51
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Skrzypczak N, Przybylski P. Structural diversity and biological relevance of benzenoid and atypical ansamycins and their congeners. Nat Prod Rep 2022; 39:1678-1704. [PMID: 35262153 DOI: 10.1039/d2np00004k] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Covering: 2011 to 2021The structural division of ansamycins, including those of atypical cores and different lengths of the ansa chains, is presented. Recently discovered benzenoid and atypical ansamycin scaffolds are presented in relation to their natural source and biosynthetic routes realized in bacteria as well as their muta and semisynthetic modifications influencing biological properties. To better understand the structure-activity relationships among benzenoid ansamycins structural aspects together with mechanisms of action regarding different targets in cells, are discussed. The most promising directions for structural optimizations of benzenoid ansamycins, characterized by predominant anticancer properties, were discussed in view of their potential medical and pharmaceutical applications. The bibliography of the review covers mainly years from 2011 to 2021.
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Affiliation(s)
- Natalia Skrzypczak
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland.
| | - Piotr Przybylski
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland.
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52
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Skrzypczak N, Przybylski P. Modifications, biological origin and antibacterial activity of naphthalenoid ansamycins. Nat Prod Rep 2022; 39:1653-1677. [PMID: 35244668 DOI: 10.1039/d2np00002d] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covering: 2011 to 2021Structural division of natural naphthalenoid ansamycins, regarding the type of the core and length of the ansa chain, and their biosynthetic pathways in microorganisms are discussed. The great biosynthetic plasticity of natural naphthalenoid ansamycins is reflected in their structural variety due to the alterations within ansa bridge or naphthalenoid core portions. A comparison between the biological potency of natural and semisynthetic naphthalenoid ansamycins was performed and discussed in relation to the molecular targets in cells. The antibacterial potency of naphthalenoid ansamycins seems to be dependent on the ansa chain length and conformational flexibility - the higher flexibility of the ansa chain the better biological outcome is noted.
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Affiliation(s)
- Natalia Skrzypczak
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland.
| | - Piotr Przybylski
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland.
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53
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Tamura T, Inoue M, Yoshimitsu Y, Hashimoto I, Ohashi N, Tsumura K, Suzuki K, Watanabe T, Hohsaka T. Chemical Synthesis and Cell-Free Expression of Thiazoline Ring-Bridged Cyclic Peptides and Their Properties on Biomembrane Permeability. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20210409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Takashi Tamura
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1211, Japan
- Synthetic Organic Chemistry Laboratories, FUJIFILM Corporation, 577 Ushijima, Kaisei-machi, Ashigarakami-gun, Kanagawa 258-8577, Japan
| | - Masaaki Inoue
- Synthetic Organic Chemistry Laboratories, FUJIFILM Corporation, 577 Ushijima, Kaisei-machi, Ashigarakami-gun, Kanagawa 258-8577, Japan
| | - Yuji Yoshimitsu
- Synthetic Organic Chemistry Laboratories, FUJIFILM Corporation, 577 Ushijima, Kaisei-machi, Ashigarakami-gun, Kanagawa 258-8577, Japan
| | - Ichihiko Hashimoto
- Analysis Technology Center, FUJIFILM Corporation, 210 Nakanuma, Minamiashigara, Kanagawa 258-0123, Japan
| | - Noriyuki Ohashi
- Analysis Technology Center, FUJIFILM Corporation, 210 Nakanuma, Minamiashigara, Kanagawa 258-0123, Japan
| | - Kyosuke Tsumura
- Analysis Technology Center, FUJIFILM Corporation, 210 Nakanuma, Minamiashigara, Kanagawa 258-0123, Japan
| | - Koo Suzuki
- Analysis Technology Center, FUJIFILM Corporation, 210 Nakanuma, Minamiashigara, Kanagawa 258-0123, Japan
| | - Takayoshi Watanabe
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1211, Japan
| | - Takahiro Hohsaka
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1211, Japan
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54
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Li J, Kannan S, Aronica P, Brown CJ, Partridge AW, Verma CS. Molecular descriptors suggest stapling as a strategy for optimizing membrane permeability of cyclic peptides. J Chem Phys 2022; 156:065101. [DOI: 10.1063/5.0078025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jianguo Li
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, Matrix, Singapore 138671
- Singapore Eye Research Institute, Singapore 169856, Singapore
| | | | - Pietro Aronica
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, Matrix, Singapore 138671
| | | | - Anthony W. Partridge
- MSD International, Translation Medicine Research Centre, 8 Biomedical Grove, #04-01/05 Neuros Building, Singapore 138665, Singapore
| | - Chandra S. Verma
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, Matrix, Singapore 138671
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
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55
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He S, Dong G, Cheng J, Wu Y, Sheng C. Strategies for designing proteolysis targeting chimaeras (PROTACs). Med Res Rev 2022; 42:1280-1342. [PMID: 35001407 DOI: 10.1002/med.21877] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/06/2021] [Accepted: 12/16/2021] [Indexed: 12/18/2022]
Abstract
Proteolysis targeting chimaeras (PROTACs) is a cutting edge and rapidly growing technique for new drug discovery and development. Currently, the largest challenge in the molecular design and drug development of PROTACs is efficient identification of potent and drug-like degraders. This review aims to comprehensively summarize and analyse state-of-the-art methods and strategies in the design of PROTACs. We provide a detailed illustration of the general principles and tactics for designing potent PROTACs, highlight representative case studies, and discuss the advantages and limitations of these strategies. Particularly, structure-based rational PROTAC design and emerging new types of PROTACs (e.g., homo-PROTACs, multitargeting PROTACs, photo-control PROTACs and PROTAC-based conjugates) will be focused on.
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Affiliation(s)
- Shipeng He
- Institute of Translational Medicine, Shanghai University, Shanghai, China
| | - Guoqiang Dong
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Junfei Cheng
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Ying Wu
- School of Pharmacy, Second Military Medical University, Shanghai, China.,Department of Pharmacy, 920th Hospital of Joint Logistics Support Force, Kunming, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, Shanghai, China
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56
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Linclau B, Wang Z, Jeffries B, Graton J, Carbajo RJ, Sinnaeve D, Le Questel J, Scott JS, Chiarparin E. Relating Conformational Equilibria to Conformer‐Specific Lipophilicities: New Opportunities in Drug Discovery. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202114862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Bruno Linclau
- School of Chemistry University of Southampton Highfield, Southampton SO17 1BJ UK
- Department of Organic and Macromolecular Chemistry, Ghent University Campus Sterre, S4 Krijgslaan 281 9000 Ghent Belgium
| | - Zhong Wang
- School of Chemistry University of Southampton Highfield, Southampton SO17 1BJ UK
| | - Benjamin Jeffries
- School of Chemistry University of Southampton Highfield, Southampton SO17 1BJ UK
| | - Jérôme Graton
- CEISAM UMR CNRS 6230 Université de Nantes CNRS CEISAM UMR 6230 44000 Nantes France
| | | | - Davy Sinnaeve
- Univ. Lille Inserm Institut Pasteur de Lille CHU Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 59000 Lille France
- CNRS ERL9002—Integrative Structural Biology 59000 Lille France
| | - Jean‐Yves Le Questel
- CEISAM UMR CNRS 6230 Université de Nantes CNRS CEISAM UMR 6230 44000 Nantes France
| | - James S. Scott
- Medicinal Chemistry, Oncology R&D AstraZeneca Cambridge CB4 0WG UK
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57
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Linclau B, Wang Z, Jeffries B, Graton J, Carbajo RJ, Sinnaeve D, Le Questel JY, Scott JS, Chiarparin E. Relating Conformational Equilibria to Conformer-Specific Lipophilicities: New Opportunities in Drug Discovery. Angew Chem Int Ed Engl 2021; 61:e202114862. [PMID: 34913249 PMCID: PMC9304282 DOI: 10.1002/anie.202114862] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Indexed: 11/10/2022]
Abstract
Efficient drug discovery is based on a concerted effort in optimizing bioactivity and compound properties such as lipophilicity, and is guided by efficiency metrics that reflect both aspects. While conformation–activity relationships and ligand conformational control are known strategies to improve bioactivity, the use of conformer‐specific lipophilicities (logp) is much less explored. Here we show how conformer‐specific logp values can be obtained from knowledge of the macroscopic logP value, and of the equilibrium constants between the individual species in water and in octanol. This is illustrated with fluorinated amide rotamers, with integration of rotamer 19F NMR signals as a facile, direct method to obtain logp values. The difference between logp and logP optimization is highlighted, giving rise to a novel avenue for lipophilicity control in drug discovery.
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Affiliation(s)
- Bruno Linclau
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.,Department of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre, S4, Krijgslaan 281, 9000, Ghent, Belgium
| | - Zhong Wang
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - Benjamin Jeffries
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - Jérôme Graton
- CEISAM UMR CNRS 6230, Université de Nantes, CNRS, CEISAM UMR 6230, 44000, Nantes, France
| | - Rodrigo J Carbajo
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, UK
| | - Davy Sinnaeve
- Univ. Lille, Inserm, Institut Pasteur de Lille, CHU Lille, U1167-RID-AGE-Risk Factors and Molecular, Determinants of Aging-Related Diseases, 59000, Lille, France.,CNRS, ERL9002-Integrative Structural Biology, 59000, Lille, France
| | - Jean-Yves Le Questel
- CEISAM UMR CNRS 6230, Université de Nantes, CNRS, CEISAM UMR 6230, 44000, Nantes, France
| | - James S Scott
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, UK
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58
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Zhang Z, Wang S, Li L. Emerging investigator series: the role of chemical properties in human exposure to environmental chemicals. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:1839-1862. [PMID: 34542121 DOI: 10.1039/d1em00252j] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
One of the ultimate goals of environmental exposure science is to mechanistically understand how chemical properties and human behavior interactively determine human exposure to the wide spectrum of chemicals present in the environment. This comprehensive review assembles state-of-the-art knowledge of the role of partitioning, dissociation, mass transfer, and reactive properties in human contact with and absorption of organic chemicals via oral, dermal, and respiratory routes. Existing studies have revealed that chemicals with different properties vary greatly in mass distribution and occurrence among multiple exposure media, resulting in distinct patterns of human intake from the environment. On the other hand, these chemicals encounter different levels of resistance in the passage of intestinal, dermal, and pulmonary absorption barriers and demonstrate different levels of bioavailability, due to the selectivity of biochemical, anatomical and physiological structures of these absorption barriers. Moving forward, the research community needs to gain more in-depth mechanistic insights into the complex processes in human exposure, advance the technique to better characterize and predict chemical properties, generate and leverage experimental data for a more diverse range of chemicals, and describe better the interactions between chemical properties and human behavior.
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Affiliation(s)
- Zhizhen Zhang
- School of Public Health, University of Nevada Reno, 1664 N. Virginia Street, 89557-274, Reno, Nevada, USA.
| | - Shenghong Wang
- School of Public Health, University of Nevada Reno, 1664 N. Virginia Street, 89557-274, Reno, Nevada, USA.
| | - Li Li
- School of Public Health, University of Nevada Reno, 1664 N. Virginia Street, 89557-274, Reno, Nevada, USA.
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59
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Structure-based design and synthesis of conformationally constrained derivatives of methyl-piperidinopyrazole (MPP) with estrogen receptor (ER) antagonist activity. Bioorg Chem 2021; 119:105554. [PMID: 34923243 DOI: 10.1016/j.bioorg.2021.105554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/11/2021] [Accepted: 12/08/2021] [Indexed: 11/23/2022]
Abstract
Nuclear Estrogen receptors (ER) are cytoplasmic proteins; translocated to the nucleus to induce transcriptional signals after getting bound to the estrogen hormone. ER activation implicated in cancer cell proliferation of female reproductive organs. Thus, the discovery of ER antagonists is a reliable strategy to combat estrogen-dependent breast cancer. Endometrial carcinoma is one of the complications encountered upon long-term therapy by selective estrogen receptor modulators (SERMs) like Tamoxifen (TMX) and methyl piperidinopyrazole (MPP). Thus, the ER-full antagonist is a solution to improve the safety of this class of therapeutics during the treatment of breast cancer. We selected MPP as a lead structure to design conformationally constrained analogs. Structural rigidification is a proven strategy to transform the SERMs into full antagonists. Accordingly, we synthesized 7-methoxy-3-(4-methoxyphenyl)-4,5-dihydro-2H-benzo[g]indazoles (4), (6a-c),(8-12) along with the biphenolic counterparts(13-19)that are the anticipated active metabolites. The 4-nitrophenyl derivative(4)is with the most balanced profile regardingthe in vivoanti-uterotrophic potential (EC50 = 4.160 μM); and the cytotoxicity assay of the corresponding active metabolite(13)against ER+ breast cancer cell lines (MCF-7 IC50 = 7.200 μM, T-47D IC50 = 11.710 μM). The inconsiderable uterotrophic activities of the elaborated ER-antagonists and weak antiproliferative activity of the compound(13)against ovarian cancer (SKOV-3 IC50 = 29.800 μM) highlighted it as a good start point to elaborate potential ER-full antagonists devoid of endometrial carcinoma. Extending the pendant chain that protrudes from the 2-(4-(substituted)-phenyl) ring of the new benzo-indazoles is recommended for enhancing the potency based on the binding mode of compound(13)in the ligand-binding domain (LBD) of ER.
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60
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Dard C, Leforestier B, Francisco Hilário F, Traoré MDM, Lespinasse MA, Pérès B, Molina MC, Pereira de Freitas R, Milet A, Maubon D, Wong YS. Crossing of the Cystic Barriers of Toxoplasma gondii by the Fluorescent Coumarin Tetra-Cyclopeptide. Molecules 2021; 26:7506. [PMID: 34946588 PMCID: PMC8708940 DOI: 10.3390/molecules26247506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 11/28/2021] [Accepted: 12/05/2021] [Indexed: 01/11/2023] Open
Abstract
FR235222 is a natural tetra-cyclopeptide with a strong inhibition effect on histone deacetylases, effective on mammalian cells as well as on intracellular apicomplexan parasites, such as Toxoplasma gondii, in the tachyzoite and bradyzoite stages. This molecule is characterized by two parts: the zinc-binding group, responsible for the binding to the histone deacetylase, and the cyclic tetrapeptide moiety, which plays a crucial role in cell permeability. Recently, we have shown that the cyclic tetrapeptide coupled with a fluorescent diethyl-amino-coumarin was able to maintain properties of cellular penetration on human cells. Here, we show that this property can be extended to the crossing of the Toxoplasma gondii cystic cell wall and the cell membrane of the parasite in its bradyzoite form, while maintaining a high efficacy as a histone deacetylase inhibitor. The investigation by molecular modeling allows a better understanding of the penetration mechanism.
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Affiliation(s)
- Céline Dard
- Team Host-Pathogen Interactions and Immunity to Infection, Institute for Advanced Biosciences, INSERM, CNRSINSERM U1209, CNRS UMR 5309, Univ. Grenoble Alpes, 38000 Grenoble, France; (C.D.); (D.M.)
| | - Baptiste Leforestier
- Team SITH, CNRS UMR 5250, Univ. Grenoble Alpes, CNRS, DCM, 38000 Grenoble, France; (B.L.); (A.M.)
| | - Flaviane Francisco Hilário
- Team COMET, CNRS UMR 5063, Univ. Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France; (F.F.H.); (M.D.M.T.); (M.-A.L.); (B.P.); (M.-C.M.)
| | - Mohamed Dit Mady Traoré
- Team COMET, CNRS UMR 5063, Univ. Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France; (F.F.H.); (M.D.M.T.); (M.-A.L.); (B.P.); (M.-C.M.)
| | - Marie-Ange Lespinasse
- Team COMET, CNRS UMR 5063, Univ. Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France; (F.F.H.); (M.D.M.T.); (M.-A.L.); (B.P.); (M.-C.M.)
| | - Basile Pérès
- Team COMET, CNRS UMR 5063, Univ. Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France; (F.F.H.); (M.D.M.T.); (M.-A.L.); (B.P.); (M.-C.M.)
| | - Marie-Carmen Molina
- Team COMET, CNRS UMR 5063, Univ. Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France; (F.F.H.); (M.D.M.T.); (M.-A.L.); (B.P.); (M.-C.M.)
| | - Rossimiriam Pereira de Freitas
- Departamento de Química, Universidade Federal de Minas Gerais, Av Pres Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270-901, MG, Brazil;
| | - Anne Milet
- Team SITH, CNRS UMR 5250, Univ. Grenoble Alpes, CNRS, DCM, 38000 Grenoble, France; (B.L.); (A.M.)
| | - Danièle Maubon
- Team Host-Pathogen Interactions and Immunity to Infection, Institute for Advanced Biosciences, INSERM, CNRSINSERM U1209, CNRS UMR 5309, Univ. Grenoble Alpes, 38000 Grenoble, France; (C.D.); (D.M.)
| | - Yung-Sing Wong
- Departamento de Química, Universidade Federal de Minas Gerais, Av Pres Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270-901, MG, Brazil;
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61
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Babuka D, Kolouchova K, Loukotova L, Sedlacek O, Groborz O, Skarkova A, Zhigunov A, Pavlova E, Hoogenboom R, Hruby M, Stepanek P. Self-Assembly, Drug Encapsulation, and Cellular Uptake of Block and Gradient Copolymers of 2-Methyl-2-oxazine and 2- n-Propyl/butyl-2-oxazoline. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c01794] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- David Babuka
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovskeho sq. 2, Prague 6 162 06, Czech Republic
- Department of Biophysics, Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague 2 121 16, Czech Republic
| | - Kristyna Kolouchova
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovskeho sq. 2, Prague 6 162 06, Czech Republic
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2 128 00, Czech Republic
| | - Lenka Loukotova
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovskeho sq. 2, Prague 6 162 06, Czech Republic
| | - Ondrej Sedlacek
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2 128 00, Czech Republic
- Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Ghent, Belgium
| | - Ondrej Groborz
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovskeho sq. 2, Prague 6 162 06, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo sq. 542, Prague 6 162 06, Czech Republic
- Institute of Biophysics and Informatics, Charles University, First Faculty of Medicine, Salmovská 1, Prague 2 120 00, Czech Republic
| | - Aneta Skarkova
- Department of Cell Biology, Charles University, Vinicna 7, Prague 12843, Czech Republic
- Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Prumyslova 595, Vestec u Prahy 25242, Czech Republic
| | - Alexander Zhigunov
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovskeho sq. 2, Prague 6 162 06, Czech Republic
| | - Ewa Pavlova
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovskeho sq. 2, Prague 6 162 06, Czech Republic
| | - Richard Hoogenboom
- Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Ghent, Belgium
| | - Martin Hruby
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovskeho sq. 2, Prague 6 162 06, Czech Republic
| | - Petr Stepanek
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovskeho sq. 2, Prague 6 162 06, Czech Republic
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62
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Machauer R, Lueoend R, Hurth K, Veenstra SJ, Rueeger H, Voegtle M, Tintelnot-Blomley M, Rondeau JM, Jacobson LH, Laue G, Beltz K, Neumann U. Discovery of Umibecestat (CNP520): A Potent, Selective, and Efficacious β-Secretase (BACE1) Inhibitor for the Prevention of Alzheimer's Disease. J Med Chem 2021; 64:15262-15279. [PMID: 34648711 DOI: 10.1021/acs.jmedchem.1c01300] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
After identification of lead compound 6, 5-amino-1,4-oxazine BACE1 inhibitors were optimized in order to improve potency, brain penetration, and metabolic stability. Insertion of a methyl and a trifluoromethyl group at the 6-position of the 5-amino-1,4-oxazine led to 8 (NB-360), an inhibitor with a pKa of 7.1, a very low P-glycoprotein efflux ratio, and excellent pharmacological profile, enabling high central nervous system penetration and exposure. Fur color changes observed with NB-360 in efficacy studies in preclinical animal models triggered further optimization of the series. Herein, we describe the steps leading to the discovery of 3-chloro-5-trifluoromethyl-pyridine-2-carboxylic acid [6-((3R,6R)-5-amino-3,6-dimethyl-6-trifluoromethyl-3,6-dihydro-2H-[1,4]oxazin-3-yl)-5-fluoro-pyridin-2-yl]amide 15 (CNP520, umibecestat), an inhibitor with superior BACE1/BACE2 selectivity and pharmacokinetics. CNP520 reduced significantly Aβ levels in mice and rats in acute and chronic treatment regimens without any side effects and thus qualified for Alzheimer's disease prevention studies in the clinic.
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Affiliation(s)
- Rainer Machauer
- Global Discovery Chemistry, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | - Rainer Lueoend
- Global Discovery Chemistry, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | - Konstanze Hurth
- Global Discovery Chemistry, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | - Siem J Veenstra
- Global Discovery Chemistry, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | - Heinrich Rueeger
- Global Discovery Chemistry, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | - Markus Voegtle
- Global Discovery Chemistry, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | | | - Jean-Michel Rondeau
- Chemical Biology and Therapeutics, Structural Biology Platform, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | - Laura H Jacobson
- Department of Neuroscience, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | - Grit Laue
- Pharmacokinetic-Sciences, Novartis Institutes for BioMedical Research, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | - Karen Beltz
- Pharmacokinetic-Sciences, Novartis Institutes for BioMedical Research, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | - Ulf Neumann
- Department of Neuroscience, Novartis Pharma AG, CH-4056 Basel, Switzerland
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63
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Sheikh AY, Mattei A, Miglani Bhardwaj R, Hong RS, Abraham NS, Schneider-Rauber G, Engstrom KM, Diwan M, Henry RF, Gao Y, Juarez V, Jordan E, DeGoey DA, Hutchins CW. Implications of the Conformationally Flexible, Macrocyclic Structure of the First-Generation, Direct-Acting Anti-Viral Paritaprevir on Its Solid Form Complexity and Chameleonic Behavior. J Am Chem Soc 2021; 143:17479-17491. [PMID: 34637297 DOI: 10.1021/jacs.1c06837] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Direct-acting antiviral regimens have transformed therapeutic management of hepatitis C across all prevalent genotypes. Most of the chemical matter in these regimens comprises molecules well outside the traditional drug development chemical space and presents significant challenges. Herein, the implications of high conformational flexibility and the presence of a 15-membered macrocyclic ring in paritaprevir are studied through a combination of advanced computational and experimental methods with focus on molecular chameleonicity and crystal form complexity. The ability of the molecule to toggle between high and low 3D polar surface area (PSA) conformations is underpinned by intramolecular hydrogen bonding (IMHB) interactions and intramolecular steric effects. Computational studies consequently show a very significant difference of over 75 Å2 in 3D PSA between polar and apolar environments and provide the structural basis for the perplexingly favorable passive permeability of the molecule. Crystal packing and protein binding resulting in strong intermolecular interactions disrupt these intramolecular interactions. Crystalline Form I benefits from strong intermolecular interactions, whereas the weaker intermolecular interactions in Form II are partially compensated by the energetic advantage of an IMHB. Like Form I, no IMHB is observed within the receptor-bound conformation; instead, an intermolecular H-bond contributes to the potency of the molecule. The choice of metastable Form II is derisked through strategies accounting for crystal surface and packing features to manage higher form specific solid-state chemical reactivity and specific processing requirements. Overall, the results show an unambiguous link between structural features and derived properties from crystallization to dissolution, permeation, and docking into the protein pocket.
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Affiliation(s)
- Ahmad Y Sheikh
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Alessandra Mattei
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Rajni Miglani Bhardwaj
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Richard S Hong
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Nathan S Abraham
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Gabriela Schneider-Rauber
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Kenneth M Engstrom
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Moiz Diwan
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Rodger F Henry
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Yi Gao
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Vivian Juarez
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Erin Jordan
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - David A DeGoey
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Charles W Hutchins
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
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64
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JNJ-67569762, A 2-Aminotetrahydropyridine-Based Selective BACE1 Inhibitor Targeting the S3 Pocket: From Discovery to Clinical Candidate. J Med Chem 2021; 64:14175-14191. [PMID: 34553934 DOI: 10.1021/acs.jmedchem.1c00935] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The discovery of a novel 2-aminotetrahydropyridine class of BACE1 inhibitors is described. Their pKa and lipophilicity were modulated by a pending sulfonyl group, while good permeability and brain penetration were achieved via intramolecular hydrogen bonding. BACE1 selectivity over BACE2 was achieved in the S3 pocket by a novel bicyclic ring system. An optimization addressing reactive metabolite formation, cardiovascular safety, and CNS toxicity is described, leading to the clinical candidate JNJ-67569762 (12), which gave robust dose-dependent BACE1-mediated amyloid β lowering without showing BACE2-dependent hair depigmentation in preclinical models. We show that 12 has a favorable projected human dose and PK and hence presented us with an opportunity to test a highly selective BACE1 inhibitor in humans. However, 12 was found to have a QT effect upon repeat dosing in dogs and its development was halted in favor of other selective leads, which will be reported in the future.
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65
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Wang S, König G, Roth HJ, Fouché M, Rodde S, Riniker S. Effect of Flexibility, Lipophilicity, and the Location of Polar Residues on the Passive Membrane Permeability of a Series of Cyclic Decapeptides. J Med Chem 2021; 64:12761-12773. [PMID: 34406766 DOI: 10.1021/acs.jmedchem.1c00775] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cyclic peptides have received increasing attention over the recent years as potential therapeutics for "undruggable" targets. One major obstacle is, however, their often relatively poor bioavailability. Here, we investigate the structure-permeability relationship of 24 cyclic decapeptides that share the same backbone N-methylation pattern but differ in their side chains. The peptides cover a large range of values for passive membrane permeability as well as lipophilicity and solubility. To rationalize the observed differences in permeability, we extracted for each peptide the population of the membrane-permeable conformation in water from extensive explicit-solvent molecular dynamics simulations and used this as a metric for conformational rigidity or "prefolding." The insights from the simulations together with lipophilicity measurements highlight the intricate interplay between polarity/lipophilicity and flexibility/rigidity and the possible compensating effects on permeability. The findings allow us to better understand the structure-permeability relationship of cyclic peptides and extract general guiding principles.
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Affiliation(s)
- Shuzhe Wang
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Gerhard König
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Hans-Jörg Roth
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Marianne Fouché
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Stephane Rodde
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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66
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Loukotová L, Švec P, Groborz O, Heizer T, Beneš H, Raabová H, Bělinová T, Herynek V, Hrubý M. Direct Comparison of Analogous Amphiphilic Gradient and Block Polyoxazolines. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c02674] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Lenka Loukotová
- Institute of Macromolecular Chemistry CAS, Heyrovsky sq. 2, Prague 162 00, Czech Republic
| | - Pavel Švec
- Institute of Macromolecular Chemistry CAS, Heyrovsky sq. 2, Prague 162 00, Czech Republic
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, Prague 128 43, Czech Republic
| | - Ondřej Groborz
- Institute of Macromolecular Chemistry CAS, Heyrovsky sq. 2, Prague 162 00, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, Prague 128 43, Czech Republic
| | - Tomáš Heizer
- Center for Advanced Preclinical Imaging, First Faculty of Medicine, Charles University, Salmovska 3, Prague 120 00, Czech Republic
| | - Hynek Beneš
- Institute of Macromolecular Chemistry CAS, Heyrovsky sq. 2, Prague 162 00, Czech Republic
| | - Helena Raabová
- Electron Microscopy Core Facility of the Microscopy Centre, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, Prague 142 20, Czech Republic
| | - Tereza Bělinová
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University in Prague, alej Svobody 1655/76, Pilsen 323 00, Czech Republic
| | - Vít Herynek
- Center for Advanced Preclinical Imaging, First Faculty of Medicine, Charles University, Salmovska 3, Prague 120 00, Czech Republic
| | - Martin Hrubý
- Institute of Macromolecular Chemistry CAS, Heyrovsky sq. 2, Prague 162 00, Czech Republic
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67
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Ermondi G, Lavore F, Vallaro M, Tiana G, Vasile F, Caron G. Managing Experimental 3D Structures in the Beyond-Rule-of-5 Chemical Space: The Case of Rifampicin. Chemistry 2021; 27:10394-10404. [PMID: 34114271 PMCID: PMC8361677 DOI: 10.1002/chem.202100961] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Indexed: 12/29/2022]
Abstract
The beyond-Rule-of-5 (bRo5) chemical space is a source of new oral drugs and includes large and flexible compounds. Because of their size and conformational variability, bRo5 molecules assume different privileged conformations in the compartments of human body, i. e., they can exhibit chameleonic properties. The elucidation of the ensemble of 3D structures explored by such molecules under different conditions is therefore critical to check the role played by chameleonicity to modulate cell permeability. Here we characterized the conformational ensembles of rifampicin, a bRo5 drug, in polar and nonpolar solvents and in the solid state. We performed NMR experiments, analyzed their results with a novel algorithm and set-up a pool of ad hoc in silico strategies to investigate crystallographic structures retrieved from the CSD. Moreover, a polarity descriptor often related to permeability (SA-3D-PSA) was calculated for all the conformers and its variation with the environment analyzed. Results showed that the conformational behavior of rifampicin in solution and in the solid state is not superposable. The identification of dynamic intramolecular hydrogen bonds can be assessed by NMR spectroscopy but not by X-ray structures. Moreover, SA-3D-PSA revealed that dynamic IMHBs do not provide rifampicin with chameleonic properties. Overall, this study highlights that the peculiarity of rifampicin, which is cell permeable probably because of the presence of static IMHBs but is devoid of any chameleonic behavior, can be assessed by a proper analysis of experimental 3D structures.
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Affiliation(s)
- Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Dept.Università degli Studi di Torinovia Quarello 1510135TorinoItaly
| | - Francesca Lavore
- Department of ChemistryUniversità degli Studi di Milanovia Golgi 1920133MilanoItaly
| | - Maura Vallaro
- Molecular Biotechnology and Health Sciences Dept.Università degli Studi di Torinovia Quarello 1510135TorinoItaly
| | - Guido Tiana
- Department of Physics and Center for Complexity and BiosystemsUniversità degli Studi di Milano and INFNvia Celoria 1620133MilanoItaly
| | - Francesca Vasile
- Department of ChemistryUniversità degli Studi di Milanovia Golgi 1920133MilanoItaly
| | - Giulia Caron
- Molecular Biotechnology and Health Sciences Dept.Università degli Studi di Torinovia Quarello 1510135TorinoItaly
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68
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Ermondi G, Garcia Jimenez D, Rossi Sebastiano M, Caron G. Rational Control of Molecular Properties Is Mandatory to Exploit the Potential of PROTACs as Oral Drugs. ACS Med Chem Lett 2021; 12:1056-1060. [PMID: 34262642 PMCID: PMC8274089 DOI: 10.1021/acsmedchemlett.1c00298] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
![]()
To obtain new oral
drugs in the beyond rule of five space, PROTACs
among others, molecular properties should be optimized in early drug
discovery. Degraders call for design strategies which focus on intramolecular
interaction and chameleonicity. In parallel, tailored revalidation
of permeability assessment and prediction methods becomes fundamental
in this innovative chemical space.
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Affiliation(s)
- Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Dept., CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Diego Garcia Jimenez
- Molecular Biotechnology and Health Sciences Dept., CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Matteo Rossi Sebastiano
- Molecular Biotechnology and Health Sciences Dept., CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giulia Caron
- Molecular Biotechnology and Health Sciences Dept., CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
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69
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Sugita M, Sugiyama S, Fujie T, Yoshikawa Y, Yanagisawa K, Ohue M, Akiyama Y. Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations. J Chem Inf Model 2021; 61:3681-3695. [PMID: 34236179 DOI: 10.1021/acs.jcim.1c00380] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Membrane permeability is a significant obstacle facing the development of cyclic peptide drugs. However, membrane permeation mechanisms are poorly understood. To investigate common features of permeable (and nonpermeable) designs, it is necessary to reproduce the membrane permeation process of cyclic peptides through the lipid bilayer. We simulated the membrane permeation process of 100 six-residue cyclic peptides across the lipid bilayer based on steered molecular dynamics (MD) and replica-exchange umbrella sampling simulations and predicted membrane permeability using the inhomogeneous solubility-diffusion model and a modified version of it. Furthermore, we confirmed the effectiveness of this protocol by predicting the membrane permeability of 56 eight-residue cyclic peptides with diverse chemical structures, including some confidential designs from a pharmaceutical company. As a result, a reasonable correlation between experimentally assessed and calculated membrane permeability of cyclic peptides was observed for the peptide libraries, except for strongly hydrophobic peptides. Our analysis of the MD trajectory demonstrated that most peptides were stabilized in the boundary region between bulk water and membrane and that for most peptides, the process of crossing the center of the membrane is the main obstacle to membrane permeation. The height of this barrier is well correlated with the electrostatic interaction between the peptide and the surrounding media. The structural and energetic features of the representative peptide at each vertical position within the membrane were also analyzed, revealing that peptides permeate the membrane by changing their orientation and conformation according to the surrounding environment.
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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, RGBT2-A-1C, 3-25-10 Tonomachi, Kawasaki-ku, Kawasaki City, Kanagawa 210-0821, Japan
| | - Satoshi Sugiyama
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,AIST-TokyoTech Real World Big-Data Computation Open Innovation Laboratory (RWBC-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8560, 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, RGBT2-A-1C, 3-25-10 Tonomachi, Kawasaki-ku, Kawasaki City, Kanagawa 210-0821, Japan
| | - Yasushi Yoshikawa
- 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, RGBT2-A-1C, 3-25-10 Tonomachi, Kawasaki-ku, Kawasaki City, Kanagawa 210-0821, Japan
| | - Keisuke Yanagisawa
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Middle-Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, RGBT2-A-1C, 3-25-10 Tonomachi, Kawasaki-ku, Kawasaki City, Kanagawa 210-0821, Japan
| | - Masahito Ohue
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Middle-Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, RGBT2-A-1C, 3-25-10 Tonomachi, Kawasaki-ku, Kawasaki City, Kanagawa 210-0821, Japan
| | - Yutaka Akiyama
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Middle-Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, RGBT2-A-1C, 3-25-10 Tonomachi, Kawasaki-ku, Kawasaki City, Kanagawa 210-0821, Japan
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70
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Lee D, Lee S, Choi J, Song YK, Kim MJ, Shin DS, Bae MA, Kim YC, Park CJ, Lee KR, Choi JH, Seo J. Interplay among Conformation, Intramolecular Hydrogen Bonds, and Chameleonicity in the Membrane Permeability and Cyclophilin A Binding of Macrocyclic Peptide Cyclosporin O Derivatives. J Med Chem 2021; 64:8272-8286. [PMID: 34096287 DOI: 10.1021/acs.jmedchem.1c00211] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A macrocyclic peptide scaffold with well-established structure-property relationship is desirable for tackling undruggable targets. Here, we adopted a natural macrocycle, cyclosporin O (CsO) and its derivatives (CP1-3), and evaluated the impact of conformation on membrane permeability, cyclophilin A (CypA) binding, and the pharmacokinetic (PK) profile. In nonpolar media, CsO showed a similar conformation to cyclosporin A (CsA), a well-known chameleonic macrocycle, but less chameleonic behavior in a polar environment. The weak chameleonicity of CsO resulted in decreased membrane permeability; however, the more rigid conformation of CsO was not detrimental to its PK profile. CsO exhibited a higher plasma concentration than CsA, which resulted from minimal CypA binding and lower accumulation in red blood cells and moderate oral bioavailability (F = 12%). Our study aids understanding of CsO, a macrocyclic peptide that is less explored than CsA but with greater potential for diversity generation and rational design.
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Affiliation(s)
- Dongjae Lee
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Sungjin Lee
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Jieun Choi
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Yoo-Kyung Song
- Laboratory of Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang 28116, Republic of Korea
| | - Min Ju Kim
- Laboratory of Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang 28116, Republic of Korea
| | - Dae-Seop Shin
- Bio Platform Technology Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Myung Ae Bae
- Bio Platform Technology Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Yong-Chul Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Kyeong-Ryoon Lee
- Laboratory of Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang 28116, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Jiwon Seo
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
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71
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Price E, Kalvass JC, DeGoey D, Hosmane B, Doktor S, Desino K. Global Analysis of Models for Predicting Human Absorption: QSAR, In Vitro, and Preclinical Models. J Med Chem 2021; 64:9389-9403. [PMID: 34152772 DOI: 10.1021/acs.jmedchem.1c00669] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Models intended to predict intestinal absorption are an essential part of the drug development process. Although many models exist for capturing intestinal absorption, many questions still exist around the applicability of these models to drug types like "beyond rule of 5" (bRo5) and low absorption compounds. This presents a challenge as current models have not been rigorously tested to understand intestinal absorption. Here, we assembled a large, structurally diverse dataset of ∼1000 compounds with known in vitro, preclinical, and human permeability and/or absorption data. In silico (quantitative structure-activity relationship), in vitro (Caco-2), and in vivo (rat) models were statistically evaluated for predictive performance against this human intestinal absorption dataset. We expect this evaluation to serve as a resource for DMPK scientists and medicinal/computational chemists to increase their understanding of permeability and absorption model utility and applications for academia and industry.
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Affiliation(s)
- Edward Price
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - J Cory Kalvass
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - David DeGoey
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Balakrishna Hosmane
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Stella Doktor
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Kelly Desino
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
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72
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Leeson PD, Bento AP, Gaulton A, Hersey A, Manners EJ, Radoux CJ, Leach AR. Target-Based Evaluation of "Drug-Like" Properties and Ligand Efficiencies. J Med Chem 2021; 64:7210-7230. [PMID: 33983732 PMCID: PMC7610969 DOI: 10.1021/acs.jmedchem.1c00416] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Physicochemical descriptors commonly used to define "drug-likeness" and ligand efficiency measures are assessed for their ability to differentiate marketed drugs from compounds reported to bind to their efficacious target or targets. Using ChEMBL version 26, a data set of 643 drugs acting on 271 targets was assembled, comprising 1104 drug-target pairs having ≥100 published compounds per target. Taking into account changes in their physicochemical properties over time, drugs are analyzed according to their target class, therapy area, and route of administration. Recent drugs, approved in 2010-2020, display no overall differences in molecular weight, lipophilicity, hydrogen bonding, or polar surface area from their target comparator compounds. Drugs are differentiated from target comparators by higher potency, ligand efficiency (LE), lipophilic ligand efficiency (LLE), and lower carboaromaticity. Overall, 96% of drugs have LE or LLE values, or both, greater than the median values of their target comparator compounds.
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Affiliation(s)
- Paul D Leeson
- Paul Leeson Consulting Ltd, The Malt House, Main Street, Congerstone, Nuneaton, Warkwickshire CV13 6LZ, United Kingdom
| | - A Patricia Bento
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Anna Gaulton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Anne Hersey
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Emma J Manners
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Chris J Radoux
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Andrew R Leach
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
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73
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Begnini F, Poongavanam V, Atilaw Y, Erdelyi M, Schiesser S, Kihlberg J. Cell Permeability of Isomeric Macrocycles: Predictions and NMR Studies. ACS Med Chem Lett 2021; 12:983-990. [PMID: 34136079 PMCID: PMC8201747 DOI: 10.1021/acsmedchemlett.1c00126] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/13/2021] [Indexed: 12/22/2022] Open
Abstract
![]()
Conformation-dependent 3D descriptors
have been shown to provide
better predictions of the physicochemical properties of macrocycles
than 2D descriptors. However, the computational identification of
relevant conformations for macrocycles is nontrivial. Herein, we report
that the Caco-2 cell permeability difference between a pair of diastereomeric
macrocycles correlated with their solvent accessible 3D polar surface
area and radius of gyration. The descriptors were calculated from
the macrocycles’ solution-phase conformational ensembles and
independently from ensembles obtained by conformational sampling.
Calculation of the two descriptors for three other stereo- and regioisomeric
macrocycles also allowed the correct ranking of their cell permeability.
Methods for conformational sampling may thus allow ranking of passive
permeability for moderately flexible macrocycles, thereby contributing
to the prioritization of macrocycles for synthesis in lead optimization.
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Affiliation(s)
- Fabio Begnini
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | | | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Stefan Schiesser
- Department of Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
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74
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Digiesi V, de la Oliva Roque V, Vallaro M, Caron G, Ermondi G. Permeability prediction in the beyond-Rule-of 5 chemical space: Focus on cyclic hexapeptides. Eur J Pharm Biopharm 2021; 165:259-270. [PMID: 34038796 DOI: 10.1016/j.ejpb.2021.05.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/13/2021] [Accepted: 05/18/2021] [Indexed: 11/30/2022]
Abstract
Cyclic peptides (CPs) are gaining more and more relevance in drug discovery. Since one of their main drawbacks is poor permeability, the discovery of new orally available CP drugs requires computational tools that predict CP permeability in very early drug discovery. In this study we used a literature dataset of 62 cyclic hexapeptides to evaluate the performances of a number of in silico tools based on different computational theory to model and rationalize PAMPA and Caco-2 permeability values. In particular, we submitted the dataset to a) online calculators, b) QSPR strategies, c) a physics-based tool, d) a mixed approach and e) a kinetic method. This latter is an emergent strategy in which a few relevant conformations retrieved from a set of molecular dynamics (MD) simulations by the Markov State Model (MSM) are used to establish the compounds permeability. Both free and commercial software were used. Results were compared with a model based on experimental physicochemical descriptors. All the computational approaches but online calculators performed quite well and show that lipophilicity and not polarity is the main determinant of the investigated event. A second major outcome of the study is that the impact of flexibility on the permeability of the considered dataset cannot be unambiguously assessed. Finally, our comparative analysis, which also included not common applied strategies, allowed a sound evaluation of the pros and cons of the applied computational approaches.
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Affiliation(s)
- Vito Digiesi
- University of Torino, Molecular Biotechnology and Health Sciences Dept., Via Quarello, 15, 10135 Torino, Italy
| | - Víctor de la Oliva Roque
- University of Torino, Molecular Biotechnology and Health Sciences Dept., Via Quarello, 15, 10135 Torino, Italy
| | - Maura Vallaro
- University of Torino, Molecular Biotechnology and Health Sciences Dept., Via Quarello, 15, 10135 Torino, Italy
| | - Giulia Caron
- University of Torino, Molecular Biotechnology and Health Sciences Dept., Via Quarello, 15, 10135 Torino, Italy
| | - Giuseppe Ermondi
- University of Torino, Molecular Biotechnology and Health Sciences Dept., Via Quarello, 15, 10135 Torino, Italy.
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75
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Santana K, do Nascimento LD, Lima e Lima A, Damasceno V, Nahum C, Braga RC, Lameira J. Applications of Virtual Screening in Bioprospecting: Facts, Shifts, and Perspectives to Explore the Chemo-Structural Diversity of Natural Products. Front Chem 2021; 9:662688. [PMID: 33996755 PMCID: PMC8117418 DOI: 10.3389/fchem.2021.662688] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 02/25/2021] [Indexed: 12/22/2022] Open
Abstract
Natural products are continually explored in the development of new bioactive compounds with industrial applications, attracting the attention of scientific research efforts due to their pharmacophore-like structures, pharmacokinetic properties, and unique chemical space. The systematic search for natural sources to obtain valuable molecules to develop products with commercial value and industrial purposes remains the most challenging task in bioprospecting. Virtual screening strategies have innovated the discovery of novel bioactive molecules assessing in silico large compound libraries, favoring the analysis of their chemical space, pharmacodynamics, and their pharmacokinetic properties, thus leading to the reduction of financial efforts, infrastructure, and time involved in the process of discovering new chemical entities. Herein, we discuss the computational approaches and methods developed to explore the chemo-structural diversity of natural products, focusing on the main paradigms involved in the discovery and screening of bioactive compounds from natural sources, placing particular emphasis on artificial intelligence, cheminformatics methods, and big data analyses.
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Affiliation(s)
- Kauê Santana
- Instituto de Biodiversidade, Universidade Federal do Oeste do Pará, Santarém, Brazil
| | | | - Anderson Lima e Lima
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
| | - Vinícius Damasceno
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
| | - Claudio Nahum
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
| | | | - Jerônimo Lameira
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
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76
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Gabano E, Rangone B, Perin E, Caron G, Ermondi G, Vallaro M, Gandin V, Marzano C, Barbanente A, Margiotta N, Ravera M. Pt(iv) complexes based on cyclohexanediamines and the histone deacetylase inhibitor 2-(2-propynyl)octanoic acid: synthesis, characterization, cell penetration properties and antitumor activity. Dalton Trans 2021; 50:4663-4672. [PMID: 33725031 DOI: 10.1039/d0dt04135a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Pt(iv) complexes based on (SP-4-2)-dichlorido(cyclohexane-1,4-diamine)platinum(ii) (kiteplatin) and the histone deacetylase inhibitor 2-(2-propynyl)octanoic acid (POA) were investigated. Since POA contains a chiral carbon, all the possible Pt(iv) isomers were prepared and characterized, and their antiproliferative activity on six cancer cell lines was compared with that of the corresponding Pt(iv) complexes containing the cyclohexane-1R,2R-diamine equatorial ligand. To justify the very good antiproliferative activity (nanomolar IC50), the polarity, lipophilicity, permeability, and cell accumulation of the complexes were studied. Overall, the two series of Pt(iv) complexes showed similar cell penetration properties, being significantly better than that of the Pt(ii) reference compounds. Finally, a representative compound of the whole set of complexes (i.e., that based on cyclohexane-1R,2R-diamine and racemic POA) was tested in vivo on mice bearing Lewis lung carcinoma, showing good tumor growth inhibition with negligible body weight loss.
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Affiliation(s)
- Elisabetta Gabano
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Viale Michel 11, 15121 Alessandria, Italy.
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77
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Predicting cell-penetrating peptides using machine learning algorithms and navigating in their chemical space. Sci Rep 2021; 11:7628. [PMID: 33828175 PMCID: PMC8027643 DOI: 10.1038/s41598-021-87134-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 03/24/2021] [Indexed: 02/01/2023] Open
Abstract
Cell-penetrating peptides (CPPs) are naturally able to cross the lipid bilayer membrane that protects cells. These peptides share common structural and physicochemical properties and show different pharmaceutical applications, among which drug delivery is the most important. Due to their ability to cross the membranes by pulling high-molecular-weight polar molecules, they are termed Trojan horses. In this study, we proposed a machine learning (ML)-based framework named BChemRF-CPPred (beyond chemical rules-based framework for CPP prediction) that uses an artificial neural network, a support vector machine, and a Gaussian process classifier to differentiate CPPs from non-CPPs, using structure- and sequence-based descriptors extracted from PDB and FASTA formats. The performance of our algorithm was evaluated by tenfold cross-validation and compared with those of previously reported prediction tools using an independent dataset. The BChemRF-CPPred satisfactorily identified CPP-like structures using natural and synthetic modified peptide libraries and also obtained better performance than those of previously reported ML-based algorithms, reaching the independent test accuracy of 90.66% (AUC = 0.9365) for PDB, and an accuracy of 86.5% (AUC = 0.9216) for FASTA input. Moreover, our analyses of the CPP chemical space demonstrated that these peptides break some molecular rules related to the prediction of permeability of therapeutic molecules in cell membranes. This is the first comprehensive analysis to predict synthetic and natural CPP structures and to evaluate their chemical space using an ML-based framework. Our algorithm is freely available for academic use at http://comptools.linc.ufpa.br/BChemRF-CPPred .
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78
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Comeau C, Ries B, Stadelmann T, Tremblay J, Poulet S, Fröhlich U, Côté J, Boudreault PL, Derbali RM, Sarret P, Grandbois M, Leclair G, Riniker S, Marsault É. Modulation of the Passive Permeability of Semipeptidic Macrocycles: N- and C-Methylations Fine-Tune Conformation and Properties. J Med Chem 2021; 64:5365-5383. [PMID: 33750117 DOI: 10.1021/acs.jmedchem.0c02036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Incorporating small modifications to peptidic macrocycles can have a major influence on their properties. For instance, N-methylation has been shown to impact permeability. A better understanding of the relationship between permeability and structure is of key importance as peptidic drugs are often associated with unfavorable pharmacokinetic profiles. Starting from a semipeptidic macrocycle backbone composed of a tripeptide tethered head-to-tail with an alkyl linker, we investigated two small changes: peptide-to-peptoid substitution and various methyl placements on the nonpeptidic linker. Implementing these changes in parallel, we created a collection of 36 compounds. Their permeability was then assessed in parallel artificial membrane permeability assay (PAMPA) and Caco-2 assays. Our results show a systematic improvement in permeability associated with one peptoid position in the cycle, while the influence of methyl substitution varies on a case-by-case basis. Using a combination of molecular dynamics simulations and NMR measurements, we offer hypotheses to explain such behavior.
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Affiliation(s)
- Christian Comeau
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Benjamin Ries
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Thomas Stadelmann
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Jacob Tremblay
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Sylvain Poulet
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Ulrike Fröhlich
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Jérôme Côté
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Pierre-Luc Boudreault
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Rabeb Mouna Derbali
- Faculté de pharmacie, Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Quebec, Canada H3C 3J7
| | - Philippe Sarret
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Michel Grandbois
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Grégoire Leclair
- Faculté de pharmacie, Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Quebec, Canada H3C 3J7
| | - Sereina Riniker
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Éric Marsault
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
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79
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Ermondi G, Vallaro M, Saame J, Toom L, Leito I, Ruiz R, Caron G. Rifampicin as an example of beyond-rule-of-5 compound: Ionization beyond water and lipophilicity beyond octanol/water. Eur J Pharm Sci 2021; 161:105802. [PMID: 33716188 DOI: 10.1016/j.ejps.2021.105802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 10/21/2022]
Abstract
Ionization and lipophilicity in early drug discovery are commonly characterized in water and octanol/water, respectively and thus do not consider the non-polar features of the biomembrane core. This is particularly limiting for bRo5 compounds which may adapt their properties (e.g. ionization and lipophilicity) to the environment. In this paper we used experimental methods to characterize rifampicin for its ionization properties in various water/cosolvent mixtures and in pure MeCN and its lipophilicity in octanol/water and toluene/water systems. Moreover, we also measured log k'80 PLRP-S, a chromatographic index of lipophilicity in non-polar media. Results show that the existence domain of neutral rifampicin is limited compared to the zwitterion, but the lipophilic cationic species is extremely relevant in non-polar environments.
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Affiliation(s)
- Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Dept., Università degli Studi di Torino, via Quarello 15, Torino 10135, Italy
| | - Maura Vallaro
- Molecular Biotechnology and Health Sciences Dept., Università degli Studi di Torino, via Quarello 15, Torino 10135, Italy
| | - Jaan Saame
- University of Tartu, Institute of Chemistry, Ravila 14a, Tartu 50411, Estonia
| | - Lauri Toom
- University of Tartu, Institute of Chemistry, Ravila 14a, Tartu 50411, Estonia
| | - Ivo Leito
- University of Tartu, Institute of Chemistry, Ravila 14a, Tartu 50411, Estonia
| | - Rebeca Ruiz
- Pion Inc., Forest Row Business Park, Forest Row RH18 5DW, UK
| | - Giulia Caron
- Molecular Biotechnology and Health Sciences Dept., Università degli Studi di Torino, via Quarello 15, Torino 10135, Italy.
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80
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Hoang HN, Hill TA, Fairlie DP. Connecting Hydrophobic Surfaces in Cyclic Peptides Increases Membrane Permeability. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012643] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Huy N. Hoang
- Division of Chemistry and Structural Biology and ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Timothy A. Hill
- Division of Chemistry and Structural Biology and ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology and ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
- ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
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81
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Hoang HN, Hill TA, Fairlie DP. Connecting Hydrophobic Surfaces in Cyclic Peptides Increases Membrane Permeability. Angew Chem Int Ed Engl 2021; 60:8385-8390. [PMID: 33185961 DOI: 10.1002/anie.202012643] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/04/2020] [Indexed: 12/16/2022]
Abstract
N- or C-methylation in natural and synthetic cyclic peptides can increase membrane permeability, but it remains unclear why this happens in some cases but not others. Here we compare three-dimensional structures for cyclic peptides from six families, including isomers differing only in the location of an N- or Cα-methyl substituent. We show that a single methyl group only increases membrane permeability when it connects or expands hydrophobic surface patches. Positional isomers, with the same molecular weight, hydrogen bond donors/acceptors, rotatable bonds, calculated LogP, topological polar surface area, and total hydrophobic surface area, can have different membrane permeabilities that correlate with the size of the largest continuous hydrophobic surface patch. These results illuminate a key local molecular determinant of membrane permeability.
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Affiliation(s)
- Huy N Hoang
- Division of Chemistry and Structural Biology and ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Timothy A Hill
- Division of Chemistry and Structural Biology and ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David P Fairlie
- Division of Chemistry and Structural Biology and ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
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82
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Protti ÍF, Rodrigues DR, Fonseca SK, Alves RJ, de Oliveira RB, Maltarollo VG. Do Drug-likeness Rules Apply to Oral Prodrugs? ChemMedChem 2021; 16:1446-1456. [PMID: 33471444 DOI: 10.1002/cmdc.202000805] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/12/2021] [Indexed: 12/21/2022]
Abstract
This paper describes a comparative analysis of the physicochemical and structural properties of prodrugs and their corresponding drugs with regard to drug-likeness rules. The dataset used in this work was obtained from the DrugBank. Sixty-five pairs of prodrugs/drugs were retrieved and divided into the following categories: carrier-linked to increase hydrophilic character, carrier-linked to increase absorption, and bioprecursors. We compared the physicochemical properties related to drug-likeness between prodrugs and drugs. Our results show that prodrugs do not always follow Lipinski's Rule of 5, especially as we observed 15 prodrugs with more than 10 hydrogen bond acceptors and 18 with a molecular weight greater than 500 Da. This fact highlights the importance of extending Lipinski's rules to encompass other parameters as both strategies (filtering of drug-like chemical libraries and prodrug design) aim to improve the bioavailability of compounds. Therefore, critical reasoning is fundamental to determine whether a structure has drug-like properties or could be considered a potential orally active compound in the drug-design pipeline.
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Affiliation(s)
- Ícaro F Protti
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 Pampulha, Belo Horizonte, MG, BR 31270-901, Brazil
| | - Daniel R Rodrigues
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 Pampulha, Belo Horizonte, MG, BR 31270-901, Brazil
| | - Sofia K Fonseca
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 Pampulha, Belo Horizonte, MG, BR 31270-901, Brazil
| | - Ricardo J Alves
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 Pampulha, Belo Horizonte, MG, BR 31270-901, Brazil
| | - Renata B de Oliveira
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 Pampulha, Belo Horizonte, MG, BR 31270-901, Brazil
| | - Vinícius G Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 Pampulha, Belo Horizonte, MG, BR 31270-901, Brazil
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83
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Damjanovic J, Miao J, Huang H, Lin YS. Elucidating Solution Structures of Cyclic Peptides Using Molecular Dynamics Simulations. Chem Rev 2021; 121:2292-2324. [PMID: 33426882 DOI: 10.1021/acs.chemrev.0c01087] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein-protein interactions are vital to biological processes, but the shape and size of their interfaces make them hard to target using small molecules. Cyclic peptides have shown promise as protein-protein interaction modulators, as they can bind protein surfaces with high affinity and specificity. Dozens of cyclic peptides are already FDA approved, and many more are in various stages of development as immunosuppressants, antibiotics, antivirals, or anticancer drugs. However, most cyclic peptide drugs so far have been natural products or derivatives thereof, with de novo design having proven challenging. A key obstacle is structural characterization: cyclic peptides frequently adopt multiple conformations in solution, which are difficult to resolve using techniques like NMR spectroscopy. The lack of solution structural information prevents a thorough understanding of cyclic peptides' sequence-structure-function relationship. Here we review recent development and application of molecular dynamics simulations with enhanced sampling to studying the solution structures of cyclic peptides. We describe novel computational methods capable of sampling cyclic peptides' conformational space and provide examples of computational studies that relate peptides' sequence and structure to biological activity. We demonstrate that molecular dynamics simulations have grown from an explanatory technique to a full-fledged tool for systematic studies at the forefront of cyclic peptide therapeutic design.
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Affiliation(s)
- Jovan Damjanovic
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Jiayuan Miao
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - He Huang
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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84
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Ta GH, Jhang CS, Weng CF, Leong MK. Development of a Hierarchical Support Vector Regression-Based In Silico Model for Caco-2 Permeability. Pharmaceutics 2021; 13:pharmaceutics13020174. [PMID: 33525340 PMCID: PMC7911528 DOI: 10.3390/pharmaceutics13020174] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/09/2021] [Accepted: 01/21/2021] [Indexed: 12/26/2022] Open
Abstract
Drug absorption is one of the critical factors that should be taken into account in the process of drug discovery and development. The human colon carcinoma cell layer (Caco-2) model has been frequently used as a surrogate to preliminarily investigate the intestinal absorption. In this study, a quantitative structure–activity relationship (QSAR) model was generated using the innovative machine learning-based hierarchical support vector regression (HSVR) scheme to depict the exceedingly confounding passive diffusion and transporter-mediated active transport. The HSVR model displayed good agreement with the experimental values of the training samples, test samples, and outlier samples. The predictivity of HSVR was further validated by a mock test and verified by various stringent statistical criteria. Consequently, this HSVR model can be employed to forecast the Caco-2 permeability to assist drug discovery and development.
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Affiliation(s)
- Giang Huong Ta
- Department of Chemistry, National Dong Hwa University, Shoufeng, Hualien 974301, Taiwan; (G.H.T.); (C.-S.J.)
| | - Cin-Syong Jhang
- Department of Chemistry, National Dong Hwa University, Shoufeng, Hualien 974301, Taiwan; (G.H.T.); (C.-S.J.)
| | - Ching-Feng Weng
- Department of Physiology, School of Basic Medical Science, Xiamen Medical College, Xiamen 361023, China;
| | - Max K. Leong
- Department of Chemistry, National Dong Hwa University, Shoufeng, Hualien 974301, Taiwan; (G.H.T.); (C.-S.J.)
- Correspondence: ; Tel.: +886-3-890-3609
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85
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Bogaerts J, Atilaw Y, Peintner S, Aerts R, Kihlberg J, Johannessen C, Erdélyi M. Employing complementary spectroscopies to study the conformations of an epimeric pair of side-chain stapled peptides in aqueous solution. RSC Adv 2021; 11:4200-4208. [PMID: 35424346 PMCID: PMC8694311 DOI: 10.1039/d0ra10167b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 12/21/2020] [Indexed: 12/11/2022] Open
Abstract
Understanding the conformational preferences of free ligands in solution is often necessary to rationalize structure-activity relationships in drug discovery. Herein, we examine the conformational behavior of an epimeric pair of side-chain stapled peptides that inhibit the FAD dependent amine oxidase lysine specific demethylase 1 (LSD1). The peptides differ only at a single stereocenter, but display a major difference in binding affinity. Their Raman optical activity (ROA) spectra are most likely dominated by the C-terminus, obscuring the analysis of the epimeric macrocycle. By employing NMR spectroscopy, we show a difference in conformational behavior between the two compounds and that the LSD1 bound conformation of the most potent compound is present to a measurable extent in aqueous solution. In addition, we illustrate that Molecular Dynamics (MD) simulations produce ensembles that include the most important solution conformations, but that it remains problematic to identify relevant conformations with no a priori knowledge from the large conformational pool. Furthermore, this work highlights the importance of understanding the scope and limitations of the available techniques for conducting conformational analyses. It also emphasizes the importance of conformational selection of a flexible ligand in molecular recognition.
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Affiliation(s)
| | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University SE-751 23 Uppsala Sweden
| | - Stefan Peintner
- Department of Chemistry - BMC, Uppsala University SE-751 23 Uppsala Sweden
| | - Roy Aerts
- Department of Chemistry, University of Antwerp 2020 Antwerp Belgium
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University SE-751 23 Uppsala Sweden
| | | | - Máté Erdélyi
- Department of Chemistry - BMC, Uppsala University SE-751 23 Uppsala Sweden
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86
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Atilaw Y, Poongavanam V, Svensson Nilsson C, Nguyen D, Giese A, Meibom D, Erdelyi M, Kihlberg J. Solution Conformations Shed Light on PROTAC Cell Permeability. ACS Med Chem Lett 2021; 12:107-114. [PMID: 33488971 PMCID: PMC7812666 DOI: 10.1021/acsmedchemlett.0c00556] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/18/2020] [Indexed: 12/18/2022] Open
Abstract
![]()
Proteolysis
targeting chimeras (PROTACs) induce intracellular degradation
of target proteins. Their bifunctional structure puts degraders in
a chemical space where ADME properties often complicate drug discovery.
Herein we provide the first structural insight into PROTAC cell permeability
obtained by NMR studies of a VHL-based PROTAC (1), which
is cell permeable despite having a high molecular weight and polarity
and a large number of rotatable bonds. We found that 1 populates elongated and polar conformations in solutions that mimic
extra- and intracellular compartments. Conformations were folded and
had a smaller polar surface area in chloroform, mimicking a cell membrane
interior. Formation of intramolecular and nonclassical hydrogen bonds,
π–π interactions, and shielding of amide groups
from solvent all facilitate cell permeability by minimization of size
and polarity. We conclude that molecular chameleonicity appears to
be of major importance for 1 to enter into target cells.
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Affiliation(s)
- Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | | | | | - Duy Nguyen
- Nuvisan Innovation Campus Berlin GmbH, Muellerstrasse 178, 13353 Berlin, Germany
| | - Anja Giese
- Drug Discovery Sciences, Bayer AG, 13342 Berlin, Germany
| | - Daniel Meibom
- Drug Discovery Sciences, Bayer AG, 42113 Wuppertal, Germany
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
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87
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Caron G, Kihlberg J, Goetz G, Ratkova E, Poongavanam V, Ermondi G. Steering New Drug Discovery Campaigns: Permeability, Solubility, and Physicochemical Properties in the bRo5 Chemical Space. ACS Med Chem Lett 2021; 12:13-23. [PMID: 33488959 PMCID: PMC7812602 DOI: 10.1021/acsmedchemlett.0c00581] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
An increasing number of drug discovery programs concern compounds in the beyond rule of 5 (bRo5) chemical space, such as cyclic peptides, macrocycles, and degraders. Recent results show that common paradigms of property-based drug design need revision to be applied to larger and more flexible compounds. A virtual event entitled "Solubility, permeability and physico-chemical properties in the bRo5 chemical space" was organized to provide preliminary guidance on how to make the discovery of oral drugs in the bRo5 space more effective. The four speakers emphasized the importance of the bRo5 space as a source of new oral drugs and provided examples of experimental and computational methods specifically tailored for design and optimization in this chemical space.
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Affiliation(s)
- Giulia Caron
- Molecular
Biotechnology and Health Sciences Department, University of Torino, Via Quarello, 15, 10135 Torino, Italy
| | - Jan Kihlberg
- Department
of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Gilles Goetz
- Hit
Discovery and Optimization, Discovery Sciences, WWRD, Pfizer Inc, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ekaterina Ratkova
- Medicinal
Chemistry, Research and Early Development, Cardiovascular, Renal and
Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | | | - Giuseppe Ermondi
- Molecular
Biotechnology and Health Sciences Department, University of Torino, Via Quarello, 15, 10135 Torino, Italy
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88
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Machine-learning Applications to Membrane Active Peptides. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11544-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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89
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Cipcigan F, Smith P, Crain J, Hogner A, De Maria L, Llinas A, Ratkova E. Membrane Permeability in Cyclic Peptides is Modulated by Core Conformations. J Chem Inf Model 2020; 61:263-269. [PMID: 33350828 DOI: 10.1021/acs.jcim.0c00803] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cyclic peptides have the potential to bind to challenging targets, which are undruggable with small molecules, but their application is limited by low membrane permeability. Here, using a series of cyclic pentapeptides, we showed that established physicochemical criteria of permeable peptides are heavily violated. We revealed that a dominant core conformation, stabilized by amides' shielding pattern, could guide the design of novel compounds. As a result, counter-intuitive strategies, such as incorporation of polar residues, can be beneficial for permeability. We further find that core globularity is a promising descriptor, which can extend the capability of standard predictive models.
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Affiliation(s)
- Flaviu Cipcigan
- IBM Research Europe, The Hartree Centre STFC Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, U.K
| | - Paul Smith
- IBM Research Europe, The Hartree Centre STFC Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, U.K.,King's College London, London WC2R 2LS, U.K
| | - Jason Crain
- IBM Research Europe, The Hartree Centre STFC Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, U.K.,Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
| | - Anders Hogner
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43150, Sweden
| | - Leonardo De Maria
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (RI), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43150, Sweden
| | - Antonio Llinas
- Inhalation Product Development, Pharmaceutical Technology and Development, Operations, AstraZeneca, Gothenburg 43150, Sweden
| | - Ekaterina Ratkova
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43150, Sweden
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90
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Díaz N, Suárez D. Understanding the Conformational Properties of Fluorinated Polypeptides: Molecular Modelling of Unguisin A. J Chem Inf Model 2020; 61:223-237. [PMID: 33325701 DOI: 10.1021/acs.jcim.0c00746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this work, we investigate the conformational properties of unguisin A, a natural macrocyclic heptapeptide that incorporates a γ-aminobutyric acid (Gaba), and four of its difluorinated stereoisomers at the Gaba residue. According to nuclear magnetic resonance (NMR) experiments, their secondary structure depends dramatically on the stereochemistry of the fluorinated carbon atoms. However, many molecular details of the structure and flexibility of these systems remain unknown, so that a rationale of the conformational changes induced by the fluorine atoms in the macrocycle is still missing. To fill this gap, we apply enhanced molecular dynamics (MD) techniques to explore the peptide conformational space in dimethyl sulfoxide solution followed by 4-8 μs of conventional MD simulations that provide extensive equilibrium sampling. The simulations, which compare reasonably well with the NMR-based observations, show that the secondary structure of the macrocycle is altered substantially upon fluorination, except for the (S,S) diastereomer. It also turns out that the conformations of the fluorinated peptides are visited during the enhanced MD simulation of natural unguisin A, suggesting thus that conformations accessible to the unsubstituted macrocyclic peptide may be selected by fluorination. Therefore, computational characterization of the macrocyclic peptides could be helpful in the rational design of stereoselective fluorinated peptides with fine-tuned conformation and activity.
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Affiliation(s)
- Natalia Díaz
- Departamento de Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, 33006 Oviedo, Asturias, Spain
| | - Dimas Suárez
- Departamento de Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, 33006 Oviedo, Asturias, Spain
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91
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Reyes Romero A, Ruiz-Moreno AJ, Groves MR, Velasco-Velázquez M, Dömling A. Benchmark of Generic Shapes for Macrocycles. J Chem Inf Model 2020; 60:6298-6313. [PMID: 33270455 PMCID: PMC7768607 DOI: 10.1021/acs.jcim.0c01038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Macrocycles
target proteins that are otherwise considered undruggable
because of a lack of hydrophobic cavities and the presence of extended
featureless surfaces. Increasing efforts by computational chemists
have developed effective software to overcome the restrictions of
torsional and conformational freedom that arise as a consequence of
macrocyclization. Moloc is an efficient algorithm, with an emphasis
on high interactivity, and has been constantly updated since 1986
by drug designers and crystallographers of the Roche biostructural
community. In this work, we have benchmarked the shape-guided algorithm
using a dataset of 208 macrocycles, carefully selected on the basis
of structural complexity. We have quantified the accuracy, diversity,
speed, exhaustiveness, and sampling efficiency in an automated fashion
and we compared them with four commercial (Prime, MacroModel, molecular
operating environment, and molecular dynamics) and four open-access
(experimental-torsion distance geometry with additional “basic
knowledge” alone and with Merck molecular force field minimization
or universal force field minimization, Cambridge Crystallographic
Data Centre conformer generator, and conformator) packages. With three-quarters
of the database processed below the threshold of high ring accuracy,
Moloc was identified as having the highest sampling efficiency and
exhaustiveness without producing thousands of conformations, random
ring splitting into two half-loops, and possibility to interactively
produce globular or flat conformations with diversity similar to Prime,
MacroModel, and molecular dynamics. The algorithm and the Python scripts
for full automatization of these parameters are freely available for
academic use.
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Affiliation(s)
- Atilio Reyes Romero
- Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, XB20, 9713 AV Groningen, The Netherlands
| | - Angel Jonathan Ruiz-Moreno
- Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, XB20, 9713 AV Groningen, The Netherlands.,Departamento de Farmacología y Unidad Periférica de Investigación en Biomedicina Trasnacional, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 3000, Circuito Exterior S/N, Delegación Coyoacán, Ciudad Universitaria, 04510 Ciudad de México, Mexico.,Programa de Doctorado en Ciencias Biomédicas, UNAM, Av. Universidad 3000, Circuito Exterior S/N. Delegación Coyoacán, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Matthew R Groves
- Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, XB20, 9713 AV Groningen, The Netherlands
| | - Marco Velasco-Velázquez
- Departamento de Farmacología y Unidad Periférica de Investigación en Biomedicina Trasnacional, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 3000, Circuito Exterior S/N, Delegación Coyoacán, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Alexander Dömling
- Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, XB20, 9713 AV Groningen, The Netherlands
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92
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Posada L, Davyt D, Serra G. First total synthesis of versicotide A, B and C. RSC Adv 2020; 10:43653-43659. [PMID: 35519702 PMCID: PMC9058379 DOI: 10.1039/d0ra09635k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 11/24/2020] [Indexed: 12/25/2022] Open
Abstract
The syntheses of versicotides A-C, natural products containing anthranilic acid and NMe-Ala, were achieved by solid phase peptide synthesis on 2-chlorotrityl resin followed by solution phase macrocyclization. Using an oxyma additive, the difficult coupling reactions to the deactivated aromatic amine of o-aminobenzoic acid, were performed in high yield, avoiding anthranilic rearrangements or side reactions.
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Affiliation(s)
- Laura Posada
- Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República General Flores 2124 CC1157 Montevideo Uruguay
- Graduate Program in Chemistry, Facultad de Química, Universidad de la República Uruguay
| | - Danilo Davyt
- Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República General Flores 2124 CC1157 Montevideo Uruguay
| | - Gloria Serra
- Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República General Flores 2124 CC1157 Montevideo Uruguay
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93
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Furukawa A, Schwochert J, Pye CR, Asano D, Edmondson QD, Turmon AC, Klein VG, Ono S, Okada O, Lokey RS. Drug-Like Properties in Macrocycles above MW 1000: Backbone Rigidity versus Side-Chain Lipophilicity. Angew Chem Int Ed Engl 2020; 59:21571-21577. [PMID: 32789999 PMCID: PMC7719619 DOI: 10.1002/anie.202004550] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/10/2020] [Indexed: 12/22/2022]
Abstract
Large macrocyclic peptides can achieve surprisingly high membrane permeability, although the properties that govern permeability in this chemical space are only beginning to come into focus. We generated two libraries of cyclic decapeptides with stable cross-β conformations, and found that peptoid substitutions within the β-turns of the macrocycle preserved the rigidity of the parent scaffold, whereas peptoid substitutions in the opposing β-strands led to "chameleonic" species that were rigid in nonpolar media but highly flexible in water. Both rigid and chameleonic compounds showed high permeability over a wide lipophilicity range, with peak permeabilities differing significantly depending on scaffold rigidity. Our findings indicate that modulating lipophilicity can be used to engineer favorable ADME properties into both rigid and flexible macrocyclic peptides, and that scaffold rigidity can be used to tune optimal lipophilicity.
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Affiliation(s)
- Akihiro Furukawa
- Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Joshua Schwochert
- Unnatural Products, Inc., 250 Natural Bridges Drive, Santa Cruz, CA 95060 USA
| | - Cameron R. Pye
- Unnatural Products, Inc., 250 Natural Bridges Drive, Santa Cruz, CA 95060 USA
| | - Daigo Asano
- Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Quinn D. Edmondson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, USA
| | - Alexandra C. Turmon
- Unnatural Products, Inc., 250 Natural Bridges Drive, Santa Cruz, CA 95060 USA
| | - Victoria G. Klein
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, CA 96064 USA
| | - Satoshi Ono
- Discovery Technology Laboratories, Mitsubishi Tanabe Pharma Corporation, Yokohama, 227-0033, Japan
| | - Okimasa Okada
- Discovery Technology Laboratories, Mitsubishi Tanabe Pharma Corporation, Yokohama, 227-0033, Japan
| | - R. Scott Lokey
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, CA 96064 USA
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94
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Synergistic Computational Modeling Approaches as Team Players in the Game of Solubility Predictions. J Pharm Sci 2020; 110:22-34. [PMID: 33217423 DOI: 10.1016/j.xphs.2020.10.068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/23/2020] [Accepted: 10/28/2020] [Indexed: 11/23/2022]
Abstract
Several approaches to predict and model drug solubility have been used in the drug discovery and development processes during the last decades. Each of these approaches have their own benefits and place, and are typically used as standalone approaches rather than in concert. The synergistic effects of these are often overlooked, partly due to the need of computational experts to perform the modeling and simulations as well as analyzing the data obtained. Here we provide our views on how these different approaches can be used to retrieve more information on drug solubility, ranging from multivariate data analysis over thermodynamic cycle modeling to molecular dynamics simulations. We are discussing aqueous solubility as well as solubility in more complex mixed solvents and media with colloidal structures present. We conclude that the field of computational pharmaceutics is in its early days but with a bright future ahead. However, education of computational formulators with broad knowledge of modeling and simulation approaches is imperative if computational pharmaceutics is to reach its full potential.
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95
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Buckton LK, Rahimi MN, McAlpine SR. Cyclic Peptides as Drugs for Intracellular Targets: The Next Frontier in Peptide Therapeutic Development. Chemistry 2020; 27:1487-1513. [PMID: 32875673 DOI: 10.1002/chem.201905385] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 08/26/2020] [Indexed: 12/18/2022]
Abstract
Developing macrocyclic peptides that can reach intracellular targets is a significant challenge. This review discusses the most recent strategies used to develop cell permeable cyclic peptides that maintain binding to their biological target inside the cell. Macrocyclic peptides are unique from small molecules because traditional calculated physical properties are unsuccessful for predicting cell membrane permeability. Peptide synthesis and experimental membrane permeability is the only strategy that effectively differentiates between cell permeable and cell impermeable molecules. Discussed are chemical strategies, including backbone N-methylation and stereochemical changes, which have produced molecular scaffolds with improved cell permeability. However, these improvements often come at the expense of biological activity as chemical modifications alter the peptide conformation, frequently impacting the compound's ability to bind to the target. Highlighted is the most promising approach, which involves side-chain alterations that improve cell permeability without impact binding events.
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Affiliation(s)
- Laura K Buckton
- Department of Chemistry, University of New South Wales, Sydney, Gate 2 High Street, SEB 701, Kensington, NSW, 2052, Australia
| | - Marwa N Rahimi
- Department of Chemistry, University of New South Wales, Sydney, Gate 2 High Street, SEB 701, Kensington, NSW, 2052, Australia
| | - Shelli R McAlpine
- Department of Chemistry, University of New South Wales, Sydney, Gate 2 High Street, SEB 701, Kensington, NSW, 2052, Australia
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96
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Poongavanam V, Atilaw Y, Ye S, Wieske LHE, Erdelyi M, Ermondi G, Caron G, Kihlberg J. Predicting the Permeability of Macrocycles from Conformational Sampling - Limitations of Molecular Flexibility. J Pharm Sci 2020; 110:301-313. [PMID: 33129836 DOI: 10.1016/j.xphs.2020.10.052] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 12/19/2022]
Abstract
Macrocycles constitute superior ligands for targets that have flat binding sites but often require long synthetic routes, emphasizing the need for property prediction prior to synthesis. We have investigated the scope and limitations of machine learning classification models and of regression models for predicting the cell permeability of a set of denovo-designed, drug-like macrocycles. 2D-Based classification models, which are fast to calculate, discriminated between macrocycles that had low-medium and high permeability and may be used as virtual filters in early drug discovery projects. Importantly, stereo- and regioisomer were correctly classified. QSPR studies of two small sets of comparator drugs suggested that use of 3D descriptors, calculated from biologically relevant conformations, would allow development of more precise regression models for late phase drug projects. However, a 3D permeability model could only be developed for a rigid series of macrocycles. Comparison of NMR based conformational analysis with in silico conformational sampling indicated that this shortcoming originates from the inability of the molecular mechanics force field to identify the relevant conformations for flexible macrocycles. We speculate that a Kier flexibility index of ≤10 constitutes a current upper limit for reasonably accurate 3D prediction of macrocycle cell permeability.
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Affiliation(s)
| | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Sofie Ye
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Lianne H E Wieske
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Giuseppe Ermondi
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Quarello 15, 10135 Torino, Italy
| | - Giulia Caron
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Quarello 15, 10135 Torino, Italy.
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden.
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97
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Furukawa A, Schwochert J, Pye CR, Asano D, Edmondson QD, Turmon AC, Klein VG, Ono S, Okada O, Lokey RS. Drug‐Like Properties in Macrocycles above MW 1000: Backbone Rigidity versus Side‐Chain Lipophilicity. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004550] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Akihiro Furukawa
- Daiichi Sankyo Co., Ltd. 1-2-58, Hiromachi, Shinagawa-ku Tokyo 140-8710 Japan
| | - Joshua Schwochert
- Unnatural Products, Inc. 250 Natural Bridges Drive Santa Cruz CA 95060 USA
| | - Cameron R. Pye
- Unnatural Products, Inc. 250 Natural Bridges Drive Santa Cruz CA 95060 USA
| | - Daigo Asano
- Daiichi Sankyo Co., Ltd. 1-2-58, Hiromachi, Shinagawa-ku Tokyo 140-8710 Japan
| | - Quinn D. Edmondson
- Department of Pharmaceutical Chemistry University of California, San Francisco San Francisco California 94158 USA
| | | | - Victoria G. Klein
- Department of Chemistry & Biochemistry University of California Santa Cruz Santa Cruz CA 96064 USA
| | - Satoshi Ono
- Discovery Technology Laboratories Mitsubishi Tanabe Pharma Corporation Yokohama 227-0033 Japan
| | - Okimasa Okada
- Discovery Technology Laboratories Mitsubishi Tanabe Pharma Corporation Yokohama 227-0033 Japan
| | - R. Scott Lokey
- Department of Chemistry & Biochemistry University of California Santa Cruz Santa Cruz CA 96064 USA
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98
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Di L, Artursson P, Avdeef A, Benet LZ, Houston JB, Kansy M, Kerns EH, Lennernäs H, Smith DA, Sugano K. The Critical Role of Passive Permeability in Designing Successful Drugs. ChemMedChem 2020; 15:1862-1874. [PMID: 32743945 DOI: 10.1002/cmdc.202000419] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Indexed: 12/25/2022]
Abstract
Passive permeability is a key property in drug disposition and delivery. It is critical for gastrointestinal absorption, brain penetration, renal reabsorption, defining clearance mechanisms and drug-drug interactions. Passive diffusion rate is translatable across tissues and animal species, while the extent of absorption is dependent on drug properties, as well as in vivo physiology/pathophysiology. Design principles have been developed to guide medicinal chemistry to enhance absorption, which combine the balance of aqueous solubility, permeability and the sometimes unfavorable compound characteristic demanded by the target. Permeability assays have been implemented that enable rapid development of structure-permeability relationships for absorption improvement. Future advances in assay development to reduce nonspecific binding and improve mass balance will enable more accurately measurement of passive permeability. Design principles that integrate potency, selectivity, passive permeability and other ADMET properties facilitate rapid advancement of successful drug candidates to patients.
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Affiliation(s)
- Li Di
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, CT 06340, USA
| | - Per Artursson
- Department of Pharmacy, Uppsala University, 752 36, Uppsala, Sweden
| | - Alex Avdeef
- in-ADME Research, 1732 First Avenue, #102, New York, NY 10128, USA
| | - Leslie Z Benet
- Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, CA 94143, USA
| | - J Brian Houston
- Division of Pharmacy & Optometry, Stopford Building, Oxford Road, Manchester, M13 9PT, UK
| | | | | | - Hans Lennernäs
- Department of Pharmacy, Uppsala University, 752 36, Uppsala, Sweden
| | | | - Kiyohiko Sugano
- College of Pharmaceutical Sciences, Department of Pharmacy, Ritsumeikan University, Noji-higashi, Kusatsu, Shiga, 525-8577, Japan
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99
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Velcicky J, Wilcken R, Cotesta S, Janser P, Schlapbach A, Wagner T, Piechon P, Villard F, Bouhelal R, Piller F, Harlfinger S, Stringer R, Fehlmann D, Kaupmann K, Littlewood-Evans A, Haffke M, Gommermann N. Discovery and Optimization of Novel SUCNR1 Inhibitors: Design of Zwitterionic Derivatives with a Salt Bridge for the Improvement of Oral Exposure. J Med Chem 2020; 63:9856-9875. [DOI: 10.1021/acs.jmedchem.0c01020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Juraj Velcicky
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Rainer Wilcken
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Simona Cotesta
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Philipp Janser
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Achim Schlapbach
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Trixie Wagner
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Philippe Piechon
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Frederic Villard
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Rochdi Bouhelal
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Fabian Piller
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | | | - Rowan Stringer
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | | | - Klemens Kaupmann
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | | | - Matthias Haffke
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Nina Gommermann
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
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100
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Ermondi G, Vallaro M, Caron G. Degraders early developability assessment: face-to-face with molecular properties. Drug Discov Today 2020; 25:1585-1591. [PMID: 32565163 DOI: 10.1016/j.drudis.2020.06.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/29/2020] [Accepted: 06/16/2020] [Indexed: 12/12/2022]
Abstract
Pharmaceutical scientists have huge expectations from heterobifunctional small molecule degraders to treat diseases with an unmet medical need. However, degraders are large and flexible and pose significant challenges in terms of cellular uptake and bioavailability. An efficient property-based design is therefore required to discover new oral degrader medicines. Here, we show the non‑transferability to degraders of in silico tools routinely implemented in small molecule drug discovery programs; and provide ionization, lipophilicity, polarity and chameleonicity data for a series of seven degraders. We also reveal that permeability can be modeled by Δlog kWIAM - an experimental polarity descriptor. Overall, the paper is a proof-of-concept that shows to discover new oral degrader drugs ad hoc property-based design strategies are required.
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Affiliation(s)
- Giuseppe Ermondi
- University of Torino, Molecular Biotechnology and Health Sciences Dept, CASSMedChem, via Quarello 15, 10135 Torino, Italy
| | - Maura Vallaro
- University of Torino, Molecular Biotechnology and Health Sciences Dept, CASSMedChem, via Quarello 15, 10135 Torino, Italy
| | - Giulia Caron
- University of Torino, Molecular Biotechnology and Health Sciences Dept, CASSMedChem, via Quarello 15, 10135 Torino, Italy.
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