ltd., Bangalore, 560099, Karnataka, India
| | - S R Anandakumar
- Department of Pre-clinical Research, Anthem Biosciences Pvt. Ltd., Bangalore, 560099, Karnataka, India
| | - Srinivas Seekallu
- Department of Pre-clinical Research, Anthem Biosciences Pvt. Ltd., Bangalore, 560099, Karnataka, India
| | - M B Dinesh
- Central Animal Facility, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Gajanan Jadhav
- Eurofins Advinus Biopharma Services India Pvt. Ltd., Bangalore, 560058, Karnataka, India
| | - Prem Narayan Yadav
- Neuroscience & Ageing Biology, CSIR-CDRI, Lucknow, 226031, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India.
| |
Collapse
|
4
|
Lee D, Choi J, Yang MJ, Park CJ, Seo J. Controlling the Chameleonic Behavior and Membrane Permeability of Cyclosporine Derivatives via Backbone and Side Chain Modifications. J Med Chem 2023; 66:13189-13204. [PMID: 37718494 DOI: 10.1021/acs.jmedchem.3c01140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Some macrocycles exhibit enhanced membrane permeability through conformational switching in different environmental polarities, a trait known as chameleonic behavior. In this study, we demonstrate specific backbone and side chain modifications that can control chameleonic behavior and passive membrane permeability using a cyclosporin O (CsO) scaffold. To quantify chameleonic behavior, we used a ratio of the population of the closed conformation obtained in polar solvent and nonpolar solvent for each CsO derivative. We found that β-hydroxylation at position 1 (1 and 3) can encode chameleonicity and improve permeability. However, the conformational stabilization induced by adding an additional transannular H-bond (2 and 5) leads to a much slower rate of membrane permeation. Our CsO scaffold provides a platform for the systematic study of the relationship among conformation, membrane permeability, solubility, and protein binding. This knowledge contributes to the discovery of potent beyond the rule of five (bRo5) macrocycles capable of targeting undruggable targets.
Collapse
Affiliation(s)
- Dongjae Lee
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Jieun Choi
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Min June Yang
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Jiwon Seo
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| |
Collapse
|
5
|
Moxam J, Naylon S, Richaud AD, Zhao G, Padilla A, Roche SP. Passive Membrane Permeability of Sizable Acyclic β-Hairpin Peptides. ACS Med Chem Lett 2023; 14:278-284. [PMID: 36923919 PMCID: PMC10009788 DOI: 10.1021/acsmedchemlett.2c00486] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
The recent shift toward increasingly larger drug modalities has created a significant demand for novel classes of compounds with high membrane permeability that can inhibit intracellular protein-protein interactions (PPIs). While major advances have been made in the design of cell-permeable helices, stapled β-sheets, and cyclic peptides, the development of large acyclic β-hairpins lags far behind. Therefore, we investigated a series of 26 β-hairpins (MW > 1.6 kDa) belonging to a chemical space far beyond the Lipinski "rule of five" (fbRo5) and showed that, in addition to their innate plasticity, the lipophilicity of these peptides (log D 7.4 ≈ 0 ± 0.7) can be tuned to drastically improve the balance between aqueous solubility and passive membrane permeability.
Collapse
Affiliation(s)
- Jillene Moxam
- Department
of Chemistry and Biochemistry, Florida Atlantic
University, Boca Raton, Florida 33431, United States
| | - Sarah Naylon
- Department
of Chemistry and Biochemistry, Florida Atlantic
University, Boca Raton, Florida 33431, United States
| | - Alexis D. Richaud
- Department
of Chemistry and Biochemistry, Florida Atlantic
University, Boca Raton, Florida 33431, United States
| | - Guangkuan Zhao
- Department
of Chemistry and Biochemistry, Florida Atlantic
University, Boca Raton, Florida 33431, United States
| | - Alberto Padilla
- Department
of Natural Science, Keiser University, Fort Lauderdale, Florida 33309, United States
| | - Stéphane P. Roche
- Department
of Chemistry and Biochemistry, Florida Atlantic
University, Boca Raton, Florida 33431, United States
- Center
for Molecular Biology and Biotechnology, Florida Atlantic University, Jupiter, Florida 33458, United States
| |
Collapse
|
6
|
Mazzanti L, Ha-Duong T. Understanding Passive Membrane Permeation of Peptides: Physical Models and Sampling Methods Compared. Int J Mol Sci 2023; 24:ijms24055021. [PMID: 36902455 PMCID: PMC10003141 DOI: 10.3390/ijms24055021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023] Open
Abstract
The early characterization of drug membrane permeability is an important step in pharmaceutical developments to limit possible late failures in preclinical studies. This is particularly crucial for therapeutic peptides whose size generally prevents them from passively entering cells. However, a sequence-structure-dynamics-permeability relationship for peptides still needs further insight to help efficient therapeutic peptide design. In this perspective, we conducted here a computational study for estimating the permeability coefficient of a benchmark peptide by considering and comparing two different physical models: on the one hand, the inhomogeneous solubility-diffusion model, which requires umbrella-sampling simulations, and on the other hand, a chemical kinetics model which necessitates multiple unconstrained simulations. Notably, we assessed the accuracy of the two approaches in relation to their computational cost.
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Raja R, Hemaiswarya S, Arunkumar K, Mathiyazhagan N, Sabariswaran K, Arun A, Ramasamy P. Efficacy of Eisenia bicyclis phlorotannins in the treatment of diabetes and reducing inflammation. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2023.102381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
9
|
Kusumoto Y, Hayashi K, Sato S, Yamada T, Kozono I, Nakata Z, Asada N, Mitsuki S, Watanabe A, Wakasa-Morimoto C, Uemura K, Arita S, Miki S, Mizutare T, Mikamiyama H. Highly Potent and Oral Macrocyclic Peptides as a HIV-1 Protease Inhibitor: mRNA Display-Derived Hit-to-Lead Optimization. ACS Med Chem Lett 2022; 13:1634-1641. [PMID: 36262395 PMCID: PMC9575168 DOI: 10.1021/acsmedchemlett.2c00310] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/30/2022] [Indexed: 11/30/2022] Open
Abstract
Human immunodeficiency virus type-1 (HIV-1) protease is essential for viral propagation, and its inhibitors are key anti-HIV-1 drug candidates. In this study, we discovered a novel HIV-1 protease inhibitor (compound 16) with potent antiviral activity and oral bioavailability using a structure-based drug design approach via X-ray crystal structure analysis and improved metabolic stability, starting from hit macrocyclic peptides identified by mRNA display against HIV-1 protease. We found that the improvement of the proteolytic stability of macrocyclic peptides by introducing a methyl group to the α-position of amino acid is crucial to exhibit strong antiviral activity. In addition, macrocyclic peptides, which have moderate metabolic stability and solubility in solutions containing taurocholic acid, exhibited desirable plasma total clearance and oral bioavailability. These approaches may contribute to the successful discovery and development of orally bioavailable peptide drugs.
Collapse
Affiliation(s)
- Yoshifumi Kusumoto
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Kyohei Hayashi
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Soichiro Sato
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Toru Yamada
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Iori Kozono
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Zenzaburo Nakata
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Naoya Asada
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Shungo Mitsuki
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Ayahisa Watanabe
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Chiaki Wakasa-Morimoto
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Kentaro Uemura
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Shuhei Arita
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Shinobu Miki
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Tohru Mizutare
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Hidenori Mikamiyama
- Shionogi Pharmaceutical
Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| |
Collapse
|
10
|
Bhardwaj G, O'Connor J, Rettie S, Huang YH, Ramelot TA, Mulligan VK, Alpkilic GG, Palmer J, Bera AK, Bick MJ, Di Piazza M, Li X, Hosseinzadeh P, Craven TW, Tejero R, Lauko A, Choi R, Glynn C, Dong L, Griffin R, van Voorhis WC, Rodriguez J, Stewart L, Montelione GT, Craik D, Baker D. Accurate de novo design of membrane-traversing macrocycles. Cell 2022; 185:3520-3532.e26. [PMID: 36041435 PMCID: PMC9490236 DOI: 10.1016/j.cell.2022.07.019] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 05/01/2022] [Accepted: 07/21/2022] [Indexed: 01/26/2023]
Abstract
We use computational design coupled with experimental characterization to systematically investigate the design principles for macrocycle membrane permeability and oral bioavailability. We designed 184 6-12 residue macrocycles with a wide range of predicted structures containing noncanonical backbone modifications and experimentally determined structures of 35; 29 are very close to the computational models. With such control, we show that membrane permeability can be systematically achieved by ensuring all amide (NH) groups are engaged in internal hydrogen bonding interactions. 84 designs over the 6-12 residue size range cross membranes with an apparent permeability greater than 1 × 10-6 cm/s. Designs with exposed NH groups can be made membrane permeable through the design of an alternative isoenergetic fully hydrogen-bonded state favored in the lipid membrane. The ability to robustly design membrane-permeable and orally bioavailable peptides with high structural accuracy should contribute to the next generation of designed macrocycle therapeutics.
Collapse
Affiliation(s)
- Gaurav Bhardwaj
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA; Biological Physics, Structure and Design program, University of Washington, Seattle, WA 98195, USA.
| | - Jacob O'Connor
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Biological Physics, Structure and Design program, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Stephen Rettie
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Molecular Cell and Biology program, University of Washington, Seattle, WA 98195, USA
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Theresa A Ramelot
- Department of Chemistry and Chemical Biology and Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | | | - Gizem Gokce Alpkilic
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA; Molecular Engineering and Sciences Program, University of Washington, Seattle, WA 98195, USA
| | - Jonathan Palmer
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Asim K Bera
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Matthew J Bick
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Maddalena Di Piazza
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Xinting Li
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Parisa Hosseinzadeh
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Timothy W Craven
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Roberto Tejero
- Departamento de Quίmica Fίsica, Universidad de Valencia, Avenida Dr. Moliner 50, Burjassot, 46100 Valencia, Spain
| | - Anna Lauko
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Biological Physics, Structure and Design program, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Ryan Choi
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, WA, USA
| | - Calina Glynn
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, USA
| | - Linlin Dong
- Takeda Pharmaceuticals Inc., Cambridge, MA, USA
| | | | - Wesley C van Voorhis
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, WA, USA
| | - Jose Rodriguez
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, USA
| | - Lance Stewart
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Gaetano T Montelione
- Department of Chemistry and Chemical Biology and Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - David Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
11
|
Sugita M, Fujie T, Yanagisawa K, Ohue M, Akiyama Y. Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:4549-4560. [PMID: 36053061 PMCID: PMC9516681 DOI: 10.1021/acs.jcim.2c00931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclic peptides have attracted attention as a promising pharmaceutical modality due to their potential to selectively inhibit previously undruggable targets, such as intracellular protein-protein interactions. Poor membrane permeability is the biggest bottleneck hindering successful drug discovery based on cyclic peptides. Therefore, the development of computational methods that can predict membrane permeability and support elucidation of the membrane permeation mechanism of drug candidate peptides is much sought after. In this study, we developed a protocol to simulate the behavior in membrane permeation steps and estimate the membrane permeability of large cyclic peptides with more than or equal to 10 residues. This protocol requires the use of a more realistic membrane model than a single-lipid phospholipid bilayer. To select a membrane model, we first analyzed the effect of cholesterol concentration in the model membrane on the potential of mean force and hydrogen bonding networks along the direction perpendicular to the membrane surface as predicted by molecular dynamics simulations using cyclosporine A. These results suggest that a membrane model with 40 or 50 mol % cholesterol was suitable for predicting the permeation process. Subsequently, two types of membrane models containing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine and 40 and 50 mol % cholesterol were used. To validate the efficiency of our protocol, the membrane permeability of 18 ten-residue peptides was predicted. Correlation coefficients of R > 0.8 between the experimental and calculated permeability values were obtained with both model membranes. The results of this study demonstrate that the lipid membrane is not just a medium but also among the main factors determining the membrane permeability of molecules. The computational protocol proposed in this study and the findings obtained on the effect of membrane model composition will contribute to building a schematic view of the membrane permeation process. Furthermore, the results of this study will eventually aid the elucidation of design rules for peptide drugs with high membrane permeability.
Collapse
Affiliation(s)
- Masatake Sugita
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Middle-Molecule IT-Based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Takuya Fujie
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Middle-Molecule IT-Based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Keisuke Yanagisawa
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Middle-Molecule IT-Based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Masahito Ohue
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Middle-Molecule IT-Based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Yutaka Akiyama
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Middle-Molecule IT-Based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| |
Collapse
|
12
|
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.
Collapse
|
13
|
Optimization of cyclic peptide property using chromatographic capacity factor on permeability of passive cell membrane and human induced pluripotent stem cell-derived intestinal membrane. J Pharm Sci 2022; 111:1879-1886. [DOI: 10.1016/j.xphs.2022.03.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 11/21/2022]
|
14
|
Chiral secondary amino acids, their importance, and methods of analysis. Amino Acids 2022; 54:687-719. [PMID: 35192062 DOI: 10.1007/s00726-022-03136-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 02/04/2022] [Indexed: 11/01/2022]
Abstract
Naturally occurring secondary amino acids, with proline as the main representative, contain an alpha-imino group in a cycle that is typically four-, five-, and six-membered. The unique ring structure exhibits exceptional properties-conformational rigidity, chemical stability, and specific roles in protein structure and folding. Many proline analogues have been used as valuable compounds for the study of metabolism of both prokaryotic and eukaryotic cells and for the synthesis of compounds with desired biological, pharmaceutical, or industrial properties. The D-forms of secondary amino acids play different roles in living organisms than the L-forms. They have different metabolic pathways, biological, physiological, and pharmacological effects, they can be indicators of changes and also serve as biomarkers of diseases. In the scientific literature, the number of articles examining D-amino acids in biological samples is increasing. The review summarises information on the occurrence and importance of D- and L-secondary amino acids-azetidic acid, proline, hydroxyprolines, pipecolic, nipecotic, hydroxypipecolic acids and related peptides containing these D-AAs, as well as the main analytical methods (mostly chromatographic) used for their enantiomeric determination in different matrices (biological samples, plants, food, water, and soil).
Collapse
|
15
|
Linker SM, Schellhaas C, Ries B, Roth HJ, Fouché M, Rodde S, Riniker S. Polar/apolar interfaces modulate the conformational behavior of cyclic peptides with impact on their passive membrane permeability. RSC Adv 2022; 12:5782-5796. [PMID: 35424539 PMCID: PMC8981571 DOI: 10.1039/d1ra09025a] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/10/2022] [Indexed: 02/01/2023] Open
Abstract
Cyclic peptides have the potential to vastly extend the scope of druggable proteins and lead to new therapeutics for currently untreatable diseases. However, cyclic peptides often suffer from poor bioavailability. To uncover design principles for permeable cyclic peptides, a promising strategy is to analyze the conformational dynamics of the peptides using molecular dynamics (MD) and Markov state models (MSMs). Previous MD studies have focused on the conformational dynamics in pure aqueous or apolar environments to rationalize membrane permeability. However, during the key steps of the permeation through the membrane, cyclic peptides are exposed to interfaces between polar and apolar regions. Recent studies revealed that these interfaces constitute the free energy minima of the permeation process. Thus, a deeper understanding of the behavior of cyclic peptides at polar/apolar interfaces is desired. Here, we investigate the conformational and kinetic behavior of cyclic decapeptides at a water/chloroform interface using unbiased MD simulations and MSMs. The distinct environments at the interface alter the conformational equilibrium as well as the interconversion kinetics of cyclic peptide conformations. For peptides with low population of the permeable conformation in aqueous solution, the polar/apolar interface facilitates the interconversion to the closed conformation, which is required for membrane permeation. Comparison to unbiased MD simulations with a POPC bilayer reveals that not only the conformations but also the orientations are relevant in a membrane system. These findings allow us to propose a permeability model that includes both 'prefolding' and 'non-prefolding' cyclic peptides - an extension that can lead to new design considerations for permeable cyclic peptides.
Collapse
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
| | - Benjamin Ries
- 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
| |
Collapse
|
16
|
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
| |
Collapse
|
17
|
Wang S, Krummenacher K, Landrum GA, Sellers BD, Di Lello P, Robinson SJ, Martin B, Holden JK, Tom JYK, Murthy AC, Popovych N, Riniker S. Incorporating NOE-Derived Distances in Conformer Generation of Cyclic Peptides with Distance Geometry. J Chem Inf Model 2022; 62:472-485. [PMID: 35029985 DOI: 10.1021/acs.jcim.1c01165] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nuclear magnetic resonance (NMR) data from NOESY (nuclear Overhauser enhancement spectroscopy) and ROESY (rotating frame Overhauser enhancement spectroscopy) experiments can easily be combined with distance geometry (DG) based conformer generators by modifying the molecular distance bounds matrix. In this work, we extend the modern DG based conformer generator ETKDG, which has been shown to reproduce experimental crystal structures from small molecules to large macrocycles well, to include NOE-derived interproton distances. In noeETKDG, the experimentally derived interproton distances are incorporated into the distance bounds matrix as loose upper (or lower) bounds to generate large conformer sets. Various subselection techniques can subsequently be applied to yield a conformer bundle that best reproduces the NOE data. The approach is benchmarked using a set of 24 (mostly) cyclic peptides for which NOE-derived distances as well as reference solution structures obtained by other software are available. With respect to other packages currently available, the advantages of noeETKDG are its speed and that no prior force-field parametrization is required, which is especially useful for peptides with unnatural amino acids. The resulting conformer bundles can be further processed with the use of structural refinement techniques to improve the modeling of the intramolecular nonbonded interactions. The noeETKDG code is released as a fully open-source software package available at www.github.com/rinikerlab/customETKDG.
Collapse
Affiliation(s)
- Shuzhe Wang
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Kajo Krummenacher
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Gregory A Landrum
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Benjamin D Sellers
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Paola Di Lello
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Sarah J Robinson
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Bryan Martin
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jeffrey K Holden
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Jeffrey Y K Tom
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Anastasia C Murthy
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Nataliya Popovych
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| |
Collapse
|
18
|
Asano A, Minami C, Matsuoka S, Kato T, Doi M. An Ornithine-Free Gramicidin S Analogue Using Norleucine, Cyclo(Val-Nle-Leu-D-Phe-Pro) 2, Forms Helically Aligned β-Sheets. Chem Pharm Bull (Tokyo) 2021; 69:1097-1103. [PMID: 34719592 DOI: 10.1248/cpb.c21-00548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structure of an ornithine (Orn)-free Gramicidin S (GS) analogue, cyclo(Val-Nle-Leu-D-Phe-Pro)2 (NGS), was studied. Its circular dichroism (CD) spectrum showed that NGS has a structure similar to GS, though the value of [θ] indicated smaller β-turn and sheet populations. This is probably because the Nle side chain could not form intramolecular hydrogen bonds stabilizing the sheet structure. The chemical shift perturbation of αH and JNH-αH were similar in GS and NGS. Three independent NGS molecules formed intramolecular β-sheet structures in crystal. The turn structures of D-Phe-Pro moieties were classed as type II' β-turns, but one part was unclassed. The molecules were arranged in a twisting manner, which resulted in the formation of a helical sheet. Similar structural characteristics were observed previously in a Leu-type, Orn-free GS analogue and in GS trifluoroacetic acid salt.
Collapse
Affiliation(s)
- Akiko Asano
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University
| | - Chisato Minami
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University
| | - Shiori Matsuoka
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University
| | - Takuma Kato
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University
| | - Mitsunobu Doi
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University
| |
Collapse
|
19
|
Pace JR, Lampkin BJ, Abakah C, Moyer A, Miao J, Deprey K, Cerulli RA, Lin YS, Baleja JD, Baker D, Kritzer JA. Stapled β-Hairpins Featuring 4-Mercaptoproline. J Am Chem Soc 2021; 143:15039-15044. [PMID: 34516087 DOI: 10.1021/jacs.1c04378] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptides constrained by intramolecular cross-links, especially stapled α-helices, have emerged as versatile scaffolds for drug development. However, there are fewer examples of similarly constrained scaffolds for other secondary structures. Here, we used a novel computational strategy to identify an optimal staple for antiparallel β-strands, and then we incorporated that staple within a β-hairpin peptide. The hairpin uses 4-mercaptoproline as a novel staple component, which contributes to a unique, kinked structure. The stapled hairpins show a high degree of structure in aqueous solution, excellent resistance to degradation in cell lysates, and cytosolic penetration at micromolar concentrations. They also overlay with a unique subset of kinked hairpin motifs at protein-protein interaction interfaces. Thus, these scaffolds represent promising starting points for developing inhibitors of cellular protein-protein interactions.
Collapse
Affiliation(s)
- Jennifer R Pace
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Bryan J Lampkin
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Charles Abakah
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Adam Moyer
- Molecular Engineering and Sciences Institute, University of Washington, Seattle Washington 98195, United States
| | - Jiayuan Miao
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Kirsten Deprey
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Robert A Cerulli
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts 02111, United States
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - James D Baleja
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts 02111, United States
| | - David Baker
- Molecular Engineering and Sciences Institute, University of Washington, Seattle Washington 98195, United States.,Department of Biochemistry, Institute for Protein Design, and Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, United States
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| |
Collapse
|
20
|
Wang S, König G, Roth HJ, Fouché M, Rodde S, Riniker S. Effect of Flexibility, Lipophilicity, and the Location of Polar Residues on the Passive Membrane Permeability of a Series of Cyclic Decapeptides. J Med Chem 2021; 64:12761-12773. [PMID: 34406766 DOI: 10.1021/acs.jmedchem.1c00775] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cyclic peptides have received increasing attention over the recent years as potential therapeutics for "undruggable" targets. One major obstacle is, however, their often relatively poor bioavailability. Here, we investigate the structure-permeability relationship of 24 cyclic decapeptides that share the same backbone N-methylation pattern but differ in their side chains. The peptides cover a large range of values for passive membrane permeability as well as lipophilicity and solubility. To rationalize the observed differences in permeability, we extracted for each peptide the population of the membrane-permeable conformation in water from extensive explicit-solvent molecular dynamics simulations and used this as a metric for conformational rigidity or "prefolding." The insights from the simulations together with lipophilicity measurements highlight the intricate interplay between polarity/lipophilicity and flexibility/rigidity and the possible compensating effects on permeability. The findings allow us to better understand the structure-permeability relationship of cyclic peptides and extract general guiding principles.
Collapse
Affiliation(s)
- Shuzhe Wang
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Gerhard König
- Laboratory of Physical Chemistry, 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
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| |
Collapse
|
21
|
Lee D, Lee S, Choi J, Song YK, Kim MJ, Shin DS, Bae MA, Kim YC, Park CJ, Lee KR, Choi JH, Seo J. Interplay among Conformation, Intramolecular Hydrogen Bonds, and Chameleonicity in the Membrane Permeability and Cyclophilin A Binding of Macrocyclic Peptide Cyclosporin O Derivatives. J Med Chem 2021; 64:8272-8286. [PMID: 34096287 DOI: 10.1021/acs.jmedchem.1c00211] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A macrocyclic peptide scaffold with well-established structure-property relationship is desirable for tackling undruggable targets. Here, we adopted a natural macrocycle, cyclosporin O (CsO) and its derivatives (CP1-3), and evaluated the impact of conformation on membrane permeability, cyclophilin A (CypA) binding, and the pharmacokinetic (PK) profile. In nonpolar media, CsO showed a similar conformation to cyclosporin A (CsA), a well-known chameleonic macrocycle, but less chameleonic behavior in a polar environment. The weak chameleonicity of CsO resulted in decreased membrane permeability; however, the more rigid conformation of CsO was not detrimental to its PK profile. CsO exhibited a higher plasma concentration than CsA, which resulted from minimal CypA binding and lower accumulation in red blood cells and moderate oral bioavailability (F = 12%). Our study aids understanding of CsO, a macrocyclic peptide that is less explored than CsA but with greater potential for diversity generation and rational design.
Collapse
Affiliation(s)
- Dongjae Lee
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Sungjin Lee
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Jieun Choi
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Yoo-Kyung Song
- Laboratory of Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang 28116, Republic of Korea
| | - Min Ju Kim
- Laboratory of Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang 28116, Republic of Korea
| | - Dae-Seop Shin
- Bio Platform Technology Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Myung Ae Bae
- Bio Platform Technology Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Yong-Chul Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Kyeong-Ryoon Lee
- Laboratory of Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang 28116, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Jiwon Seo
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| |
Collapse
|
22
|
Roy A, Koesema E, Kodadek T. High-Throughput Quality Control Assay for the Solid-Phase Synthesis of DNA-Encoded Libraries of Macrocycles*. Angew Chem Int Ed Engl 2021; 60:11983-11990. [PMID: 33682283 DOI: 10.1002/anie.202100230] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Indexed: 12/18/2022]
Abstract
There is considerable interest in the development of libraries of scaffold-diverse macrocycles as a source of ligands for difficult targets, such as protein-protein interaction surfaces. A classic problem in the synthesis of high-quality macrocyclic libraries is that some linear precursors will cyclize efficiently while some will not, depending on their conformational preferences. We report here a powerful quality control method that can be employed to readily distinguish between scaffolds that do and do not cyclize efficiently during solid-phase synthesis of thioether macrocycles without the need for tedious liquid chromatography/mass spectrometry analysis. We demonstrate that this assay can be employed to identify linear impurities in a DNA-encoded library of macrocycles. We also use the method to establish a useful quality control protocol for re-synthesis of putative macrocyclic screening hits.
Collapse
Affiliation(s)
- Animesh Roy
- Deluge Biotechnologies, 6671 W. Indiantown Rd., Suite 50-325, Jupiter, FL, 33458, USA
| | - Eric Koesema
- Deluge Biotechnologies, 6671 W. Indiantown Rd., Suite 50-325, Jupiter, FL, 33458, USA
| | - Thomas Kodadek
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| |
Collapse
|
23
|
Roy A, Koesema E, Kodadek T. High‐Throughput Quality Control Assay for the Solid‐Phase Synthesis of DNA‐Encoded Libraries of Macrocycles**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Animesh Roy
- Deluge Biotechnologies 6671 W. Indiantown Rd., Suite 50–325 Jupiter FL 33458 USA
| | - Eric Koesema
- Deluge Biotechnologies 6671 W. Indiantown Rd., Suite 50–325 Jupiter FL 33458 USA
| | - Thomas Kodadek
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| |
Collapse
|
24
|
Golosov AA, Flyer AN, Amin J, Babu C, Gampe C, Li J, Liu E, Nakajima K, Nettleton D, Patel TJ, Reid PC, Yang L, Monovich LG. Design of Thioether Cyclic Peptide Scaffolds with Passive Permeability and Oral Exposure. J Med Chem 2021; 64:2622-2633. [PMID: 33629858 DOI: 10.1021/acs.jmedchem.0c01505] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Advances in the design of permeable peptides and in the synthesis of large arrays of macrocyclic peptides with diverse amino acids have evolved on parallel but independent tracks. Less precedent combines their respective attributes, thereby limiting the potential to identify permeable peptide ligands for key targets. Herein, we present novel 6-, 7-, and 8-mer cyclic peptides (MW 774-1076 g·mol-1) with passive permeability and oral exposure that feature the amino acids and thioether ring-closing common to large array formats, including DNA- and RNA-templated synthesis. Each oral peptide herein, selected from virtual libraries of partially N-methylated peptides using in silico methods, reflects the subset consistent with low energy conformations, low desolvation penalties, and passive permeability. We envision that, by retaining the backbone N-methylation pattern and consequent bias toward permeability, one can generate large peptide arrays with sufficient side chain diversity to identify permeability-biased ligands to a variety of protein targets.
Collapse
Affiliation(s)
- Andrei A Golosov
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Alec N Flyer
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jakal Amin
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Charles Babu
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Christian Gampe
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jingzhou Li
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Eugene Liu
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Katsumasa Nakajima
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - David Nettleton
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Tajesh J Patel
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Patrick C Reid
- PeptiDream, Inc., 3-25-23 Tonomachi, Kawasaki-Ku, Kawasaki, Kanagawa 210-0821, Japan
| | - Lihua Yang
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Lauren G Monovich
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
25
|
Kelly CN, Townsend CE, Jain AN, Naylor MR, Pye CR, Schwochert J, Lokey RS. Geometrically Diverse Lariat Peptide Scaffolds Reveal an Untapped Chemical Space of High Membrane Permeability. J Am Chem Soc 2021; 143:705-714. [PMID: 33381960 PMCID: PMC8514148 DOI: 10.1021/jacs.0c06115] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Constrained, membrane-permeable peptides offer the possibility of engaging challenging intracellular targets. Structure-permeability relationships have been extensively studied in cyclic peptides whose backbones are cyclized from head to tail, like the membrane permeable and orally bioavailable natural product cyclosporine A. In contrast, the physicochemical properties of lariat peptides, which are cyclized from one of the termini onto a side chain, have received little attention. Many lariat peptide natural products exhibit interesting biological activities, and some, such as griselimycin and didemnin B, are membrane permeable and have intracellular targets. To investigate the structure-permeability relationships in the chemical space exemplified by these natural products, we generated a library of scaffolds using stable isotopes to encode stereochemistry and determined the passive membrane permeability of over 1000 novel lariat peptide scaffolds with molecular weights around 1000. Many lariats were surprisingly permeable, comparable to many known orally bioavailable drugs. Passive permeability was strongly dependent on N-methylation, stereochemistry, and ring topology. A variety of structure-permeability trends were observed including a relationship between alternating stereochemistry and high permeability, as well as a set of highly permeable consensus sequences. For the first time, robust structure-permeability relationships are established in synthetic lariat peptides exceeding 1000 compounds.
Collapse
Affiliation(s)
- Colin N. Kelly
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, USA
| | - Chad E. Townsend
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, USA
| | - Ajay N. Jain
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, USA
| | - Matthew R. Naylor
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, USA
| | | | | | - R. Scott Lokey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, USA
| |
Collapse
|
26
|
Furukawa A, Schwochert J, Pye CR, Asano D, Edmondson QD, Turmon AC, Klein VG, Ono S, Okada O, Lokey RS. Drug-Like Properties in Macrocycles above MW 1000: Backbone Rigidity versus Side-Chain Lipophilicity. Angew Chem Int Ed Engl 2020; 59:21571-21577. [PMID: 32789999 PMCID: PMC7719619 DOI: 10.1002/anie.202004550] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/10/2020] [Indexed: 12/22/2022]
Abstract
Large macrocyclic peptides can achieve surprisingly high membrane permeability, although the properties that govern permeability in this chemical space are only beginning to come into focus. We generated two libraries of cyclic decapeptides with stable cross-β conformations, and found that peptoid substitutions within the β-turns of the macrocycle preserved the rigidity of the parent scaffold, whereas peptoid substitutions in the opposing β-strands led to "chameleonic" species that were rigid in nonpolar media but highly flexible in water. Both rigid and chameleonic compounds showed high permeability over a wide lipophilicity range, with peak permeabilities differing significantly depending on scaffold rigidity. Our findings indicate that modulating lipophilicity can be used to engineer favorable ADME properties into both rigid and flexible macrocyclic peptides, and that scaffold rigidity can be used to tune optimal lipophilicity.
Collapse
Affiliation(s)
- Akihiro Furukawa
- Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Joshua Schwochert
- Unnatural Products, Inc., 250 Natural Bridges Drive, Santa Cruz, CA 95060 USA
| | - Cameron R. Pye
- Unnatural Products, Inc., 250 Natural Bridges Drive, Santa Cruz, CA 95060 USA
| | - Daigo Asano
- Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Quinn D. Edmondson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, USA
| | - Alexandra C. Turmon
- Unnatural Products, Inc., 250 Natural Bridges Drive, Santa Cruz, CA 95060 USA
| | - Victoria G. Klein
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, CA 96064 USA
| | - Satoshi Ono
- Discovery Technology Laboratories, Mitsubishi Tanabe Pharma Corporation, Yokohama, 227-0033, Japan
| | - Okimasa Okada
- Discovery Technology Laboratories, Mitsubishi Tanabe Pharma Corporation, Yokohama, 227-0033, Japan
| | - R. Scott Lokey
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, CA 96064 USA
| |
Collapse
|
27
|
Furukawa A, Schwochert J, Pye CR, Asano D, Edmondson QD, Turmon AC, Klein VG, Ono S, Okada O, Lokey RS. Drug‐Like Properties in Macrocycles above MW 1000: Backbone Rigidity versus Side‐Chain Lipophilicity. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004550] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Akihiro Furukawa
- Daiichi Sankyo Co., Ltd. 1-2-58, Hiromachi, Shinagawa-ku Tokyo 140-8710 Japan
| | - Joshua Schwochert
- Unnatural Products, Inc. 250 Natural Bridges Drive Santa Cruz CA 95060 USA
| | - Cameron R. Pye
- Unnatural Products, Inc. 250 Natural Bridges Drive Santa Cruz CA 95060 USA
| | - Daigo Asano
- Daiichi Sankyo Co., Ltd. 1-2-58, Hiromachi, Shinagawa-ku Tokyo 140-8710 Japan
| | - Quinn D. Edmondson
- Department of Pharmaceutical Chemistry University of California, San Francisco San Francisco California 94158 USA
| | | | - Victoria G. Klein
- Department of Chemistry & Biochemistry University of California Santa Cruz Santa Cruz CA 96064 USA
| | - Satoshi Ono
- Discovery Technology Laboratories Mitsubishi Tanabe Pharma Corporation Yokohama 227-0033 Japan
| | - Okimasa Okada
- Discovery Technology Laboratories Mitsubishi Tanabe Pharma Corporation Yokohama 227-0033 Japan
| | - R. Scott Lokey
- Department of Chemistry & Biochemistry University of California Santa Cruz Santa Cruz CA 96064 USA
| |
Collapse
|
28
|
Kamenik AS, Kraml J, Hofer F, Waibl F, Quoika PK, Kahler U, Schauperl M, Liedl KR. Macrocycle Cell Permeability Measured by Solvation Free Energies in Polar and Apolar Environments. J Chem Inf Model 2020; 60:3508-3517. [PMID: 32551643 PMCID: PMC7388155 DOI: 10.1021/acs.jcim.0c00280] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The relation of surface polarity and conformational preferences is decisive for cell permeability and thus bioavailability of macrocyclic drugs. Here, we employ grid inhomogeneous solvation theory (GIST) to calculate solvation free energies for a series of six macrocycles in water and chloroform as a measure of passive membrane permeability. We perform accelerated molecular dynamics simulations to capture a diverse structural ensemble in water and chloroform, allowing for a direct profiling of solvent-dependent conformational preferences. Subsequent GIST calculations facilitate a quantitative measure of solvent preference in the form of a transfer free energy, calculated from the ensemble-averaged solvation free energies in water and chloroform. Hence, the proposed method considers how the conformational diversity of macrocycles in polar and apolar solvents translates into transfer free energies. Following this strategy, we find a striking correlation of 0.92 between experimentally determined cell permeabilities and calculated transfer free energies. For the studied model systems, we find that the transfer free energy exceeds the purely water-based solvation free energies as a reliable estimate of cell permeability and that conformational sampling is imperative for a physically meaningful model. We thus recommend this purely physics-based approach as a computational tool to assess cell permeabilities of macrocyclic drug candidates.
Collapse
Affiliation(s)
- Anna S Kamenik
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, Innsbruck A-6020 Austria
| | - Johannes Kraml
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, Innsbruck A-6020 Austria
| | - Florian Hofer
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, Innsbruck A-6020 Austria
| | - Franz Waibl
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, Innsbruck A-6020 Austria
| | - Patrick K Quoika
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, Innsbruck A-6020 Austria
| | - Ursula Kahler
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, Innsbruck A-6020 Austria
| | - Michael Schauperl
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, Innsbruck A-6020 Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, Innsbruck A-6020 Austria
| |
Collapse
|
29
|
Brayden D, Hill T, Fairlie D, Maher S, Mrsny R. Systemic delivery of peptides by the oral route: Formulation and medicinal chemistry approaches. Adv Drug Deliv Rev 2020; 157:2-36. [PMID: 32479930 DOI: 10.1016/j.addr.2020.05.007] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 02/07/2023]
Abstract
In its 33 years, ADDR has published regularly on the po5tential of oral delivery of biologics especially peptides and proteins. In the intervening period, analysis of the preclinical and clinical trial failures of many purported platform technologies has led to reflection on the true status of the field and reigning in of expectations. Oral formulations of semaglutide, octreotide, and salmon calcitonin have completed Phase III trials, with oral semaglutide being approved by the FDA in 2019. The progress made with oral peptide formulations based on traditional permeation enhancers is against a background of low and variable oral bioavailability values of ~1%, leading to a current perception that only potent peptides with a viable cost of synthesis can be realistically considered. Desirable features of candidates should include a large therapeutic index, some stability in the GI tract, a long elimination half-life, and a relatively low clearance rate. Administration in nanoparticle formats have largely disappointed, with few prototypes reaching clinical trials: insufficient particle loading, lack of controlled release, low epithelial particle uptake, and lack of scalable synthesis being the main reasons for discontinuation. Disruptive technologies based on engineered devices promise improvements, but scale-up and toxicology aspects are issues to address. In parallel, medicinal chemists are synthesizing stable hydrophobic macrocyclic candidate peptides of lower molecular weight and with potential for greater oral bioavailability than linear peptides, but perhaps without the same requirement for elaborate drug delivery systems. In summary, while there have been advances in understanding the limitations of peptides for oral delivery, low membrane permeability, metabolism, and high clearance rates continue to hamper progress.
Collapse
|
30
|
Le Roux A, Blaise É, Boudreault PL, Comeau C, Doucet A, Giarrusso M, Collin MP, Neubauer T, Kölling F, Göller AH, Seep L, Tshitenge DT, Wittwer M, Kullmann M, Hillisch A, Mittendorf J, Marsault E. Structure-Permeability Relationship of Semipeptidic Macrocycles-Understanding and Optimizing Passive Permeability and Efflux Ratio. J Med Chem 2020; 63:6774-6783. [PMID: 32453569 DOI: 10.1021/acs.jmedchem.0c00013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We herein report the first thorough analysis of the structure-permeability relationship of semipeptidic macrocycles. In total, 47 macrocycles were synthesized using a hybrid solid-phase/solution strategy, and then their passive and cellular permeability was assessed using the parallel artificial membrane permeability assay (PAMPA) and Caco-2 assay, respectively. The results indicate that semipeptidic macrocycles generally possess high passive permeability based on the PAMPA, yet their cellular permeability is governed by efflux, as reported in the Caco-2 assay. Structural variations led to tractable structure-permeability and structure-efflux relationships, wherein the linker length, stereoinversion, N-methylation, and peptoids site-specifically impact the permeability and efflux. Extensive nuclear magnetic resonance, molecular dynamics, and ensemble-based three-dimensional polar surface area (3D-PSA) studies showed that ensemble-based 3D-PSA is a good predictor of passive permeability.
Collapse
Affiliation(s)
- Antoine Le Roux
- Department of Pharmacology-Physiology, Institut de Pharmacologie de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec J1H 5N4, Canada
| | - Émilie Blaise
- Department of Pharmacology-Physiology, Institut de Pharmacologie de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec J1H 5N4, Canada
| | - Pierre-Luc Boudreault
- Department of Pharmacology-Physiology, Institut de Pharmacologie de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec J1H 5N4, Canada
| | - Christian Comeau
- Department of Pharmacology-Physiology, Institut de Pharmacologie de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec J1H 5N4, Canada
| | - Annie Doucet
- Department of Pharmacology-Physiology, Institut de Pharmacologie de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec J1H 5N4, Canada
| | - Marilena Giarrusso
- Department of Pharmacology-Physiology, Institut de Pharmacologie de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec J1H 5N4, Canada
| | | | - Thomas Neubauer
- Drug Discovery, Pharmaceuticals, Bayer AG, Wuppertal D-42096, Germany
| | - Florian Kölling
- Drug Discovery, Pharmaceuticals, Bayer AG, Wuppertal D-42096, Germany
| | - Andreas H Göller
- Drug Discovery, Pharmaceuticals, Bayer AG, Wuppertal D-42096, Germany
| | - Lea Seep
- Drug Discovery, Pharmaceuticals, Bayer AG, Wuppertal D-42096, Germany
| | | | - Matthias Wittwer
- Drug Discovery, Pharmaceuticals, Bayer AG, Wuppertal D-42096, Germany
| | | | | | | | - Eric Marsault
- Department of Pharmacology-Physiology, Institut de Pharmacologie de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec J1H 5N4, Canada
| |
Collapse
|
31
|
Wang S, Witek J, Landrum GA, Riniker S. Improving Conformer Generation for Small Rings and Macrocycles Based on Distance Geometry and Experimental Torsional-Angle Preferences. J Chem Inf Model 2020; 60:2044-2058. [PMID: 32155061 DOI: 10.1021/acs.jcim.0c00025] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The conformer generator ETKDG is a stochastic search method that utilizes distance geometry together with knowledge derived from experimental crystal structures. It has been shown to generate good conformers for acyclic, flexible molecules. This work builds on ETKDG to improve conformer generation of molecules containing small or large aliphatic (i.e., non-aromatic) rings. For one, we devise additional torsional-angle potentials to describe small aliphatic rings and adapt the previously developed potentials for acyclic bonds to facilitate the sampling of macrocycles. However, due to the larger number of degrees of freedom of macrocycles, the conformational space to sample is much broader than for small molecules, creating a challenge for conformer generators. We therefore introduce different heuristics to restrict the search space of macrocycles and bias the sampling toward more experimentally relevant structures. Specifically, we show the usage of elliptical geometry and customizable Coulombic interactions as heuristics. The performance of the improved ETKDG is demonstrated on test sets of diverse macrocycles and cyclic peptides. The code developed here will be incorporated into the 2020.03 release of the open-source cheminformatics library RDKit.
Collapse
Affiliation(s)
- Shuzhe Wang
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Jagna Witek
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | | | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| |
Collapse
|
32
|
Abstract
Approximately 75% of all disease-relevant human proteins, including those involved in intracellular protein-protein interactions (PPIs), are undruggable with the current drug modalities (i.e., small molecules and biologics). Macrocyclic peptides provide a potential solution to these undruggable targets because their larger sizes (relative to conventional small molecules) endow them the capability of binding to flat PPI interfaces with antibody-like affinity and specificity. Powerful combinatorial library technologies have been developed to routinely identify cyclic peptides as potent, specific inhibitors against proteins including PPI targets. However, with the exception of a very small set of sequences, the vast majority of cyclic peptides are impermeable to the cell membrane, preventing their application against intracellular targets. This Review examines common structural features that render most cyclic peptides membrane impermeable, as well as the unique features that allow the minority of sequences to enter the cell interior by passive diffusion, endocytosis/endosomal escape, or other mechanisms. We also present the current state of knowledge about the molecular mechanisms of cell penetration, the various strategies for designing cell-permeable, biologically active cyclic peptides against intracellular targets, and the assay methods available to quantify their cell-permeability.
Collapse
Affiliation(s)
- Patrick G. Dougherty
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43210, United States
| | - Ashweta Sahni
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43210, United States
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43210, United States
| |
Collapse
|
33
|
Vinogradov AA, Yin Y, Suga H. Macrocyclic Peptides as Drug Candidates: Recent Progress and Remaining Challenges. J Am Chem Soc 2019; 141:4167-4181. [PMID: 30768253 DOI: 10.1021/jacs.8b13178] [Citation(s) in RCA: 412] [Impact Index Per Article: 82.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Peptides as a therapeutic modality attract much attention due to their synthetic accessibility, high degree of specific binding, and the ability to target protein surfaces traditionally considered "undruggable". Unfortunately, at the same time, other pharmacological properties of a generic peptide, such as metabolic stability and cell permeability, are quite poor, which limits the success of de novo discovered biologically active peptides as drug candidates. Here, we review how macrocyclization as well as the incorporation of nonproteogenic amino acids and various conjugation strategies may be utilized to improve on these characteristics to create better drug candidates. We analyze recent progress and remaining challenges in improving individual pharmacological properties of bioactive peptides, and offer our opinion on interfacing these, often conflicting, considerations, to create balanced drug candidates as a potential way to make further progress in this area.
Collapse
Affiliation(s)
- Alexander A Vinogradov
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Yizhen Yin
- 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
| |
Collapse
|
34
|
Tajimi T, Wakui N, Yanagisawa K, Yoshikawa Y, Ohue M, Akiyama Y. Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques. BMC Bioinformatics 2018; 19:527. [PMID: 30598072 PMCID: PMC6311893 DOI: 10.1186/s12859-018-2529-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Cyclic peptide-based drug discovery is attracting increasing interest owing to its potential to avoid target protein depletion. In drug discovery, it is important to maintain the biostability of a drug within the proper range. Plasma protein binding (PPB) is the most important index of biostability, and developing a computational method to predict PPB of drug candidate compounds contributes to the acceleration of drug discovery research. PPB prediction of small molecule drug compounds using machine learning has been conducted thus far; however, no study has investigated cyclic peptides because experimental information of cyclic peptides is scarce. RESULTS First, we adopted sparse modeling and small molecule information to construct a PPB prediction model for cyclic peptides. As cyclic peptide data are limited, applying multidimensional nonlinear models involves concerns regarding overfitting. However, models constructed by sparse modeling can avoid overfitting, offering high generalization performance and interpretability. More than 1000 PPB data of small molecules are available, and we used them to construct a prediction models with two enumeration methods: enumerating lasso solutions (ELS) and forward beam search (FBS). The accuracies of the prediction models constructed by ELS and FBS were equal to or better than those of conventional non-linear models (MAE = 0.167-0.174) on cross-validation of a small molecule compound dataset. Moreover, we showed that the prediction accuracies for cyclic peptides were close to those for small molecule compounds (MAE = 0.194-0.288). Such high accuracy could not be obtained by a simple method of learning from cyclic peptide data directly by lasso regression (MAE = 0.286-0.671) or ridge regression (MAE = 0.244-0.354). CONCLUSION In this study, we proposed a machine learning techniques that uses low-dimensional sparse modeling to predict the PPB value of cyclic peptides computationally. The low-dimensional sparse model not only exhibits excellent generalization performance but also improves interpretation of the prediction model. This can provide common an noteworthy knowledge for future cyclic peptide drug discovery studies.
Collapse
Affiliation(s)
- Takashi Tajimi
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Naoki Wakui
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Middle Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, RGBT2-A-1C 3-25-10 Tonomachi, Kawasaki-ku, Kawasaki city, Kanagawa, 210-0821, Japan
| | - Keisuke Yanagisawa
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Yasushi Yoshikawa
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Middle Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, RGBT2-A-1C 3-25-10 Tonomachi, Kawasaki-ku, Kawasaki city, Kanagawa, 210-0821, Japan
| | - Masahito Ohue
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Middle Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, RGBT2-A-1C 3-25-10 Tonomachi, Kawasaki-ku, Kawasaki city, Kanagawa, 210-0821, Japan
| | - Yutaka Akiyama
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. .,Middle Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, RGBT2-A-1C 3-25-10 Tonomachi, Kawasaki-ku, Kawasaki city, Kanagawa, 210-0821, Japan. .,Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
| |
Collapse
|
35
|
Witek J, Wang S, Schroeder B, Lingwood R, Dounas A, Roth HJ, Fouché M, Blatter M, Lemke O, Keller B, Riniker S. Rationalization of the Membrane Permeability Differences in a Series of Analogue Cyclic Decapeptides. J Chem Inf Model 2018; 59:294-308. [PMID: 30457855 DOI: 10.1021/acs.jcim.8b00485] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cyclization and selected backbone N-methylations are found to be often necessary but not sufficient conditions for peptidic drugs to have a good bioavailability. Thus, the design of cyclic peptides with good passive membrane permeability and good solubility remains a challenge. The backbone scaffold of a recently published series of cyclic decapeptides with six selected backbone N-methylations was designed to favor the adoption of a closed conformation with β-turns and four transannular hydrogen bonds. Although this conformation was indeed adopted by the peptides as determined by NMR measurements, substantial differences in the membrane permeability were observed. In this work, we aim to rationalize the impact of discrete side chain modifications on membrane permeability for six of these cyclic decapeptides. The thermodynamic and kinetic properties were investigated using molecular dynamics simulations and Markov state modeling in water and chloroform. The study highlights the influence that side-chain modifications can have on the backbone conformation. Peptides with a d-proline in the β-turns were more likely to adopt, even in water, the closed conformation with transannular hydrogen bonds, which facilitates transition through the membrane. The population of the closed conformation in water was found to correlate positively with PAMPA log Pe.
Collapse
Affiliation(s)
- Jagna Witek
- Laboratory of Physical Chemistry , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Shuzhe Wang
- Laboratory of Physical Chemistry , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Benjamin Schroeder
- Laboratory of Physical Chemistry , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Robin Lingwood
- Laboratory of Physical Chemistry , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Andreas Dounas
- Laboratory of Physical Chemistry , 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
| | - Markus Blatter
- Novartis Institutes for BioMedical Research , Novartis Pharma AG, Novartis Campus , 4056 Basel , Switzerland
| | - Oliver Lemke
- Department of Biology, Chemistry, Pharmacy , Freie Universität Berlin , Takustrasse 3 , 14195 Berlin , Germany
| | - Bettina Keller
- Department of Biology, Chemistry, Pharmacy , Freie Universität Berlin , Takustrasse 3 , 14195 Berlin , Germany
| | - Sereina Riniker
- Department of Biology, Chemistry, Pharmacy , Freie Universität Berlin , Takustrasse 3 , 14195 Berlin , Germany
| |
Collapse
|
36
|
Babii O, Afonin S, Ishchenko AY, Schober T, Negelia AO, Tolstanova GM, Garmanchuk LV, Ostapchenko LI, Komarov IV, Ulrich AS. Structure–Activity Relationships of Photoswitchable Diarylethene-Based β-Hairpin Peptides as Membranolytic Antimicrobial and Anticancer Agents. J Med Chem 2018; 61:10793-10813. [DOI: 10.1021/acs.jmedchem.8b01428] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Oleg Babii
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany
| | - Aleksandr Yu. Ishchenko
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Vul. Volodymyrska 60, 01601 Kyiv, Ukraine
- Enamine Ltd., Vul. Chervonotkatska 78, 02066 Kyiv, Ukraine
| | - Tim Schober
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Anatoliy O. Negelia
- Institute of Biology and Medicine, Taras Shevchenko National University of Kyiv, Prosp. Hlushkova 2, 03022 Kyiv, Ukraine
| | - Ganna M. Tolstanova
- Institute of Biology and Medicine, Taras Shevchenko National University of Kyiv, Prosp. Hlushkova 2, 03022 Kyiv, Ukraine
| | - Liudmyla V. Garmanchuk
- Institute of Biology and Medicine, Taras Shevchenko National University of Kyiv, Prosp. Hlushkova 2, 03022 Kyiv, Ukraine
| | - Liudmyla I. Ostapchenko
- Institute of Biology and Medicine, Taras Shevchenko National University of Kyiv, Prosp. Hlushkova 2, 03022 Kyiv, Ukraine
| | - Igor V. Komarov
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Vul. Volodymyrska 60, 01601 Kyiv, Ukraine
- Enamine Ltd., Vul. Chervonotkatska 78, 02066 Kyiv, Ukraine
- Lumobiotics GmbH, Auerstraße 2, 76227 Karlsruhe, Germany
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| |
Collapse
|
37
|
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
| |
Collapse
|
38
|
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
| |
Collapse
|
39
|
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.
Collapse
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
| |
Collapse
|
40
|
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
| |
Collapse
|
41
|
Slough DP, McHugh SM, Lin YS. Understanding and designing head-to-tail cyclic peptides. Biopolymers 2018; 109:e23113. [PMID: 29528114 PMCID: PMC6135719 DOI: 10.1002/bip.23113] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 01/30/2023]
Abstract
Cyclic peptides (CPs) are an exciting class of molecules with a variety of applications. However, design strategies for CP therapeutics, for example, are generally limited by a poor understanding of their sequence-structure relationships. This knowledge gap often leads to a trial-and-error approach for designing CPs for a specific purpose, which is both costly and time-consuming. Herein, we describe the current experimental and computational efforts in understanding and designing head-to-tail CPs along with their respective challenges. In addition, we provide several future directions in the field of computational CP design to improve its accuracy, efficiency and applicability. These advances, combined with experimental techniques, shall ultimately provide a better understanding of these interesting molecules and a reliable working platform to rationally design CPs with desired characteristics.
Collapse
Affiliation(s)
| | | | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts, 02155, United States
| |
Collapse
|
42
|
Kamenik AS, Lessel U, Fuchs JE, Fox T, Liedl KR. Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization. J Chem Inf Model 2018; 58:982-992. [PMID: 29652495 PMCID: PMC5974701 DOI: 10.1021/acs.jcim.8b00097] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Macrocycles are of considerable interest as highly specific drug candidates, yet they challenge standard conformer generators with their large number of rotatable bonds and conformational restrictions. Here, we present a molecular dynamics-based routine that bypasses current limitations in conformational sampling and extensively profiles the free energy landscape of peptidic macrocycles in solution. We perform accelerated molecular dynamics simulations to capture a diverse conformational ensemble. By applying an energetic cutoff, followed by geometric clustering, we demonstrate the striking robustness and efficiency of the approach in identifying highly populated conformational states of cyclic peptides. The resulting structural and thermodynamic information is benchmarked against interproton distances from NMR experiments and conformational states identified by X-ray crystallography. Using three different model systems of varying size and flexibility, we show that the method reliably reproduces experimentally determined structural ensembles and is capable of identifying key conformational states that include the bioactive conformation. Thus, the described approach is a robust method to generate conformations of peptidic macrocycles and holds promise for structure-based drug design.
Collapse
Affiliation(s)
- Anna S Kamenik
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck , University of Innsbruck , 6020 Innsbruck , Austria
| | - Uta Lessel
- Medicinal Chemistry , Boehringer Ingelheim Pharma GmbH & Co. KG , 88397 Biberach , Germany
| | - Julian E Fuchs
- Department of Medicinal Chemistry , Boehringer Ingelheim RCV GmbH & Co KG , 1120 Vienna , Austria
| | - Thomas Fox
- Medicinal Chemistry , Boehringer Ingelheim Pharma GmbH & Co. KG , 88397 Biberach , Germany
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck , University of Innsbruck , 6020 Innsbruck , Austria
| |
Collapse
|
43
|
Kaneda M, Inuki S, Ohno H, Oishi S. Total Synthesis and Stereochemical Revision of Stereocalpin A: Mirror-Image Approach for Stereochemical Assignments of the Peptide-Polyketide Macrocycle. J Org Chem 2018; 83:3047-3060. [PMID: 29470088 DOI: 10.1021/acs.joc.8b00118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Stereocalpin A is a cyclic depsipeptide with cytotoxic activity isolated from the Antarctic lichen Stereocaulon alpinum. Although a number of synthetic investigations of the unprecedented 12-membered macrocycle of stereocalpin A with a dipeptide segment and a polyketide substructure have been conducted, the configurational assignment has not been completed. In this study, we achieved the first total synthesis and stereochemical revision of stereocalpin A. To facilitate the comprehensive assessment of eight possible stereocalpin A isomers, four stereoisomers of polyketide precursors were conjugated with l-Phe-l-MePhe and d-Phe-d-MePhe dipeptides (MePhe: N-methylphenylalanine) to provide four possible isomers and four mirror-image structures of the remaining isomers, respectively. The comparative NMR analysis of a series of stereoisomers revealed that stereocalpin A possesses 2 R,4 S,5 R-configurations, which is unique among the related 12-membered hybrid peptide-polyketide natural products reported recently. The NOE correlations in the polyketide substructure of stereocalpin A were also retrospectively analyzed among the eight possible stereoisomers.
Collapse
Affiliation(s)
- Masato Kaneda
- Graduate School of Pharmaceutical Sciences , Kyoto University , Sakyo-ku, Kyoto 606-8501 , Japan
| | - Shinsuke Inuki
- Graduate School of Pharmaceutical Sciences , Kyoto University , Sakyo-ku, Kyoto 606-8501 , Japan
| | - Hiroaki Ohno
- Graduate School of Pharmaceutical Sciences , Kyoto University , Sakyo-ku, Kyoto 606-8501 , Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences , Kyoto University , Sakyo-ku, Kyoto 606-8501 , Japan
| |
Collapse
|
44
|
|
45
|
Moore AF, Newman DJ, Ranganathan S, Liu F. Imaginative Order from Reasonable Chaos: Conformation-Driven Activity and Reactivity in Exploring Protein–Ligand Interactions. Aust J Chem 2018. [DOI: 10.1071/ch18416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Sir Derek Barton’s seminal work on steroid conformational analysis opened up a new era of enquiry into how the preferred conformation of any molecule could have profound effects on its physical–chemical properties and activities. Conformation-based effects on molecular activity and reactivity continue to manifest, with one key area of investigation currently focussed on conformational entropy in driving protein–ligand interactions. Carrying on from Barton’s initial insight on natural product conformational properties, new questions now address how conformational flexibility within a bioactive natural product structural framework (reasonable chaos), can be directed to confer dynamically new protein–ligand interactions beyond the basic lock–key model (imaginative order). Here we summarise our work on exploring conformational diversity from fluorinated natural product fragments, and how this approach of conformation-coupled diversity-oriented synthesis can be used to iteratively derive ligands with enhanced specificity against highly homologous protein domains. Our results demonstrate that the conformation entropic states of highly conserved protein domains differ significantly, and this conformational diversity, beyond primary sequence analysis, can be duly captured and exploited by natural-product derived ligands with complementary conformational dynamics for enhancing recognition specificity in drug lead discovery.
Collapse
|
46
|
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]
|
47
|
Stutz K, Müller AT, Hiss JA, Schneider P, Blatter M, Pfeiffer B, Posselt G, Kanfer G, Kornmann B, Wrede P, Altmann KH, Wessler S, Schneider G. Peptide-Membrane Interaction between Targeting and Lysis. ACS Chem Biol 2017; 12:2254-2259. [PMID: 28763193 DOI: 10.1021/acschembio.7b00504] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Certain cationic peptides interact with biological membranes. These often-complex interactions can result in peptide targeting to the membrane, or in membrane permeation, rupture, and cell lysis. We investigated the relationship between the structural features of membrane-active peptides and these effects, to better understand these processes. To this end, we employed a computational method for morphing a membranolytic antimicrobial peptide into a nonmembranolytic mitochondrial targeting peptide by "directed simulated evolution." The results obtained demonstrate that superficially subtle sequence modifications can strongly affect the peptides' membranolytic and membrane-targeting abilities. Spectroscopic and computational analyses suggest that N- and C-terminal structural flexibility plays a crucial role in determining the mode of peptide-membrane interaction.
Collapse
Affiliation(s)
- Katharina Stutz
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Alex T. Müller
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Jan A. Hiss
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Petra Schneider
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Markus Blatter
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Bernhard Pfeiffer
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Gernot Posselt
- Department
of Molecular Biology, Division of Microbiology, Paris-Lodron University of Salzburg, 5020 Salzburg, Austria
| | - Gil Kanfer
- Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), Otto-Stern-Weg-3, 8093 Zurich, Switzerland
| | - Benoît Kornmann
- Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), Otto-Stern-Weg-3, 8093 Zurich, Switzerland
| | - Paul Wrede
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Karl-Heinz Altmann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Silja Wessler
- Department
of Molecular Biology, Division of Microbiology, Paris-Lodron University of Salzburg, 5020 Salzburg, Austria
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| |
Collapse
|
48
|
Cyclic peptide natural products chart the frontier of oral bioavailability in the pursuit of undruggable targets. Curr Opin Chem Biol 2017; 38:141-147. [DOI: 10.1016/j.cbpa.2017.04.012] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 04/13/2017] [Accepted: 04/18/2017] [Indexed: 01/23/2023]
|
49
|
Nielsen DS, Shepherd NE, Xu W, Lucke AJ, Stoermer MJ, Fairlie DP. Orally Absorbed Cyclic Peptides. Chem Rev 2017; 117:8094-8128. [PMID: 28541045 DOI: 10.1021/acs.chemrev.6b00838] [Citation(s) in RCA: 266] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Peptides and proteins are not orally bioavailable in mammals, although a few peptides are intestinally absorbed in small amounts. Polypeptides are generally too large and polar to passively diffuse through lipid membranes, while most known active transport mechanisms facilitate cell uptake of only very small peptides. Systematic evaluations of peptides with molecular weights above 500 Da are needed to identify parameters that influence oral bioavailability. Here we describe 125 cyclic peptides containing four to thirty-seven amino acids that are orally absorbed by mammals. Cyclization minimizes degradation in the gut, blood, and tissues by removing cleavable N- and C-termini and by shielding components from metabolic enzymes. Cyclization also folds peptides into bioactive conformations that determine exposure of polar atoms to solvation by water and lipids and therefore can influence oral bioavailability. Key chemical properties thought to influence oral absorption and bioavailability are analyzed, including molecular weight, octanol-water partitioning, hydrogen bond donors/acceptors, rotatable bonds, and polar surface area. The cyclic peptides violated to different degrees all of the limits traditionally considered to be important for oral bioavailability of drug-like small molecules, although fewer hydrogen bond donors and reduced flexibility generally favored oral absorption.
Collapse
Affiliation(s)
- Daniel S Nielsen
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Nicholas E Shepherd
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Weijun Xu
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Andrew J Lucke
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Martin J Stoermer
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - David P Fairlie
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| |
Collapse
|
50
|
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.
Collapse
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
| |
Collapse
|