1
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Britton D, Katsara O, Mishkit O, Wang A, Pandya N, Liu C, Mao H, Legocki J, Jia S, Xiao Y, Aristizabal O, Paul D, Deng Y, Schneider R, Wadghiri YZ, Montclare JK. Engineered coiled-coil HIF1α protein domain mimic. Biomater Sci 2024; 12:2951-2959. [PMID: 38656316 PMCID: PMC11191652 DOI: 10.1039/d4bm00354c] [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] [Indexed: 04/26/2024]
Abstract
The development of targeted anti-cancer therapeutics offers the potential for increased efficacy of drugs and diagnostics. Utilizing modalities agnostic to tumor type, such as the hypoxic tumor microenvironment (TME), may assist in the development of universal tumor targeting agents. The hypoxia-inducible factor (HIF), in particular HIF1, plays a key role in tumor adaptation to hypoxia, and inhibiting its interaction with p300 has been shown to provide therapeutic potential. Using a multivalent assembled protein (MAP) approach based on the self-assembly of the cartilage oligomeric matrix protein coiled-coil (COMPcc) domain fused to the critical residues of the C-terminal transactivation domain (C-TAD) of the α subunit of HIF1 (HIF1α), we generate HIF1α-MAP (H-MAP). The resulting H-MAP demonstrates picomolar binding affinity to p300, the ability to downregulate hypoxia-inducible genes, and in vivo tumor targeting capability.
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Affiliation(s)
- Dustin Britton
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Olga Katsara
- Department of Microbiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Orin Mishkit
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Andrew Wang
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
- Department of Biomedical Engineering, State University of New York Downstate Medical Center, Brooklyn, New York, 11203, USA
- College of Medicine, State University of New York Downstate Medical Center, Brooklyn, New York, 11203, USA
| | - Neelam Pandya
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Chengliang Liu
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Heather Mao
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Jakub Legocki
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Sihan Jia
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Yingxin Xiao
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Orlando Aristizabal
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Deven Paul
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Yan Deng
- Microscopy Laboratory, New York University Langone Health, New York, NY, 10016, USA
| | - Robert Schneider
- Department of Microbiology, New York University School of Medicine, New York, New York, 10016, USA
- Department of Radiation Oncology, New York University School of Medicine, New York, New York, 10016, USA
| | - Youssef Z Wadghiri
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Department of Chemistry, New York University, New York, New York, 10012, USA
- Department of Biomaterials, New York University College of Dentistry, New York, New York, 10010, USA
- Department of Biomedical Engineering, New York University, New York, NY, 11201, USA
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2
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Mermet S, Voisin M, Mordier J, Dubos T, Tutois S, Tuffery P, Baroux C, Tamura K, Probst AV, Vanrobays E, Tatout C. Evolutionarily conserved protein motifs drive interactions between the plant nucleoskeleton and nuclear pores. THE PLANT CELL 2023; 35:4284-4303. [PMID: 37738557 PMCID: PMC10689174 DOI: 10.1093/plcell/koad236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/07/2023] [Accepted: 08/14/2023] [Indexed: 09/24/2023]
Abstract
The nucleoskeleton forms a filamentous meshwork under the nuclear envelope and contributes to the regulation of nuclear shape and gene expression. To understand how the Arabidopsis (Arabidopsis thaliana) nucleoskeleton physically connects to the nuclear periphery in plants, we investigated the Arabidopsis nucleoskeleton protein KAKU4 and sought for functional regions responsible for its localization at the nuclear periphery. We identified 3 conserved peptide motifs within the N-terminal region of KAKU4, which are required for intermolecular interactions of KAKU4 with itself, interaction with the nucleoskeleton protein CROWDED NUCLEI (CRWN), localization at the nuclear periphery, and nuclear elongation in differentiated tissues. Unexpectedly, we find these motifs to be present also in NUP82 and NUP136, 2 plant-specific nucleoporins from the nuclear pore basket. We further show that NUP82, NUP136, and KAKU4 have a common evolutionary history predating nonvascular land plants with KAKU4 mainly localizing outside the nuclear pore suggesting its divergence from an ancient nucleoporin into a new nucleoskeleton component. Finally, we demonstrate that both NUP82 and NUP136, through their shared N-terminal motifs, interact with CRWN and KAKU4 proteins revealing the existence of a physical continuum between the nuclear pore and the nucleoskeleton in plants.
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Affiliation(s)
- Sarah Mermet
- iGReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Maxime Voisin
- iGReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Joris Mordier
- iGReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Tristan Dubos
- iGReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Sylvie Tutois
- iGReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Pierre Tuffery
- Université Paris Cité, CNRS UMR 8251, INSERM ERL U1133, 75013 Paris, France
| | - Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, 8008 Zürich, Switzerland
| | - Kentaro Tamura
- Department of Environmental and Life Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Aline V Probst
- iGReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Emmanuel Vanrobays
- iGReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Christophe Tatout
- iGReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
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3
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Webb KR, Hess KA, Shmidt A, Segner KD, Buchanan LE. Probing local changes to α-helical structures with 2D IR spectroscopy and isotope labeling. Biophys J 2023; 122:1491-1502. [PMID: 36906800 PMCID: PMC10147839 DOI: 10.1016/j.bpj.2023.03.014] [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: 05/24/2022] [Revised: 10/13/2022] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
α-Helical secondary structures impart specific mechanical and physiochemical properties to peptides and proteins, enabling them to perform a vast array of molecular tasks ranging from membrane insertion to molecular allostery. Loss of α-helical content in specific regions can inhibit native protein function or induce new, potentially toxic, biological activities. Thus, identifying specific residues that exhibit loss or gain of helicity is critical for understanding the molecular basis of function. Two-dimensional infrared (2D IR) spectroscopy coupled with isotope labeling is capable of capturing detailed structural changes in polypeptides. Yet, questions remain regarding the inherent sensitivity of isotope-labeled modes to local changes in α-helicity, such as terminal fraying; the origin of spectral shifts (hydrogen-bonding versus vibrational coupling); and the ability to definitively detect coupled isotopic signals in the presence of overlapping side chains. Here, we address each of these points individually by characterizing a short, model α-helix (DPAEAAKAAAGR-NH2) with 2D IR and isotope labeling. These results demonstrate that pairs of 13C18O probes placed three residues apart can detect subtle structural changes and variations along the length of the model peptide as the α-helicity is systematically tuned. Comparison of singly and doubly labeled peptides affirm that frequency shifts arise primarily from hydrogen-bonding, while vibrational coupling between paired isotopes leads to increased peak areas that can be clearly differentiated from underlying side-chain modes or uncoupled isotope labels not participating in helical structures. These results demonstrate that 2D IR in tandem with i,i+3 isotope-labeling schemes can capture residue-specific molecular interactions within a single turn of an α-helix.
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Affiliation(s)
| | - Kayla Anne Hess
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Alisa Shmidt
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
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4
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Kell S, Wang Z, Ji H. Common Structural Features of Hydrophobic α-Helical Hot Spots: Insights for the Design of Novel α-Helix Mimetics. ACS Med Chem Lett 2022; 13:1670-1677. [PMID: 36262397 PMCID: PMC9575182 DOI: 10.1021/acsmedchemlett.2c00296] [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: 06/29/2022] [Accepted: 09/02/2022] [Indexed: 11/28/2022] Open
Abstract
The binding conformations of α-helical hydrophobic hot spots are convergent into two spatial areas in protein-protein complex structures. The physical basis for convergence was disclosed, which allows the development of pharmacophore models for i/i + 4/i + 7 or i/i + 3/i + 4 α-helical hot spots. Further investigation revealed that this convergence of binding conformations is common among all hydrophobic hot spots regardless of their α-helical positions. This observation led to a streamlined generation of pharmacophore models for hydrophobic hot spots at any positions along the α-helix. These successfully evaluated pharmacophore models may be useful for designing novel α-helical hot spot mimetics.
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Affiliation(s)
- Shelby
R. Kell
- Drug
Discovery Department, H. Lee Moffitt Cancer
Center & Research Institute, Tampa, Florida 33612, United States
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Zhen Wang
- Drug
Discovery Department, H. Lee Moffitt Cancer
Center & Research Institute, Tampa, Florida 33612, United States
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Haitao Ji
- Drug
Discovery Department, H. Lee Moffitt Cancer
Center & Research Institute, Tampa, Florida 33612, United States
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
- Department
of Oncologic Sciences, University of South
Florida, Tampa, Florida 33620, United
States
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5
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Kim DI, Han SH, Park H, Choi S, Kaur M, Hwang E, Han SJ, Ryu JY, Cheong HK, Barnwal RP, Lim YB. Pseudo-Isolated α-Helix Platform for the Recognition of Deep and Narrow Targets. J Am Chem Soc 2022; 144:15519-15528. [PMID: 35972994 DOI: 10.1021/jacs.2c03858] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although interest in stabilized α-helical peptides as next-generation therapeutics for modulating biomolecular interfaces is increasing, peptides have limited functionality and stability due to their small size. In comparison, α-helical ligands based on proteins can make steric clash with targets due to their large size. Here, we report the design of a monomeric pseudo-isolated α-helix (mPIH) system in which proteins behave as if they are peptides. The designed proteins contain α-helix ligands that do not require any covalent chemical modification, do not have frayed ends, and importantly can make sterically favorable interactions similar to isolated peptides. An optimal mPIH showed a more than 100-fold increase in target selectivity, which might be related to the advantages in conformational selection due to the absence of frayed ends. The α-helical ligand in the mPIH displayed high thermal stability well above human body temperature and showed reversible and rapid folding/unfolding transitions. Thus, mPIH can become a promising protein-based platform for developing stabilized α-helix pharmaceuticals.
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Affiliation(s)
- Dong-In Kim
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - So-Hee Han
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Hahnbeom Park
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Sehwan Choi
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Mandeep Kaur
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Euimin Hwang
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Seong-Jae Han
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jung-Yeon Ryu
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Hae-Kap Cheong
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang 28119, Republic of Korea
| | | | - Yong-Beom Lim
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
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6
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Mahtarin R, Islam S, Islam MJ, Ullah MO, Ali MA, Halim MA. Structure and dynamics of membrane protein in SARS-CoV-2. J Biomol Struct Dyn 2022; 40:4725-4738. [PMID: 33353499 PMCID: PMC7784837 DOI: 10.1080/07391102.2020.1861983] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/05/2020] [Indexed: 12/15/2022]
Abstract
SARS-CoV-2 membrane (M) protein performs a variety of critical functions in virus infection cycle. However, the expression and purification of membrane protein structure is difficult despite tremendous progress. In this study, the 3 D structure is modeled followed by intensive validation and molecular dynamics simulation. The lack of suitable homologous templates (>30% sequence identities) leads us to construct the membrane protein models using template-free modeling (de novo or ab initio) approach with Robetta and trRosetta servers. Comparing with other model structures, it is evident that trRosetta (TM-score: 0.64; TM region RMSD: 2 Å) can provide the best model than Robetta (TM-score: 0.61; TM region RMSD: 3.3 Å) and I-TASSER (TM-score: 0.45; TM region RMSD: 6.5 Å). 100 ns molecular dynamics simulations are performed on the model structures by incorporating membrane environment. Moreover, secondary structure elements and principal component analysis (PCA) have also been performed on MD simulation data. Finally, trRosetta model is utilized for interpretation and visualization of interacting residues during protein-protein interactions. The common interacting residues including Phe103, Arg107, Met109, Trp110, Arg131, and Glu135 in the C-terminal domain of M protein are identified in membrane-spike and membrane-nucleocapsid protein complexes. The active site residues are also predicted for potential drug and peptide binding. Overall, this study might be helpful to design drugs and peptides against the modeled membrane protein of SARS-CoV-2 to accelerate further investigation. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rumana Mahtarin
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Shafiqul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md. Jahirul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - M Obayed Ullah
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Mohammad A. Halim
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
- Department of Physical Sciences, University of Arkansas - Fort Smith, Fort Smith, AR, USA
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7
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McCoy MA, Spicer D, Wells N, Hoogewijs K, Fiedler M, Baud MGJ. Biophysical Survey of Small-Molecule β-Catenin Inhibitors: A Cautionary Tale. J Med Chem 2022; 65:7246-7261. [PMID: 35581674 PMCID: PMC9150122 DOI: 10.1021/acs.jmedchem.2c00228] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The canonical Wingless-related
integration site signaling pathway
plays a critical role in human physiology, and its dysregulation can
lead to an array of diseases. β-Catenin is a multifunctional
protein within this pathway and an attractive yet challenging therapeutic
target, most notably in oncology. This has stimulated the search for
potent small-molecule inhibitors binding directly to the β-catenin
surface to inhibit its protein–protein interactions and downstream
signaling. Here, we provide an account of the claimed (and some putative)
small-molecule ligands of β-catenin from the literature. Through
in silico analysis, we show that most of these molecules contain promiscuous
chemical substructures notorious for interfering with screening assays.
Finally, and in line with this analysis, we demonstrate using orthogonal
biophysical techniques that none of the examined small molecules bind
at the surface of β-catenin. While shedding doubts on their
reported mode of action, this study also reaffirms β-catenin
as a prominent target in drug discovery.
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Affiliation(s)
- Michael A McCoy
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Dominique Spicer
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Neil Wells
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Kurt Hoogewijs
- National University of Ireland, University Road, Galway H91 TK33, Ireland
| | - Marc Fiedler
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Matthias G J Baud
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
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8
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Nakaya T, Aizawa K, Taguchi Y, Tsuji K, Sekine S, Murakami K, Kasai M, Nakano H, Kondoh Y, Dan S, Yoshimori A, Kouji H, Takehara D, Suzuki T, Osada H, Murata M, Tanaka A, Nagai R. Development of Low-Molecular-Weight Compounds Targeting the Cancer-Associated KLF5 Transcription Factor. ACS Med Chem Lett 2022; 13:687-694. [PMID: 35450365 PMCID: PMC9014505 DOI: 10.1021/acsmedchemlett.1c00721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/11/2022] [Indexed: 11/28/2022] Open
Abstract
Krüppel-like factor 5 (KLF5) is a potential target for anticancer drugs. However, as an intrinsically disordered protein (IDP) whose tertiary structure cannot be solved, innovative strategies are needed. We focused on its hydrophobic α-helix structure, defined as an induced helical motif (IHM), which is a possible interface for protein-protein interaction. Using mathematical analyses predicting the α-helix's structure and hydrophobicity, a 4-amino-acid site (V-A-I-F) was identified as an IHM. Low-molecular-weight compounds that mimic the main chain conformation of the α-helix with the four side chains of V-A-I-F were synthesized using bicyclic pyrazinooxadiazine-4,7-dione. These compounds selectively suppressed the proliferation and survival of cancer cells but not noncancer cells and decreased the protein but not mRNA levels of KLF5 in addition to reducing proteins of Wnt signaling. The compounds further suppressed transplanted colorectal cancer cells in vivo without side effects. Our approach appears promising for developing drugs against key IDPs.
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Affiliation(s)
- Takeo Nakaya
- Department of Pathology, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Kenichi Aizawa
- Department of Clinical Pharmacology, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Yuki Taguchi
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo,
Meguro-ku, Tokyo 153-8902, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
| | - Kentaro Tsuji
- Department of Pathology, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Sachi Sekine
- Department of Pathology and Department of Pediatric Surgery , Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Kazuhiro Murakami
- Department of Pathology, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
- Department of Dentistry and Oral Surgery, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Masaji Kasai
- PRISM BioLab Co., Ltd., Fujisawa, Kanagawa 251-8555, Japan
| | | | - Yasumitsu Kondoh
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Shingo Dan
- Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, Japan
| | - Atsushi Yoshimori
- Institute for Theoretical Medicine, Inc., Fujisawa Kanagawa 251-0012, Japan
| | - Hiroyuki Kouji
- PRISM BioLab Co., Ltd., Fujisawa, Kanagawa 251-8555, Japan
- ¶Oita University Institute of Advanced Medicine, Inc., Fujisawa, Kanagawa 251-0052, Japan
| | - Dai Takehara
- PRISM BioLab Co., Ltd., Fujisawa, Kanagawa 251-8555, Japan
| | - Toru Suzuki
- Department of Cardiovascular Sciences, University of Leicester Cardiovascular Research Centre, Glenfield Hospital, Leicester LE39QP, U.K
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Masayuki Murata
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo,
Meguro-ku, Tokyo 153-8902, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
| | - Akira Tanaka
- Department of Pathology, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Ryozo Nagai
- Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
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9
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Wang Z, Ji H. Characterization of Hydrophilic α-Helical Hot Spots on the Protein-Protein Interaction Interfaces for the Design of α-Helix Mimetics. J Chem Inf Model 2022; 62:1873-1890. [PMID: 35385659 DOI: 10.1021/acs.jcim.1c01556] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cooperativity index, Kc, was developed to examine the binding synergy between hot spots of the ligand-protein. For the first time, the convergence of the side-chain spatial arrangements of hydrophilic α-helical hot spots Thr, Tyr, Asp, Asn, Ser, Cys, and His in protein-protein interaction (PPI) complex structures was disclosed and quantified by developing novel clustering models. In-depth analyses revealed the driving force for the protein-protein binding conformation convergence of hydrophilic α-helical hot spots. This observation allows deriving pharmacophore models to design new mimetics for hydrophilic α-helical hot spots. A computational protocol was developed to search amino acid analogues and small-molecule mimetics for each hydrophilic α-helical hot spot. As a pilot study, diverse building blocks of commercially available nonstandard L-type α-amino acids and the phenyl ring-containing small-molecule fragments were obtained, which serve as a fragment collection to mimic hydrophilic α-helical hot spots for the improvement of binding affinity, selectivity, physicochemical properties, and synthesis accessibility of α-helix mimetics.
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Affiliation(s)
- Zhen Wang
- Drug Discovery Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612-9497, United States.,Departments of Chemistry and Oncologic Sciences, University of South Florida, Tampa, Florida 33620-9497, United States
| | - Haitao Ji
- Drug Discovery Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612-9497, United States.,Departments of Chemistry and Oncologic Sciences, University of South Florida, Tampa, Florida 33620-9497, United States
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10
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Trobe M, Vareka M, Schreiner T, Dobrounig P, Doler C, Holzinger EB, Steinegger A, Breinbauer R. Modular Synthesis of Teraryl‐based alpha ‐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] [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
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Martin Vareka
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Till Schreiner
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Patrick Dobrounig
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Carina Doler
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Ella B. Holzinger
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Andreas Steinegger
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Rolf Breinbauer
- Technische Universitat Graz Institute of Organic Chemistry Stremayrgasse 9 A-8010 Graz AUSTRIA
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11
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Trobe M, Blesl J, Vareka M, Schreiner T, Breinbauer R. Modular Synthesis of Teraryl‐based alpha‐Helix Mimetics, Part 4: Core Fragments with two Halide Leaving Groups Featuring Side Chains of Proteinogenic Amino Acids. European J Org Chem 2022; 2022:e202101279. [PMID: 35910460 PMCID: PMC9304293 DOI: 10.1002/ejoc.202101279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/08/2022] [Indexed: 12/03/2022]
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 halide leaving groups of differentiated reactivity in the Pd‐catalyzed cross‐coupling used for teraryl assembly. The use of para‐bromo iodoarene core fragments resolved the issue of hydrolysis during cross‐coupling that was observed when using triflate as a leaving group. We report a complete set of para‐bromoiodoarene core fragments decorated with side chains of all proteinogenic amino acids relevant for PPI (Ala, Arg, Asn, Asp, Cys, Gln, Glu, His, Ile, Leu, Lys, Met, Phe, Ser, Thr, Trp, Tyr and Val). In order to be compatible with general cross‐coupling conditions, some of the nucleophilic side chains had to be provided in a protected form to serve as stable building blocks.
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Affiliation(s)
- Melanie Trobe
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Julia Blesl
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Martin Vareka
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Till Schreiner
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Rolf Breinbauer
- Technische Universitat Graz Institute of Organic Chemistry Stremayrgasse 9 A-8010 Graz AUSTRIA
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12
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Rational design of a helical peptide inhibitor targeting c-Myb–KIX interaction. Sci Rep 2022; 12:816. [PMID: 35058484 PMCID: PMC8776815 DOI: 10.1038/s41598-021-04497-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/22/2021] [Indexed: 01/05/2023] Open
Abstract
The transcription factor c-Myb promotes the proliferation of hematopoietic cells by interacting with the KIX domain of CREB-binding protein; however, its aberrant expression causes leukemia. Therefore, inhibitors of the c-Myb–KIX interaction are potentially useful as antitumor drugs. Since the intrinsically disordered transactivation domain (TAD) of c-Myb binds KIX via a conformational selection mechanism where helix formation precedes binding, stabilizing the helical structure of c-Myb TAD is expected to increase the KIX-binding affinity. Here, to develop an inhibitor of the c-Myb–KIX interaction, we designed mutants of the c-Myb TAD peptide fragment where the helical structure is stabilized, based on theoretical predictions using AGADIR. Three of the four initially designed peptides each had a different Lys-to-Arg substitution on the helix surface opposite the KIX-binding interface. Furthermore, the triple mutant with three Lys-to-Arg substitutions, named RRR, showed a high helical propensity and achieved three-fold higher affinity to KIX than the wild-type TAD with a dissociation constant of 80 nM. Moreover, the RRR inhibitor efficiently competed out the c-Myb–KIX interaction. These results suggest that stabilizing the helical structure based on theoretical predictions, especially by conservative Lys-to-Arg substitutions, is a simple and useful strategy for designing helical peptide inhibitors of protein–protein interactions.
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13
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Islam MS, Junod SL, Zhang S, Buuh ZY, Guan Y, Zhao M, Kaneria KH, Kafley P, Cohen C, Maloney R, Lyu Z, Voelz VA, Yang W, Wang RE. Unprotected peptide macrocyclization and stapling via a fluorine-thiol displacement reaction. Nat Commun 2022; 13:350. [PMID: 35039490 PMCID: PMC8763920 DOI: 10.1038/s41467-022-27995-5] [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] [Received: 09/01/2020] [Accepted: 12/19/2021] [Indexed: 12/31/2022] Open
Abstract
We report the discovery of a facile peptide macrocyclization and stapling strategy based on a fluorine thiol displacement reaction (FTDR), which renders a class of peptide analogues with enhanced stability, affinity, cellular uptake, and inhibition of cancer cells. This approach enabled selective modification of the orthogonal fluoroacetamide side chains in unprotected peptides in the presence of intrinsic cysteines. The identified benzenedimethanethiol linker greatly promoted the alpha helicity of a variety of peptide substrates, as corroborated by molecular dynamics simulations. The cellular uptake of benzenedimethanethiol stapled peptides appeared to be universally enhanced compared to the classic ring-closing metathesis (RCM) stapled peptides. Pilot mechanism studies suggested that the uptake of FTDR-stapled peptides may involve multiple endocytosis pathways in a distinct pattern in comparison to peptides stapled by RCM. Consistent with the improved cell permeability, the FTDR-stapled lead Axin and p53 peptide analogues demonstrated enhanced inhibition of cancer cells over the RCM-stapled analogues and the unstapled peptides. Strategies capable of stapling unprotected peptides in a straightforward, chemoselective, and clean manner, as well as promoting cellular uptake are of great interest. Here the authors report a peptide macrocyclization and stapling strategy which satisfies those criteria, based on a fluorine thiol displacement reaction.
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Affiliation(s)
- Md Shafiqul Islam
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Samuel L Junod
- Department of Biology, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA
| | - Si Zhang
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Zakey Yusuf Buuh
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Yifu Guan
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Mi Zhao
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Kishan H Kaneria
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Parmila Kafley
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Carson Cohen
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Robert Maloney
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Zhigang Lyu
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Vincent A Voelz
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Weidong Yang
- Department of Biology, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA
| | - Rongsheng E Wang
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA.
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14
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Hetherington K, Dutt S, Ibarra AA, Cawood EE, Hobor F, Woolfson DN, Edwards TA, Nelson A, Sessions RB, Wilson AJ. Towards optimizing peptide-based inhibitors of protein-protein interactions: predictive saturation variation scanning (PreSaVS). RSC Chem Biol 2021; 2:1474-1478. [PMID: 34704051 PMCID: PMC8495968 DOI: 10.1039/d1cb00137j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 07/30/2021] [Indexed: 12/21/2022] Open
Abstract
A simple-to-implement and experimentally validated computational workflow for sequence modification of peptide inhibitors of protein–protein interactions (PPIs) is described. An experimentally validated approach for in silico modification of peptide based protein–protein interaction inhibitors is described.![]()
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Affiliation(s)
- Kristina Hetherington
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK .,School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Som Dutt
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK .,School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Amaurys A Ibarra
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
| | - Emma E Cawood
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK .,School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Fruzsina Hobor
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK .,School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Derek N Woolfson
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK .,School of Chemistry, University of Bristol, Cantock's Close Bristol BS8 1TS UK.,BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK .,School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Adam Nelson
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK .,School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK .,BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK .,School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
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15
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Higo J, Takashima H, Fukunishi Y, Yoshimori A. Generalized-ensemble method study: A helix-mimetic compound inhibits protein-protein interaction by long-range and short-range intermolecular interactions. J Comput Chem 2021; 42:956-969. [PMID: 33755222 DOI: 10.1002/jcc.26516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 12/30/2022]
Abstract
A heterocyclic compound mS-11 is a helix-mimetic designed to inhibit binding of an intrinsic disordered protein neural restrictive silence factor/repressor element 1 silencing factor (NRSF/REST) to a receptor protein mSin3B. We apply a generalized ensemble method, multi-dimensional virtual-system coupled molecular dynamics developed by ourselves recently, to a system consisting of mS-11 and mSin3B, and obtain a thermally equilibrated distribution, which is comprised of the bound and unbound states extensively. The lowest free-energy position of mS-11 coincides with the NRSF/REST position in the experimentally-determined NRSF/REST-mSin3B complex. Importantly, the molecular orientation of mS-11 is ordering in a wide region around mSin3B. The resultant binding scenario is: When mS-11 is distant from the binding site of mSin3B, mS-11 descends the free-energy slope toward the binding site maintaining the molecular orientation to be advantageous for binding. Then, finally a long and flexible hydrophobic sidechain of mS-11 fits into the binding site, which is the lowest-free-energy complex structure inhibiting NRSF/REST binding to mSin3B.
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Affiliation(s)
- Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Japan
| | - Hajime Takashima
- Department of Research and Development, PRISM BioLab Co., Ltd., Fujisawa, Japan
| | - Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Atsushi Yoshimori
- Chemoinformatics & AI Research Group, Institute for Theoretical Medicine, Inc., Fujisawa, Japan
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16
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Jedhe GS, Arora PS. Hydrogen bond surrogate helices as minimal mimics of protein α-helices. Methods Enzymol 2021; 656:1-25. [PMID: 34325784 DOI: 10.1016/bs.mie.2021.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Examination of complexes of proteins with biomolecular ligands reveals that proteins tend to interact with partners via folded sub-domains, in which the backbone possesses secondary structure. α-Helices comprising the largest class of protein secondary structures, play fundamental roles in a multitude of highly specific protein-protein and protein-nucleic acid interactions. We have demonstrated a unique strategy for stabilization of the α-helical conformation that involves replacement of one of the main chain i and i+4 hydrogen bonds in the target α-helix with a covalent bond. We termed this synthetic strategy a hydrogen bond surrogate (HBS) approach. Two salient features of this approach are: (1) the internal placement of the crosslink allows development of helices such that none of the solvent-exposed surfaces are blocked by the constraining element, i.e., all side chains of the constrained helices remain available for molecular recognition. (2) This approach can be deployed to constrain very short peptides (<10 amino acid residues) into highly stable α-helices. This chapter presents the biophysical basis for the development of the hydrogen bond surrogate approach, as well as methods for the synthesis and conformational analysis of the artificial helices.
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Affiliation(s)
- Ganesh S Jedhe
- Department of Chemistry, New York University, New York, NY, United States
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY, United States.
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17
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Abstract
Wnt/β-catenin signaling is crucial both in normal embryonic development and throughout the life of an organism. Moreover, aberrant Wnt signaling has been associated with various diseases, especially cancer and fibrosis. Recent research suggests that direct targeting of the β-catenin/BCL9 protein-protein interaction (PPI) is a promising strategy to block the Wnt pathway. Progress in understanding the cocrystalline complex and mechanism of action of the β-catenin/BCL9 interaction facilitates the discovery process of its inhibitors, but only a few inhibitors have been reported. In this review, the discovery and development of β-catenin/BCL9 PPI inhibitors in the areas of drug design, structure-activity relationships and biological and biochemical properties are summarized. In addition, perspectives for the future development of β-catenin/BCL9 PPI inhibitors are explored.
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18
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A novel peptide antagonist of the human growth hormone receptor. J Biol Chem 2021; 296:100588. [PMID: 33774052 PMCID: PMC8086144 DOI: 10.1016/j.jbc.2021.100588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/09/2021] [Accepted: 03/23/2021] [Indexed: 12/11/2022] Open
Abstract
Excess circulating human growth hormone (hGH) in vivo is linked to metabolic and growth disorders such as cancer, diabetes, and acromegaly. Consequently, there is considerable interest in developing antagonists of hGH action. Here, we present the design, synthesis, and characterization of a 16-residue peptide (site 1-binding helix [S1H]) that inhibits hGH-mediated STAT5 phosphorylation in cultured cells. S1H was designed as a direct sequence mimetic of the site 1 mini-helix (residues 36-51) of wild-type hGH and acts by inhibiting the interaction of hGH with the human growth hormone receptor (hGHR). In vitro studies indicated that S1H is stable in human serum and can adopt an α-helix in solution. Our results also show that S1H mitigates phosphorylation of STAT5 in cells co-treated with hGH, reducing intracellular STAT5 phosphorylation levels to those observed in untreated controls. Furthermore, S1H was found to attenuate the activity of the hGHR and the human prolactin receptor, suggesting that this peptide acts as an antagonist of both lactogenic and somatotrophic hGH actions. Finally, we used alanine scanning to determine how discrete amino acids within the S1H sequence contribute to its structural organization and biological activity. We observed a strong correlation between helical propensity and inhibitory effect, indicating that S1H-mediated antagonism of the hGHR is largely dependent on the ability for S1H to adopt an α-helix. Taken together, these results show that S1H not only acts as a novel peptide-based antagonist of the hGHR but can also be applied as a chemical tool to study the molecular nature of hGH-hGHR interactions.
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19
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Koirala M, Alexov E. Ab-initio binding of barnase–barstar with DelPhiForce steered Molecular Dynamics (DFMD) approach. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2020. [DOI: 10.1142/s0219633620500169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Receptor–ligand interactions are involved in various biological processes, therefore understanding the binding mechanism and ability to predict the binding mode are essential for many biological investigations. While many computational methods exist to predict the 3D structure of the corresponding complex provided the knowledge of the monomers, here we use the newly developed DelPhiForce steered Molecular Dynamics (DFMD) approach to model the binding of barstar to barnase to demonstrate that first-principles methods are also capable of modeling the binding. Essential component of DFMD approach is enhancing the role of long-range electrostatic interactions to provide guiding force of the monomers toward their correct binding orientation and position. Thus, it is demonstrated that the DFMD can successfully dock barstar to barnase even if the initial positions and orientations of both are completely different from the correct ones. Thus, the electrostatics provides orientational guidance along with pulling force to deliver the ligand in close proximity to the receptor.
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Affiliation(s)
- Mahesh Koirala
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
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20
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Bueno AB, Sun B, Willard FS, Feng D, Ho JD, Wainscott DB, Showalter AD, Vieth M, Chen Q, Stutsman C, Chau B, Ficorilli J, Agejas FJ, Cumming GR, Jiménez A, Rojo I, Kobilka TS, Kobilka BK, Sloop KW. Structural insights into probe-dependent positive allosterism of the GLP-1 receptor. Nat Chem Biol 2020; 16:1105-1110. [PMID: 32690941 DOI: 10.1038/s41589-020-0589-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 06/09/2020] [Indexed: 12/19/2022]
Abstract
Drugs that promote the association of protein complexes are an emerging therapeutic strategy. We report discovery of a G protein-coupled receptor (GPCR) ligand that stabilizes an active state conformation by cooperatively binding both the receptor and orthosteric ligand, thereby acting as a 'molecular glue'. LSN3160440 is a positive allosteric modulator of the GLP-1R optimized to increase the affinity and efficacy of GLP-1(9-36), a proteolytic product of GLP-1(7-36). The compound enhances insulin secretion in a glucose-, ligand- and GLP-1R-dependent manner. Cryo-electron microscopy determined the structure of the GLP-1R bound to LSN3160440 in complex with GLP-1 and heterotrimeric Gs. The modulator binds high in the helical bundle at an interface between TM1 and TM2, allowing access to the peptide ligand. Pharmacological characterization showed strong probe dependence of LSN3160440 for GLP-1(9-36) versus oxyntomodulin that is driven by a single residue. Our findings expand protein-protein modulation drug discovery to uncompetitive, active state stabilizers for peptide hormone receptors.
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Affiliation(s)
| | | | - Francis S Willard
- Quantitative Biology, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Dan Feng
- ConfometRx, Santa Clara, CA, USA
| | - Joseph D Ho
- Lilly Biotechnology Center San Diego, San Diego, CA, USA
| | - David B Wainscott
- Quantitative Biology, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Aaron D Showalter
- Diabetes and Complications, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Michal Vieth
- Lilly Biotechnology Center San Diego, San Diego, CA, USA
| | - Qi Chen
- Discovery Chemistry Research and Technologies, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Cynthia Stutsman
- Diabetes and Complications, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Betty Chau
- Lilly Biotechnology Center San Diego, San Diego, CA, USA
| | - James Ficorilli
- Diabetes and Complications, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | | | | | | | | | | | | | - Kyle W Sloop
- Diabetes and Complications, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA.
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21
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Synthesis of a Bcl9 Alpha-Helix Mimetic for Inhibition of PPIs by a Combination of Electrooxidative Phenol Coupling and Pd-Catalyzed Cross Coupling. Catalysts 2020. [DOI: 10.3390/catal10030340] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Teraryl-based alpha-helix mimetics have resulted in efficient inhibitors of protein-protein interactions (PPIs). Extending the concept to even longer oligoarene systems would allow for the mimicking of even larger interaction sites. We present a highly efficient synthetic modular access to quateraryl alpha-helix mimetics, in which, at first, two phenols undergo electrooxidative dehydrogenative cross-coupling. The resulting 4,4′-biphenol is then activated by conversion to nonaflates, which serve as leaving groups for iterative Pd-catalyzed Suzuki-cross-coupling reactions with suitably substituted pyridine boronic acids. This work, for the first time, demonstrates the synthetic efficiency of using both electroorganic as well as transition-metal catalyzed cross-coupling in the assembly of oligoarene structures.
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22
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Merritt HI, Sawyer N, Arora PS. Bent Into Shape: Folded Peptides to Mimic Protein Structure and Modulate Protein Function. Pept Sci (Hoboken) 2020; 112:e24145. [PMID: 33575525 PMCID: PMC7875438 DOI: 10.1002/pep2.24145] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 12/11/2019] [Indexed: 12/16/2022]
Abstract
Protein secondary and tertiary structure mimics have served as model systems to probe biophysical parameters that guide protein folding and as attractive reagents to modulate protein interactions. Here we review contemporary methods to reproduce loop, helix, sheet and coiled-coil conformations in short peptides.
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Affiliation(s)
| | | | - Paramjit S. Arora
- Department of Chemistry New York University, New York, New York 10003, United States
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23
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Chen Z, Yu X, Zhang A, Wang F, Xing Y. De Novo Hydrocarbon-Stapling Design of Single-Turn α-Helical Antimicrobial Peptides. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09964-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Yang W, Sun X, Zhang C, Lai L. Discovery of novel helix binding sites at protein-protein interfaces. Comput Struct Biotechnol J 2019; 17:1396-1403. [PMID: 31768230 PMCID: PMC6872852 DOI: 10.1016/j.csbj.2019.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 10/29/2019] [Accepted: 11/01/2019] [Indexed: 01/09/2023] Open
Abstract
Protein-protein interactions (PPIs) play a key role in numerous biological processes. Many efforts have been undertaken to develop PPI modulators for therapeutic applications; however, to date, most of the peptide binders designed to target PPIs are derived from native binding helices or using the native helix binding site, which has limited the applications of protein-protein interface binding peptide design. Here, we developed a general computational algorithm, HPer (Helix Positioner), that locates single-helix binding sites at protein-protein interfaces based on the structure of protein targets. HPer performed well on known single-helix-mediated PPIs and recaptured the key interactions and hot-spot residues of native helical binders. We also screened non-helical-mediated PPIs in the PDBbind database and identified 17 PPIs that were suitable for helical peptide binding, and the helical binding sites in these PPIs were also predicted for designing novel peptide ligands. The L2 domain of EGFR, which was the top ranked, was selected as an example to show the protocol and results of designing novel helical peptide ligands on the searched binding site. The binding stability of the designed sequences were further investigated using molecular dynamics simulations.
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Affiliation(s)
- Wei Yang
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Quantitative Biology, AAIS, Peking University, Beijing 100871, China
| | - Xiangyu Sun
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Changsheng Zhang
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Luhua Lai
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, AAIS, Peking University, Beijing 100084, China
- Center for Quantitative Biology, AAIS, Peking University, Beijing 100871, China
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25
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Wang Z, Ji H. Targeting the Side-Chain Convergence of Hydrophobic α-Helical Hot Spots To Design Small-Molecule Mimetics: Key Binding Features for i, i + 3, and i + 7. J Med Chem 2019; 62:9906-9917. [PMID: 31593458 DOI: 10.1021/acs.jmedchem.9b01324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The conformational convergence of hydrophobic α-helical hot spots was revealed by analyzing α-helix-mediated protein-protein interaction (PPI) complex structures. The pharmacophore models were derived for hydrophobic α-helical hot spots at positions i, i + 3, and i + 7. These provide the foundation for designing generalizable scaffolds that can directly mimic the binding mode of the side chains of α-helical hot spots, offering a new class of small-molecule α-helix mimetics. For the first time, the protocol was developed to identify the PPI targets that have similar binding pockets, allowing evaluation of inhibitor selectivities between α-helix-mediated PPIs. The mimicry efficiency of the previously designed scaffold 1 was disclosed. The close positioning of this small molecule to the additional α-helical hot spots suggests that the decoration of this series of generalizable scaffolds can conveniently reach the binding pockets of additional α-helical hot spots to produce potent small-molecule inhibitors for α-helix-mediated PPIs.
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Affiliation(s)
- Zhen Wang
- Drug Discovery Department , H. Lee Moffitt Cancer Center & Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612-9497 , United States.,Departments of Chemistry and Oncologic Sciences , University of South Florida , Tampa , Florida 33620-9497 , United States
| | - Haitao Ji
- Drug Discovery Department , H. Lee Moffitt Cancer Center & Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612-9497 , United States.,Departments of Chemistry and Oncologic Sciences , University of South Florida , Tampa , Florida 33620-9497 , United States
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26
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Lim SI. Site-specific bioconjugation and self-assembly technologies for multi-functional biologics: on the road to the clinic. Drug Discov Today 2019; 25:168-176. [PMID: 31610287 DOI: 10.1016/j.drudis.2019.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/28/2019] [Accepted: 10/03/2019] [Indexed: 01/02/2023]
Abstract
The expanding portfolio of biotherapeutics both in the research and development (R&D) and market sectors is shaping new opportunities towards multifunctional biologics (MFBs). The combination of new or pre-existing therapeutic agents into a single multifunctional format makes it possible to develop new pharmacological actions to significantly improve their efficacy and safety. In this review, I focus on novel platform technologies that are being exploited in the biotech industry to produce MFBs with potential therapeutic benefits that include half-life extension, targeted delivery, T cell engagement, and improved vaccination. In this regard, technologies of key importance are site-specific bioconjugation and self-assembly, which allow homogeneous, defined, and scalable process developments for several MFBs that are advancing towards clinical applications.
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Affiliation(s)
- Sung In Lim
- Department of Chemical Engineering, Pukyong National University, 45 Yongso-ro, Nam-gu, Busan, Republic of Korea.
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27
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Sun B, Vaughan D, Tikunova S, Creamer TP, Davis JP, Kekenes-Huskey PM. Calmodulin-Calcineurin Interaction beyond the Calmodulin-Binding Region Contributes to Calcineurin Activation. Biochemistry 2019; 58:4070-4085. [PMID: 31483613 DOI: 10.1021/acs.biochem.9b00626] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Calcineurin (CaN) is a calcium-dependent phosphatase involved in numerous signaling pathways. Its activation is in part driven by the binding of calmodulin (CaM) to a CaM recognition region (CaMBR) within CaN's regulatory domain (RD). However, secondary interactions between CaM and the CaN RD may be necessary to fully activate CaN. Specifically, it is established that the CaN RD folds upon CaM binding and a region C-terminal to CaMBR, the "distal helix", assumes an α-helix fold and contributes to activation [Dunlap, T. B., et al. (2013) Biochemistry 52, 8643-8651]. We hypothesized in that previous study that this distal helix can bind CaM in a region distinct from the canonical CaMBR. To test this hypothesis, we utilized molecular simulations, including replica-exchange molecular dynamics, protein-protein docking, and computational mutagenesis, to determine potential distal helix-binding sites on CaM's surface. We isolated a potential binding site on CaM (site D) that facilitates moderate-affinity interprotein interactions and predicted that mutation of site D residues K30 and G40 on CaM would weaken CaN distal helix binding. We experimentally confirmed that two variants (K30E and G40D) indicate weaker binding of a phosphate substrate p-nitrophenyl phosphate to the CaN catalytic site by a phosphatase assay. This weakened substrate affinity is consistent with competitive binding of the CaN autoinhibition domain to the catalytic site, which we suggest is due to the weakened distal helix-CaM interactions. This study therefore suggests a novel mechanism for CaM regulation of CaN that may extend to other CaM targets.
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Affiliation(s)
- Bin Sun
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40506 , United States
| | - Darin Vaughan
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40506 , United States
| | - Svetlana Tikunova
- Department of Physiology and Cell Biology , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Trevor P Creamer
- Center for Structural Biology and Department of Molecular & Cellular Biochemistry , University of Kentucky , Lexington , Kentucky 40536 , United States
| | - Jonathan P Davis
- Department of Physiology and Cell Biology , The Ohio State University , Columbus , Ohio 43210 , United States
| | - P M Kekenes-Huskey
- Department of Chemical and Materials Engineering , University of Kentucky , Lexington , Kentucky 40506 , United States.,Department of Cell and Molecular Physiology , Loyola University Chicago , Maywood , Illinois 60153 , United States
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28
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Flack T, Romain C, White AJP, Haycock PR, Barnard A. Design, Synthesis, and Conformational Analysis of Oligobenzanilides as Multifacial α-Helix Mimetics. Org Lett 2019; 21:4433-4438. [PMID: 31188616 PMCID: PMC6593395 DOI: 10.1021/acs.orglett.9b01115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Indexed: 01/19/2023]
Abstract
The design, synthesis, and conformational analysis of an oligobenzanilide helix mimetic scaffold capable of simultaneous mimicry of two faces of an α-helix is reported. The synthetic methodology provides access to diverse monomer building blocks amenable to solid-phase assembly in just four synthetic steps. The conformational flexibility of model dimers was investigated using a combination of solid and solution state methodologies supplemented with DFT calculations. The lack of noncovalent constraints allows for significant conformational plasticity in the scaffold, thus permitting it to successfully mimic residues i, i+2, i+4, i+6, i+7, and i+9 of a canonical α-helix.
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Affiliation(s)
- Theo Flack
- Department of Chemistry,
Molecular Sciences Research Hub, Imperial
College London, London W12 0BZ, U.K.
| | - Charles Romain
- Department of Chemistry,
Molecular Sciences Research Hub, Imperial
College London, London W12 0BZ, U.K.
| | - Andrew J. P. White
- Department of Chemistry,
Molecular Sciences Research Hub, Imperial
College London, London W12 0BZ, U.K.
| | - Peter R. Haycock
- Department of Chemistry,
Molecular Sciences Research Hub, Imperial
College London, London W12 0BZ, U.K.
| | - Anna Barnard
- Department of Chemistry,
Molecular Sciences Research Hub, Imperial
College London, London W12 0BZ, U.K.
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29
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Valeur E, Jimonet P. New Modalities, Technologies, and Partnerships in Probe and Lead Generation: Enabling a Mode-of-Action Centric Paradigm. J Med Chem 2018; 61:9004-9029. [DOI: 10.1021/acs.jmedchem.8b00378] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Eric Valeur
- Medicinal Chemistry, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal 431 83, Sweden
| | - Patrick Jimonet
- External Innovation Drug Discovery, Global Business Development & Licensing, Sanofi, 13 quai Jules Guesde, 94400 Vitry-sur-Seine, France
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30
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Sawyer TK, Partridge AW, Kaan HYK, Juang YC, Lim S, Johannes C, Yuen TY, Verma C, Kannan S, Aronica P, Tan YS, Sherborne B, Ha S, Hochman J, Chen S, Surdi L, Peier A, Sauvagnat B, Dandliker PJ, Brown CJ, Ng S, Ferrer F, Lane DP. Macrocyclic α helical peptide therapeutic modality: A perspective of learnings and challenges. Bioorg Med Chem 2018; 26:2807-2815. [PMID: 29598901 DOI: 10.1016/j.bmc.2018.03.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 03/03/2018] [Accepted: 03/06/2018] [Indexed: 12/20/2022]
Abstract
Macrocyclic α-helical peptides have emerged as a compelling new therapeutic modality to tackle targets confined to the intracellular compartment. Within the scope of hydrocarbon-stapling there has been significant progress to date, including the first stapled α-helical peptide to enter into clinical trials. The principal design concept of stapled α-helical peptides is to mimic a cognate (protein) ligand relative to binding its target via an α-helical interface. However, it was the proclivity of such stapled α-helical peptides to exhibit cell permeability and proteolytic stability that underscored their promise as unique macrocyclic peptide drugs for intracellular targets. This perspective highlights key learnings as well as challenges in basic research with respect to structure-based design, innovative chemistry, cell permeability and proteolytic stability that are essential to fulfill the promise of stapled α-helical peptide drug development.
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31
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A High-Throughput Synthetic Platform Enables the Discovery of Proteomimetic Cell Penetrating Peptides and Bioportides. Int J Pept Res Ther 2018. [DOI: 10.1007/s10989-018-9681-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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32
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Shin YH, Gellman SH. Impact of Backbone Pattern and Residue Substitution on Helicity in α/β/γ-Peptides. J Am Chem Soc 2018; 140:1394-1400. [PMID: 29350033 DOI: 10.1021/jacs.7b10868] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have evaluated the impact of changes in the chemical structure of peptidic oligomers containing α-, β-, and γ-amino acid residues (α/β/γ-peptides) on the propensities of these oligomers to adopt helical conformations in aqueous and alcoholic solutions. These studies were inspired by our previous discovery that α/β/γ-peptides containing a regular αγααβα hexad repeat adopt an α-helix-like conformation in which the β and γ residues are aligned in a stripe along one side, and the remainder of the helix surface is defined by the α residues. This helix was found to be most stable when the β and γ residues were rigidified with specific cyclic constraints. Relaxation of the β residue constraints caused profound conformational destabilization, but relaxation of the γ residue constraints led to only a moderate drop in helicity. The new work more broadly characterizes the effect of γ residue substitution on helix stability, based on circular dichroism and two-dimensional NMR measurements. We find that even a fully unsubstituted γ residue (derived from γ-aminobutyric acid) supports a moderate helical propensity, which is surprising in light of the strong destabilizing effect of glycine residues on α-helix stability. Additional studies examine the effects of altering sequence in terms of amino acid type, by comparing a prototype with the αγααβα hexad pattern to isomers with irregular arrangements of the α, β, and γ residues along the backbone. The data indicate that the strong helix-forming propensity previously discovered for α/β/γ-peptide 12-mers is retained when sequence is varied, with small variations detected across diverse α-β-γ placements. These structural findings suggest that α/β/γ-peptide scaffolds represent versatile scaffolds for the design of peptidic foldamers that display specific functions.
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Affiliation(s)
- Young-Hee Shin
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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33
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Yu X, Li Y, Lou Y, Wang T. Molecular design and engineering of phosphopeptide ligands to target lung cancer polo-like kinase. BIOTECHNOL BIOPROC E 2017. [DOI: 10.1007/s12257-016-0441-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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34
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Watkins AM, Bonneau R, Arora PS. Modeling and Design of Peptidomimetics to Modulate Protein-Protein Interactions. Methods Mol Biol 2017; 1561:291-307. [PMID: 28236245 DOI: 10.1007/978-1-4939-6798-8_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We describe a modular approach to identify and inhibit protein-protein interactions (PPIs) that are mediated by protein secondary and tertiary structures with rationally designed peptidomimetics. Our analysis begins with entries of high-resolution complexes in the Protein Data Bank and utilizes conformational sampling, scoring, and design capabilities of advanced biomolecular modeling software to develop peptidomimetics.
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Affiliation(s)
| | - Richard Bonneau
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Computer Science Department, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, 29 Washington Place, Brown Bldg., Room 360, New York, NY, USA.
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35
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Zhang Q, Jiang F, Zhao B, Lin H, Tian Y, Xie M, Bai G, Gilbert AM, Goetz GH, Liras S, Mathiowetz AA, Price DA, Song K, Tu M, Wu Y, Wang T, Flanagan ME, Wu YD, Li Z. Chiral Sulfoxide-Induced Single Turn Peptide α-Helicity. Sci Rep 2016; 6:38573. [PMID: 27934919 PMCID: PMC5146914 DOI: 10.1038/srep38573] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 11/09/2016] [Indexed: 11/25/2022] Open
Abstract
Inducing α-helicity through side-chain cross-linking is a strategy that has been pursued to improve peptide conformational rigidity and bio-availability. Here we describe the preparation of small peptides tethered to chiral sulfoxide-containing macrocyclic rings. Furthermore, a study of structure-activity relationships (SARs) disclosed properties with respect to ring size, sulfur position, oxidation state, and stereochemistry that show a propensity to induce α-helicity. Supporting data include circular dichroism spectroscopy (CD), NMR spectroscopy, and a single crystal X-ray structure for one such stabilized peptide. Finally, theoretical studies are presented to elucidate the effect of chiral sulfoxides in inducing backbone α-helicity.
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Affiliation(s)
- Qingzhou Zhang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Fan Jiang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Bingchuan Zhao
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Huacan Lin
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Yuan Tian
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Mingsheng Xie
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Guoyun Bai
- Cardiovascular and Metabolic Diseases Medicinal Chemistry, Pfizer, Inc., 620 Memorial Drive, Cambridge, MA, 02142, USA
| | - Adam M Gilbert
- Cardiovascular and Metabolic Diseases Medicinal Chemistry, Pfizer, Inc., 620 Memorial Drive, Cambridge, MA, 02142, USA
| | - Gilles H Goetz
- Cardiovascular and Metabolic Diseases Medicinal Chemistry, Pfizer, Inc., 620 Memorial Drive, Cambridge, MA, 02142, USA
| | - Spiros Liras
- Cardiovascular and Metabolic Diseases Medicinal Chemistry, Pfizer, Inc., 620 Memorial Drive, Cambridge, MA, 02142, USA
| | - Alan A Mathiowetz
- Cardiovascular and Metabolic Diseases Medicinal Chemistry, Pfizer, Inc., 620 Memorial Drive, Cambridge, MA, 02142, USA
| | - David A Price
- Cardiovascular and Metabolic Diseases Medicinal Chemistry, Pfizer, Inc., 620 Memorial Drive, Cambridge, MA, 02142, USA
| | - Kun Song
- Cardiovascular and Metabolic Diseases Medicinal Chemistry, Pfizer, Inc., 620 Memorial Drive, Cambridge, MA, 02142, USA
| | - Meihua Tu
- Cardiovascular and Metabolic Diseases Medicinal Chemistry, Pfizer, Inc., 620 Memorial Drive, Cambridge, MA, 02142, USA
| | - Yujie Wu
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Tao Wang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Mark E Flanagan
- Center for Chemistry Innovation and Excellence, Pfizer Inc., Eastern Point Road, Groton, CT, 06340, USA
| | - Yun-Dong Wu
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.,College of Chemistry, Peking University, Beijing, 100871, China
| | - Zigang Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
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36
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Watkins AM, Bonneau R, Arora PS. Side-Chain Conformational Preferences Govern Protein-Protein Interactions. J Am Chem Soc 2016; 138:10386-9. [PMID: 27483190 DOI: 10.1021/jacs.6b04892] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein secondary structures serve as geometrically constrained scaffolds for the display of key interacting residues at protein interfaces. Given the critical role of secondary structures in protein folding and the dependence of folding propensities on backbone dihedrals, secondary structure is expected to influence the identity of residues that are important for complex formation. Counter to this expectation, we find that a narrow set of residues dominates the binding energy in protein-protein complexes independent of backbone conformation. This finding suggests that the binding epitope may instead be substantially influenced by the side-chain conformations adopted. We analyzed side-chain conformational preferences in residues that contribute significantly to binding. This analysis suggests that preferred rotamers contribute directly to specificity in protein complex formation and provides guidelines for peptidomimetic inhibitor design.
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Affiliation(s)
| | - Richard Bonneau
- Center for Computational Biology, Simons Foundation , New York, New York 10010, United States
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37
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Checco JW, Gellman SH. Targeting recognition surfaces on natural proteins with peptidic foldamers. Curr Opin Struct Biol 2016; 39:96-105. [PMID: 27390896 DOI: 10.1016/j.sbi.2016.06.014] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 05/22/2016] [Accepted: 06/15/2016] [Indexed: 11/30/2022]
Abstract
Molecules intended to antagonize protein-protein interactions or augment polypeptide-based signaling must bind tightly to large and specific surfaces on target proteins. Some types of unnatural oligomers with discrete folding propensities ('foldamers') have recently been shown to display this capability. This review covers important recent advances among several classes of foldamers, including α-peptides with secondary structures stabilized by covalent bonds, d-α-peptides, α/β-peptides and oligo-oxopiperazines. Recent advances in this area have involved enhancing membrane permeability to provide access to intracellular protein targets, improving pharmacokinetics and duration of action in vivo, and developing strategies appropriate for targeting large and irregularly-shaped protein surfaces.
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Affiliation(s)
- James W Checco
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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38
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Rezaei Araghi R, Keating AE. Designing helical peptide inhibitors of protein-protein interactions. Curr Opin Struct Biol 2016; 39:27-38. [PMID: 27123812 DOI: 10.1016/j.sbi.2016.04.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/28/2016] [Accepted: 04/03/2016] [Indexed: 02/04/2023]
Abstract
Short helical peptides combine characteristics of small molecules and large proteins and provide an exciting area of opportunity in protein design. A growing number of studies report novel helical peptide inhibitors of protein-protein interactions. New techniques have been developed for peptide design and for chemically stabilizing peptides in a helical conformation, which frequently improves protease resistance and cell permeability. We summarize advances in peptide crosslinking chemistry and give examples of peptide design studies targeting coiled-coil transcription factors, Bcl-2 family proteins, MDM2/MDMX, and HIV gp41, among other targets.
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Affiliation(s)
- Raheleh Rezaei Araghi
- MIT Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Amy E Keating
- MIT Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; MIT Department of Biological Engineering, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.
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39
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40
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Tian Y, Li J, Zhao H, Zeng X, Wang D, Liu Q, Niu X, Huang X, Xu N, Li Z. Stapling of unprotected helical peptides via photo-induced intramolecular thiol-yne hydrothiolation. Chem Sci 2016; 7:3325-3330. [PMID: 29997825 PMCID: PMC6006495 DOI: 10.1039/c6sc00106h] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 02/03/2016] [Indexed: 12/27/2022] Open
Abstract
Peptide stapling emerged as a versatile strategy to recapitulate the bioactive helical conformation of unstructured short peptides in water to improve their therapeutic properties in targeting intracellular "undruggable" targets. Here, we describe the development of photo-induced intramolecular thiol-yne macrocyclization for rapid access to short stapled peptides with enhanced biophysical properties. This new peptide stapling technique provides rapid access to conformationally constrained helices with satisfying functional group tolerance. Notably, the vinyl sulfide linkage shows distinct lipophilicity with reduced membrane toxicity compared to the corresponding all-hydrocarbon analogue. As a proof of principle, we constructed stabilized helices modulating intracellular estrogen receptor (ER)-coactivator interactions with a nanomolar binding affinity, enhanced serum stability, a diffuse cellular distribution and selective cytotoxicity towards ER-positive MCF-7 cells.
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Affiliation(s)
- Yuan Tian
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen , 518055 , China .
| | - Jingxu Li
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen , 518055 , China .
| | - Hui Zhao
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen , 518055 , China .
| | - Xiangze Zeng
- Department of Chemistry , Center of Systems Biology and Human Health , School of Science and Institute for Advance Study , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon , Hong Kong , China
| | - Dongyuan Wang
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen , 518055 , China .
| | - Qisong Liu
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen , 518055 , China .
| | - Xiaogang Niu
- College of Chemistry and Molecular Engineering , Beijing Nuclear Magnetic Resonance Center , Peking University , Beijing , 100871 , China
| | - Xuhui Huang
- Department of Chemistry , Center of Systems Biology and Human Health , School of Science and Institute for Advance Study , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon , Hong Kong , China
| | - Naihan Xu
- Key Lab in Healthy Science and Technology , Division of Life Science , Shenzhen Graduate School of Tsinghua University , Shenzhen , 518055 , China .
| | - Zigang Li
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen , 518055 , China .
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41
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Tian Y, Wang D, Li J, Shi C, Zhao H, Niu X, Li Z. A proline-derived transannular N-cap for nucleation of short α-helical peptides. Chem Commun (Camb) 2016; 52:9275-8. [DOI: 10.1039/c6cc04672j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report herein a simple and practical proline-derived transannular N-cap as a helix nucleating template in diverse bio-related peptide sequences via macrolactamization on resin.
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Affiliation(s)
- Yuan Tian
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
| | - Dongyuan Wang
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
| | - Jingxu Li
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
| | - Chuan Shi
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
| | - Hui Zhao
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
| | - Xiaogang Niu
- College of Chemistry and Molecular Engineering
- Beijing Nuclear Magnetic Resonance Center
- Peking University
- Beijing
- China
| | - Zigang Li
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
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42
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Trobe M, Breinbauer R. Improved and scalable synthesis of building blocks for the modular synthesis of teraryl-based alpha-helix mimetics. MONATSHEFTE FUR CHEMIE 2015. [DOI: 10.1007/s00706-015-1599-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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43
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Maffucci I, Clayden J, Contini A. Origin of Helical Screw Sense Selectivity Induced by Chiral Constrained Cα-Tetrasubstituted α-Amino Acids in Aib-based Peptides. J Phys Chem B 2015; 119:14003-13. [PMID: 26457452 DOI: 10.1021/acs.jpcb.5b07050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The mechanisms behind the propensity of chiral constrained Cα-tetrasubstituted amino acids (cCTAAs) to induce one particular helical screw sense, when included in the Ac-Aib2-cCTAA-Aib2-NHMe peptide model, were studied through replica exchange molecular dynamics, potential of mean force, and quantum theory of atoms in molecules calculations. We observed that cCTAAs exert their effect on helical screw sense selectivity through the positioning of the side chain to generate steric hindrance in either the (-x, +y, +z) or (+x, +y, -z) sectors of a right-handed 3D Cartesian space, where the z axis corresponds to the axis of the helix and the Cα lies on the +y semiaxis (0, +y, 0). The different strengthening of the noncovalent interactions, also comprising C-H···O interactions, exerted by the cCTAA in the right-handed or left-handed helix was also found important to define the preference of a cCTAA for a particular helix screw sense.
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Affiliation(s)
- Irene Maffucci
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano , Via Venezian, 21, 20133 Milano, Italy
| | - Jonathan Clayden
- School of Chemistry, University of Manchester , Oxford Road, Manchester M13 9PL, U.K
| | - Alessandro Contini
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano , Via Venezian, 21, 20133 Milano, Italy
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44
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Cromm PM, Spiegel J, Grossmann TN, Waldmann H. Direkte Modulation von Aktivität und Funktion kleiner GTPasen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504357] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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45
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Cromm PM, Spiegel J, Grossmann TN, Waldmann H. Direct Modulation of Small GTPase Activity and Function. Angew Chem Int Ed Engl 2015; 54:13516-37. [DOI: 10.1002/anie.201504357] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Indexed: 12/19/2022]
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46
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Abstract
Interactions between polypeptide chains containing amino acid residues with opposite absolute configurations have long been a source of interest and speculation, but there is very little structural information for such heterochiral associations. The need to address this lacuna has grown in recent years because of increasing interest in the use of peptides generated from d amino acids (d peptides) as specific ligands for natural proteins, e.g., to inhibit deleterious protein-protein interactions. Coiled-coil interactions, between or among α-helices, represent the most common tertiary and quaternary packing motif in proteins. Heterochiral coiled-coil interactions were predicted over 50 years ago by Crick, and limited experimental data obtained in solution suggest that such interactions can indeed occur. To address the dearth of atomic-level structural characterization of heterochiral helix pairings, we report two independent crystal structures that elucidate coiled-coil packing between l- and d-peptide helices. Both structures resulted from racemic crystallization of a peptide corresponding to the transmembrane segment of the influenza M2 protein. Networks of canonical knobs-into-holes side-chain packing interactions are observed at each helical interface. However, the underlying patterns for these heterochiral coiled coils seem to deviate from the heptad sequence repeat that is characteristic of most homochiral analogs, with an apparent preference for a hendecad repeat pattern.
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47
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Hoggard LR, Zhang Y, Zhang M, Panic V, Wisniewski JA, Ji H. Rational design of selective small-molecule inhibitors for β-catenin/B-cell lymphoma 9 protein-protein interactions. J Am Chem Soc 2015; 137:12249-60. [PMID: 26352795 DOI: 10.1021/jacs.5b04988] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Selective inhibition of α-helix-mediated protein-protein interactions (PPIs) with small organic molecules provides great potential for the discovery of chemical probes and therapeutic agents. Protein Data Bank data mining using the HippDB database indicated that (1) the side chains of hydrophobic projecting hot spots at positions i, i + 3, and i + 7 of an α-helix had few orientations when interacting with the second protein and (2) the hot spot pockets of PPI complexes had different sizes, shapes, and chemical groups when interacting with the same hydrophobic projecting hot spots of α-helix. On the basis of these observations, a small organic molecule, 4'-fluoro-N-phenyl-[1,1'-biphenyl]-3-carboxamide, was designed as a generic scaffold that itself directly mimics the binding mode of the side chains of hydrophobic projecting hot spots at positions i, i + 3, and i + 7 of an α-helix. Convenient decoration of this generic scaffold led to the selective disruption of α-helix-mediated PPIs. A series of small-molecule inhibitors selective for β-catenin/B-cell lymphoma 9 (BCL9) over β-catenin/cadherin PPIs was designed and synthesized. The binding mode of new inhibitors was characterized by site-directed mutagenesis and structure-activity relationship studies. This new class of inhibitors can selectively disrupt β-catenin/BCL9 over β-catenin/cadherin PPIs, suppress the transactivation of canonical Wnt signaling, downregulate the expression of Wnt target genes, and inhibit the growth of Wnt/β-catenin-dependent cancer cells.
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Affiliation(s)
- Logan R Hoggard
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Yongqiang Zhang
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Min Zhang
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Vanja Panic
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - John A Wisniewski
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Haitao Ji
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
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Watkins A, Wuo MG, Arora PS. Protein-Protein Interactions Mediated by Helical Tertiary Structure Motifs. J Am Chem Soc 2015; 137:11622-30. [PMID: 26302018 PMCID: PMC4577960 DOI: 10.1021/jacs.5b05527] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Indexed: 12/26/2022]
Abstract
The modulation of protein-protein interactions (PPIs) by means of creating or stabilizing secondary structure conformations is a rapidly growing area of research. Recent success in the inhibition of difficult PPIs by secondary structure mimetics also points to potential limitations, because often, specific cases require tertiary structure mimetics. To streamline protein structure-based inhibitor design, we have previously described the examination of protein complexes in the Protein Data Bank where α-helices or β-strands form critical contacts. Here, we examined coiled coils and helix bundles that mediate complex formation to create a platform for the discovery of potential tertiary structure mimetics. Though there has been extensive analysis of coiled coil motifs, the interactions between pre-formed coiled coils and globular proteins have not been systematically analyzed. This article identifies critical features of these helical interfaces with respect to coiled coil and other helical PPIs. We expect the analysis to prove useful for the rational design of modulators of this fundamental class of protein assemblies.
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Affiliation(s)
- Andrew
M. Watkins
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Michael G. Wuo
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, New York, New York 10003, United States
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49
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Library construction, selection and modification strategies to generate therapeutic peptide-based modulators of protein-protein interactions. Future Med Chem 2015; 6:2073-92. [PMID: 25531969 DOI: 10.4155/fmc.14.134] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In the modern age of proteomics, vast numbers of protein-protein interactions (PPIs) are being identified as causative agents in pathogenesis, and are thus attractive therapeutic targets for intervention. Although traditionally regarded unfavorably as druggable agents relative to small molecules, peptides in recent years have gained considerable attention. Their previous dismissal had been largely due to the susceptibility of unmodified peptides to the barriers and pressures exerted by the circulation, immune system, proteases, membranes and other stresses. However, recent advances in high-throughput peptide isolation techniques, as well as a huge variety of direct modification options and approaches to allow targeted delivery, mean that peptides and their mimetics can now be designed to circumvent many of these traditional barriers. As a result, an increasing number of peptide-based drugs are reaching clinical trials and patients beyond.
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50
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Pollock J, Borkin D, Lund G, Purohit T, Dyguda-Kazimierowicz E, Grembecka J, Cierpicki T. Rational Design of Orthogonal Multipolar Interactions with Fluorine in Protein-Ligand Complexes. J Med Chem 2015; 58:7465-74. [PMID: 26288158 PMCID: PMC4584387 DOI: 10.1021/acs.jmedchem.5b00975] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
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Multipolar interactions involving
fluorine and the protein backbone
have been frequently observed in protein–ligand complexes.
Such fluorine–backbone interactions may substantially contribute
to the high affinity of small molecule inhibitors. Here we found that
introduction of trifluoromethyl groups into two different sites in
the thienopyrimidine class of menin–MLL inhibitors considerably
improved their inhibitory activity. In both cases, trifluoromethyl
groups are engaged in short interactions with the backbone of menin.
In order to understand the effect of fluorine, we synthesized a series
of analogues by systematically changing the number of fluorine atoms,
and we determined high-resolution crystal structures of the complexes
with menin. We found that introduction of fluorine at favorable geometry
for interactions with backbone carbonyls may improve the activity
of menin–MLL inhibitors as much as 5- to 10-fold. In order
to facilitate the design of multipolar fluorine–backbone interactions
in protein–ligand complexes, we developed a computational algorithm
named FMAP, which calculates fluorophilic sites in proximity to the
protein backbone. We demonstrated that FMAP could be used to rationalize
improvement in the activity of known protein inhibitors upon introduction
of fluorine. Furthermore, FMAP may also represent a valuable tool
for designing new fluorine substitutions and support ligand optimization
in drug discovery projects. Analysis of the menin–MLL inhibitor
complexes revealed that the backbone in secondary structures is particularly
accessible to the interactions with fluorine. Considering that secondary
structure elements are frequently exposed at protein interfaces, we
postulate that multipolar fluorine–backbone interactions may
represent a particularly attractive approach to improve inhibitors
of protein–protein interactions.
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Affiliation(s)
- Jonathan Pollock
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Dmitry Borkin
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - George Lund
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Trupta Purohit
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Edyta Dyguda-Kazimierowicz
- Molecular Modeling and Quantum Chemistry Group, Department of Chemistry, Wrocław University of Technology , Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
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