1
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Bi T, Cui Y, Liu S, Yu H, Qiu W, Hou KQ, Zou J, Yu Z, Zhang F, Xu Z, Zhang J, Xu X, Yang W. Ligand-Enabled Pd-Catalyzed sp 3 C-H Macrocyclization: Synthesis and Evaluation of Macrocyclic Sulfonamide for the Treatment of Parkinson's Disease. Angew Chem Int Ed Engl 2024; 63:e202412296. [PMID: 39078406 DOI: 10.1002/anie.202412296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 07/31/2024]
Abstract
The development of simplified synthetic strategy to create structurally and functionally diverse pseudo-natural macrocyclic molecules is highly appealing but poses a marked challenge. Inspired by natural scaffolds, herein, we describe a practical and concise ligand-enabled Pd(II)-catalyzed sp3 C-H alkylation, olefination and arylation macrocyclization, which could offer a novel set of pseudo-natural macrocyclic sulfonamides. Interestingly, the potential of ligand acceleration in C-H activation is also demonstrated by an unprecedented enantioselective sp3 C-H alkylation macrocyclization. Moreover, a combination of in silico screening and biological evaluation led to the identification of a novel spiro-grafted macrocyclic sulfonamide 2 a, which showed a promising efficacy for the treatment of Parkinson's disease (PD) in a mouse model through the activation of silent information regulator sirtuin 3 (SIRT3).
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Affiliation(s)
- Tongyu Bi
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunxia Cui
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Shuai Liu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Haiyue Yu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weirong Qiu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Ke-Qiang Hou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiaqi Zou
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210000, China
| | - Zhipeng Yu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210000, China
| | - Feili Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhongliang Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Zhang
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaojun Xu
- Center for Innovative Traditional Chinese Medicine Target and New Drug Research, International Institutes of Medicine, Zhejiang University, Yiwu, Zhejiang, 322000, China
| | - Weibo Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
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2
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Galamba N. Sickle Cell Hemoglobin "Drugged" with Cyclic Peptides Is Aggregation Incompetent. J Phys Chem B 2024; 128:8662-8671. [PMID: 39205400 PMCID: PMC11403655 DOI: 10.1021/acs.jpcb.4c03805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Sickle cell disease (SCD) is a monogenic blood disorder associated with a mutation in the hemoglobin subunit β gene encoding for the β-globin of normal adult hemoglobin (HbA). This mutation transcribes into a Glu-β6 → Val-β6 substitution in the β-globins, inducing the polymerization of this hemoglobin form (HbS) when in the T-state. Despite advances in stem cell and gene therapy, and the recent approval of a new antisickling drug, therapeutic limitations persist. Herein, we demonstrate through molecular dynamics and umbrella sampling, that (unrestrained) blockage of the hydrophobic pocket involved in the lateral contact of the HbS fibers by 5-mer cyclic peptides, recently proposed as SCD aggregation inhibitors (Neto, V.; J. Med. Chem. 2023, 66, 16062-16074), is enough to turn the dimerization of HbS thermodynamically unfavorable. Among these potential drugs, some exhibit an estimated pocket abandonment probability of around 15-20% within the simulations' time frame, and an impressive specificity toward the mutated Val-β6. Additionally, we show that the dimerization can be thermodynamically unfavored by blocking a nearby region while the pocket remains vacant. These results are compared with curcumin, an antisickling molecule and a pan-assay interference compound, with a good binding affinity for different proteins and protein domains. Our results confirm the potential of some of these cyclic peptides as antisickling drug candidates to reduce the concentration of aggregation-competent HbS.
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Affiliation(s)
- N Galamba
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Edifício C8, Campo Grande, 1749-016 Lisboa, Portugal
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3
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Aida-Ficken V, Kelly JA, Chatterjee P, Jenks MH, McMullan LK, Albariño CG, Montgomery JM, Seley-Radtke KL, Spiropoulou CF, Flint M. Identification of a macrocyclic compound targeting the lassa virus polymerase. Antiviral Res 2024; 228:105923. [PMID: 38844175 DOI: 10.1016/j.antiviral.2024.105923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/20/2024] [Accepted: 06/02/2024] [Indexed: 06/21/2024]
Abstract
There are no approved vaccines or therapeutics for Lassa virus (LASV) infections. To identify compounds with anti-LASV activity, we conducted a cell-based screening campaign at biosafety level 4 and tested almost 60,000 compounds for activity against an infectious reporter LASV. Hits from this screen included several structurally related macrocycles. The most potent, Mac128, had a sub-micromolar EC50 against the reporter virus, inhibited wild-type clade IV LASV, and reduced viral titers by 4 orders of magnitude. Mechanistic studies suggested that Mac128 inhibited viral replication at the level of the polymerase.
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Affiliation(s)
- Virginia Aida-Ficken
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Jamie A Kelly
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Payel Chatterjee
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - M Harley Jenks
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Laura K McMullan
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - César G Albariño
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Joel M Montgomery
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Katherine L Seley-Radtke
- Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, USA
| | - Christina F Spiropoulou
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mike Flint
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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4
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Zhao H, Jiang D, Shen C, Zhang J, Zhang X, Wang X, Nie D, Hou T, Kang Y. Comprehensive Evaluation of 10 Docking Programs on a Diverse Set of Protein-Cyclic Peptide Complexes. J Chem Inf Model 2024; 64:2112-2124. [PMID: 38483249 DOI: 10.1021/acs.jcim.3c01921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Cyclic peptides have emerged as a highly promising class of therapeutic molecules owing to their favorable pharmacokinetic properties, including stability and permeability. Currently, many clinically approved cyclic peptides are derived from natural products or their derivatives, and the development of molecular docking techniques for cyclic peptide discovery holds great promise for expanding the applications and potential of this class of molecules. Given the availability of numerous docking programs, there is a pressing need for a systematic evaluation of their performance, specifically on protein-cyclic peptide systems. In this study, we constructed an extensive benchmark data set called CPSet, consisting of 493 protein-cyclic peptide complexes. Based on this data set, we conducted a comprehensive evaluation of 10 docking programs, including Rosetta, AutoDock CrankPep, and eight protein-small molecule docking programs (i.e., AutoDock, AudoDock Vina, Glide, GOLD, LeDock, rDock, MOE, and Surflex). The evaluation encompassed the assessment of the sampling power, docking power, and scoring power of these programs. The results revealed that all of the tested protein-small molecule docking programs successfully sampled the binding conformations when using the crystal conformations as the initial structures. Among them, rDock exhibited outstanding performance, achieving a remarkable 94.3% top-100 sampling success rate. However, few programs achieved successful predictions of the binding conformations using tLEaP-generated conformations as the initial structures. Within this scheme, AutoDock CrankPep yielded the highest top-100 sampling success rate of 29.6%. Rosetta's scoring function outperformed the others in selecting optimal conformations, resulting in an impressive top-1 docking success rate of 87.6%. Nevertheless, all the tested scoring functions displayed limited performance in predicting binding affinity, with MOE@Affinity dG exhibiting the highest Pearson's correlation coefficient of 0.378. It is therefore suggested to use an appropriate combination of different docking programs for given tasks in real applications. We expect that this work will offer valuable insights into selecting the appropriate docking programs for protein-cyclic peptide complexes.
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Affiliation(s)
- Huifeng Zhao
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang China
- Hangzhou Carbonsilicon AI Technology Co., Ltd, Hangzhou 310018, Zhejiang China
| | - Dejun Jiang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang China
- Hangzhou Carbonsilicon AI Technology Co., Ltd, Hangzhou 310018, Zhejiang China
| | - Chao Shen
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang China
- Hangzhou Carbonsilicon AI Technology Co., Ltd, Hangzhou 310018, Zhejiang China
| | - Jintu Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang China
| | - Xujun Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang China
| | - Xiaorui Wang
- Hangzhou Carbonsilicon AI Technology Co., Ltd, Hangzhou 310018, Zhejiang China
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao 999078, China
| | - Dou Nie
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang China
| | - Yu Kang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang China
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5
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Zhang C, Liu F, Zhang Y, Song C. Macrocycles and macrocyclization in anticancer drug discovery: Important pieces of the puzzle. Eur J Med Chem 2024; 268:116234. [PMID: 38401189 DOI: 10.1016/j.ejmech.2024.116234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/10/2024] [Accepted: 02/11/2024] [Indexed: 02/26/2024]
Abstract
Increasing disease-related proteins have been identified as novel therapeutic targets. Macrocycles are emerging as potential solutions, bridging the gap between conventional small molecules and biomacromolecules in drug discovery. Inspired by successful macrocyclic drugs of natural origins, macrocycles are attracting more attention for enhanced binding affinity and target selectivity. Due to the conformation constraint and structure preorganization, macrocycles can reach bioactive conformations more easily than parent acyclic compounds. Also, rational macrocyclization combined with sequent structural modification will help improve oral bioavailability and combat drug resistance. This review introduces various strategies to enhance membrane permeability in macrocyclization and subsequent modification, such as N-methylation, intramolecular hydrogen bonding modulation, isomerization, and reversible bicyclization. Several case studies highlight macrocyclic inhibitors targeting kinases, HDAC, and protein-protein interactions. Finally, some macrocyclic agents targeting tumor microenvironments are illustrated.
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Affiliation(s)
- Chao Zhang
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Fenfen Liu
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Chun Song
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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6
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Ly HM, Desgagné M, Nguyen DT, Comeau C, Froehlich U, Marsault É, Boudreault PL. Insights on Structure-Passive Permeability Relationship in Pyrrole and Furan-Containing Macrocycles. J Med Chem 2024; 67:3711-3726. [PMID: 38417040 PMCID: PMC10946398 DOI: 10.1021/acs.jmedchem.3c02162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/19/2023] [Accepted: 01/11/2024] [Indexed: 03/01/2024]
Abstract
Macrocycles have recognized therapeutic potential, but their limited cellular permeability can hinder their development as oral drugs. To better understand the structure-permeability relationship of heterocycle-containing, semipeptidic macrocycles, a library was synthesized. These compounds were created by developing two novel reactions described herein: the reduction of activated oximes by LiBH4 and the aqueous reductive mono-N-alkylation of aldehydes using catalytic SmI2 and stoichiometric Zn. The permeability of the macrocycles was evaluated through a parallel artificial membrane permeability assay (PAMPA), and the results indicated that macrocycles with a furan incorporated into the structure have better passive permeability than those with a pyrrole moiety. Compounds bearing a 2,5-disubstituted pyrrole (endo orientation) were shown to be implicated in intramolecular H-bonds, enhancing their permeability. This study highlighted the impact of heterocycles moieties in semipeptides, creating highly permeable macrocycles, thus showing promising avenues for passive diffusion of drugs beyond the rule-of-five chemical space.
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Affiliation(s)
- Huy M Ly
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, QC J1H5N4, Canada
| | - Michael Desgagné
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, QC J1H5N4, Canada
| | - Duc Tai Nguyen
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, QC J1H5N4, Canada
| | - Christian Comeau
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, QC J1H5N4, Canada
| | - Ulrike Froehlich
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, QC J1H5N4, Canada
| | - Éric Marsault
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, QC J1H5N4, Canada
| | - Pierre-Luc Boudreault
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, QC J1H5N4, Canada
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7
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Abstract
Cyclic peptides are fascinating molecules abundantly found in nature and exploited as molecular format for drug development as well as other applications, ranging from research tools to food additives. Advances in peptide technologies made over many years through improved methods for synthesis and drug development have resulted in a steady stream of new drugs, with an average of around one cyclic peptide drug approved per year. Powerful technologies for screening random peptide libraries, and de novo generating ligands, have enabled the development of cyclic peptide drugs independent of naturally derived molecules and now offer virtually unlimited development opportunities. In this review, we feature therapeutically relevant cyclic peptides derived from nature and discuss the unique properties of cyclic peptides, the enormous technological advances in peptide ligand development in recent years, and current challenges and opportunities for developing cyclic peptides that address unmet medical needs.
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Affiliation(s)
- Xinjian Ji
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Alexander L Nielsen
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
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8
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Ferková S, Froehlich U, Nepveu-Traversy MÉ, Murza A, Azad T, Grandbois M, Sarret P, Lavigne P, Boudreault PL. Comparative Analysis of Cyclization Techniques in Stapled Peptides: Structural Insights into Protein-Protein Interactions in a SARS-CoV-2 Spike RBD/hACE2 Model System. Int J Mol Sci 2023; 25:166. [PMID: 38203338 PMCID: PMC10778704 DOI: 10.3390/ijms25010166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Medicinal chemistry is constantly searching for new approaches to develop more effective and targeted therapeutic molecules. The design of peptidomimetics is a promising emerging strategy that is aimed at developing peptides that mimic or modulate the biological activity of proteins. Among these, stapled peptides stand out for their unique ability to stabilize highly frequent helical motifs, but they have failed to be systematically reported. Here, we exploit chemically diverse helix-inducing i, i + 4 constraints-lactam, hydrocarbon, triazole, double triazole and thioether-on two distinct short sequences derived from the N-terminal peptidase domain of hACE2 upon structural characterization and in silico alanine scan. Our overall objective was to provide a sequence-independent comparison of α-helix-inducing staples using circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. We identified a 9-mer lactam stapled peptide derived from the hACE2 sequence (His34-Gln42) capable of reaching its maximal helicity of 55% with antiviral activity in bioreporter- and pseudovirus-based inhibition assays. To the best of our knowledge, this study is the first comprehensive investigation comparing several cyclization methods with the goal of generating stapled peptides and correlating their secondary structures with PPI inhibitions using a highly topical model system (i.e., the interaction of SARS-CoV-2 Spike RBD with hACE2).
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Affiliation(s)
| | | | | | | | | | | | | | | | - Pierre-Luc Boudreault
- Department of Pharmacology and Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, QC J1H 5N4, Canada; (S.F.); (M.-É.N.-T.); (A.M.); (T.A.)
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9
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Neto V, Victor BL, Galamba N. Cyclic Peptides as Aggregation Inhibitors for Sickle Cell Disease. J Med Chem 2023; 66:16062-16074. [PMID: 37988411 DOI: 10.1021/acs.jmedchem.3c01484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Sickle cell disease is a missense genetic disorder characterized by the aggregation of deoxy-HbS into helical fibers that distort erythrocytes into a sickle-like shape. Herein, we investigate, through molecular dynamics, the effect of nine 5-mer cyclic peptides (CPs), tailor-designed to block key lateral contacts of the fibers. Our results show that the CPs bind orthogonally to the main HbS pocket involved in the latter contacts, with some revealing exceedingly long residence times. These CPs display moderate to high specificity, exhibiting molecular recognition events even at a HbS/CP (1:1) ratio. A much lower HbS-CP binding free energy, longer residence times, and higher specificity are also found relative to a previously reported CP with modest in vitro antisickling activity. These results indicate that some of these CPs have the potential to reduce the concentration of aggregation-competent deoxy-HbS, precluding or delaying the formation of lateral contact at the homogeneous nucleation stage.
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Affiliation(s)
- Vasco Neto
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Edifício C8, Campo Grande 1749-016, Lisboa, Portugal
| | - Bruno Lourenço Victor
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Edifício C8, Campo Grande 1749-016, Lisboa, Portugal
| | - Nuno Galamba
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Edifício C8, Campo Grande 1749-016, Lisboa, Portugal
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10
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Pepanian A, Binbay FA, Roy S, Nubbemeyer B, Koley A, Rhodes CA, Ammer H, Pei D, Ghosh P, Imhof D. Bicyclic Peptide Library Screening for the Identification of Gαi Protein Modulators. J Med Chem 2023; 66:12396-12406. [PMID: 37587416 PMCID: PMC11000586 DOI: 10.1021/acs.jmedchem.3c00873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Noncanonical G protein activation and inactivation, particularly for the Gαi/s protein subfamilies, have long been a focus of chemical research. Combinatorial libraries were already effectively applied to identify modulators of the guanine-nucleotide exchange, as can be exemplified with peptides such as KB-752 and GPM-1c/d, the so-called guanine-nucleotide exchange modulators. In this study, we identified novel bicyclic peptides from a combinatorial library screening that show prominent properties as molecular switch-on/off modulators of Gαi signaling. Among the series of hits, the exceptional paradigm of GPM-3, a protein and state-specific bicyclic peptide, is the first chemically identified GAP (GTPase-activating protein) modulator with a high binding affinity for Gαi protein. Computational analyses identified and assessed the structure of the bicyclic peptides, novel ligand-protein interaction sites, and their subsequent impact on the nucleotide binding site. This approach can therefore lead the way for the development of efficient chemical biological probes targeting Gαi protein modulation within a cellular context.
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Affiliation(s)
- Anna Pepanian
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Furkan Ayberk Binbay
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Suchismita Roy
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Britta Nubbemeyer
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Amritendu Koley
- Department of Chemistry and Biochemistry, The Ohio State University, 578 Biological Sciences Building, 484 W 12th Avenue, Columbus, OH 43210, USA
| | - Curran A. Rhodes
- Department of Chemistry and Biochemistry, The Ohio State University, 578 Biological Sciences Building, 484 W 12th Avenue, Columbus, OH 43210, USA
| | - Hermann Ammer
- Institute of Pharmacology Toxicology and Pharmacy, Veterinary Faculty, Ludwig Maximilian University of Munich, Königinstr. 16, 80539 Munich, Germany
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 578 Biological Sciences Building, 484 W 12th Avenue, Columbus, OH 43210, USA
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
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11
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Seidel T, Permann C, Wieder O, Kohlbacher SM, Langer T. High-Quality Conformer Generation with CONFORGE: Algorithm and Performance Assessment. J Chem Inf Model 2023; 63:5549-5570. [PMID: 37624145 PMCID: PMC10498443 DOI: 10.1021/acs.jcim.3c00563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Indexed: 08/26/2023]
Abstract
Knowledge of the putative bound-state conformation of a molecule is an essential prerequisite for the successful application of many computer-aided drug design methods that aim to assess or predict its capability to bind to a particular target receptor. An established approach to predict bioactive conformers in the absence of receptor structure information is to sample the low-energy conformational space of the investigated molecules and derive representative conformer ensembles that can be expected to comprise members closely resembling possible bound-state ligand conformations. The high relevance of such conformer generation functionality led to the development of a wide panel of dedicated commercial and open-source software tools throughout the last decades. Several published benchmarking studies have shown that open-source tools usually lag behind their commercial competitors in many key aspects. In this work, we introduce the open-source conformer ensemble generator CONFORGE, which aims at delivering state-of-the-art performance for all types of organic molecules in drug-like chemical space. The ability of CONFORGE and several well-known commercial and open-source conformer ensemble generators to reproduce experimental 3D structures as well as their computational efficiency and robustness has been assessed thoroughly for both typical drug-like molecules and macrocyclic structures. For small molecules, CONFORGE clearly outperformed all other tested open-source conformer generators and performed at least equally well as the evaluated commercial generators in terms of both processing speed and accuracy. In the case of macrocyclic structures, CONFORGE achieved the best average accuracy among all benchmarked generators, with RDKit's generator coming close in second place.
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Affiliation(s)
- Thomas Seidel
- Department
of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Christian Permann
- NeGeMac
Research Platform, Department of Pharmaceutical Sciences, Division
of Pharmaceutical Chemistry, University
of Vienna, Josef-Holaubek-Platz
2, 1090 Vienna, Austria
| | - Oliver Wieder
- Christian
Doppler Laboratory for Molecular Informatics in the Biosciences, Department
of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Stefan M. Kohlbacher
- Department
of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Thierry Langer
- Department
of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
- NeGeMac
Research Platform, Department of Pharmaceutical Sciences, Division
of Pharmaceutical Chemistry, University
of Vienna, Josef-Holaubek-Platz
2, 1090 Vienna, Austria
- Christian
Doppler Laboratory for Molecular Informatics in the Biosciences, Department
of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
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12
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Tosh D, Fisher CL, Salmaso V, Wan TC, Campbell RG, Chen E, Gao ZG, Auchampach JA, Jacobson KA. First Potent Macrocyclic A 3 Adenosine Receptor Agonists Reveal G-Protein and β-Arrestin2 Signaling Preferences. ACS Pharmacol Transl Sci 2023; 6:1288-1305. [PMID: 37705595 PMCID: PMC10496144 DOI: 10.1021/acsptsci.3c00126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Indexed: 09/15/2023]
Abstract
(N)-Methanocarba adenosine derivatives (A3 adenosine receptor (AR) agonists containing bicyclo[3.1.0]hexane replacing furanose) were chain-extended at N6 and C2 positions with terminal alkenes for ring closure. The resulting macrocycles of 17-20 atoms retained affinity, indicating a spatially proximal orientation of these receptor-bound chains, consistent with molecular modeling of 12. C2-Arylethynyl-linked macrocycle 19 was more A3AR-selective than 2-ether-linked macrocycle 12 (both 5'-methylamides, human (h) A3AR affinities (Ki): 22.1 and 25.8 nM, respectively), with lower mouse A3AR affinities. Functional hA3AR comparison of two sets of open/closed analogues in β-arrestin2 and Gi/o protein assays showed certain signaling preferences divergent from reference agonist Cl-IB-MECA 1. The potencies of 1 at all three Gαi isoforms were slightly less than its hA3AR binding affinity (Ki: 1.4 nM), while the Gαi1 and Gαi2 potencies of macrocycle 12 were roughly an order of magnitude higher than its radioligand binding affinity. Gαi2-coupling was enhanced in macrocycle 12 (EC50 2.56 nM, ∼40% greater maximal efficacy than 1). Di-O-allyl precursor 18 cyclized to form 19, increasing the Gαi1 potency by 7.5-fold. The macrocycles 12 and 19 and their open precursors 11 and 18 potently stimulated β-arrestin2 recruitment, with EC50 values (nM) of 5.17, 4.36, 1.30, and 4.35, respectively, and with nearly 50% greater efficacy compared to 1. This example of macrocyclization altering the coupling pathways of small-molecule (nonpeptide) GPCR agonists is the first for potent and selective macrocyclic AR agonists. These initial macrocyclic derivatives can serve as a guide for the future design of macrocyclic AR agonists displaying unanticipated pharmacology.
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Affiliation(s)
- Dilip
K. Tosh
- Laboratory
of Bioorganic Chemistry, National Institute of Diabetes and Digestive
and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - Courtney L. Fisher
- Department
of Pharmacology & Toxicology and the Cardiovascular Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Veronica Salmaso
- Laboratory
of Bioorganic Chemistry, National Institute of Diabetes and Digestive
and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
- Molecular
Modeling Section, Department of Pharmaceutical and Pharmacological
Sciences, University of Padua, Padua 35131, Italy
| | - Tina C. Wan
- Department
of Pharmacology & Toxicology and the Cardiovascular Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Ryan G. Campbell
- Laboratory
of Bioorganic Chemistry, National Institute of Diabetes and Digestive
and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - Eric Chen
- Laboratory
of Bioorganic Chemistry, National Institute of Diabetes and Digestive
and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - Zhan-Guo Gao
- Laboratory
of Bioorganic Chemistry, National Institute of Diabetes and Digestive
and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - John A. Auchampach
- Department
of Pharmacology & Toxicology and the Cardiovascular Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Kenneth A. Jacobson
- Laboratory
of Bioorganic Chemistry, National Institute of Diabetes and Digestive
and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
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13
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Diao Y, Liu D, Ge H, Zhang R, Jiang K, Bao R, Zhu X, Bi H, Liao W, Chen Z, Zhang K, Wang R, Zhu L, Zhao Z, Hu Q, Li H. Macrocyclization of linear molecules by deep learning to facilitate macrocyclic drug candidates discovery. Nat Commun 2023; 14:4552. [PMID: 37507402 PMCID: PMC10382584 DOI: 10.1038/s41467-023-40219-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Interest in macrocycles as potential therapeutic agents has increased rapidly. Macrocyclization of bioactive acyclic molecules provides a potential avenue to yield novel chemical scaffolds, which can contribute to the improvement of the biological activity and physicochemical properties of these molecules. In this study, we propose a computational macrocyclization method based on Transformer architecture (which we name Macformer). Leveraging deep learning, Macformer explores the vast chemical space of macrocyclic analogues of a given acyclic molecule by adding diverse linkers compatible with the acyclic molecule. Macformer can efficiently learn the implicit relationships between acyclic and macrocyclic structures represented as SMILES strings and generate plenty of macrocycles with chemical diversity and structural novelty. In data augmentation scenarios using both internal ChEMBL and external ZINC test datasets, Macformer display excellent performance and generalisability. We showcase the utility of Macformer when combined with molecular docking simulations and wet lab based experimental validation, by applying it to the prospective design of macrocyclic JAK2 inhibitors.
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Affiliation(s)
- Yanyan Diao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Dandan Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Huan Ge
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Rongrong Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Kexin Jiang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Runhui Bao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Xiaoqian Zhu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Hongjie Bi
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Wenjie Liao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Ziqi Chen
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Kai Zhang
- Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai, 200062, China
| | - Rui Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Lili Zhu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Zhenjiang Zhao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Qiaoyu Hu
- Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai, 200062, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China.
- Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai, 200062, China.
- Lingang Laboratory, Shanghai, 200031, China.
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14
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Hosono Y, Uchida S, Shinkai M, Townsend CE, Kelly CN, Naylor MR, Lee HW, Kanamitsu K, Ishii M, Ueki R, Ueda T, Takeuchi K, Sugita M, Akiyama Y, Lokey SR, Morimoto J, Sando S. Amide-to-ester substitution as a stable alternative to N-methylation for increasing membrane permeability in cyclic peptides. Nat Commun 2023; 14:1416. [PMID: 36932083 PMCID: PMC10023679 DOI: 10.1038/s41467-023-36978-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
Naturally occurring peptides with high membrane permeability often have ester bonds on their backbones. However, the impact of amide-to-ester substitutions on the membrane permeability of peptides has not been directly evaluated. Here we report the effect of amide-to-ester substitutions on the membrane permeability and conformational ensemble of cyclic peptides related to membrane permeation. Amide-to-ester substitutions are shown to improve the membrane permeability of dipeptides and a model cyclic hexapeptide. NMR-based conformational analysis and enhanced sampling molecular dynamics simulations suggest that the conformational transition of the cyclic hexapeptide upon membrane permeation is differently influenced by an amide-to-ester substitution and an amide N-methylation. The effect of amide-to-ester substitution on membrane permeability of other cyclic hexapeptides, cyclic octapeptides, and a cyclic nonapeptide is also investigated to examine the scope of the substitution. Appropriate utilization of amide-to-ester substitution based on our results will facilitate the development of membrane-permeable peptides.
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Affiliation(s)
- Yuki Hosono
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Satoshi Uchida
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Moe Shinkai
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Chad E Townsend
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Colin N Kelly
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Matthew R Naylor
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Hsiau-Wei Lee
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Kayoko Kanamitsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Mayumi Ishii
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ryosuke Ueki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Koh Takeuchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Masatake Sugita
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
- Middle-Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Yutaka Akiyama
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
- Middle-Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
| | - Scott R Lokey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA.
| | - Jumpei Morimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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15
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Menke AJ, Gloor CJ, Claton LE, Mekhail MA, Pan H, Stewart MD, Green KN, Reibenspies JH, Pavan GM, Capelli R, Simanek EE. A Model for the Rapid Assessment of Solution Structures for 24-Atom Macrocycles: The Impact of β-Branched Amino Acids on Conformation. J Org Chem 2023; 88:2692-2702. [PMID: 36780253 PMCID: PMC10903118 DOI: 10.1021/acs.joc.2c01984] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Experiment and computation are used to develop a model to rapidly predict solution structures of macrocycles sharing the same Murcko framework. These 24-atom triazine macrocycles result from the quantitative dimerization of identical monomers presenting a hydrazine group and an acetal tethered to an amino acid linker. Monomers comprising glycine and the β-branched amino acids threonine, valine, and isoleucine yield macrocycles G-G, T-T, V-V, and I-I, respectively. Elements common to all members of the framework include the efficiency of macrocyclization (quantitative), the solution- and solid-state structures (folded), the site of protonation (opposite the auxiliary dimethylamine group), the geometry of the hydrazone (E), the C2 symmetry of the subunits (conserved), and the rotamer state adopted. In aggregate, the data reveal metrics predictive of the three-dimensional solution structure that derive from the fingerprint region of the 1D 1H spectrum and a network of rOes from a single resonance. The metrics also afford delineation of more nuanced structural features that allow subpopulations to be identified among the members of the framework. Well-tempered metadynamics provides free energy surfaces and population distributions of these macrocycles. The areas of the free energy surface decrease with increasing steric bulk (G-G > V-V ∼ T-T > I-I). In addition, the surfaces are increasingly isoenergetic with decreasing steric bulk (G-G > V-V ∼ T-T > I-I).
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Affiliation(s)
- Alexander J Menke
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Camryn J Gloor
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Liam E Claton
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Magy A Mekhail
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Hongjun Pan
- Department of Chemistry, University of North Texas, Denton, Texas 76203, United States
| | - Mikaela D Stewart
- Department of Biology, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Kayla N Green
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Joseph H Reibenspies
- Department of Chemistry, Texas A&M University, College Station, Texas 77845, United States
| | - Giovanni M Pavan
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano, Viganello, 6962 Lugano, Switzerland
- Department of Applied Science and Technology, Politecnico di Torino, 10129 Torino, Italy
| | - Riccardo Capelli
- Department of Biosciences, Université degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Eric E Simanek
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
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16
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Linker S, Schellhaas C, Kamenik AS, Veldhuizen MM, Waibl F, Roth HJ, Fouché M, Rodde S, Riniker S. Lessons for Oral Bioavailability: How Conformationally Flexible Cyclic Peptides Enter and Cross Lipid Membranes. J Med Chem 2023; 66:2773-2788. [PMID: 36762908 PMCID: PMC9969412 DOI: 10.1021/acs.jmedchem.2c01837] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Indexed: 02/11/2023]
Abstract
Cyclic peptides extend the druggable target space due to their size, flexibility, and hydrogen-bonding capacity. However, these properties impact also their passive membrane permeability. As the "journey" through membranes cannot be monitored experimentally, little is known about the underlying process, which hinders rational design. Here, we use molecular simulations to uncover how cyclic peptides permeate a membrane. We show that side chains can act as "molecular anchors", establishing the first contact with the membrane and enabling insertion. Once inside, the peptides are positioned between headgroups and lipid tails─a unique polar/apolar interface. Only one of two distinct orientations at this interface allows for the formation of the permeable "closed" conformation. In the closed conformation, the peptide crosses to the lower leaflet via another "anchoring" and flipping mechanism. Our findings provide atomistic insights into the permeation process of flexible cyclic peptides and reveal design considerations for each step of the process.
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Affiliation(s)
- Stephanie
M. Linker
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Christian Schellhaas
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Anna S. Kamenik
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Mac M. Veldhuizen
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Franz Waibl
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Hans-Jörg Roth
- Novartis
Institutes for BioMedical Research, Novartis
Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Marianne Fouché
- Novartis
Institutes for BioMedical Research, Novartis
Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Stephane Rodde
- Novartis
Institutes for BioMedical Research, Novartis
Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Sereina Riniker
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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17
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Lasso-grafted designer cytokines. Nat Biomed Eng 2023; 7:89-91. [PMID: 36424466 DOI: 10.1038/s41551-022-00974-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Sakai K, Sugano-Nakamura N, Mihara E, Rojas-Chaverra NM, Watanabe S, Sato H, Imamura R, Voon DCC, Sakai I, Yamasaki C, Tateno C, Shibata M, Suga H, Takagi J, Matsumoto K. Designing receptor agonists with enhanced pharmacokinetics by grafting macrocyclic peptides into fragment crystallizable regions. Nat Biomed Eng 2023; 7:164-176. [PMID: 36344661 PMCID: PMC9991925 DOI: 10.1038/s41551-022-00955-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 09/26/2022] [Indexed: 11/09/2022]
Abstract
Short half-lives in circulation and poor transport across the blood-brain barrier limit the utility of cytokines and growth factors acting as receptor agonists. Here we show that surrogate receptor agonists with longer half-lives in circulation and enhanced transport rates across the blood-brain barrier can be generated by genetically inserting macrocyclic peptide pharmacophores into the structural loops of the fragment crystallizable (Fc) region of a human immunoglobulin. We used such 'lasso-grafting' approach, which preserves the expression levels of the Fc region and its affinity for the neonatal Fc receptor, to generate Fc-based protein scaffolds with macrocyclic peptides binding to the receptor tyrosine protein kinase Met. The Met agonists dimerized Met, inducing biological responses that were similar to those induced by its natural ligand. Moreover, lasso-grafting of the Fc region of the mouse anti-transferrin-receptor antibody with Met-binding macrocyclic peptides enhanced the accumulation of the resulting Met agonists in brain parenchyma in mice. Lasso-grafting may allow for designer protein therapeutics with enhanced stability and pharmacokinetics.
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Affiliation(s)
- Katsuya Sakai
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa, Japan.
- WPI-Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan.
| | - Nozomi Sugano-Nakamura
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Suita, Japan
| | - Emiko Mihara
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Suita, Japan
| | | | - Sayako Watanabe
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Suita, Japan
| | - Hiroki Sato
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
- Tumor Microenvironment Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Ryu Imamura
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
- WPI-Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Dominic Chih-Cheng Voon
- Inflammation and Epithelial Plasticity Unit, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
- Cancer Model Research Innovative Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Itsuki Sakai
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Chihiro Yamasaki
- Research and Development Department, PhoenixBio Co. Ltd, Higashihiroshima, Japan
| | - Chise Tateno
- Research and Development Department, PhoenixBio Co. Ltd, Higashihiroshima, Japan
| | - Mikihiro Shibata
- WPI-Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
- High-speed AFM for Biological Application Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Junichi Takagi
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Suita, Japan.
| | - Kunio Matsumoto
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa, Japan.
- WPI-Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan.
- Tumor Microenvironment Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan.
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19
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Ikeda K, Maezawa Y, Yonezawa T, Shimizu Y, Tashiro T, Kanai S, Sugaya N, Masuda Y, Inoue N, Niimi T, Masuya K, Mizuguchi K, Furuya T, Osawa M. DLiP-PPI library: An integrated chemical database of small-to-medium-sized molecules targeting protein-protein interactions. Front Chem 2023; 10:1090643. [PMID: 36700083 PMCID: PMC9868583 DOI: 10.3389/fchem.2022.1090643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 12/09/2022] [Indexed: 01/11/2023] Open
Abstract
Protein-protein interactions (PPIs) are recognized as important targets in drug discovery. The characteristics of molecules that inhibit PPIs differ from those of small-molecule compounds. We developed a novel chemical library database system (DLiP) to design PPI inhibitors. A total of 32,647 PPI-related compounds are registered in the DLiP. It contains 15,214 newly synthesized compounds, with molecular weight ranging from 450 to 650, and 17,433 active and inactive compounds registered by extracting and integrating known compound data related to 105 PPI targets from public databases and published literature. Our analysis revealed that the compounds in this database contain unique chemical structures and have physicochemical properties suitable for binding to the protein-protein interface. In addition, advanced functions have been integrated with the web interface, which allows users to search for potential PPI inhibitor compounds based on types of protein-protein interfaces, filter results by drug-likeness indicators important for PPI targeting such as rule-of-4, and display known active and inactive compounds for each PPI target. The DLiP aids the search for new candidate molecules for PPI drug discovery and is available online (https://skb-insilico.com/dlip).
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Affiliation(s)
- Kazuyoshi Ikeda
- HPC—and AI-driven Drug Development Platform Division, Center for Computational Science, Yokohama, Kanagawa, Japan,Division of Physics for Life Functions, Keio University Faculty of Pharmacy, Tokyo, Japan,*Correspondence: Kazuyoshi Ikeda,
| | | | - Tomoki Yonezawa
- Division of Physics for Life Functions, Keio University Faculty of Pharmacy, Tokyo, Japan
| | - Yugo Shimizu
- Division of Physics for Life Functions, Keio University Faculty of Pharmacy, Tokyo, Japan
| | | | | | | | | | - Naoko Inoue
- PeptiDream Inc., Chiyoda-Ku, Kanagawa, Japan
| | | | | | - Kenji Mizuguchi
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan,Institute for Protein Research, Osaka University, Osaka, Japan
| | | | - Masanori Osawa
- Division of Physics for Life Functions, Keio University Faculty of Pharmacy, Tokyo, Japan
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20
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Zhao Z, Dong R, Cui K, You Q, Jiang Z. An updated patent review of Nrf2 activators (2020-present). Expert Opin Ther Pat 2023; 33:29-49. [PMID: 36800917 DOI: 10.1080/13543776.2023.2178299] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
INTRODUCTION The nuclear factor erythroid 2-related factor 2 (Nrf2) is a pivotal transcription factor that controls the expression of numerous cytoprotective genes and regulates cellular defense system against oxidative insults. Thus, activating the Nrf2 pathway is a promising strategy for the treatment of various chronic diseases characterized by oxidative stress. AREAS COVERED This review first discusses the biological effects of Nrf2 and the regulatory mechanism of Kelch-like ECH-associated protein 1-Nrf2-antioxidant response element (Keap1-Nrf2-ARE) pathway. Then, Nrf2 activators (2020-present) are summarized based on the mechanism of action. The case studies consist of chemical structures, biological activities, structural optimization, and clinical development. EXPERT OPINION Extensive efforts have been devoted to developing novel Nrf2 activators with improved potency and drug-like properties. These Nrf2 activators have exhibited beneficial effects in in vitro and in vivo models of oxidative stress-related chronic diseases. However, some specific problems, such as target selectivity and brain blood barrier (BBB) permeability, still need to be addressed in the future.
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Affiliation(s)
- Ziquan Zhao
- State Key Laboratory of Natural Medicines, and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Ruitian Dong
- State Key Laboratory of Natural Medicines, and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Keni Cui
- State Key Laboratory of Natural Medicines, and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Qidong You
- State Key Laboratory of Natural Medicines, and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Zhengyu Jiang
- State Key Laboratory of Natural Medicines, and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
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21
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Yang J, Zhu Q, Wu Y, Qu X, Liu H, Jiang B, Ge D, Song X. Utilization of macrocyclic peptides to target protein-protein interactions in cancer. Front Oncol 2022; 12:992171. [PMID: 36465350 PMCID: PMC9714258 DOI: 10.3389/fonc.2022.992171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/24/2022] [Indexed: 07/30/2023] Open
Abstract
Protein-protein interactions (PPIs) play vital roles in normal cellular processes. Dysregulated PPIs are involved in the process of various diseases, including cancer. Thus, these PPIs may serve as potential therapeutic targets in cancer treatment. However, despite rapid advances in small-molecule drugs and biologics, it is still hard to target PPIs, especially for those intracellular PPIs. Macrocyclic peptides have gained growing attention for their therapeutic properties in targeting dysregulated PPIs. Macrocyclic peptides have some unique features, such as moderate sizes, high selectivity, and high binding affinities, which make them good drug candidates. In addition, some oncology macrocyclic peptide drugs have been approved by the US Food and Drug Administration (FDA) for clinical use. Here, we reviewed the recent development of macrocyclic peptides in cancer treatment. The opportunities and challenges were also discussed to inspire new perspectives.
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Affiliation(s)
- Jiawen Yang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Qiaoliang Zhu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yifan Wu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojuan Qu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haixia Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Di Ge
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaoling Song
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
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22
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Schaub J, Zander J, Zielesny A, Steinbeck C. Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK). J Cheminform 2022; 14:79. [PMID: 36357931 PMCID: PMC9650898 DOI: 10.1186/s13321-022-00656-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 10/30/2022] [Indexed: 11/12/2022] Open
Abstract
The concept of molecular scaffolds as defining core structures of organic molecules is utilised in many areas of chemistry and cheminformatics, e.g. drug design, chemical classification, or the analysis of high-throughput screening data. Here, we present Scaffold Generator, a comprehensive open library for the generation, handling, and display of molecular scaffolds, scaffold trees and networks. The new library is based on the Chemistry Development Kit (CDK) and highly customisable through multiple settings, e.g. five different structural framework definitions are available. For display of scaffold hierarchies, the open GraphStream Java library is utilised. Performance snapshots with natural products (NP) from the COCONUT (COlleCtion of Open Natural prodUcTs) database and drug molecules from DrugBank are reported. The generation of a scaffold network from more than 450,000 NP can be achieved within a single day.
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Affiliation(s)
- Jonas Schaub
- grid.9613.d0000 0001 1939 2794Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessing Strasse 8, 07743 Jena, Germany
| | - Julian Zander
- grid.454254.60000 0004 0647 4362Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665 Recklinghausen, Germany
| | - Achim Zielesny
- grid.454254.60000 0004 0647 4362Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665 Recklinghausen, Germany
| | - Christoph Steinbeck
- grid.9613.d0000 0001 1939 2794Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessing Strasse 8, 07743 Jena, Germany
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23
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Multicomponent coupling and macrocyclization enabled by Rh(III)-catalyzed dual C–H activation: Macrocyclic oxime inhibitor of influenza H1N1. Chem 2022. [DOI: 10.1016/j.chempr.2022.10.019] [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]
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24
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Capelli R, Menke AJ, Pan H, Janesko BG, Simanek EE, Pavan GM. Well-Tempered Metadynamics Simulations Predict the Structural and Dynamic Properties of a Chiral 24-Atom Macrocycle in Solution. ACS OMEGA 2022; 7:30291-30296. [PMID: 36061685 PMCID: PMC9434777 DOI: 10.1021/acsomega.2c03536] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Inspired by therapeutic potential, the molecular engineering of macrocycles is garnering increased interest. Exercising control with design, however, is challenging due to the dynamic behavior that these molecules must demonstrate in order to be bioactive. Herein, the value of metadynamics simulations is demonstrated: the free-energy surfaces calculated reveal folded and flattened accessible conformations of a 24-atom macrocycle separated by barriers of ∼6 kT under experimentally relevant conditions. Simulations reveal that the dominant conformer is folded-an observation consistent with a solid-state structure determined by X-ray crystallography and a network of rOes established by 1H NMR. Simulations suggest that the macrocycle exists as a rapidly interconverting pair of enantiomeric, folded structures. Experimentally, 1H NMR shows a single species at room temperature. However, at lower temperature, the interconversion rate between these enantiomers becomes markedly slower, resulting in the decoalescence of enantiotopic methylene protons into diastereotopic, distinguishable resonances due to the persistence of conformational chirality. The emergence of conformational chirality provides critical experimental support for the simulations, revealing the dynamic nature of the scaffold-a trait deemed critical for oral bioactivity.
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Affiliation(s)
- Riccardo Capelli
- Department
of Applied Science and Technology, Politecnico
di Torino, 10129 Torino, Italy
| | - Alexander J. Menke
- Department
of Chemistry & Biochemistry, Texas Christian
University, Fort Worth, Texas 76129, United States
| | - Hongjun Pan
- Department
of Chemistry, University of North Texas, Denton, Texas 76129, United States
| | - Benjamin G. Janesko
- Department
of Chemistry & Biochemistry, Texas Christian
University, Fort Worth, Texas 76129, United States
| | - Eric E. Simanek
- Department
of Chemistry & Biochemistry, Texas Christian
University, Fort Worth, Texas 76129, United States
| | - Giovanni M. Pavan
- Department
of Applied Science and Technology, Politecnico
di Torino, 10129 Torino, Italy
- Department
of Innovative Technologies, University of
Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano, 6962 Lugano-Viganello, Switzerland
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25
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Pei D. Designing Cell-Permeable Peptide Therapeutics That Enter the Cell by Endocytosis. ACS SYMPOSIUM SERIES. AMERICAN CHEMICAL SOCIETY 2022; 1417:179-197. [PMID: 37621949 PMCID: PMC10448808 DOI: 10.1021/bk-2022-1417.ch007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
Intracellular protein-protein interactions (PPIs) represent a large class of exciting as well as challenging drug targets for traditional drug modalities (i.e., small molecules and biologics). Peptides (especially cyclic peptides) have proven highly effective as PPI inhibitors in vitro but are generally impermeable to the cell membrane. The recent discovery of a family of highly active cyclic cell-penetrating peptides (CPPs) has enabled the delivery of peptides into the cytosol of mammalian cells at therapeutically relevant levels. This chapter describes the various strategies that have been developed to conjugate or integrate different types of peptidyl cargoes (e.g., linear, cyclic, and stapled peptides) with cyclic CPPs to generate cell-permeable, metabolically stable, and biologically active macrocyclic peptides against intracellular targets including PPIs.
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Affiliation(s)
- Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
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26
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Chen Y, Rosenkranz C, Hirte S, Kirchmair J. Ring systems in natural products: structural diversity, physicochemical properties, and coverage by synthetic compounds. Nat Prod Rep 2022; 39:1544-1556. [PMID: 35708009 DOI: 10.1039/d2np00001f] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: up to 2021The structural core of most small-molecule drugs is formed by a ring system, often derived from natural products. However, despite the importance of natural product ring systems in bioactive small molecules, there is still a lack of a comprehensive overview and understanding of natural product ring systems and how their full potential can be harnessed in drug discovery and related fields. Herein, we present a comprehensive cheminformatic analysis of the structural and physicochemical properties of 38 662 natural product ring systems, and the coverage of natural product ring systems by readily purchasable, synthetic compounds that are commonly explored in virtual screening and high-throughput screening. The analysis stands out by the use of comprehensive, curated data sets, the careful consideration of stereochemical information, and a robust analysis of the 3D molecular shape and electrostatic properties of ring systems. Among the key findings of this study are the facts that only about 2% of the ring systems observed in NPs are present in approved drugs but that approximately one in two NP ring systems are represented by ring systems with identical or related 3D shape and electrostatic properties in compounds that are typically used in (high-throughput) screening.
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Affiliation(s)
- Ya Chen
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria.
| | - Cara Rosenkranz
- Center for Bioinformatics (ZBH), Universität Hamburg, 20146 Hamburg, Germany
| | - Steffen Hirte
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria. .,Vienna Doctoral School of Pharmaceutical, Nutritional and Sport Sciences (PhaNuSpo), University of Vienna, 1090 Vienna, Austria
| | - Johannes Kirchmair
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria.
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27
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Garrigou M, Sauvagnat B, Duggal R, Boo N, Gopal P, Johnston JM, Partridge A, Sawyer T, Biswas K, Boyer N. Accelerated Identification of Cell Active KRAS Inhibitory Macrocyclic Peptides using Mixture Libraries and Automated Ligand Identification System (ALIS) Technology. J Med Chem 2022; 65:8961-8974. [PMID: 35707970 PMCID: PMC9289880 DOI: 10.1021/acs.jmedchem.2c00154] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Macrocyclic
peptides can disrupt previously intractable protein–protein
interactions (PPIs) relevant to oncology targets such as KRAS. Early
hits often lack cellular activity and require meticulous improvement
of affinity, permeability, and metabolic stability to become viable
leads. We have validated the use of the Automated Ligand Identification
System (ALIS) to screen oncogenic KRASG12D (GDP) against
mass-encoded mini-libraries of macrocyclic peptides and accelerate
our structure–activity relationship (SAR) exploration. These
mixture libraries were generated by premixing various unnatural amino
acids without the need for the laborious purification of individual
peptides. The affinity ranking of the peptide sequences provided SAR-rich
data sets that led to the selection of novel potency-enhancing substitutions
in our subsequent designs. Additional stability and permeability optimization
resulted in the identification of peptide 7 that inhibited
pERK activity in a pancreatic cancer cell line. More broadly, this
methodology offers an efficient alternative to accelerate the fastidious
hit-to-lead optimization of PPI peptide inhibitors.
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Affiliation(s)
| | | | - Ruchia Duggal
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Nicole Boo
- MSD International, Singapore 138665, Singapore
| | - Pooja Gopal
- MSD International, Singapore 138665, Singapore
| | | | | | - Tomi Sawyer
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Kaustav Biswas
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Nicolas Boyer
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
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28
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Marine Cyclic Peptides: Antimicrobial Activity and Synthetic Strategies. Mar Drugs 2022; 20:md20060397. [PMID: 35736200 PMCID: PMC9230156 DOI: 10.3390/md20060397] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/06/2022] [Accepted: 06/13/2022] [Indexed: 01/29/2023] Open
Abstract
Oceans are a rich source of structurally unique bioactive compounds from the perspective of potential therapeutic agents. Marine peptides are a particularly interesting group of secondary metabolites because of their chemistry and wide range of biological activities. Among them, cyclic peptides exhibit a broad spectrum of antimicrobial activities, including against bacteria, protozoa, fungi, and viruses. Moreover, there are several examples of marine cyclic peptides revealing interesting antimicrobial activities against numerous drug-resistant bacteria and fungi, making these compounds a very promising resource in the search for novel antimicrobial agents to revert multidrug-resistance. This review summarizes 174 marine cyclic peptides with antibacterial, antifungal, antiparasitic, or antiviral properties. These natural products were categorized according to their sources—sponges, mollusks, crustaceans, crabs, marine bacteria, and fungi—and chemical structure—cyclic peptides and depsipeptides. The antimicrobial activities, including against drug-resistant microorganisms, unusual structural characteristics, and hits more advanced in (pre)clinical studies, are highlighted. Nocathiacins I–III (91–93), unnarmicins A (114) and C (115), sclerotides A (160) and B (161), and plitidepsin (174) can be highlighted considering not only their high antimicrobial potency in vitro, but also for their promising in vivo results. Marine cyclic peptides are also interesting models for molecular modifications and/or total synthesis to obtain more potent compounds, with improved properties and in higher quantity. Solid-phase Fmoc- and Boc-protection chemistry is the major synthetic strategy to obtain marine cyclic peptides with antimicrobial properties, and key examples are presented guiding microbiologist and medicinal chemists to the discovery of new antimicrobial drug candidates from marine sources.
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29
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Charitou V, van Keulen SC, Bonvin AMJJ. Cyclization and Docking Protocol for Cyclic Peptide-Protein Modeling Using HADDOCK2.4. J Chem Theory Comput 2022; 18:4027-4040. [PMID: 35652781 PMCID: PMC9202357 DOI: 10.1021/acs.jctc.2c00075] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An emerging class of therapeutic molecules are cyclic peptides with over 40 cyclic peptide drugs currently in clinical use. Their mode of action is, however, not fully understood, impeding rational drug design. Computational techniques could positively impact their design, but modeling them and their interactions remains challenging due to their cyclic nature and their flexibility. This study presents a step-by-step protocol for generating cyclic peptide conformations and docking them to their protein target using HADDOCK2.4. A dataset of 30 cyclic peptide-protein complexes was used to optimize both cyclization and docking protocols. It supports peptides cyclized via an N- and C-terminus peptide bond and/or a disulfide bond. An ensemble of cyclic peptide conformations is then used in HADDOCK to dock them onto their target protein using knowledge of the binding site on the protein side to drive the modeling. The presented protocol predicts at least one acceptable model according to the critical assessment of prediction of interaction criteria for each complex of the dataset when the top 10 HADDOCK-ranked single structures are considered (100% success rate top 10) both in the bound and unbound docking scenarios. Moreover, its performance in both bound and fully unbound docking is similar to the state-of-the-art software in the field, Autodock CrankPep. The presented cyclization and docking protocol should make HADDOCK a valuable tool for rational cyclic peptide-based drug design and high-throughput screening.
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Affiliation(s)
- Vicky Charitou
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science─Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Siri C van Keulen
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science─Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Alexandre M J J Bonvin
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science─Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
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30
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Abstract
Peptides have traditionally been perceived as poor drug candidates due to unfavorable characteristics mainly regarding their pharmacokinetic behavior, including plasma stability, membrane permeability and circulation half-life. Nonetheless, in recent years, general strategies to tackle those shortcomings have been established, and peptides are subsequently gaining increasing interest as drugs due to their unique ability to combine the advantages of antibodies and small molecules. Macrocyclic peptides are a special focus of drug development efforts due to their ability to address so called ‘undruggable’ targets characterized by large and flat protein surfaces lacking binding pockets. Here, the main strategies developed to date for adapting peptides for clinical use are summarized, which may soon help usher in an age highly shaped by peptide-based therapeutics. Nonetheless, limited membrane permeability is still to overcome before peptide therapeutics will be broadly accepted.
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31
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Abstract
Being able to effectively target RNA with potent ligands will open up a large number of potential therapeutic options. The knowledge on how to achieve this is ever expanding but an important question that remains open is what chemical matter is suitable to achieve this goal. The high flexibility of an RNA as well as its more limited chemical diversity and featureless binding sites can be difficult to target selectively but can be addressed by well-designed cyclic peptides. In this review we will provide an overview of reported cyclic peptide ligands for therapeutically relevant RNA targets and discuss the methods used to discover them. We will also provide critical insights into the properties required for potent and selective interaction and suggestions on how to assess these parameters. The use of cyclic peptides to target RNA is still in its infancy but the lessons learned from past examples can be adopted for the development of novel potent and selective ligands.
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Affiliation(s)
- Sunit Pal
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Peter 't Hart
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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32
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Trobe M, Vareka M, Schreiner T, Dobrounig P, Doler C, Holzinger EB, Steinegger A, Breinbauer R. A Modular Synthesis of Teraryl-Based α-Helix Mimetics, Part 3: Iodophenyltriflate Core Fragments Featuring Side Chains of Proteinogenic Amino Acids. European J Org Chem 2022; 2022:e202101278. [PMID: 35910459 PMCID: PMC9306992 DOI: 10.1002/ejoc.202101278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/08/2022] [Indexed: 11/18/2022]
Abstract
Teraryl-based α-helix mimetics have proven to be useful compounds for the inhibition of protein-protein interactions (PPI). We have developed a modular and flexible approach for the synthesis of teraryl-based α-helix mimetics using a benzene core unit featuring two leaving groups of differentiated reactivity in the Pd-catalyzed cross-coupling used for teraryl assembly. In previous publications we have introduced the methodology of 4-iodophenyltriflates decorated with the side chains of some of the proteinogenic amino acids. We herein report the core fragments corresponding to the previously missing amino acids Arg, Asn, Asp, Met, Trp and Tyr. Therefore, our set now encompasses all relevant amino acid analogues with the exception of His. In order to be compatible with the triflate moiety, some of the nucleophilic side chains had to be provided in a protected form to serve as stable building blocks. Additionally, cross-coupling procedures for the assembly of teraryls were investigated.
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Affiliation(s)
- Melanie Trobe
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
| | - Martin Vareka
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
| | - Till Schreiner
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
| | - Patrick Dobrounig
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
| | - Carina Doler
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
| | - Ella B. Holzinger
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
| | - Andreas Steinegger
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
| | - Rolf Breinbauer
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
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33
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Olivet J, Maseko SB, Volkov AN, Salehi-Ashtiani K, Das K, Calderwood MA, Twizere JC, Gorgulla C. A systematic approach to identify host targets and rapidly deliver broad-spectrum antivirals. Mol Ther 2022; 30:1797-1800. [PMID: 35231394 PMCID: PMC8884476 DOI: 10.1016/j.ymthe.2022.02.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/10/2021] [Accepted: 02/11/2022] [Indexed: 11/24/2022] Open
Affiliation(s)
- Julien Olivet
- Structural Biology Unit, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research and Department of Microbiology, Immunology and Transplantation, Catholic University of Leuven (KU Leuven), Leuven, Belgium; Laboratory of Viral Interactomes Networks, Unit of Molecular Biology of Diseases, Interdisciplinary Cluster for Applied Genoproteomics (GIGA Institute), University of Liège, Liège, Belgium
| | - Sibusiso B Maseko
- Laboratory of Viral Interactomes Networks, Unit of Molecular Biology of Diseases, Interdisciplinary Cluster for Applied Genoproteomics (GIGA Institute), University of Liège, Liège, Belgium
| | - Alexander N Volkov
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium; Jean Jeener NMR Centre, Free University of Brussels (VUB), Brussels, Belgium
| | | | - Kalyan Das
- Structural Biology Unit, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research and Department of Microbiology, Immunology and Transplantation, Catholic University of Leuven (KU Leuven), Leuven, Belgium
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | - Jean-Claude Twizere
- Laboratory of Viral Interactomes Networks, Unit of Molecular Biology of Diseases, Interdisciplinary Cluster for Applied Genoproteomics (GIGA Institute), University of Liège, Liège, Belgium; Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro Bio-tech, University of Liège, Gembloux, Belgium.
| | - Christoph Gorgulla
- Department of Cancer Biology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA; Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA.
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34
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Bi T, Xu Y, Xu X, Tang B, Yang Q, Zang Y, Lin Z, Li J, Yang W. Natural scaffolds-inspired synthesis of CF3-substituted macrolides enabled by Rh-catalyzed C–H alkylation macrocyclization. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.10.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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35
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Yonezawa H, Ikeda A, Takahashi R, Endo H, Sugawara Y, Goto M, Kanno M, Ogawa S, Nakamura K, Ujiie H, Iwatsuki M, Hirose T, Sunazuka T, Uehara Y, Nishiya N. Ivermectin represses Wnt/β-catenin signaling by binding to TELO2, a regulator of phosphatidylinositol 3-kinase-related kinases. iScience 2022; 25:103912. [PMID: 35530256 PMCID: PMC9072907 DOI: 10.1016/j.isci.2022.103912] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 12/10/2021] [Accepted: 02/08/2022] [Indexed: 11/19/2022] Open
Abstract
Ivermectin (IVM), an avermectin-derivative anthelmintic, specifically binds to glutamate-gated chloride ion channels (GluCls), causing paralysis in invertebrates. IVM also exhibits other biological activities such as Wnt/β-catenin pathway inhibition in vertebrates that do not possess GluCls. This study showed that affinity purification using immobilized IVM B1a isolated TELO2, a cofactor of phosphatidylinositol 3-kinase-related kinases (PIKKs), as a specific IVM B1a-binding protein. TELO2 knockdown reduced cytoplasmic β-catenin and the transcriptional activation of β-catenin/TCF. IVM B1a bound to TELO2 through the C-terminal α-helix, in which mutations conferred IVM resistance. IVM reduced the TELO2 and PIKK protein levels and the AKT and S6 kinase phosphorylation levels. The inhibition of mTOR kinase reduced the cytoplasmic β-catenin level. Therefore, IVM binds to TELO2, inhibiting PIKKs and reducing the cytoplasmic β-catenin level. In conclusion, our data indicate TELO2 as a druggable target for human diseases involving abnormalities of the Wnt/β-catenin pathway and PIKKs, including mTOR. Ivermectin is a chemical suppressor of the eyeless phenotype in zebrafish embryos Ivermectin physically interacts with TELO2 TELO2 mediates Wnt/β-catenin signaling inhibition by ivermectin Ivermectin reduces the PIKK protein levels and downstream signaling
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Affiliation(s)
- Honami Yonezawa
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, Iwate Medical University School of Pharmacy, Shiwa-gun, Yahaba-cho, Iwate 028-3694, Japan
| | - Akari Ikeda
- Ōmura Satoshi Memorial Institute and Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Minato-ku 108-8641, Japan
| | - Ryo Takahashi
- Ōmura Satoshi Memorial Institute and Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Minato-ku 108-8641, Japan
| | - Haruka Endo
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, Iwate Medical University School of Pharmacy, Shiwa-gun, Yahaba-cho, Iwate 028-3694, Japan
| | - Yasuyo Sugawara
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, Iwate Medical University School of Pharmacy, Shiwa-gun, Yahaba-cho, Iwate 028-3694, Japan
| | - Mikako Goto
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, Iwate Medical University School of Pharmacy, Shiwa-gun, Yahaba-cho, Iwate 028-3694, Japan
| | - Mirute Kanno
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, Iwate Medical University School of Pharmacy, Shiwa-gun, Yahaba-cho, Iwate 028-3694, Japan
| | - Sosuke Ogawa
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, Iwate Medical University School of Pharmacy, Shiwa-gun, Yahaba-cho, Iwate 028-3694, Japan
| | - Karin Nakamura
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, Iwate Medical University School of Pharmacy, Shiwa-gun, Yahaba-cho, Iwate 028-3694, Japan
| | - Haruki Ujiie
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, Iwate Medical University School of Pharmacy, Shiwa-gun, Yahaba-cho, Iwate 028-3694, Japan
| | - Masato Iwatsuki
- Ōmura Satoshi Memorial Institute and Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Minato-ku 108-8641, Japan
| | - Tomoyasu Hirose
- Ōmura Satoshi Memorial Institute and Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Minato-ku 108-8641, Japan
| | - Toshiaki Sunazuka
- Ōmura Satoshi Memorial Institute and Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Minato-ku 108-8641, Japan
| | - Yoshimasa Uehara
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, Iwate Medical University School of Pharmacy, Shiwa-gun, Yahaba-cho, Iwate 028-3694, Japan
| | - Naoyuki Nishiya
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, Iwate Medical University School of Pharmacy, Shiwa-gun, Yahaba-cho, Iwate 028-3694, Japan
- Corresponding author
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36
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Buyanova M, Pei D. Targeting intracellular protein-protein interactions with macrocyclic peptides. Trends Pharmacol Sci 2022; 43:234-248. [PMID: 34911657 PMCID: PMC8840965 DOI: 10.1016/j.tips.2021.11.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/23/2021] [Accepted: 11/09/2021] [Indexed: 01/07/2023]
Abstract
Intracellular protein-protein interactions (PPIs) are challenging targets for traditional drug modalities. Macrocyclic peptides (MPs) prove highly effective PPI inhibitors in vitro and can be rapidly discovered against PPI targets by rational design or screening combinatorial libraries but are generally impermeable to the cell membrane. Recent advances in MP science and technology are allowing for the development of 'drug-like' MPs that potently and specifically modulate intracellular PPI targets in cell culture and animal models. In this review, we highlight recent progress in generating cell-permeable MPs that enter the mammalian cell by passive diffusion, endocytosis followed by endosomal escape, or as-yet unknown mechanisms.
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Affiliation(s)
- Marina Buyanova
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA.
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37
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Ali M, Latif A, Bibi S, Ali S, Ali A, Ahmad M, Ahmad R, Khan AA, Khan A, Ribeiro AI, Al‐Harrasi A, Farooq U. Facile Synthesis of the Shape‐Persistent 4‐Hydroxybenzaldehyde Based Macrocycles and Exploration of their Key Electronic Properties: An Experimental and DFT Approach. ChemistrySelect 2022. [DOI: 10.1002/slct.202102715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mumtaz Ali
- Department of Chemistry University of Malakand Lower 18800 Khyber Pakhtunkhwa Pakistan
| | - Abdul Latif
- Department of Chemistry University of Malakand Lower 18800 Khyber Pakhtunkhwa Pakistan
| | - Saeeda Bibi
- Department of Chemistry University of Malakand Lower 18800 Khyber Pakhtunkhwa Pakistan
| | - Sardar Ali
- Department of Chemistry University of Malakand Lower 18800 Khyber Pakhtunkhwa Pakistan
| | - Akbar Ali
- Department of Chemistry Government College University Faisalabad Faisalabad 38000 Pakistan
| | - Manzoor Ahmad
- Department of Chemistry University of Malakand Lower 18800 Khyber Pakhtunkhwa Pakistan
| | - Rashid Ahmad
- Department of Chemistry University of Malakand Lower 18800 Khyber Pakhtunkhwa Pakistan
- Center for Computational Materials Science University of Malakand Dir Lower
| | - Adnan Ali Khan
- Department of Chemistry University of Malakand Lower 18800 Khyber Pakhtunkhwa Pakistan
- Center for Computational Materials Science University of Malakand Dir Lower
| | - Ajmal Khan
- Natural and Medical Sciences Research Center University of Nizwa PO Box 33, 616 Birkat Al Mauz Nizwa Oman
| | - Alany Ingrid Ribeiro
- Department of Chemistry Federal University of São Carlos Rod. Washington Luís, Km 265 São Carlos Brazil
| | - Ahmed Al‐Harrasi
- Natural and Medical Sciences Research Center University of Nizwa PO Box 33, 616 Birkat Al Mauz Nizwa Oman
| | - Umar Farooq
- Department of Chemistry COMSATS University Islamabad Abbottabad Campus, KPK 22060 Islamabad 45550 Pakistan
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38
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Linker SM, Schellhaas C, Ries B, Roth HJ, Fouché M, Rodde S, Riniker S. Polar/apolar interfaces modulate the conformational behavior of cyclic peptides with impact on their passive membrane permeability. RSC Adv 2022; 12:5782-5796. [PMID: 35424539 PMCID: PMC8981571 DOI: 10.1039/d1ra09025a] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/10/2022] [Indexed: 02/01/2023] Open
Abstract
Cyclic peptides have the potential to vastly extend the scope of druggable proteins and lead to new therapeutics for currently untreatable diseases. However, cyclic peptides often suffer from poor bioavailability. To uncover design principles for permeable cyclic peptides, a promising strategy is to analyze the conformational dynamics of the peptides using molecular dynamics (MD) and Markov state models (MSMs). Previous MD studies have focused on the conformational dynamics in pure aqueous or apolar environments to rationalize membrane permeability. However, during the key steps of the permeation through the membrane, cyclic peptides are exposed to interfaces between polar and apolar regions. Recent studies revealed that these interfaces constitute the free energy minima of the permeation process. Thus, a deeper understanding of the behavior of cyclic peptides at polar/apolar interfaces is desired. Here, we investigate the conformational and kinetic behavior of cyclic decapeptides at a water/chloroform interface using unbiased MD simulations and MSMs. The distinct environments at the interface alter the conformational equilibrium as well as the interconversion kinetics of cyclic peptide conformations. For peptides with low population of the permeable conformation in aqueous solution, the polar/apolar interface facilitates the interconversion to the closed conformation, which is required for membrane permeation. Comparison to unbiased MD simulations with a POPC bilayer reveals that not only the conformations but also the orientations are relevant in a membrane system. These findings allow us to propose a permeability model that includes both 'prefolding' and 'non-prefolding' cyclic peptides - an extension that can lead to new design considerations for permeable cyclic peptides.
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Affiliation(s)
- Stephanie M Linker
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - Christian Schellhaas
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - Benjamin Ries
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - Hans-Jörg Roth
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus 4056 Basel Switzerland
| | - Marianne Fouché
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus 4056 Basel Switzerland
| | - Stephane Rodde
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus 4056 Basel Switzerland
| | - Sereina Riniker
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
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39
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Ellipyrones A-B, from oval bone cuttlefish Sepia elliptica: Antihyperglycemic γ-pyrone enclosed macrocyclic polyketides attenuate dipeptidyl peptidase-4 and carbolytic enzymes. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02846-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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40
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Bérubé C, Borgia A, Voyer N. Total synthesis of the macrocyclic peptide stylopeptide II using oxime resin. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.153677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Xu W, Brown LE, Porco JA. Divergent, C-C Bond Forming Macrocyclizations Using Modular Sulfonylhydrazone and Derived Substrates. J Org Chem 2021; 86:16485-16510. [PMID: 34730970 PMCID: PMC8783553 DOI: 10.1021/acs.joc.1c01848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A divergent approach to C-C bond forming macrocycle construction is described. Modular sulfonylhydrazone and derived pyridotriazole substrates with three key building blocks have been constructed and cyclized to afford diverse macrocyclic frameworks. Broad substrate scope and functional group tolerance have been demonstrated. In addition, site-selective postfunctionalization allowed for further diversification of macrocyclic cores.
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Affiliation(s)
- Wenqing Xu
- Department of Chemistry, Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts 02215, United States
| | - Lauren E. Brown
- Department of Chemistry, Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts 02215, United States
| | - John A. Porco
- Department of Chemistry, Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts 02215, United States
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42
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Shi M, Zhou X, Cai Y, Li P, Qin D, Yan X, Du M, Li S, Xu D. Inhibition mechanism of hydroxyproline-like small inhibitors to disorder HIF-VHL interaction by molecular dynamic simulations and binding free energy calculations. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2110198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Mingsong Shi
- State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xin Zhou
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Yao Cai
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Penghui Li
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Dengxue Qin
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Xinrong Yan
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Meng Du
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Shuo Li
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Dingguo Xu
- College of Chemistry, Sichuan University, Chengdu 610064, China
- Research Center for Material Genome Engineering, Sichuan University, Chengdu 610065, China
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43
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Richaud AD, Zhao G, Hobloss S, Roche SP. Folding in Place: Design of β-Strap Motifs to Stabilize the Folding of Hairpins with Long Loops. J Org Chem 2021; 86:13535-13547. [PMID: 34499510 PMCID: PMC8576641 DOI: 10.1021/acs.joc.1c01442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Despite their pivotal role in defining antibody affinity and protein function, β-hairpins harboring long noncanonical loops remain synthetically challenging because of the large entropic penalty associated with their conformational folding. Little is known about the contribution and impact of stabilizing motifs on the folding of β-hairpins with loops of variable length and plasticity. Here, we report a design of minimalist β-straps (strap = strand + cap) that offset the entropic cost of long-loop folding. The judicious positioning of noncovalent interactions (hydrophobic cluster and salt-bridge) within the novel 8-mer β-strap design RW(V/H)W···WVWE stabilizes hairpins with up to 10-residue loops of varying degrees of plasticity (Tm up to 52 °C; 88 ± 1% folded at 18 °C). This "hyper" thermostable β-strap outperforms the previous gold-standard technology of β-strand-β-cap (16-mer) and provides a foundation for producing new classes of long hairpins as a viable and practical alternative to macrocyclic peptides.
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Affiliation(s)
- Alexis D Richaud
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Guangkuan Zhao
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Samir Hobloss
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Stéphane P Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
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44
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Bechtler C, Lamers C. Macrocyclization strategies for cyclic peptides and peptidomimetics. RSC Med Chem 2021; 12:1325-1351. [PMID: 34447937 PMCID: PMC8372203 DOI: 10.1039/d1md00083g] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/01/2021] [Indexed: 12/12/2022] Open
Abstract
Peptides are a growing therapeutic class due to their unique spatial characteristics that can target traditionally "undruggable" protein-protein interactions and surfaces. Despite their advantages, peptides must overcome several key shortcomings to be considered as drug leads, including their high conformational flexibility and susceptibility to proteolytic cleavage. As a general approach for overcoming these challenges, macrocyclization of a linear peptide can usually improve these characteristics. Their synthetic accessibility makes peptide macrocycles very attractive, though traditional synthetic methods for macrocyclization can be challenging for peptides, especially for head-to-tail cyclization. This review provides an updated summary of the available macrocyclization chemistries, such as traditional lactam formation, azide-alkyne cycloadditions, ring-closing metathesis as well as unconventional cyclization reactions, and it is structured according to the obtained functional groups. Keeping peptide chemistry and screening in mind, the focus is given to reactions applicable in solution, on solid supports, and compatible with contemporary screening methods.
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Affiliation(s)
- Clément Bechtler
- Department Pharmaceutical Sciences, University of Basel Klingelbergstr. 50 4056 Basel Switzerland
| | - Christina Lamers
- Department Pharmaceutical Sciences, University of Basel Klingelbergstr. 50 4056 Basel Switzerland
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45
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Gironda-Martínez A, Donckele EJ, Samain F, Neri D. DNA-Encoded Chemical Libraries: A Comprehensive Review with Succesful Stories and Future Challenges. ACS Pharmacol Transl Sci 2021; 4:1265-1279. [PMID: 34423264 PMCID: PMC8369695 DOI: 10.1021/acsptsci.1c00118] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Indexed: 12/27/2022]
Abstract
DNA-encoded chemical libraries (DELs) represent a versatile and powerful technology platform for the discovery of small-molecule ligands to protein targets of biological and pharmaceutical interest. DELs are collections of molecules, individually coupled to distinctive DNA tags serving as amplifiable identification barcodes. Thanks to advances in DNA-compatible reactions, selection methodologies, next-generation sequencing, and data analysis, DEL technology allows the construction and screening of libraries of unprecedented size, which has led to the discovery of highly potent ligands, some of which have progressed to clinical trials. In this Review, we present an overview of diverse approaches for the generation and screening of DEL molecular repertoires. Recent success stories are described, detailing how novel ligands were isolated from DEL screening campaigns and were further optimized by medicinal chemistry. The goal of the Review is to capture some of the most recent developments in the field, while also elaborating on future challenges to further improve DEL technology as a therapeutic discovery platform.
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Affiliation(s)
| | | | - Florent Samain
- Philochem
AG, Libernstrasse 3, CH-8112 Otelfingen, Switzerland
| | - Dario Neri
- Department
of Chemistry and Applied Biosciences, Swiss
Federal Institute of Technology, CH-8093 Zürich, Switzerland
- Philogen
S.p.A, 53100 Siena, Italy
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46
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Jiang Y, Liu S, Tian G, Cheung HJH, Li X, Li XD. Concise solid-phase synthesis enables derivatisation of YEATS domain cyclopeptide inhibitors for improved cellular uptake. Bioorg Med Chem 2021; 45:116342. [PMID: 34364221 DOI: 10.1016/j.bmc.2021.116342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022]
Abstract
YEATS domains, which are newly identified epigenetic readers of histone lysine acetylation and crotonylation, have emerged as promising anti-cancer drug targets. We recently developed AF9 YEATS domain-selective cyclopeptide inhibitors. However, the cumbersome and time-consuming synthesis of the cyclopeptides limited further structural derivatisation and applications. Here, we reported a concise method for the solid-phase synthesis of the cyclopeptides, which substantially reduced the amount of time required for the preparation of the cyclopeptides and led to a higher overall yield. Moreover, this new synthetic route also allowed further derivatisation of the cyclopeptides with various functional modules, including fluorescent dye and cell-penetrating peptide. We demonstrated that the conjugation of the cyclopeptide with cell-penetrating peptide TAT led to a significantly increased cellular uptake.
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Affiliation(s)
- Yixiang Jiang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Sha Liu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Gaofei Tian
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Hayden Jit Hei Cheung
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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47
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Raubo P, Carbajo RJ, McCoull W, Raubo J, Thomas M. Diversity-orientated synthesis of macrocyclic heterocycles using a double S NAr approach. Org Biomol Chem 2021; 19:6274-6290. [PMID: 34195728 DOI: 10.1039/d1ob00612f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An efficient macrocyclisation approach based on the double aromatic nucleophilic substitution (SNACK) was developed. This methodology allows a facile incorporation of heterocyclic motifs into macrocyclic rings and rapid synthesis of a significant number of structurally diverse macrocycles. SNACK macrocyclisation enables preparation of stable diastereoisomers of conformationally restricted macrocycles (atropisomers). Practical application of SNACK macrocyclisation in a drug discovery project was exemplified by the identification of high affinity macrocyclic binders of B-cell lymphoma 6 (BCL6).
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Affiliation(s)
- Piotr Raubo
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK.
| | - Rodrigo J Carbajo
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK.
| | - William McCoull
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK.
| | - Joanna Raubo
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK.
| | - Morgan Thomas
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK.
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48
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Mochizuki K, Matsukura L, Ito Y, Miyashita N, Taki M. A medium-firm drug-candidate library of cryptand-like structures on T7 phage: design and selection of a strong binder for Hsp90. Org Biomol Chem 2021; 19:146-150. [PMID: 33095213 DOI: 10.1039/d0ob01855d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We designed and synthesized a medium-firm drug-candidate library of cryptand-like structures possessing a randomized peptide linker on the bacteriophage T7. From the macrocyclic library with a 109 diversity, we obtained a binder toward a cancer-related protein (Hsp90) with an antibody-like strong affinity (KD = 62 nM) and the binding was driven by the enthalpy. The selected supramolecular ligand inhibited Hsp90 activity by site-specific binding outside of the well-known ATP-binding pocket on the N-terminal domain (NTD).
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Affiliation(s)
- Kazuto Mochizuki
- Department of Engineering Science, Bioscience and Technology Program, The Graduate School of Informatics and Engineering, The University of Electro-Communications (UEC), 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
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49
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Alexa A, Ember O, Szabó I, Mo'ath Y, Póti ÁL, Reményi A, Bánóczi Z. Peptide Based Inhibitors of Protein Binding to the Mitogen-Activated Protein Kinase Docking Groove. Front Mol Biosci 2021; 8:690429. [PMID: 34277705 PMCID: PMC8281026 DOI: 10.3389/fmolb.2021.690429] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/18/2021] [Indexed: 11/21/2022] Open
Abstract
Mitogen-activated protein kinases (MAPK) are important regulatory units in cells and they take part in the regulation of many cellular functions such as cell division, differentiation or apoptosis. All MAPKs have a shallow docking groove that interacts with linear binding motifs of their substrate proteins and their regulatory proteins such as kinases, phosphatases, scaffolds. Inhibition of these protein–protein interactions may reduce or abolish the activity of the targeted kinase. Based on the wide range of their biological activity, this kind of inhibition can be useful in the treatment of many disorders like tumors, inflammation or undesired cell apoptosis. In this study a linear binding motif from the RHDF1 protein—a 15 amino acids long peptide—was selected for optimization to increase its cellular uptake but retaining its low micromolar binding affinity. First, we synthesized an octaarginine conjugate that showed efficient cellular uptake. Next, we set out to reduce the size of this construct. We were able to decrease the length of the original peptide, and to increase its cellular uptake with specific chemical modifications. These new constructs bound better to ERK2 and p38 kinases than the original peptide and they showed markedly increased cellular uptake. The new octaarginine conjugate and one of the minimized bicyclic derivatives could inhibit the phosphorylation of intracellular ERK or p38. However, the modulation of MAPK phosphorylation levels by these cell-penetrating peptides were complex, despite that in biochemical assays they all inhibited MAPK-substrate binding as well as phosphorylation. The optimized peptides depending on the applied concentration caused an expected decrease, but also some unexpected increase in MAPK phosphorylation patterns in the cell. This possibly reflects the complexity of MAPK docking groove mediated protein–protein interactions including bone fide MAPK clients such activator kinases, deactivating phosphatases or regulatory scaffolds. Thus, our findings with optimized cell-penetrating “inhibitory” peptides highlight the opportunities but also the pitfalls of docking peptide based MAPK activity regulation and call for a better quantitative understanding of MAPK mediated protein–protein interactions in cells.
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Affiliation(s)
- Anita Alexa
- Biomolecular Interactions Laboratory, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Orsolya Ember
- Biomolecular Interactions Laboratory, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary.,Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - Ildikó Szabó
- MTA-ELTE Research Group of Peptide Chemistry, Eötvös Loránd Research Network (ELKH), Eötvös L. University, Budapest, Hungary
| | - Yousef Mo'ath
- Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - Ádám L Póti
- Biomolecular Interactions Laboratory, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Attila Reményi
- Biomolecular Interactions Laboratory, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Zoltán Bánóczi
- Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
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Adaligil E, Song A, Hallenbeck KK, Cunningham CN, Fairbrother WJ. Ribosomal Synthesis of Macrocyclic Peptides with β 2- and β 2,3-Homo-Amino Acids for the Development of Natural Product-Like Combinatorial Libraries. ACS Chem Biol 2021; 16:1011-1018. [PMID: 34008946 DOI: 10.1021/acschembio.1c00062] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The development of large, natural-product-like, combinatorial macrocyclic peptide libraries is essential in the quest to develop therapeutics for "undruggable" cellular targets. Herein we report the ribosomal synthesis of macrocyclic peptides containing one or more β2-homo-amino acids (β2haa) to enable their incorporation into mRNA display-based selection libraries. We confirmed the compatibility of 14 β2-homo-amino acids, (S)- and (R)-stereochemistry, for single incorporation into a macrocyclic peptide with low to high translation efficiency. Interestingly, N-methylation of the backbone amide of β2haa prevented the incorporation of this amino acid subclass by the ribosome. Additionally, we designed and incorporated several α,β-disubstituted β2,3-homo-amino acids (β2,3haa) with different R-groups on the α- and β-carbons of the same amino acid. Incorporation of these β2,3haa enables increased diversity in a single position of a macrocyclic peptide without significantly increasing the overall molecular weight, which is an important consideration for passive cell permeability. We also successfully incorporated multiple (S)-β2hAla into a single macrocycle with other non-proteinogenic amino acids, confirming that this class of β-amino acid is suitable for development of large scale macrocyclic peptide libraries.
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Affiliation(s)
- Emel Adaligil
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Aimin Song
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Kenneth K. Hallenbeck
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Christian N. Cunningham
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Wayne J. Fairbrother
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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