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Subramanian G, Manchanda K, Mo Y, Sathe RY, Bharatam PV. Monovalent cation binding to model systems and the macrocyclic depsipeptide, emodepside. J Comput Chem 2024; 45:2409-2423. [PMID: 38924119 DOI: 10.1002/jcc.27451] [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: 03/20/2024] [Revised: 05/13/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024]
Abstract
This study focuses on the systematic exploration of the emodepside conformations bound to monovalent K+ ion using quantum mechanical density functional theory (DFT) calculations at the M06-2X/6-31+G(d,p) level of theory. Nine conformers of emodepside and their complexes with K+ ion were characterized as stationary points on the potential energy surface. The conformational isomers were examined for their 3D structures, bonding, energetics, and interactions with the cation. A cavitand-like structure (CC) is identified to be the energetically most stable arrangement. To arrive at a better understanding of the K+ ion binding, calculations were initially performed on complexes formed by the K+ and Na+ ions with model ligands (methyl ester and N,N-dimethyl acetamide). Both the natural bond orbital (NBO) method and the block-localized wavefunction (BLW) energy decomposition approach was employed to assess the bonding and energetic contributions stabilizing the ion-bound model complexes. Finally, the solvent effect was evaluated through complete geometry optimizations and energy minimizations for the model ion-ligand complexes and the emodepside-K+ bound complexes using an implicit solvent model mimicking water and DMSO.
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Affiliation(s)
| | - Kanika Manchanda
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S Nagar (Mohali), Punjab, India
| | - Yirong Mo
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Rohit Y Sathe
- Department of Biological Sciences and Biotechnology, Institute of Chemical Technology, Mumbai, Maharashtra, India
| | - Prasad V Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S Nagar (Mohali), Punjab, India
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2
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Li Y, Wu M, Fu Y, Xue J, Yuan F, Qu T, Rissanou AN, Wang Y, Li X, Hu H. Therapeutic stapled peptides: Efficacy and molecular targets. Pharmacol Res 2024; 203:107137. [PMID: 38522761 DOI: 10.1016/j.phrs.2024.107137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/26/2024]
Abstract
Peptide stapling, by employing a stable, preformed alpha-helical conformation, results in the production of peptides with improved membrane permeability and enhanced proteolytic stability, compared to the original peptides, and provides an effective solution to accelerate the rapid development of peptide drugs. Various reviews present peptide stapling chemistries, anchoring residues and one- or two-component cyclization, however, therapeutic stapled peptides have not been systematically summarized, especially focusing on various disease-related targets. This review highlights the latest advances in therapeutic peptide drug development facilitated by the application of stapling technology, including different stapling techniques, synthetic accessibility, applicability to biological targets, potential for solving biological problems, as well as the current status of development. Stapled peptides as therapeutic drug candidates have been classified and analysed mainly by receptor- and ligand-based stapled peptide design against various diseases, including cancer, infectious diseases, inflammation, and diabetes. This review is expected to provide a comprehensive reference for the rational design of stapled peptides for different diseases and targets to facilitate the development of therapeutic peptides with enhanced pharmacokinetic and biological properties.
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Affiliation(s)
- Yulei Li
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China.
| | - Minghao Wu
- School of Medicine, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Yinxue Fu
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Jingwen Xue
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Fei Yuan
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Tianci Qu
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Anastassia N Rissanou
- Theoretical & Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 11635, Greece
| | - Yilin Wang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, 131 Dong'an Road, Shanghai 200032, China
| | - Xiang Li
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China.
| | - Honggang Hu
- School of Medicine, Shanghai University, 99 Shangda Road, Shanghai 200444, China.
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Wilson DM, Driedger DJ, Liu DY, Keerthisinghe S, Hermann A, Bieniossek C, Linington RG, Britton RA. Targeted sampling of natural product space to identify bioactive natural product-like polyketide macrolides. Nat Commun 2024; 15:2534. [PMID: 38514617 PMCID: PMC10958047 DOI: 10.1038/s41467-024-46721-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 03/01/2024] [Indexed: 03/23/2024] Open
Abstract
Polyketide or polyketide-like macrolides (pMLs) continue to serve as a source of inspiration for drug discovery. However, their inherent structural and stereochemical complexity challenges efforts to explore related regions of chemical space more broadly. Here, we report a strategy termed the Targeted Sampling of Natural Product space (TSNaP) that is designed to identify and assess regions of chemical space bounded by this important class of molecules. Using TSNaP, a family of tetrahydrofuran-containing pMLs are computationally assembled from pML inspired building blocks to provide a large collection of natural product-like virtual pMLs. By scoring functional group and volumetric overlap against their natural counterparts, a collection of compounds are prioritized for targeted synthesis. Using a modular and stereoselective synthetic approach, a library of polyketide-like macrolides are prepared to sample these unpopulated regions of pML chemical space. Validation of this TSNaP approach by screening this library against a panel of whole-cell biological assays, reveals hit rates exceeding those typically encountered in small molecule libraries. This study suggests that the TSNaP approach may be more broadly useful for the design of improved chemical libraries for drug discovery.
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Affiliation(s)
- Darryl M Wilson
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Daniel J Driedger
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Dennis Y Liu
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Sandra Keerthisinghe
- Center for High-Throughput Chemical Biology, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Adrian Hermann
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Christoph Bieniossek
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
- Center for High-Throughput Chemical Biology, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
| | - Robert A Britton
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
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Poongavanam V, Wieske LHE, Peintner S, Erdélyi M, Kihlberg J. Molecular chameleons in drug discovery. Nat Rev Chem 2024; 8:45-60. [PMID: 38123688 DOI: 10.1038/s41570-023-00563-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
Molecular chameleons possess a flexibility that allows them to dynamically shield or expose polar functionalities in response to the properties of the environment. Although the concept of molecular chameleons was introduced already in 1970, interest in them has grown considerably since the 2010s, when drug discovery has focused to an increased extent on new chemical modalities. Such modalities include cyclic peptides, macrocycles and proteolysis-targeting chimeras, all of which reside in a chemical space far from that of traditional small-molecule drugs. Both cell permeability and aqueous solubility are required for the oral absorption of drugs. Engineering these properties, and potent target binding, into the larger new modalities is a more daunting task than for traditional small-molecule drugs. The ability of chameleons to adapt to different environments may be essential for success. In this Review, we provide both general and theoretical insights into the realm of molecular chameleons. We discuss why chameleons have come into fashion and provide a do-it-yourself toolbox for their design; we then provide a glimpse of how advanced in silico methods can support molecular chameleon design.
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Affiliation(s)
| | | | - Stefan Peintner
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Máté Erdélyi
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.
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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.
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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.)
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Koziolek M, Augustijns P, Berger C, Cristofoletti R, Dahlgren D, Keemink J, Matsson P, McCartney F, Metzger M, Mezler M, Niessen J, Polli JE, Vertzoni M, Weitschies W, Dressman J. Challenges in Permeability Assessment for Oral Drug Product Development. Pharmaceutics 2023; 15:2397. [PMID: 37896157 PMCID: PMC10609725 DOI: 10.3390/pharmaceutics15102397] [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: 07/10/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Drug permeation across the intestinal epithelium is a prerequisite for successful oral drug delivery. The increased interest in oral administration of peptides, as well as poorly soluble and poorly permeable compounds such as drugs for targeted protein degradation, have made permeability a key parameter in oral drug product development. This review describes the various in vitro, in silico and in vivo methodologies that are applied to determine drug permeability in the human gastrointestinal tract and identifies how they are applied in the different stages of drug development. The various methods used to predict, estimate or measure permeability values, ranging from in silico and in vitro methods all the way to studies in animals and humans, are discussed with regard to their advantages, limitations and applications. A special focus is put on novel techniques such as computational approaches, gut-on-chip models and human tissue-based models, where significant progress has been made in the last few years. In addition, the impact of permeability estimations on PK predictions in PBPK modeling, the degree to which excipients can affect drug permeability in clinical studies and the requirements for colonic drug absorption are addressed.
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Affiliation(s)
- Mirko Koziolek
- NCE Drug Product Development, Development Sciences, AbbVie Deutschland GmbH & Co. KG, 67061 Ludwigshafen, Germany
| | - Patrick Augustijns
- Drug Delivery and Disposition, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Constantin Berger
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg, 97070 Würzburg, Germany;
| | - Rodrigo Cristofoletti
- Department of Pharmaceutics, University of Florida, 6550 Sanger Road, Orlando, FL 32827, USA
| | - David Dahlgren
- Department of Pharmaceutical Biosciences, Uppsala University, 75124 Uppsala, Sweden (J.N.)
| | - Janneke Keemink
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland;
| | - Pär Matsson
- Department of Pharmacology and SciLifeLab Gothenburg, University of Gothenburg, 40530 Gothenburg, Sweden;
| | - Fiona McCartney
- School of Veterinary Medicine, University College Dublin, D04 V1W8 Dublin, Ireland;
| | - Marco Metzger
- Translational Center for Regenerative Therapies (TLZ-RT) Würzburg, Branch of the Fraunhofer Institute for Silicate Research (ISC), 97082 Würzburg, Germany
| | - Mario Mezler
- Quantitative, Translational & ADME Sciences, AbbVie Deutschland GmbH & Co. KG, 67061 Ludwigshafen, Germany;
| | - Janis Niessen
- Department of Pharmaceutical Biosciences, Uppsala University, 75124 Uppsala, Sweden (J.N.)
| | - James E. Polli
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD 21021, USA;
| | - Maria Vertzoni
- Department of Pharmacy, National and Kapodistrian University of Athens, 157 84 Zografou, Greece;
| | - Werner Weitschies
- Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
| | - Jennifer Dressman
- Fraunhofer Institute of Translational Medicine and Pharmacology, 60596 Frankfurt, Germany
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