1
|
Kage M, Hayashi R, Matsuo A, Tamiya M, Kuramoto S, Ohara K, Irie M, Chiyoda A, Takano K, Ito T, Kotake T, Takeyama R, Ishikawa S, Nomura K, Furuichi N, Morita Y, Hashimoto S, Kawada H, Nishimura Y, Nii K, Sase H, Ohta A, Kojima T, Iikura H, Tanada M, Shiraishi T. Structure-activity relationships of middle-size cyclic peptides, KRAS inhibitors derived from an mRNA display. Bioorg Med Chem 2024; 110:117830. [PMID: 38981216 DOI: 10.1016/j.bmc.2024.117830] [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: 05/27/2024] [Revised: 06/30/2024] [Accepted: 07/01/2024] [Indexed: 07/11/2024]
Abstract
Cyclic peptides are attracting attention as therapeutic agents due to their potential for oral absorption and easy access to tough intracellular targets. LUNA18, a clinical KRAS inhibitor, was transformed-without scaffold hopping-from the initial hit by using an mRNA display library that met our criteria for drug-likeness. In drug discovery using mRNA display libraries, hit compounds always possess a site linked to an mRNA tag. Here, we describe our examination of the Structure-Activity Relationship (SAR) using X-ray structures for chemical optimization near the site linked to the mRNA tag, equivalent to the C-terminus. Structural modifications near the C-terminus demonstrated a relatively wide range of tolerance for side chains. Furthermore, we show that a single atom modification is enough to change the pharmacokinetic (PK) profile. Since there are four positions where side chain modification is permissible in terms of activity, it is possible to flexibly adjust the pharmacokinetic profile by structurally optimizing the side chain. The side chain transformation findings demonstrated here may be generally applicable to hits obtained from mRNA display libraries.
Collapse
Affiliation(s)
- Mirai Kage
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Ryuji Hayashi
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan.
| | - Atsushi Matsuo
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Minoru Tamiya
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Shino Kuramoto
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Kazuhiro Ohara
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Machiko Irie
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Aya Chiyoda
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Koji Takano
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Toshiya Ito
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Tomoya Kotake
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Ryuuichi Takeyama
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Shiho Ishikawa
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Kenichi Nomura
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Noriyuki Furuichi
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Yuya Morita
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Satoshi Hashimoto
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Hatsuo Kawada
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Yoshikazu Nishimura
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Keiji Nii
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Hitoshi Sase
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Atsushi Ohta
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Tetsuo Kojima
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Hitoshi Iikura
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Mikimasa Tanada
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan.
| | - Takuya Shiraishi
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan.
| |
Collapse
|
2
|
You S, McIntyre G, Passioura T. The coming of age of cyclic peptide drugs: an update on discovery technologies. Expert Opin Drug Discov 2024; 19:961-973. [PMID: 38872502 DOI: 10.1080/17460441.2024.2367024] [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: 04/25/2024] [Accepted: 06/07/2024] [Indexed: 06/15/2024]
Abstract
INTRODUCTION Cyclic peptides are an established class of pharmaceuticals, with the ability to bind to a broader range of protein targets than traditional small molecules while also being capable of oral availability and cell penetration. Historically, cyclic peptide drugs have been discovered almost exclusively through natural product mining approaches; however, the last two decades have seen the development of display screening approaches capable of rapidly identifying de novo (i.e. not natural product derived) cyclic peptide ligands to targets of interest. AREAS COVERED In this review, the authors describe the current clinical landscape for cyclic peptide pharmaceuticals. This article focuses on the discovery approaches that have led to the development of different classes of molecules and how the development of newer technologies, particularly phage and mRNA display, has broadened the clinical applicability of such molecules. EXPERT OPINION The field of de novo cyclic peptide drug discovery is reaching maturity, with the first drugs identified through display screening approaches reaching the market in recent years. Many more are in clinical trials; however, significant technical challenges remain. Technological improvements will be required over the coming years to facilitate the identification of membrane permeable cyclic peptides capable of oral availability and targeting intracellular proteins.
Collapse
Affiliation(s)
- Sophia You
- Insamo South, Chippendale, NSW, Australia
| | | | - Toby Passioura
- School of Chemistry, The University of Sydney, Camperdown, NSW, Australia
| |
Collapse
|
3
|
Appavoo SD, Heller NW, van Campenhout CT, Saunders GJ, Yudin AK. Identification of "Structural Pin" Interactions and their Significance for the Conformational Control of Macrocyclic Scaffolds. Angew Chem Int Ed Engl 2024; 63:e202402372. [PMID: 38499461 DOI: 10.1002/anie.202402372] [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: 02/01/2024] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 03/20/2024]
Abstract
While peptide macrocycles with rigidified conformations have proven to be useful in the design of chemical probes of protein targets, conformational flexibility and rapid interconversion can be equally vital for biological activity and favorable physicochemical properties. This study introduces the concept of "structural pin", which describes a hydrogen bond that is largely responsible for stabilizing the entire macrocycle backbone conformation. Structural analysis of macrocycles using nuclear magnetic resonance (NMR), molecular modelling and X-ray diffraction indicates that disruption of the structural pin can drastically influence the conformation of the entire ring, resulting in novel states with increased flexibility. This finding provides a new tool to interrogate dynamic behaviour of macrocycles. Identification of structural pins offers a useful conceptual framework to understand positions that can either be modified to give flexible structures or retained to maintain the rigidity of the scaffold.
Collapse
Affiliation(s)
- Solomon D Appavoo
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, Canada, M5S 3H6
| | - Nicholas W Heller
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, Canada, M5S 3H6
| | - Christian T van Campenhout
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, Canada, M5S 3H6
| | - George J Saunders
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, Canada, M5S 3H6
| | - Andrei K Yudin
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, Canada, M5S 3H6
| |
Collapse
|
4
|
Starnovskaya SS, Nesterenko LE, Popov RS, Kirichuk NN, Chausova VE, Chingizova EA, Chingizov AR, Isaeva MP, Yurchenko EA, Yurchenko AN. Metabolite profiles of Paragliomastix luzulae (formerly named as Acremonium striatisporum) KMM 4401 and its co-cultures with Penicillium hispanicum KMM 4689. NATURAL PRODUCTS AND BIOPROSPECTING 2024; 14:38. [PMID: 38886261 PMCID: PMC11182996 DOI: 10.1007/s13659-024-00459-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024]
Abstract
The marine holothurian-derived fungal strain KMM 4401 has been identified as Paragliomastix luzulae using 28S rDNA, ITS regions and the partial TEF1 gene sequences. The metabolite profile of the fungal culture was studied by UPLC-MS technique. The strain KMM 4401 is a source of various virescenoside-type isopimarane glycosides suggested as chemotaxonomic feature for this fungal species. Also Px. luzulae KMM 4401 was proposed as possible source of new bioactive secondary metabolites especially antimicrobials. Moreover, the co-cultures of Px. luzulae KMM 4401 with another marine fungus Penicillium hispanicum KMM 4689 inoculated simultaneously or after two weeks were investigated by same way. It was shown, that P. hispanicum KMM 4689 suppressed the production of most of Px. luzulae KMM 4401 metabolites. On the other hand, the co-cultivation of P. hispanicum KMM 4689 and Px. luzulae KMM 4401 resulted in increasing of production of main deoxyisoaustamide alkaloids of P. hispanicum KMM 4689 on 50-190%.
Collapse
Affiliation(s)
- Sofya S Starnovskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 159 Prospect 100-Letiya Vladivostoka, Vladivostok, 690022, Russian Federation
| | - Liliana E Nesterenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 159 Prospect 100-Letiya Vladivostoka, Vladivostok, 690022, Russian Federation
| | - Roman S Popov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 159 Prospect 100-Letiya Vladivostoka, Vladivostok, 690022, Russian Federation
| | - Natalya N Kirichuk
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 159 Prospect 100-Letiya Vladivostoka, Vladivostok, 690022, Russian Federation
| | - Viktoria E Chausova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 159 Prospect 100-Letiya Vladivostoka, Vladivostok, 690022, Russian Federation
| | - Ekaterina A Chingizova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 159 Prospect 100-Letiya Vladivostoka, Vladivostok, 690022, Russian Federation
| | - Artur R Chingizov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 159 Prospect 100-Letiya Vladivostoka, Vladivostok, 690022, Russian Federation
| | - Marina P Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 159 Prospect 100-Letiya Vladivostoka, Vladivostok, 690022, Russian Federation
| | - Ekaterina A Yurchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 159 Prospect 100-Letiya Vladivostoka, Vladivostok, 690022, Russian Federation
| | - Anton N Yurchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 159 Prospect 100-Letiya Vladivostoka, Vladivostok, 690022, Russian Federation.
| |
Collapse
|
5
|
Miao J, Ghosh AP, Ho MN, Li C, Huang X, Pentelute BL, Baleja JD, Lin YS. Assessing the Performance of Peptide Force Fields for Modeling the Solution Structural Ensembles of Cyclic Peptides. J Phys Chem B 2024; 128:5281-5292. [PMID: 38785765 PMCID: PMC11163431 DOI: 10.1021/acs.jpcb.4c00157] [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: 01/08/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
Molecular dynamics simulation is a powerful tool for characterizing the solution structural ensembles of cyclic peptides. However, the ability of simulation to recapitulate experimental results and make accurate predictions largely depends on the force fields used. In our work here, we evaluate the performance of seven state-of-the-art force fields in recapitulating the experimental NMR results in water of 12 benchmark cyclic peptides, consisting of 6 cyclic pentapeptides, 4 cyclic hexapeptides, and 2 cyclic heptapeptides. The results show that RSFF2+TIP3P, RSFF2C+TIP3P, and Amber14SB+TIP3P exhibit similar and the best performance, all recapitulating the NMR-derived structure information on 10 cyclic peptides. Amber19SB+OPC successfully recapitulates the NMR-derived structure information on 8 cyclic peptides. In contrast, OPLS-AA/M+TIP4P, Amber03+TIP3P, and Amber14SBonlysc+GB-neck2 could only recapitulate the NMR-derived structure information on 5 cyclic peptides, the majority of which are not well-structured.
Collapse
Affiliation(s)
- Jiayuan Miao
- Department
of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Arghya Pratim Ghosh
- Department
of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Minh Ngoc Ho
- Department
of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Chengxi Li
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
- College
of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310030, China
- Engineering
Research Center of Functional Materials Intelligent Manufacturing
of Zhejiang Province, ZJU-Hangzhou Global
Scientific and Technological Innovation Center, Hangzhou, Zhejiang 311215, China
| | - Xuejian Huang
- Graduate
Program in Pharmacology and Experimental Therapeutics, Graduate School
of Biomedical Sciences, Tufts University, Boston, Massachusetts 02111, United States
| | - Bradley L. Pentelute
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - James D. Baleja
- Graduate
Program in Pharmacology and Experimental Therapeutics, 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
| |
Collapse
|
6
|
Limbach M, Lindberg ET, Olivos HJ, van Tetering L, Steren CA, Martens J, Ngo VA, Oomens J, Do TD. Taming Conformational Heterogeneity on Ion Racetrack to Unveil Principles that Drive Membrane Permeation of Cyclosporines. JACS AU 2024; 4:1458-1470. [PMID: 38665661 PMCID: PMC11040698 DOI: 10.1021/jacsau.4c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 04/28/2024]
Abstract
Our study reveals the underlying principles governing the passive membrane permeability in three large N-methylated macrocyclic peptides (N-MeMPs): cyclosporine A (CycA), Alisporivir (ALI), and cyclosporine H (CycH). We determine a series of conformers required for robust passive membrane diffusion and those relevant to other functions, such as binding to protein targets or intermediates, in the presence of solvent additives. We investigate the conformational interconversions and establish correlations with the membrane permeability. Nuclear magnetic resonance (NMR) and cyclic ion-mobility spectrometry-mass spectrometry (cIMS-MS) are employed to characterize conformational heterogeneity and identify cis-amides relevant for good membrane permeability. In addition, ion mobility selected cIMS-MS and infrared (IR) multiple-photon dissociation (IRMPD) spectroscopy experiments are conducted to evaluate the energy barriers between conformations. We observe that CycA and ALI, both cyclosporines with favorable membrane permeabilities, display multiple stable and well-defined conformers. In contrast, CycH, an epimer of CycA with limited permeability, exhibits fewer and fewer stable conformers. We demonstrate the essential role of the conformational shift from the aqueous cis MeVal11-MeBmt1 state (A1) to the closed conformation featuring cis MeLeu9-MeLeu10 (C1) in facilitating membrane permeation. Additionally, we highlight that the transition from A1 to the all-trans open conformation (O1) is specifically triggered by the presence of CaCl2. We also capture a set of conformers with cis Sar3-MeLeu4, MeLeu9-MeLeu10, denoted as I. Conformationally selected cIMS-MS and IRMPD data of [CycA+Ca]2+ show immediate repopulation of the original population distribution, suggesting that CaCl2 smooths out the energy barriers. Finally, our work presents an improved sampling molecular dynamics approach based on a refined force field that not only consistently and accurately captures established conformers of cyclosporines but also exhibits strong predictive capabilities for novel conformers.
Collapse
Affiliation(s)
- Miranda
N. Limbach
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Edward T. Lindberg
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | | | - Lara van Tetering
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, Nijmegen 6525 ED, The Netherlands
| | - Carlos A. Steren
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jonathan Martens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, Nijmegen 6525 ED, The Netherlands
| | - Van A. Ngo
- Advanced
Computing for Life Sciences and Engineering Group, Science Engagement
Section, National Center for Computational Sciences, Computing and
Computational Sciences Directorate, Oak
Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Jos Oomens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, Nijmegen 6525 ED, The Netherlands
| | - Thanh D. Do
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| |
Collapse
|
7
|
Zhang C, Liu F, Zhang Y, Song C. Macrocycles and macrocyclization in anticancer drug discovery: Important pieces of the puzzle. Eur J Med Chem 2024; 268:116234. [PMID: 38401189 DOI: 10.1016/j.ejmech.2024.116234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/10/2024] [Accepted: 02/11/2024] [Indexed: 02/26/2024]
Abstract
Increasing disease-related proteins have been identified as novel therapeutic targets. Macrocycles are emerging as potential solutions, bridging the gap between conventional small molecules and biomacromolecules in drug discovery. Inspired by successful macrocyclic drugs of natural origins, macrocycles are attracting more attention for enhanced binding affinity and target selectivity. Due to the conformation constraint and structure preorganization, macrocycles can reach bioactive conformations more easily than parent acyclic compounds. Also, rational macrocyclization combined with sequent structural modification will help improve oral bioavailability and combat drug resistance. This review introduces various strategies to enhance membrane permeability in macrocyclization and subsequent modification, such as N-methylation, intramolecular hydrogen bonding modulation, isomerization, and reversible bicyclization. Several case studies highlight macrocyclic inhibitors targeting kinases, HDAC, and protein-protein interactions. Finally, some macrocyclic agents targeting tumor microenvironments are illustrated.
Collapse
Affiliation(s)
- Chao Zhang
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Fenfen Liu
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Chun Song
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| |
Collapse
|
8
|
Mácha H, Zápal J, Kuzma M, Luptáková D, Lemr K, Havlíček V. Exploring the Effects of Cyclosporin A to Isocyclosporin A Rearrangement on Ion Mobility Separation. Anal Chem 2024; 96:4163-4170. [PMID: 38430121 PMCID: PMC10938282 DOI: 10.1021/acs.analchem.3c05165] [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: 11/15/2023] [Revised: 02/05/2024] [Accepted: 02/15/2024] [Indexed: 03/03/2024]
Abstract
Cyclosporin A (CycA) is a peptide secondary metabolite derived from fungi that plays a crucial role in transplantation surgery. Cyclic traveling wave ion mobility mass spectrometry (IM-MS) revealed an N → O peptidyl shift in singly protonated CycA to isocyclosporin A (isoA), whereas no such isomerization was observed for doubly protonated and sodiated molecules. CycA and isoA were able to be separated by considering doubly protonated precursors using a specific ion fragment. In parallel, sodium ion stabilization facilitated the simultaneous separation and quantitation of singly charged cyclosporin isomers with the limit of detection and coefficient of determination of 1.3% and 0.9908 for CycA in isoA and 1.0% and 0.9830 for isoA in CycA, respectively. Finally, 1H-13C gHSQC NMR experiments permitted parallel recording of up to 11 cyclosporin conformers. The ratios were determined by integrating the volume of cross-peaks of the upfield resonating hydrogen in the diastereotopic methylene group of sarcosine-3.
Collapse
Affiliation(s)
- Hynek Mácha
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 142 00, Czech Republic
- Department
of Analytical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, Olomouc 771 46, Czech Republic
| | - Jakub Zápal
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 142 00, Czech Republic
| | - Marek Kuzma
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 142 00, Czech Republic
- Department
of Analytical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, Olomouc 771 46, Czech Republic
| | - Dominika Luptáková
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 142 00, Czech Republic
| | - Karel Lemr
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 142 00, Czech Republic
- Department
of Analytical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, Olomouc 771 46, Czech Republic
| | - Vladimír Havlíček
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 142 00, Czech Republic
- Department
of Analytical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, Olomouc 771 46, Czech Republic
| |
Collapse
|
9
|
Jiang Y, Tao M, Chen J, Luo L, You Q, Wu H, Zhang N. Calcineurin inhibitors in the treatment of systemic lupus erythematosus during pregnancy: A narrative review with emphasis on efficacy and safety. Eur J Obstet Gynecol Reprod Biol 2024; 294:148-155. [PMID: 38245953 DOI: 10.1016/j.ejogrb.2023.12.039] [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: 10/22/2023] [Revised: 11/21/2023] [Accepted: 12/31/2023] [Indexed: 01/23/2024]
Abstract
Systemic lupus erythematosus (SLE) predominantly affects child-bearing women, leading to an elevated risk of maternal and fetal complications and adverse pregnancy outcomes. Since some medications can cross the placental barrier that persist a threat to both mother and fetus, the risk-benefit ratio of SLE medications should be taken into consideration during pregnancy. Calcineurin inhibitor (CNI), mainly including cyclosporin A, tacrolimus, and voclosporin, is a category of immunosuppressive agents that inhibit calcium/calmodulin-dependent phosphatase calcineurin to block T cell activation. Based on the current clinical evidence, CNI is an alternative in pregnant SLE patients with persistent disease activity (especially lupus nephritis patients) and non-responders to azathioprine. However, there is no comprehensive review that summarizes the efficacy and safety profile of CNI for SLE management during pregnancy. This review presents a summary on the utilization of CNI for SLE management during pregnancy, including the mechanism of action, gestational amelioration of lupus flare, and the balance of maternal benefit-fetal risk, which may provide more references for the management of SLE pregnancies.
Collapse
Affiliation(s)
- Yi Jiang
- Department of Rheumatology and Immunology, The First Hospital Affiliated to Army Medical University, Chongqing 400038, China
| | - Min Tao
- Department of Pediatrics, The First Hospital Affiliated to Army Medical University, Chongqing 400038, China
| | - Jingjing Chen
- Department of Rheumatology and Immunology, The First Hospital Affiliated to Army Medical University, Chongqing 400038, China
| | - Lihua Luo
- Department of Rheumatology and Immunology, The First Hospital Affiliated to Army Medical University, Chongqing 400038, China
| | - Qingxia You
- Department of Rheumatology and Immunology, The First Hospital Affiliated to Army Medical University, Chongqing 400038, China
| | - Hong Wu
- Department of Rheumatology and Immunology, The First Hospital Affiliated to Army Medical University, Chongqing 400038, China
| | - Nian Zhang
- Department of Traditional Chinese Medicine, The Second Hospital Affiliated to Army Medical University, Chongqing 400037, China.
| |
Collapse
|
10
|
Möbitz H. Design Principles for Balancing Lipophilicity and Permeability in beyond Rule of 5 Space. ChemMedChem 2024; 19:e202300395. [PMID: 37986275 DOI: 10.1002/cmdc.202300395] [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: 07/27/2023] [Revised: 10/13/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023]
Abstract
An ab initio conformational analysis of oral beyond Rule of 5 (bRo5) drugs was complemented with measured permeability and logP(octanol) to derive design principles conferring oral bioavailability. 3D polar surface area (PSA) thresholds for oral bRo5 drugs coincided with those reported for Ro5 space. The majority of oral bRo5 drugs exceeded the Ro5 logP threshold of 5, reflecting a bias for permeability. Above 500 Da molecular weight (MW), oral drugs and highly permeable Novartis compounds occupy a narrow polarity range (topological or TPSA/MW) of 0.1-0.3 Å2 /Da, whose upper half coincides with the lower 90 percentiles of the Novartis logP set. This TPSA/MW range and 3D PSA below 100 Å2 define the "Rule of ~1 /₅" for balancing lipophilicity and permeability. Neutral TPSA, defined as TPSA minus 3D PSA occurs independent of conformation, intramolecular hydrogen bonds (IMHB) and MW, suggesting it is an intrinsic molecular property. Neutral TPSA increased in the lead optimization (LO) campaigns of three first in class de novo designed bRo5 drugs and may be a useful design parameter in bRo5 space.
Collapse
Affiliation(s)
- Henrik Möbitz
- Computer-Aided Drug Design, Global Discovery Chemistry, Novartis BioMedical Research, 4002, Basel, Switzerland
| |
Collapse
|
11
|
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
|
12
|
Abstract
Cyclic peptides are fascinating molecules abundantly found in nature and exploited as molecular format for drug development as well as other applications, ranging from research tools to food additives. Advances in peptide technologies made over many years through improved methods for synthesis and drug development have resulted in a steady stream of new drugs, with an average of around one cyclic peptide drug approved per year. Powerful technologies for screening random peptide libraries, and de novo generating ligands, have enabled the development of cyclic peptide drugs independent of naturally derived molecules and now offer virtually unlimited development opportunities. In this review, we feature therapeutically relevant cyclic peptides derived from nature and discuss the unique properties of cyclic peptides, the enormous technological advances in peptide ligand development in recent years, and current challenges and opportunities for developing cyclic peptides that address unmet medical needs.
Collapse
Affiliation(s)
- Xinjian Ji
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Alexander L Nielsen
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| |
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
Tang X, Kokot J, Waibl F, Fernández-Quintero ML, Kamenik AS, Liedl KR. Addressing Challenges of Macrocyclic Conformational Sampling in Polar and Apolar Solvents: Lessons for Chameleonicity. J Chem Inf Model 2023; 63:7107-7123. [PMID: 37943023 PMCID: PMC10685455 DOI: 10.1021/acs.jcim.3c01123] [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: 07/23/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 11/10/2023]
Abstract
We evaluated a workflow to reliably sample the conformational space of a set of 47 peptidic macrocycles. Starting from SMILES strings, we use accelerated molecular dynamics simulations to overcome high energy barriers, in particular, the cis-trans isomerization of peptide bonds. We find that our approach performs very well in polar solvents like water and dimethyl sulfoxide. Interestingly, the protonation state of a secondary amine in the ring only slightly influences the conformational ensembles of our test systems. For several of the macrocycles, determining the conformational distribution in chloroform turns out to be considerably more challenging. Especially, the choice of partial charges crucially influences the ensembles in chloroform. We address these challenges by modifying initial structures and the choice of partial charges. Our results suggest that special care has to be taken to understand the configurational distribution in apolar solvents, which is a key step toward a reliable prediction of membrane permeation of macrocycles and their chameleonic properties.
Collapse
Affiliation(s)
- Xuechen Tang
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Janik Kokot
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Franz Waibl
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, 8093 Zürich, Switzerland
| | | | - Anna S. Kamenik
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
| |
Collapse
|
15
|
Yu L, Barros SA, Sun C, Somani S. Cyclic Peptide Linker Design and Optimization by Molecular Dynamics Simulations. J Chem Inf Model 2023; 63:6863-6876. [PMID: 37903231 DOI: 10.1021/acs.jcim.3c01359] [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: 11/01/2023]
Abstract
Cyclic peptides are an emerging therapeutic modality that can target protein-protein interaction sites with high affinity and selectivity. A common medicinal chemistry strategy for the optimization of peptide hits is conformational stabilization through macrocyclization. We present a method based on explicit solvent enhanced sampling molecular dynamics simulations for estimating the impact of varying linker lengths and chemistry on the conformational stability of a peptide. The method is demonstrated on three cyclic peptide series that bind to proteins PCSK9, trypsin, and MDM2 adopting loop, β-sheet, and helical secondary structures. In general, the simulations show greater solution stability of the receptor-bound conformation for the higher-affinity peptides, consistent with the idea that preorganizing a ligand for binding can enhance binding affinity. The impact of the force field and sampling is discussed for one series that does not follow this trend. We have successfully applied this method to internal discovery programs to design peptides with increased potency and chemical stability.
Collapse
Affiliation(s)
- Lei Yu
- Janssen Research & Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Stephanie A Barros
- Janssen Research & Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Chengzao Sun
- Janssen Research & Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Sandeep Somani
- Janssen Research & Development, LLC, Spring House, Pennsylvania 19477, United States
| |
Collapse
|
16
|
Ohta A, Tanada M, Shinohara S, Morita Y, Nakano K, Yamagishi Y, Takano R, Kariyuki S, Iida T, Matsuo A, Ozeki K, Emura T, Sakurai Y, Takano K, Higashida A, Kojima M, Muraoka T, Takeyama R, Kato T, Kimura K, Ogawa K, Ohara K, Tanaka S, Kikuchi Y, Hisada N, Hayashi R, Nishimura Y, Nomura K, Tachibana T, Irie M, Kawada H, Torizawa T, Murao N, Kotake T, Tanaka M, Ishikawa S, Miyake T, Tamiya M, Arai M, Chiyoda A, Akai S, Sase H, Kuramoto S, Ito T, Shiraishi T, Kojima T, Iikura H. Validation of a New Methodology to Create Oral Drugs beyond the Rule of 5 for Intracellular Tough Targets. J Am Chem Soc 2023; 145:24035-24051. [PMID: 37874670 DOI: 10.1021/jacs.3c07145] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Establishing a technological platform for creating clinical compounds inhibiting intracellular protein-protein interactions (PPIs) can open the door to many valuable drugs. Although small molecules and antibodies are mainstream modalities, they are not suitable for a target protein that lacks a deep cavity for a small molecule to bind or a protein found in intracellular space out of an antibody's reach. One possible approach to access these targets is to utilize so-called middle-size cyclic peptides (defined here as those with a molecular weight of 1000-2000 g/mol). In this study, we validated a new methodology to create oral drugs beyond the rule of 5 for intracellular tough targets by elucidating structural features and physicochemical properties for drug-like cyclic peptides and developing library technologies to afford highly N-alkylated cyclic peptide hits. We discovered a KRAS inhibitory clinical compound (LUNA18) as the first example of our platform technology.
Collapse
Affiliation(s)
- Atsushi Ohta
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Mikimasa Tanada
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Shojiro Shinohara
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Yuya Morita
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Kazuhiko Nakano
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Yusuke Yamagishi
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Ryusuke Takano
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Shiori Kariyuki
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Takeo Iida
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Atsushi Matsuo
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Kazuhisa Ozeki
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Takashi Emura
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Yuuji Sakurai
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Koji Takano
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Atsuko Higashida
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Miki Kojima
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Terushige Muraoka
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Ryuuichi Takeyama
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Tatsuya Kato
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Kaori Kimura
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Kotaro Ogawa
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Kazuhiro Ohara
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Shota Tanaka
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Yasufumi Kikuchi
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Nozomi Hisada
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Ryuji Hayashi
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Yoshikazu Nishimura
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Kenichi Nomura
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Tatsuhiko Tachibana
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Machiko Irie
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Hatsuo Kawada
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Takuya Torizawa
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Naoaki Murao
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Tomoya Kotake
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Masahiko Tanaka
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Shiho Ishikawa
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Taiji Miyake
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Minoru Tamiya
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Masako Arai
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Aya Chiyoda
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Sho Akai
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Hitoshi Sase
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Shino Kuramoto
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Toshiya Ito
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Takuya Shiraishi
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Tetsuo Kojima
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Hitoshi Iikura
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| |
Collapse
|
17
|
Kale A, Shelke V, Lei Y, Gaikwad AB, Anders HJ. Voclosporin: Unique Chemistry, Pharmacology and Toxicity Profile, and Possible Options for Implementation into the Management of Lupus Nephritis. Cells 2023; 12:2440. [PMID: 37887284 PMCID: PMC10605893 DOI: 10.3390/cells12202440] [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: 09/14/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
Calcineurin inhibitors (CNI) can suppress allo- and autoimmunity by suppressing T cell function but also have anti-proteinuric effects by stabilizing the cellular components of the kidney's filtration barrier. Therefore, CNI are used in autoimmune kidney diseases with proteinuria. However, the traditional CNI, cyclosporine A and tacrolimus, have a narrow therapeutic range, need monitoring of drug levels, and their use is associated with nephrotoxicity and metabolic alterations. Voclosporin (VOC), a novel CNI, no longer requires drug level monitoring and seems to lack these adverse effects, although hypertension and drug-drug interactions still occur. VOC demonstrated efficacy superior to standard-of-care in controlling active lupus nephritis in the phase 2 AURA-LV and the phase 3 AURORA-1 trials and was approved for the treatment of active lupus nephritis. However, how to implement VOC into the current and changing treatment landscape of lupus nephritis is still debated. Here, we review the unique chemistry, pharmacology, and toxicity profile of VOC, summarize the efficacy and safety data from the AURA-LV and AURORA-1 trials, and discuss the following four possible options to implement VOC into the management of lupus nephritis, namely regarding B cell-targeting therapy with belimumab (BEL). These include: 1. patient stratification to either VOC or BEL, 2. VOC/BEL combination therapy, 3. VOC-BEL sequential therapy, or 4. alternative options for the rapid antiproteinuric effect of VOC.
Collapse
Affiliation(s)
- Ajinath Kale
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani 333031, Rajasthan, India; (A.K.); (V.S.); (A.B.G.)
| | - Vishwadeep Shelke
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani 333031, Rajasthan, India; (A.K.); (V.S.); (A.B.G.)
| | - Yutian Lei
- Division of Diabetology, Department of Internal Medicine IV, Hospital of the Ludwig Maximilians University Munich, 333031 Munich, Germany;
| | - Anil Bhanudas Gaikwad
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani 333031, Rajasthan, India; (A.K.); (V.S.); (A.B.G.)
| | - Hans-Joachim Anders
- Division of Nephrology, Department of Internal Medicine IV, Hospital of the Ludwig Maximilians University Munich, 80336 Munich, Germany
| |
Collapse
|
18
|
L'Exact M, Comeau C, Bourhis A, Boisvert O, Fröhlich U, Létourneau D, Marsault É, Lavigne P, Grandbois M, Boudreault PL. Beyond Rule-of-five: Permeability Assessment of Semipeptidic Macrocycles. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184196. [PMID: 37400050 DOI: 10.1016/j.bbamem.2023.184196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/08/2023] [Accepted: 06/26/2023] [Indexed: 07/05/2023]
Abstract
Compounds beyond the rule-of-five are generating interest as they expand the molecular toolbox for modulating targets previously considered "undruggable". Macrocyclic peptides are an efficient class of molecules for modulating protein-protein interactions. However, predicting their permeability is difficult as they differ from small molecules. Although constrained by macrocyclization, they generally retain some conformational flexibility associated with an enhanced ability to cross biological membranes. In this study, we investigated the relationship between the structure of semi-peptidic macrocycles and their membrane permeability through structural modifications. Based on a scaffold of four amino acids and a linker, we synthesized 56 macrocycles incorporating modifications in either stereochemistry, N-methylation, or lipophilicity and assessed their passive permeability using the parallel artificial membrane permeability assay (PAMPA). Our results show that some semi-peptidic macrocycles have adequate passive permeability even with properties outside the Lipinski rule of five. We found that N-methylation in position 2 and the addition of lipophilic groups to the side chain of tyrosine led to an improvement in permeability with a decrease in tPSA and 3D-PSA. This enhancement could be attributed to the shielding effect of the lipophilic group on some regions of the macrocycle, which in turn, facilitates a favorable macrocycle conformation for permeability, suggesting some degree of chameleonic behavior.
Collapse
Affiliation(s)
- Marion L'Exact
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Christian Comeau
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Alix Bourhis
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Olivier Boisvert
- Institut de Pharmacologie de Sherbrooke, Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Ulrike Fröhlich
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Danny Létourneau
- Institut de Pharmacologie de Sherbrooke, Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Éric Marsault
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Pierre Lavigne
- Institut de Pharmacologie de Sherbrooke, Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Michel Grandbois
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Pierre-Luc Boudreault
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada.
| |
Collapse
|
19
|
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
|
20
|
Mizuno-Kaneko M, Hashimoto I, Miyahara K, Kochi M, Ohashi N, Tsumura K, Suzuki K, Tamura T. Molecular Design of Cyclic Peptides with Cell Membrane Permeability and Development of MDMX-p53 Inhibitor. ACS Med Chem Lett 2023; 14:1174-1178. [PMID: 37736191 PMCID: PMC10510666 DOI: 10.1021/acsmedchemlett.3c00102] [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: 04/04/2023] [Accepted: 08/07/2023] [Indexed: 09/23/2023] Open
Abstract
Cyclic peptides have been expected to be one of the modalities of intracellular protein-protein interaction (PPI) inhibitors, but they are generally known to have low cell membrane permeability. In this study, we focused on the conformation of cyclic peptides in the cell membrane to determine the requirement for their cell membrane permeability through passive diffusion. Utilizing the requirement, we searched for structures with high affinity for MDMX via computational chemistry and acquired cyclic peptide 19 (Papp = 0.80 × 10-6 cm s-1, IC50 = 0.07 μM).
Collapse
Affiliation(s)
- Mai Mizuno-Kaneko
- 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-shi, Kanagawa 250-0193, Japan
| | - Kenta Miyahara
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Masahiro Kochi
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Noriyuki Ohashi
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Kyosuke Tsumura
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Koo Suzuki
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Takashi Tamura
- Synthetic
Organic Chemistry Laboratories, FUJIFILM
Corporation, 577, Ushijima, Kaisei-machi, Ashigarakami-gun, Kanagawa 258-8577, Japan
| |
Collapse
|
21
|
Ramelot TA, Palmer J, Montelione GT, Bhardwaj G. Cell-permeable chameleonic peptides: Exploiting conformational dynamics in de novo cyclic peptide design. Curr Opin Struct Biol 2023; 80:102603. [PMID: 37178478 PMCID: PMC10923192 DOI: 10.1016/j.sbi.2023.102603] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/05/2023] [Indexed: 05/15/2023]
Abstract
Membrane-traversing peptides offer opportunities for targeting intracellular proteins and oral delivery. Despite progress in understanding the mechanisms underlying membrane traversal in natural cell-permeable peptides, there are still several challenges to designing membrane-traversing peptides with diverse shapes and sizes. Conformational flexibility appears to be a key determinant of membrane permeability of large macrocycles. We review recent developments in the design and validation of chameleonic cyclic peptides, which can switch between alternative conformations to enable improved permeability through cell membranes, while still maintaining reasonable solubility and exposed polar functional groups for target protein binding. Finally, we discuss the principles, strategies, and practical considerations for rational design, discovery, and validation of permeable chameleonic peptides.
Collapse
Affiliation(s)
- Theresa A Ramelot
- Department of Chemistry and Chemical Biology and Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, 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
| | - Gaetano T Montelione
- Department of Chemistry and Chemical Biology and Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
| | - Gaurav Bhardwaj
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA; Department of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA.
| |
Collapse
|
22
|
Ono T, Tabata KV, Noji H, Morimoto J, Sando S. Each side chain of cyclosporin A is not essential for high passive permeability across lipid bilayers. RSC Adv 2023; 13:8394-8397. [PMID: 36922944 PMCID: PMC10010161 DOI: 10.1039/d3ra01358h] [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] [Received: 02/28/2023] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
We compared the passive permeability of cyclosporin A (CsA) derivatives with side chain deletions across lipid bilayers. CsA maintained passive permeability after losing any one of the side chains, which suggests that the propensity of the backbone of CsA is an important component for high passive permeability.
Collapse
Affiliation(s)
- Takahiro Ono
- Department of Chemistry & Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Kazuhito V Tabata
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Hiroyuki Noji
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan.,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Jumpei Morimoto
- Department of Chemistry & Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Shinsuke Sando
- Department of Chemistry & Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan .,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| |
Collapse
|
23
|
Kuschert S, Stroet M, Chin YKY, Conibear AC, Jia X, Lee T, Bartling CRO, Strømgaard K, Güntert P, Rosengren KJ, Mark AE, Mobli M. Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMR. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2023; 4:57-72. [PMID: 37904802 PMCID: PMC10583272 DOI: 10.5194/mr-4-57-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/07/2023] [Indexed: 11/01/2023]
Abstract
Peptides and proteins containing non-canonical amino acids (ncAAs) are a large and important class of biopolymers. They include non-ribosomally synthesised peptides, post-translationally modified proteins, expressed or synthesised proteins containing unnatural amino acids, and peptides and proteins that are chemically modified. Here, we describe a general procedure for generating atomic descriptions required to incorporate ncAAs within popular NMR structure determination software such as CYANA, CNS, Xplor-NIH and ARIA. This procedure is made publicly available via the existing Automated Topology Builder (ATB) server (https://atb.uq.edu.au, last access: 17 February 2023) with all submitted ncAAs stored in a dedicated database. The described procedure also includes a general method for linking of side chains of amino acids from CYANA templates. To ensure compatibility with other systems, atom names comply with IUPAC guidelines. In addition to describing the workflow, 3D models of complex natural products generated by CYANA are presented, including vancomycin. In order to demonstrate the manner in which the templates for ncAAs generated by the ATB can be used in practice, we use a combination of CYANA and CNS to solve the structure of a synthetic peptide designed to disrupt Alzheimer-related protein-protein interactions. Automating the generation of structural templates for ncAAs will extend the utility of NMR spectroscopy to studies of more complex biomolecules, with applications in the rapidly growing fields of synthetic biology and chemical biology. The procedures we outline can also be used to standardise the creation of structural templates for any amino acid and thus have the potential to impact structural biology more generally.
Collapse
Affiliation(s)
- Sarah Kuschert
- Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Martin Stroet
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yanni Ka-Yan Chin
- Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Anne Claire Conibear
- Institute of Applied Synthetic Chemistry, Technische Universität Wien, Getreidemarkt 9/163, Wien 1060, Vienna, Austria
| | - Xinying Jia
- Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Lee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Peter Güntert
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zurich, Switzerland
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Department of Chemistry, Tokyo Metropolitan University, Hachiōji, Tokyo 192-0397, Japan
| | - Karl Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alan Edward Mark
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| |
Collapse
|
24
|
Jyrkäs J, Lassila T, Tolonen A. Extrahepatic in vitro metabolism of peptides; comparison of human kidney and intestinal S9 fraction, human plasma and proximal tubule cells, using cyclosporine A, leuprorelin, and cetrorelix as model compounds. J Pharm Biomed Anal 2023; 225:115219. [PMID: 36630767 DOI: 10.1016/j.jpba.2022.115219] [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: 10/15/2022] [Revised: 12/06/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
Peptide therapeutics showcase number of advantages compared to the traditional small molecule drugs, e,g. they usually have higher affinity to target and lower toxicity profiles. Endogenous peptides are mostly cleared from the body through renal clearance or proteolytic hydrolysis. As a part of drug discovery, metabolite identification is an important part in their development to identify metabolic hot spots and to further improve their stability. As the catabolism of the peptides and peptide-like drugs is often considered to be extrahepatic, the use of in vitro systems derived from these organs might be beneficial. In this study, multiple extrahepatic metabolic systems were evaluated for the applicability for peptide metabolism studies. Three peptide drugs (leuprorelin, cetrorelix, cyclosporin) were incubated in kidney and intestinal S9 fraction ( ± NADPH), fresh plasma (anticoagulants EDTA and heparin separately), and plated proximal tubule cells. Additionally, leuprorelin was also incubated with human kidney microsomes and cytosol to further investigate the NADPH-dependent metabolism detected in kidney S9 fraction. Both substrate disappearance and metabolite formation were monitored, using UPLC/HR-MS analysis of the collected samples.Overall, the largest number of metabolites was formed in the incubation with kidney S9 fraction, followed by intestinal S9, while incubations with proximal tubule cells produced lower number of metabolites All investigated peptides were stable in plasma and only a few metabolites were detected, likely because the studied peptide drugs have been optimized to be stable in plasma. Leuprorelin showed NADPH-dependent metabolite formation in kidney S9 fraction, while the metabolism of cetrorelix was more NADPH independent. As expected, formation of cytochrome P450 (CYP) catalyzed metabolism of cyclosporine was not observed with the employed extrahepatic systems. The NADPH-dependent metabolism of leuprorelin was detected also in the incubation with kidney cytosol, but not with kidney microsomes, and was thus not caused by CYPs or FMOs, but with cytosolic NADPH-dependent drug metabolizing enzymes. These enzymes could, in principle, activate the amide bond via reductive or oxidative metabolism outside the amide bond. The identity of the involved drug metabolizing enzymes in this process is still unknown.
Collapse
Affiliation(s)
- Juha Jyrkäs
- Admescope Ltd, Typpitie 1, 90620 Oulu, Finland; Research Unit of Sustainable Chemistry, Faculty of Technology, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland.
| | | | - Ari Tolonen
- Admescope Ltd, Typpitie 1, 90620 Oulu, Finland
| |
Collapse
|
25
|
Wieske LHE, Atilaw Y, Poongavanam V, Erdélyi M, Kihlberg J. Going Viral: An Investigation into the Chameleonic Behaviour of Antiviral Compounds. Chemistry 2023; 29:e202202798. [PMID: 36286339 PMCID: PMC10107787 DOI: 10.1002/chem.202202798] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 12/15/2022]
Abstract
The ability to adjust conformations in response to the polarity of the environment, i.e. molecular chameleonicity, is considered to be important for conferring both high aqueous solubility and high cell permeability to drugs in chemical space beyond Lipinski's rule of 5. We determined the conformational ensembles populated by the antiviral drugs asunaprevir, simeprevir, atazanavir and daclatasvir in polar (DMSO-d6 ) and non-polar (chloroform) environments with NMR spectroscopy. Daclatasvir was fairly rigid, whereas the first three showed large flexibility in both environments, that translated into major differences in solvent accessible 3D polar surface area within each conformational ensemble. No significant differences in size and polar surface area were observed between the DMSO-d6 and chloroform ensembles of these three drugs. We propose that such flexible compounds are characterized as "partial molecular chameleons" and hypothesize that their ability to adopt conformations with low polar surface area contributes to their membrane permeability and oral absorption.
Collapse
Affiliation(s)
- Lianne H E Wieske
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | | | - Máté Erdélyi
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| |
Collapse
|
26
|
Saphier S, Katalan S, Yacov G, Berliner A, Redy-Keisar O, Fridkin G, Ghindes-Azaria L, Columbus I, Pevzner A, Drug E, Prihed H, Gershonov E, Eichen Y, Elias S, Parvari G, Zafrani Y. Placing CF 2 in the Center: Major Physicochemical Changes Upon a Minor Structural Alteration in Gem-Difunctional Compounds. Chemistry 2023; 29:e202202939. [PMID: 36374157 DOI: 10.1002/chem.202202939] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/07/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]
Abstract
Fluorine atoms play an important role in all branches of chemistry and accordingly, it is very important to study their unique and varied effects systematically, in particular, the structure-physicochemical properties relationship. The present study describes exceptional physicochemical effects resulting from a H/F exchange at the methylene bridge of gem-difunctional compounds. The Δlog P(CF2-CH2) values, that is, the change in lipophilicity, observed for the CH2 /CF2 replacement in various α,α-phenoxy- and thiophenoxy-esters/amides, diketones, benzodioxoles and more, fall in the range of 0.6-1.4 units, which for most cases, is far above the values expected for such a replacement. Moreover, for compounds holding more than one such gem-difunctional moiety, the effect is nearly additive, so one can switch from a hydrophilic compound to a lipophilic one in a limited number of H/F exchanges. DFT studies of some of these systems revealed that polarity, conformational preference as well as charge distributions are strongly affected by such hydrogen to fluorine atom substitution. The pronounced effects described, are a result of the interplay between changes in polarity, H-bond basicity and molecular volume, which were obtained with a very low 'cost' in terms of molecular weight or steric effects and may have a great potential for implementation in various fields of chemical sciences.
Collapse
Affiliation(s)
- Sigal Saphier
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona, 74100, Israel
| | - Shahaf Katalan
- Department of Pharmacology, Israel Institute for Biological Research, Ness-Ziona, 74100, Israel
| | - Guy Yacov
- Department of Pharmacology, Israel Institute for Biological Research, Ness-Ziona, 74100, Israel
| | - Anat Berliner
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona, 74100, Israel
| | - Orit Redy-Keisar
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona, 74100, Israel
| | - Gil Fridkin
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona, 74100, Israel
| | - Lee Ghindes-Azaria
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona, 74100, Israel
| | - Ishay Columbus
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona, 74100, Israel
| | - Alexander Pevzner
- Department of Physical Chemistry, Israel Institute for Biological Research, Ness-Ziona, 74100, Israel
| | - Eyal Drug
- Department of Analytical Chemistry, Israel Institute for Biological Research, Ness-Ziona, 74100, Israel
| | - Hagit Prihed
- Department of Analytical Chemistry, Israel Institute for Biological Research, Ness-Ziona, 74100, Israel
| | - Eytan Gershonov
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona, 74100, Israel
| | - Yoav Eichen
- Schulich Faculty of Chemistry Technion, Israel Institute of Technology, Technion City, Haifa, 3200008, Israel
| | - Shlomi Elias
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona, 74100, Israel
| | - Galit Parvari
- Schulich Faculty of Chemistry Technion, Israel Institute of Technology, Technion City, Haifa, 3200008, Israel
| | - Yossi Zafrani
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona, 74100, Israel
| |
Collapse
|
27
|
Ono T, Tabata KV, Goto Y, Saito Y, Suga H, Noji H, Morimoto J, Sando S. Label-free quantification of passive membrane permeability of cyclic peptides across lipid bilayers: penetration speed of cyclosporin A across lipid bilayers. Chem Sci 2023; 14:345-349. [PMID: 36687349 PMCID: PMC9811578 DOI: 10.1039/d2sc05785a] [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] [Received: 10/18/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
Cyclic peptides that passively penetrate cell membranes are under active investigation in drug discovery research. PAMPA (Parallel Artificial Membrane Permeability Assay) and Caco-2 assay are mainly used for permeability measurements in these studies. However, permeability rates across the artificial membrane and the cell monolayer used for these assays are intrinsically different from the ones across pure lipid bilayers. There are also membrane permeability assays for peptides using reconstructed lipid bilayers, but they require labeling for detection, and the absolute membrane permeability of the natural peptides themselves could not be determined. Here, we constructed a lipid bilayer permeability assay and realized the first label-free measurements of the lipid bilayer permeability of cyclic peptides. Quantitative permeability values across lipid bilayers were determined for model cyclic hexapeptides and an important natural product, cyclosporin A (CsA). The obtained quantitative permeability values will provide new and advanced knowledge about the passive permeability of cyclic peptides.
Collapse
Affiliation(s)
- Takahiro Ono
- Department of Chemistry & Biotechnology, Graduate School of Engineering, The University of Tokyo7-3-1 HongoBunkyo-kuTokyo 113-8656Japan
| | - Kazuhito V. Tabata
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo7-3-1 HongoBunkyo-kuTokyo 113-8656Japan
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of TokyoBunkyo-kuTokyo 113-0033Japan
| | - Yutaro Saito
- Department of Chemistry & Biotechnology, Graduate School of Engineering, The University of Tokyo7-3-1 HongoBunkyo-kuTokyo 113-8656Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of TokyoBunkyo-kuTokyo 113-0033Japan
| | - Hiroyuki Noji
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo7-3-1 HongoBunkyo-kuTokyo 113-8656Japan,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo7-3-1 HongoBunkyo-kuTokyo 113-8656Japan
| | - Jumpei Morimoto
- Department of Chemistry & Biotechnology, Graduate School of Engineering, The University of Tokyo7-3-1 HongoBunkyo-kuTokyo 113-8656Japan
| | - Shinsuke Sando
- Department of Chemistry & Biotechnology, Graduate School of Engineering, The University of Tokyo7-3-1 HongoBunkyo-kuTokyo 113-8656Japan,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo7-3-1 HongoBunkyo-kuTokyo 113-8656Japan
| |
Collapse
|
28
|
Saunders GJ, Yudin AK. A focus on the discovery of potent and selective cyclic peptide scaffolds for drug development. Chem Sci 2022; 13:12942-12944. [PMID: 36425493 PMCID: PMC9667955 DOI: 10.1039/d2sc90214a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024] Open
Abstract
In the past, cyclic peptide drugs were commonly discovered by isolation of natural products. However, recent efforts predominantly use high-throughput synthetic or genetically encoded libraries to find potent and selective hits against a range of challenging therapeutic targets. Kawamura et al. (Chem. Sci., 2022, 13, 3256-3262, https://doi.org/10.1039/D1SC06844J) developed a new workflow that can be applied to mRNA display, using high-throughput clustering, SAR investigations and in silico structural studies. This led to the discovery of nanomolar, serum-stable cyclic peptides against the human glucose-dependent insulinotropic peptide receptor (hGIP-R).
Collapse
Affiliation(s)
- George J Saunders
- Davenport Research Laboratories, University of Toronto 80 St. George St Toronto M5S 3H6 Ontario Canada
| | - Andrei K Yudin
- Davenport Research Laboratories, University of Toronto 80 St. George St Toronto M5S 3H6 Ontario Canada
| |
Collapse
|
29
|
Williams-Noonan BJ, Speer MN, Le TC, Sadek MM, Thompson PE, Norton RS, Yuriev E, Barlow N, Chalmers DK, Yarovsky I. Membrane Permeating Macrocycles: Design Guidelines from Machine Learning. J Chem Inf Model 2022; 62:4605-4619. [PMID: 36178379 DOI: 10.1021/acs.jcim.2c00809] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability to predict cell-permeable candidate molecules has great potential to assist drug discovery projects. Large molecules that lie beyond the Rule of Five (bRo5) are increasingly important as drug candidates and tool molecules for chemical biology. However, such large molecules usually do not cross cell membranes and cannot access intracellular targets or be developed as orally bioavailable drugs. Here, we describe a random forest (RF) machine learning model for the prediction of passive membrane permeation rates developed using a set of over 1000 bRo5 macrocyclic compounds. The model is based on easily calculated chemical features/descriptors as independent variables. Our random forest (RF) model substantially outperforms a multiple linear regression model based on the same features and achieves better performance metrics than previously reported models using the same underlying data. These features include: (1) polar surface area in water, (2) the octanol-water partitioning coefficient, (3) the number of hydrogen-bond donors, (4) the sum of the topological distances between nitrogen atoms, (5) the sum of the topological distances between nitrogen and oxygen atoms, and (6) the multiple molecular path count of order 2. The last three features represent molecular flexibility, the ability of the molecule to adopt different conformations in the aqueous and membrane interior phases, and the molecular "chameleonicity." Guided by the model, we propose design guidelines for membrane-permeating macrocycles. It is anticipated that this model will be useful in guiding the design of large, bioactive molecules for medicinal chemistry and chemical biology applications.
Collapse
Affiliation(s)
- Billy J Williams-Noonan
- School of Engineering, RMIT University, Melbourne3001, Australia.,Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - Melissa N Speer
- University of Melbourne, Faculty of Engineering and Information Technology, Carlton3053, Australia
| | - Tu C Le
- School of Engineering, RMIT University, Melbourne3001, Australia
| | - Maiada M Sadek
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia.,ARC Centre for Fragment-Based Design, Monash University, Parkville, 3052, Australia
| | - Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - Nicholas Barlow
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - David K Chalmers
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, Melbourne3001, Australia
| |
Collapse
|
30
|
Li X, Craven TW, Levine PM. Cyclic Peptide Screening Methods for Preclinical Drug Discovery. J Med Chem 2022; 65:11913-11926. [PMID: 36074956 DOI: 10.1021/acs.jmedchem.2c01077] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclic peptides are among the most diverse architectures for current drug discovery efforts. Their size, stability, and ease of synthesis provide attractive scaffolds to engage and modulate some of the most challenging targets, including protein-protein interactions and those considered to be "undruggable". With a variety of sophisticated screening technologies to produce libraries of cyclic peptides, including phage display, mRNA display, split intein circular ligation of peptides, and in silico screening, a new era of cyclic peptide drug discovery is at the forefront of modern medicine. In this perspective, we begin by discussing cyclic peptides approved for clinical use in the past two decades. Particular focus is placed around synthetic chemistries to generate de novo libraries of cyclic peptides and novel methods to screen them. The perspective culminates with future prospects for generating cyclic peptides as viable therapeutic options and discusses the advantages and disadvantages currently being faced with bringing them to market.
Collapse
Affiliation(s)
- Xinting Li
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Timothy W Craven
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Paul M Levine
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
31
|
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
|
32
|
Dubinin MV, Sharapov VA, Ilzorkina AI, Efimov SV, Klochkov VV, Gudkov SV, Belosludtsev KN. Comparison of structural properties of cyclosporin A and its analogue alisporivir and their effects on mitochondrial bioenergetics and membrane behavior. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183972. [PMID: 35643328 DOI: 10.1016/j.bbamem.2022.183972] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/18/2022]
Abstract
The paper considers the effect of the MPT pore inhibitor cyclosporin A (CsA) and its non-immunosuppressive analogue alisporivir (Ali) on the functioning of rat skeletal muscle mitochondria. We have shown that both agents at a standard in vitro concentration of 1 μM increase the calcium capacity of organelles and have no effect on the parameters of oxidative phosphorylation. However, an increase in their concentration to 5 μM leads to the suppression of oxygen consumption by mitochondria, which is more pronounced in the case of Ali. This effect is accompanied by a decrease in the membrane potential of organelles and, apparently, is based on the inhibition of electron transport along the mitochondrial respiratory chain due to limited mobility of coenzyme Q. We have noted that both agents do not affect the production of hydrogen peroxide by isolated mitochondria. NMR spectroscopy and molecular dynamics simulation did not reveal significant differences in the structure and backbone flexibility of CsA and Ali. Both agents decrease the overall fluidity of the membrane of DPPC liposomes, inducing an increase in laurdan generalized polarization parameter. A similar effect was also found in the case of mitochondrial membranes. We suggested that these effects of CsA and Ali, associated with their lipophilic nature and the ability to accumulate in the lipid phase of membranes, may cause a decrease in the efficiency of electron transport in the respiratory chain of mitochondria and suppression of the bioenergetics of these organelles.
Collapse
Affiliation(s)
- Mikhail V Dubinin
- Mari State University, pl. Lenina 1, Yoshkar-Ola, Mari El 424001, Russia.
| | | | - Anna I Ilzorkina
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya 3, Pushchino, Moscow, Region, 142290, Russia; Pushchino State Institute of Natural Science, Prospekt nauki 3, Pushchino, Moscow Region 142290, Russia
| | - Sergey V Efimov
- Institute of Physics, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Vladimir V Klochkov
- Institute of Physics, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Sergey V Gudkov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilova 38, Moscow 119991, Russia
| | - Konstantin N Belosludtsev
- Mari State University, pl. Lenina 1, Yoshkar-Ola, Mari El 424001, Russia; Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya 3, Pushchino, Moscow, Region, 142290, Russia
| |
Collapse
|
33
|
Rzepiela AA, Viarengo-Baker LA, Tatarskii V, Kombarov R, Whitty A. Conformational Effects on the Passive Membrane Permeability of Synthetic Macrocycles. J Med Chem 2022; 65:10300-10317. [PMID: 35861996 DOI: 10.1021/acs.jmedchem.1c02090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Macrocyclic compounds (MCs) can have complex conformational properties that affect pharmacologically important behaviors such as membrane permeability. We measured the passive permeability of 3600 diverse nonpeptidic MCs and used machine learning to analyze the results. Incorporating selected properties based on the three-dimensional (3D) conformation gave models that predicted permeability with Q2 = 0.81. A biased spatial distribution of polar versus nonpolar regions was particularly important for good permeability, consistent with a mechanism in which the initial insertion of nonpolar portions of a MC helps facilitate the subsequent membrane entry of more polar parts. We also examined effects on permeability of 800 substructural elements by comparing matched molecular pairs. Some substitutions were invariably beneficial or invariably deleterious to permeability, while the influence of others was highly contextual. Overall, the work provides insights into how the permeability of MCs is influenced by their 3D conformational properties and suggests design hypotheses for achieving macrocycles with high membrane permeability.
Collapse
Affiliation(s)
- Anna A Rzepiela
- Pyxis Discovery, Delftechpark 26, 2628XH Delft, The Netherlands
| | - Lauren A Viarengo-Baker
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Victor Tatarskii
- Asinex Corporation, 101 N Chestnut St # 104, Winston-Salem, North Carolina 27101,United States
| | - Roman Kombarov
- Asinex Corporation, 101 N Chestnut St # 104, Winston-Salem, North Carolina 27101,United States
| | - Adrian Whitty
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.,Center for Molecular Discovery, Boston University, 24 Cummington Mall, Boston, Massachusetts 02215, United States
| |
Collapse
|
34
|
Limbach MN, Antevska A, Oluwatoba DS, Gray ALH, Carroll XB, Hoffmann CM, Wang X, Voehler MW, Steren CA, Do TD. Atomic View of Aqueous Cyclosporine A: Unpacking a Decades-Old Mystery. J Am Chem Soc 2022; 144:12602-12607. [PMID: 35786958 DOI: 10.1021/jacs.2c01743] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An atomic view of a main aqueous conformation of cyclosporine A (CycA), an important 11-amino-acid macrocyclic immunosuppressant, is reported. For decades, it has been a grand challenge to determine the conformation of free CycA in an aqueous-like solution given its poor water solubility. Using a combination of X-ray and single-crystal neutron diffraction, we unambiguously resolve a unique conformer (A1) with a novel cis-amide between residues 11 and 1 and two water ligands that stabilize hydrogen bond networks. NMR spectroscopy and titration experiments indicate that the novel conformer is as abundant as the closed conformer in 90/10 (v/v) methanol/water and is the main conformer at 10/90 methanol/water. Five other conformers were also detected in 90/10 methanol/water, one in slow exchange with A1, another one in slow exchange with the closed form and three minor ones, one of which contains two cis amides Abu2-Sar3 and MeBmt1-MeVal11. These conformers help better understand the wide spectrum of membrane permeability observed for CycA analogues and, to some extent, the binding of CycA to protein targets.
Collapse
Affiliation(s)
- Miranda N Limbach
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Aleksandra Antevska
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Damilola S Oluwatoba
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Amber L H Gray
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Xian B Carroll
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Christina M Hoffmann
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Xiaoping Wang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Markus W Voehler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Carlos A Steren
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Thanh D Do
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| |
Collapse
|
35
|
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
|
36
|
Ono S, Naylor MR, Townsend CE, Okumura C, Okada O, Lee HW, Lokey RS. Cyclosporin A: Conformational Complexity and Chameleonicity. J Chem Inf Model 2021; 61:5601-5613. [PMID: 34672629 DOI: 10.1021/acs.jcim.1c00771] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The chameleonic behavior of cyclosporin A (CsA) was investigated through conformational ensembles employing multicanonical molecular dynamics simulations that could sample the cis and trans isomers of N-methylated amino acids; these assessments were conducted in explicit water, dimethyl sulfoxide, acetonitrile, methanol, chloroform, cyclohexane (CHX), and n-hexane (HEX) using AMBER ff03, AMBER10:EHT, AMBER12:EHT, and AMBER14:EHT force fields. The conformational details were discussed employing the free-energy landscapes (FELs) at T = 300 K; it was observed that the experimentally determined structures of CsA were only a part of the conformational space. Comparing the ROESY measurements in CHX-d12 and HEX-d14, the major conformations in those apolar solvents were essentially the same as that in CDCl3 except for the observation of some sidechain rotamers. The effects of the metal ions on the conformations, including the cis/trans isomerization, were also investigated. Based on the analysis of FELs, it was concluded that the AMBER ff03 force field best described the experimentally derived conformations, indicating that CsA intrinsically formed membrane-permeable conformations and that the metal ions might be the key to the cis/trans isomerization of N-methylated amino acids before binding a partner protein.
Collapse
Affiliation(s)
- Satoshi Ono
- Modality Laboratories, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Matthew R Naylor
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Chad E Townsend
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Chieko Okumura
- Modality Laboratories, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Okimasa Okada
- Modality Laboratories, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Hsiau-Wei Lee
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| |
Collapse
|