1
|
Obermann R, Yemane B, Jarvis C, Franco FM, Kyriukha Y, Nolan W, Gohara B, Krezel AM, Wildman SA, Janetka JW. Small Molecule Antagonists of the DNA Repair ERCC1/XPA Protein-Protein Interaction. ChemMedChem 2024; 19:e202300648. [PMID: 38300970 PMCID: PMC11031295 DOI: 10.1002/cmdc.202300648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/03/2024]
Abstract
The DNA excision repair protein ERCC1 and the DNA damage sensor protein, XPA are highly overexpressed in patient samples of cisplatin-resistant solid tumors including lung, bladder, ovarian, and testicular cancer. The repair of cisplatin-DNA crosslinks is dependent upon nucleotide excision repair (NER) that is modulated by protein-protein binding interactions of ERCC1, the endonuclease, XPF, and XPA. Thus, inhibition of their function is a potential therapeutic strategy for the selective sensitization of tumors to DNA-damaging platinum-based cancer therapy. Here, we report on new small-molecule antagonists of the ERCC1/XPA protein-protein interaction (PPI) discovered using a high-throughput competitive fluorescence polarization binding assay. We discovered a unique structural class of thiopyridine-3-carbonitrile PPI antagonists that block a truncated XPA polypeptide from binding to ERCC1. Preliminary hit-to-lead studies from compound 1 reveal structure-activity relationships (SAR) and identify lead compound 27 o with an EC50 of 4.7 μM. Furthermore, chemical shift perturbation mapping by NMR confirms that 1 binds within the same site as the truncated XPA67-80 peptide. These novel ERCC1 antagonists are useful chemical biology tools for investigating DNA damage repair pathways and provide a good starting point for medicinal chemistry optimization as therapeutics for sensitizing tumors to DNA damaging agents and overcoming resistance to platinum-based chemotherapy.
Collapse
Affiliation(s)
| | | | - Cassie Jarvis
- Washington University School of Medicine, Department of Biochemistry and Molecular Biophysics, 660 S. Euclid Ave., Box 8231, St. Louis, MO 63110 USA
| | - Francisco M. Franco
- Washington University School of Medicine, Department of Biochemistry and Molecular Biophysics, 660 S. Euclid Ave., Box 8231, St. Louis, MO 63110 USA
| | - Yevhenii Kyriukha
- Washington University School of Medicine, Department of Biochemistry and Molecular Biophysics, 660 S. Euclid Ave., Box 8231, St. Louis, MO 63110 USA
| | - William Nolan
- Washington University School of Medicine, Department of Biochemistry and Molecular Biophysics, 660 S. Euclid Ave., Box 8231, St. Louis, MO 63110 USA
| | - Beth Gohara
- Washington University School of Medicine, Department of Biochemistry and Molecular Biophysics, 660 S. Euclid Ave., Box 8231, St. Louis, MO 63110 USA
| | - Andrzej M. Krezel
- Washington University School of Medicine, Department of Biochemistry and Molecular Biophysics, 660 S. Euclid Ave., Box 8231, St. Louis, MO 63110 USA
| | - Scott A. Wildman
- Washington University School of Medicine, Department of Biochemistry and Molecular Biophysics, 660 S. Euclid Ave., Box 8231, St. Louis, MO 63110 USA
| | - James W. Janetka
- Washington University School of Medicine, Department of Biochemistry and Molecular Biophysics, 660 S. Euclid Ave., Box 8231, St. Louis, MO 63110 USA
| |
Collapse
|
2
|
Zhang Z, Zhao L, Gao M, Chen Y, Wang J, Wang C. PPII-AEAT: Prediction of protein-protein interaction inhibitors based on autoencoders with adversarial training. Comput Biol Med 2024; 172:108287. [PMID: 38503089 DOI: 10.1016/j.compbiomed.2024.108287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/21/2024] [Accepted: 03/12/2024] [Indexed: 03/21/2024]
Abstract
Protein-protein interactions (PPIs) have shown increasing potential as novel drug targets. The design and development of small molecule inhibitors targeting specific PPIs are crucial for the prevention and treatment of related diseases. Accordingly, effective computational methods are highly desired to meet the emerging need for the large-scale accurate prediction of PPI inhibitors. However, existing machine learning models rely heavily on the manual screening of features and lack generalizability. Here, we propose a new PPI inhibitor prediction method based on autoencoders with adversarial training (named PPII-AEAT) that can adaptively learn molecule representation to cope with different PPI targets. First, Extended-connectivity fingerprints and Mordred descriptors are employed to extract the primary features of small molecular compounds. Then, an autoencoder architecture is trained in three phases to learn high-level representations and predict inhibitory scores. We evaluate PPII-AEAT on nine PPI targets and two different tasks, including the PPI inhibitor identification task and inhibitory potency prediction task. The experimental results show that our proposed PPII-AEAT outperforms state-of-the-art methods.
Collapse
Affiliation(s)
- Zitong Zhang
- Faculty of Computing, Harbin Institute of Technology, Harbin, 150001, China
| | - Lingling Zhao
- Faculty of Computing, Harbin Institute of Technology, Harbin, 150001, China
| | - Mengyao Gao
- Faculty of Computing, Harbin Institute of Technology, Harbin, 150001, China
| | - Yuanlong Chen
- Faculty of Computing, Harbin Institute of Technology, Harbin, 150001, China
| | - Junjie Wang
- Department of Medical Informatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, 211166, China
| | - Chunyu Wang
- Faculty of Computing, Harbin Institute of Technology, Harbin, 150001, China.
| |
Collapse
|
3
|
Seidel T, Permann C, Wieder O, Kohlbacher SM, Langer T. High-Quality Conformer Generation with CONFORGE: Algorithm and Performance Assessment. J Chem Inf Model 2023; 63:5549-5570. [PMID: 37624145 PMCID: PMC10498443 DOI: 10.1021/acs.jcim.3c00563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Indexed: 08/26/2023]
Abstract
Knowledge of the putative bound-state conformation of a molecule is an essential prerequisite for the successful application of many computer-aided drug design methods that aim to assess or predict its capability to bind to a particular target receptor. An established approach to predict bioactive conformers in the absence of receptor structure information is to sample the low-energy conformational space of the investigated molecules and derive representative conformer ensembles that can be expected to comprise members closely resembling possible bound-state ligand conformations. The high relevance of such conformer generation functionality led to the development of a wide panel of dedicated commercial and open-source software tools throughout the last decades. Several published benchmarking studies have shown that open-source tools usually lag behind their commercial competitors in many key aspects. In this work, we introduce the open-source conformer ensemble generator CONFORGE, which aims at delivering state-of-the-art performance for all types of organic molecules in drug-like chemical space. The ability of CONFORGE and several well-known commercial and open-source conformer ensemble generators to reproduce experimental 3D structures as well as their computational efficiency and robustness has been assessed thoroughly for both typical drug-like molecules and macrocyclic structures. For small molecules, CONFORGE clearly outperformed all other tested open-source conformer generators and performed at least equally well as the evaluated commercial generators in terms of both processing speed and accuracy. In the case of macrocyclic structures, CONFORGE achieved the best average accuracy among all benchmarked generators, with RDKit's generator coming close in second place.
Collapse
Affiliation(s)
- Thomas Seidel
- Department
of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Christian Permann
- NeGeMac
Research Platform, Department of Pharmaceutical Sciences, Division
of Pharmaceutical Chemistry, University
of Vienna, Josef-Holaubek-Platz
2, 1090 Vienna, Austria
| | - Oliver Wieder
- Christian
Doppler Laboratory for Molecular Informatics in the Biosciences, Department
of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Stefan M. Kohlbacher
- Department
of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Thierry Langer
- Department
of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
- NeGeMac
Research Platform, Department of Pharmaceutical Sciences, Division
of Pharmaceutical Chemistry, University
of Vienna, Josef-Holaubek-Platz
2, 1090 Vienna, Austria
- Christian
Doppler Laboratory for Molecular Informatics in the Biosciences, Department
of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| |
Collapse
|
4
|
Bhuyan S, Das D, Chakraborty A, Mandal S, Dhanabal K, Roy BG. A Carbohydrate-based Synthetic Approach to Diverse Structurally and Stereochemically Complex Chiral Polyheterocycles. Chem Asian J 2021; 16:4108-4121. [PMID: 34706155 DOI: 10.1002/asia.202101123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 10/22/2021] [Indexed: 12/27/2022]
Abstract
Chiral polyheterocycles are one of the most frequently encountered scaffolds in natural products and in current drugs repertoire. A carbohydrate-based diversity oriented synthetic (DOS) approach has been employed for gaining access to many structurally diverse and stereochemically complex rigid polyheterocyclic molecules with multiple chiral hydroxyl groups to enhance aqueous solubility. Inexpensive chiral pool of D-Glucose has been judiciously exploited to get access of complex chiral polyheterocyclic structures using inexpensive, common achiral reagents and domino-Knoevenagel hetero-Diels-Alder (DKHDA) reaction as one of the key synthetic tools. Stereochemistry of newly generated stereocenters of polycyclic structures are unambiguously determined through NMR and X-ray crystallographic study. A chemoinformatic comparison (PCA and PMI) with 40 branded blockbuster drugs showed that newly generated polyheterocycles have good three-dimensional scaffold diversity and most of these pass the Lipinski filter of drug-likeness.
Collapse
Affiliation(s)
- Samuzal Bhuyan
- Department of Chemistry, Sikkim University, 6th Mile, Tadong, Gangtok, Sikkim, 737102, India
| | - Dharmendra Das
- Department of Chemistry, Sikkim University, 6th Mile, Tadong, Gangtok, Sikkim, 737102, India
| | - Amit Chakraborty
- Department of Mathematics, Sikkim University, 6th Mile, Tadong, Gangtok, Sikkim, 737102, India
| | - Susanta Mandal
- Department of Chemistry, Sikkim University, 6th Mile, Tadong, Gangtok, Sikkim, 737102, India
| | | | - Biswajit Gopal Roy
- Department of Chemistry, Sikkim University, 6th Mile, Tadong, Gangtok, Sikkim, 737102, India
| |
Collapse
|
5
|
Furiassi L, Tonogai EJ, Hergenrother PJ. Limonin as a Starting Point for the Construction of Compounds with High Scaffold Diversity. Angew Chem Int Ed Engl 2021; 60:16119-16128. [PMID: 33973348 PMCID: PMC8260459 DOI: 10.1002/anie.202104228] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Indexed: 12/21/2022]
Abstract
Structurally complex natural products have been a fruitful source for the discovery and development of new drugs. In an effort to construct a compound collection populated by architecturally complex members with unique scaffolds, we have used the natural product limonin as a starting point. Limonin is an abundant triterpenoid natural product and, through alteration of its heptacyclic core ring system using short synthetic sequences, a collection of 98 compounds was created, including multiple members with novel ring systems. The reactions leveraged in the construction of these compounds include novel ring cleavage, rearrangements, and cyclizations, and this work is highlighted by the discovery of a novel B-ring cleavage reaction, a unique B/C-ring rearrangement, an atypical D-ring cyclization, among others. Computational analysis shows that 52 different scaffolds/ring systems were produced during the course of this work, of which 36 are unprecedented. Phenotypic screening and structure-activity relationships identified compounds with activity against a panel of cancer cell lines.
Collapse
Affiliation(s)
- Lucia Furiassi
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Emily J Tonogai
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Paul J Hergenrother
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| |
Collapse
|
6
|
Furiassi L, Tonogai EJ, Hergenrother PJ. Limonin as a Starting Point for the Construction of Compounds with High Scaffold Diversity. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104228] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Lucia Furiassi
- Department of Chemistry Carl R. Woese Institute for Genomic Biology Cancer Center at Illinois University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Emily J. Tonogai
- Department of Chemistry Carl R. Woese Institute for Genomic Biology Cancer Center at Illinois University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Paul J. Hergenrother
- Department of Chemistry Carl R. Woese Institute for Genomic Biology Cancer Center at Illinois University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| |
Collapse
|
7
|
Reyes Romero A, Ruiz-Moreno AJ, Groves MR, Velasco-Velázquez M, Dömling A. Benchmark of Generic Shapes for Macrocycles. J Chem Inf Model 2020; 60:6298-6313. [PMID: 33270455 PMCID: PMC7768607 DOI: 10.1021/acs.jcim.0c01038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Macrocycles
target proteins that are otherwise considered undruggable
because of a lack of hydrophobic cavities and the presence of extended
featureless surfaces. Increasing efforts by computational chemists
have developed effective software to overcome the restrictions of
torsional and conformational freedom that arise as a consequence of
macrocyclization. Moloc is an efficient algorithm, with an emphasis
on high interactivity, and has been constantly updated since 1986
by drug designers and crystallographers of the Roche biostructural
community. In this work, we have benchmarked the shape-guided algorithm
using a dataset of 208 macrocycles, carefully selected on the basis
of structural complexity. We have quantified the accuracy, diversity,
speed, exhaustiveness, and sampling efficiency in an automated fashion
and we compared them with four commercial (Prime, MacroModel, molecular
operating environment, and molecular dynamics) and four open-access
(experimental-torsion distance geometry with additional “basic
knowledge” alone and with Merck molecular force field minimization
or universal force field minimization, Cambridge Crystallographic
Data Centre conformer generator, and conformator) packages. With three-quarters
of the database processed below the threshold of high ring accuracy,
Moloc was identified as having the highest sampling efficiency and
exhaustiveness without producing thousands of conformations, random
ring splitting into two half-loops, and possibility to interactively
produce globular or flat conformations with diversity similar to Prime,
MacroModel, and molecular dynamics. The algorithm and the Python scripts
for full automatization of these parameters are freely available for
academic use.
Collapse
Affiliation(s)
- Atilio Reyes Romero
- Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, XB20, 9713 AV Groningen, The Netherlands
| | - Angel Jonathan Ruiz-Moreno
- Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, XB20, 9713 AV Groningen, The Netherlands.,Departamento de Farmacología y Unidad Periférica de Investigación en Biomedicina Trasnacional, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 3000, Circuito Exterior S/N, Delegación Coyoacán, Ciudad Universitaria, 04510 Ciudad de México, Mexico.,Programa de Doctorado en Ciencias Biomédicas, UNAM, Av. Universidad 3000, Circuito Exterior S/N. Delegación Coyoacán, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Matthew R Groves
- Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, XB20, 9713 AV Groningen, The Netherlands
| | - Marco Velasco-Velázquez
- Departamento de Farmacología y Unidad Periférica de Investigación en Biomedicina Trasnacional, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 3000, Circuito Exterior S/N, Delegación Coyoacán, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Alexander Dömling
- Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, XB20, 9713 AV Groningen, The Netherlands
| |
Collapse
|
8
|
Bruns D, Gawehn E, Kumar KS, Schneider P, Baumgartner M, Schneider G. Identification of Synthetic Activators of Cancer Cell Migration by Hybrid Deep Learning. Chembiochem 2020; 21:500-507. [PMID: 31418992 DOI: 10.1002/cbic.201900346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/07/2019] [Indexed: 12/22/2022]
Abstract
Deep convolutional neural networks (CNNs) are a method of choice for image recognition. Herein a hybrid CNN approach is presented for molecular pattern recognition in drug discovery. Using self-organizing map images of molecular pharmacophores as input, CNN models were trained to identify chemokine receptor CXCR4 modulators with high accuracy. This machine learning classifier identified first-in-class synthetic CXCR4 full agonists. The receptor-activating effects were confirmed by intracellular cAMP response and in a phenotypic spheroid invasion assay of medulloblastoma cell invasion. Additional macromolecular targets of the small molecules were predicted in silico and tested in vitro, revealing modulatory effects on dopamine receptors and CCR1. These results positively advocate the applicability of molecular image recognition by CNNs to ligand-based virtual compound screening, and demonstrate the complementarity of machine intelligence and human expert knowledge.
Collapse
Affiliation(s)
- Dominique Bruns
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, RETHINK, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Erik Gawehn
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, RETHINK, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Karthiga Santhana Kumar
- Paediatric Neuro-Oncology Research Group, Department of Oncology, Children's Research Center, University Children's Hospital Zürich, Lengghalde 5, 8008, Zürich, Switzerland
| | - Petra Schneider
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, RETHINK, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Martin Baumgartner
- Paediatric Neuro-Oncology Research Group, Department of Oncology, Children's Research Center, University Children's Hospital Zürich, Lengghalde 5, 8008, Zürich, Switzerland
| | - Gisbert Schneider
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, RETHINK, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| |
Collapse
|
9
|
van der Vlag R, Yagiz Unver M, Felicetti T, Twarda‐Clapa A, Kassim F, Ermis C, Neochoritis CG, Musielak B, Labuzek B, Dömling A, Holak TA, Hirsch AKH. Optimized Inhibitors of MDM2 via an Attempted Protein-Templated Reductive Amination. ChemMedChem 2020; 15:370-375. [PMID: 31774938 PMCID: PMC7064911 DOI: 10.1002/cmdc.201900574] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/21/2019] [Indexed: 12/17/2022]
Abstract
Innovative and efficient hit-identification techniques are required to accelerate drug discovery. Protein-templated fragment ligations represent a promising strategy in early drug discovery, enabling the target to assemble and select its binders from a pool of building blocks. Development of new protein-templated reactions to access a larger structural diversity and expansion of the variety of targets to demonstrate the scope of the technique are of prime interest for medicinal chemists. Herein, we present our attempts to use a protein-templated reductive amination to target protein-protein interactions (PPIs), a challenging class of drug targets. We address a flexible pocket, which is difficult to achieve by structure-based drug design. After careful analysis we did not find one of the possible products in the kinetic target-guided synthesis (KTGS) approach, however subsequent synthesis and biochemical evaluation of each library member demonstrated that all the obtained molecules inhibit MDM2. The most potent library member (Ki =0.095 μm) identified is almost as active as Nutlin-3, a potent inhibitor of the p53-MDM2 PPI.
Collapse
Affiliation(s)
- Ramon van der Vlag
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - M. Yagiz Unver
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - Tommaso Felicetti
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
- Department of Pharmaceutical SciencesUniversity of PerugiaVia del Liceo 106123PerugiaItaly
| | | | - Fatima Kassim
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - Cagdas Ermis
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - Constantinos G. Neochoritis
- Department of Pharmacy, Drug Design groupUniversity of GroningenA. Deusinglaan 1GroningenThe Netherlands
- Chemistry departmentUniversity of Crete70013HeraklionGreece
| | - Bogdan Musielak
- Faculty of ChemistryJagiellonian UniversityGronostajowa 230-387KrakowPoland
| | - Beata Labuzek
- Faculty of ChemistryJagiellonian UniversityGronostajowa 230-387KrakowPoland
| | - Alexander Dömling
- Department of Pharmacy, Drug Design groupUniversity of GroningenA. Deusinglaan 1GroningenThe Netherlands
| | - Tad A. Holak
- Faculty of ChemistryJagiellonian UniversityGronostajowa 230-387KrakowPoland
| | - Anna K. H. Hirsch
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus Building E8.166123SaarbrückenGermany
| |
Collapse
|
10
|
Paciaroni NG, Perry DL, Norwood VM, Murillo-Solano C, Collins J, Tenneti S, Chakrabarti D, Huigens RW. Re-Engineering of Yohimbine's Biological Activity through Ring Distortion: Identification and Structure-Activity Relationships of a New Class of Antiplasmodial Agents. ACS Infect Dis 2020; 6:159-167. [PMID: 31913597 DOI: 10.1021/acsinfecdis.9b00380] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Select natural products are ideal starting points for ring distortion, or the dramatic altering of inherently complex molecules through short synthetic pathways, to generate an array of novel compounds with diverse skeletal architectures. A major goal of our ring distortion approach is to re-engineer the biological activity of indole alkaloids to identify new compounds with diverse biological activities in areas of significance to human health and medicine. In this study, we re-engineered the biological activity of the indole alkaloid yohimbine through ring rearrangement and ring cleavage synthesis pathways to discover new series of antiplasmodial agents. One new compound, Y7j, was found to demonstrate good potency against chloroquine-resistant Plasmodium falciparum Dd2 cells (EC50 = 0.33 μM) without eliciting cytotoxicity against HepG2 cells (EC50 > 40 μM). Y7j demonstrated stage-specific action against parasites at the late ring/trophozoite stage. A series of analogues was synthesized to gain structure-activity relationship insights, and we learned that both benzyl groups of Y7j are required for activity and fine-tuning of antiplasmodial activities could be accomplished by changing substitution patterns on the benzyl moieties. This study demonstrates the potential for ring distortion to drive new discoveries and change paradigms in chemical biology and drug discovery.
Collapse
Affiliation(s)
- Nicholas G. Paciaroni
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
| | - David L. Perry
- Division of Molecular Biology and Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, 12722 Research Parkway, Orlando, Florida 32826, United States
| | - Verrill M. Norwood
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
| | - Claribel Murillo-Solano
- Division of Molecular Biology and Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, 12722 Research Parkway, Orlando, Florida 32826, United States
| | - Jennifer Collins
- Division of Molecular Biology and Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, 12722 Research Parkway, Orlando, Florida 32826, United States
| | - Srinivasarao Tenneti
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
| | - Debopam Chakrabarti
- Division of Molecular Biology and Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, 12722 Research Parkway, Orlando, Florida 32826, United States
| | - Robert W. Huigens
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
| |
Collapse
|
11
|
Hitting on the move: Targeting intrinsically disordered protein states of the MDM2-p53 interaction. Eur J Med Chem 2019; 182:111588. [PMID: 31421630 DOI: 10.1016/j.ejmech.2019.111588] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/22/2019] [Accepted: 08/04/2019] [Indexed: 01/17/2023]
Abstract
Intrinsically disordered proteins are an emerging class of proteins without a folded structure and currently disorder-based drug targeting remains a challenge. p53 is the principal regulator of cell division and growth whereas MDM2 consists its main negative regulator. The MDM2-p53 recognition is a dynamic and multistage process that amongst other, employs the dissociation of a transient α-helical N-terminal ''lid'' segment of MDM2 from the proximity of the p53-complementary interface. Several small molecule inhibitors have been reported to inhibit the formation of the p53-MDM2 complex with the vast majority mimicking the p53 residues Phe19, Trp23 and Leu26. Recently, we have described the transit from the 3-point to 4-point pharmacophore model stabilizing this intrinsically disordered N-terminus by increasing the binding affinity by a factor of 3. Therefore, we performed a thorough SAR analysis, including chiral separation of key compound which was evaluated by FP and 2D NMR. Finally, p53-specific anti-cancer activity towards p53-wild-type cancer cells was observed for several representative compounds.
Collapse
|
12
|
Balasubramanian K, Gupta SP. Quantum Molecular Dynamics, Topological, Group Theoretical and Graph Theoretical Studies of Protein-Protein Interactions. Curr Top Med Chem 2019; 19:426-443. [PMID: 30836919 DOI: 10.2174/1568026619666190304152704] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 11/08/2018] [Accepted: 11/28/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Protein-protein interactions (PPIs) are becoming increasingly important as PPIs form the basis of multiple aggregation-related diseases such as cancer, Creutzfeldt-Jakob, and Alzheimer's diseases. This mini-review presents hybrid quantum molecular dynamics, quantum chemical, topological, group theoretical, graph theoretical, and docking studies of PPIs. We also show how these theoretical studies facilitate the discovery of some PPI inhibitors of therapeutic importance. OBJECTIVE The objective of this review is to present hybrid quantum molecular dynamics, quantum chemical, topological, group theoretical, graph theoretical, and docking studies of PPIs. We also show how these theoretical studies enable the discovery of some PPI inhibitors of therapeutic importance. METHODS This article presents a detailed survey of hybrid quantum dynamics that combines classical and quantum MD for PPIs. The article also surveys various developments pertinent to topological, graph theoretical, group theoretical and docking studies of PPIs and highlight how the methods facilitate the discovery of some PPI inhibitors of therapeutic importance. RESULTS It is shown that it is important to include higher-level quantum chemical computations for accurate computations of free energies and electrostatics of PPIs and Drugs with PPIs, and thus techniques that combine classical MD tools with quantum MD are preferred choices. Topological, graph theoretical and group theoretical techniques are shown to be important in studying large network of PPIs comprised of over 100,000 proteins where quantum chemical and other techniques are not feasible. Hence, multiple techniques are needed for PPIs. CONCLUSION Drug discovery and our understanding of complex PPIs require multifaceted techniques that involve several disciplines such as quantum chemistry, topology, graph theory, knot theory and group theory, thus demonstrating a compelling need for a multi-disciplinary approach to the problem.
Collapse
Affiliation(s)
- Krishnan Balasubramanian
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, AZ 85287-1604, United States
| | - Satya P Gupta
- Department of Pharmaceutical Technology, Meerut Institute of Engineering Technology, Meerut-250002, India
| |
Collapse
|
13
|
Mishra V, Pathak C. Structural insights into pharmacophore-assisted in silico identification of protein-protein interaction inhibitors for inhibition of human toll-like receptor 4 - myeloid differentiation factor-2 (hTLR4-MD-2) complex. J Biomol Struct Dyn 2018; 37:1968-1991. [PMID: 29842849 DOI: 10.1080/07391102.2018.1474804] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Toll-like receptor 4 (TLR4) is a member of Toll-Like Receptors (TLRs) family that serves as a receptor for bacterial lipopolysaccharide (LPS). TLR4 alone cannot recognize LPS without aid of co-receptor myeloid differentiation factor-2 (MD-2). Binding of LPS with TLR4 forms a LPS-TLR4-MD-2 complex and directs downstream signaling for activation of immune response, inflammation and NF-κB activation. Activation of TLR4 signaling is associated with various pathophysiological consequences. Therefore, targeting protein-protein interaction (PPI) in TLR4-MD-2 complex formation could be an attractive therapeutic approach for targeting inflammatory disorders. The aim of present study was directed to identify small molecule PPI inhibitors (SMPPIIs) using pharmacophore mapping-based approach of computational drug discovery. Here, we had retrieved the information about the hot spot residues and their pharmacophoric features at both primary (TLR4-MD-2) and dimerization (MD-2-TLR4*) protein-protein interaction interfaces in TLR4-MD-2 homo-dimer complex using in silico methods. Promising candidates were identified after virtual screening, which may restrict TLR4-MD-2 protein-protein interaction. In silico off-target profiling over the virtually screened compounds revealed other possible molecular targets. Two of the virtually screened compounds (C11 and C15) were predicted to have an inhibitory concentration in μM range after HYDE assessment. Molecular dynamics simulation study performed for these two compounds in complex with target protein confirms the stability of the complex. After virtual high throughput screening we found selective hTLR4-MD-2 inhibitors, which may have therapeutic potential to target chronic inflammatory diseases.
Collapse
Affiliation(s)
- Vinita Mishra
- a Department of Cell Biology, School of Biological Sciences & Biotechnology , Indian Institute of Advanced Research, Koba Institutional Area , Gandhinagar , India
| | - Chandramani Pathak
- a Department of Cell Biology, School of Biological Sciences & Biotechnology , Indian Institute of Advanced Research, Koba Institutional Area , Gandhinagar , India
| |
Collapse
|
14
|
Bojadzic D, Buchwald P. Toward Small-Molecule Inhibition of Protein-Protein Interactions: General Aspects and Recent Progress in Targeting Costimulatory and Coinhibitory (Immune Checkpoint) Interactions. Curr Top Med Chem 2018; 18:674-699. [PMID: 29848279 PMCID: PMC6067980 DOI: 10.2174/1568026618666180531092503] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/27/2018] [Accepted: 05/11/2018] [Indexed: 02/06/2023]
Abstract
Protein-Protein Interactions (PPIs) that are part of the costimulatory and coinhibitory (immune checkpoint) signaling are critical for adequate T cell response and are important therapeutic targets for immunomodulation. Biologics targeting them have already achieved considerable clinical success in the treatment of autoimmune diseases or transplant recipients (e.g., abatacept, belatacept, and belimumab) as well as cancer (e.g., ipilimumab, nivolumab, pembrolizumab, atezolizumab, durvalumab, and avelumab). In view of such progress, there have been only relatively limited efforts toward developing small-molecule PPI inhibitors (SMPPIIs) targeting these cosignaling interactions, possibly because they, as all other PPIs, are difficult to target by small molecules and were not considered druggable. Nevertheless, substantial progress has been achieved during the last decade. SMPPIIs proving the feasibility of such approaches have been identified through various strategies for a number of cosignaling interactions including CD40-CD40L, OX40-OX40L, BAFFR-BAFF, CD80-CD28, and PD-1-PD-L1s. Here, after an overview of the general aspects and challenges of SMPPII-focused drug discovery, we review them briefly together with relevant structural, immune-signaling, physicochemical, and medicinal chemistry aspects. While so far only a few of these SMPPIIs have shown activity in animal models (DRI-C21045 for CD40-D40L, KR33426 for BAFFR-BAFF) or reached clinical development (RhuDex for CD80-CD28, CA-170 for PD-1-PD-L1), there is proof-of-principle evidence for the feasibility of such approaches in immunomodulation. They can result in products that are easier to develop/ manufacture and are less likely to be immunogenic or encounter postmarket safety events than corresponding biologics, and, contrary to them, can even become orally bioavailable.
Collapse
Affiliation(s)
- Damir Bojadzic
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Peter Buchwald
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, Florida, USA
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, Florida, USA
| |
Collapse
|
15
|
Abstract
Natural products (NPs) have been used as traditional medicines since antiquity. With more than 1060 estimated compounds with molecular weights less than 500 Da representing chemical space, NPs occupy a very small percentage; however, they are significantly overrepresented in biologically relevant chemical space. The classical approach concentrates on identifying one or more NPs with biological activity from a source organism. There is much more to be learned from NPs than we can discover this narrow view. In this review, we discuss ways to harness the global properties of NPs.
Collapse
Affiliation(s)
- Asmaa Boufridi
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; ,
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; ,
| |
Collapse
|
16
|
Twarda-Clapa A, Krzanik S, Kubica K, Guzik K, Labuzek B, Neochoritis CG, Khoury K, Kowalska K, Czub M, Dubin G, Dömling A, Skalniak L, Holak TA. 1,4,5-Trisubstituted Imidazole-Based p53–MDM2/MDMX Antagonists with Aliphatic Linkers for Conjugation with Biological Carriers. J Med Chem 2017; 60:4234-4244. [DOI: 10.1021/acs.jmedchem.7b00104] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Aleksandra Twarda-Clapa
- Faculty
of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Cracow, Poland
| | - Sylwia Krzanik
- Faculty
of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Cracow, Poland
| | - Katarzyna Kubica
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
| | - Katarzyna Guzik
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
| | - Beata Labuzek
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
| | - Constantinos G. Neochoritis
- Department
of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Kareem Khoury
- Department
of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Kaja Kowalska
- Max Plank Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Miroslawa Czub
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
| | - Grzegorz Dubin
- Faculty
of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Cracow, Poland
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Cracow, Poland
| | - Alexander Dömling
- Department
of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Lukasz Skalniak
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
| | - Tad A. Holak
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
- Max Plank Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Cracow, Poland
| |
Collapse
|
17
|
Shaabani S, Neochoritis CG, Twarda-Clapa A, Musielak B, Holak TA, Dömling A. Scaffold hopping via ANCHOR.QUERY: β-lactams as potent p53-MDM2 antagonists †. MEDCHEMCOMM 2017; 8:1046-1052. [PMID: 29034069 DOI: 10.1039/c7md00058h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using the pharmacophore-based virtual screening platform ANCHOR.QUERY, we morphed our recently described Ugi-4CR scaffold towards a β-lactam scaffold with potent p53-MDM2 antagonizing activities. 2D-HSQC and FP measurements confirm potent MDM2 binding. Molecular modeling studies are used to understand the observed SAR in the β-lactam series.
Collapse
Affiliation(s)
- S Shaabani
- Department of Drug Design, University of Groningen, The Netherlands.,Faculty of Chemistry, Shahid Beheshti University, Tehran, Iran
| | - C G Neochoritis
- Department of Drug Design, University of Groningen, The Netherlands
| | - A Twarda-Clapa
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - B Musielak
- Department of Chemistry, Jagiellonian University, Krakow, Poland
| | - T A Holak
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.,Department of Chemistry, Jagiellonian University, Krakow, Poland
| | - A Dömling
- Department of Drug Design, University of Groningen, The Netherlands
| |
Collapse
|
18
|
Paciaroni NG, Ratnayake R, Matthews JH, Norwood VM, Arnold AC, Dang LH, Luesch H, Huigens RW. A Tryptoline Ring-Distortion Strategy Leads to Complex and Diverse Biologically Active Molecules from the Indole Alkaloid Yohimbine. Chemistry 2017; 23:4327-4335. [PMID: 27900785 DOI: 10.1002/chem.201604795] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Indexed: 02/06/2023]
Abstract
High-throughput screening (HTS) is the primary driver to current drug-discovery efforts. New therapeutic agents that enter the market are a direct reflection of the structurally simple compounds that make up screening libraries. Unlike medically relevant natural products (e.g., morphine), small molecules currently being screened have a low fraction of sp3 character and few, if any, stereogenic centers. Although simple compounds have been useful in drugging certain biological targets (e.g., protein kinases), more sophisticated targets (e.g., transcription factors) have largely evaded the discovery of new clinical agents from screening collections. Herein, a tryptoline ring-distortion strategy is described that enables the rapid synthesis of 70 complex and diverse compounds from yohimbine (1); an indole alkaloid. The compounds that were synthesized had architecturally complex and unique scaffolds, unlike 1 and other scaffolds. These compounds were subjected to phenotypic screens and reporter gene assays, leading to the identification of new compounds that possessed various biological activities, including antiproliferative activities against cancer cells with functional hypoxia-inducible factors, nitric oxide inhibition, and inhibition and activation of the antioxidant response element. This tryptoline ring-distortion strategy can begin to address diversity problems in screening libraries, while occupying biologically relevant chemical space in areas critical to human health.
Collapse
Affiliation(s)
- Nicholas G Paciaroni
- Department of Medicinal Chemistry, University of Florida, Gainesville, FL, 32610, USA.,Center for Natural Product Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL, 32610, USA
| | - Ranjala Ratnayake
- Department of Medicinal Chemistry, University of Florida, Gainesville, FL, 32610, USA.,Center for Natural Product Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL, 32610, USA
| | - James H Matthews
- Department of Medicinal Chemistry, University of Florida, Gainesville, FL, 32610, USA.,Center for Natural Product Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL, 32610, USA
| | - Verrill M Norwood
- Department of Medicinal Chemistry, University of Florida, Gainesville, FL, 32610, USA.,Center for Natural Product Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL, 32610, USA
| | - Austin C Arnold
- Department of Medicinal Chemistry, University of Florida, Gainesville, FL, 32610, USA
| | - Long H Dang
- Department of Medicinal Chemistry, University of Florida, Gainesville, FL, 32610, USA.,Center for Natural Product Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL, 32610, USA.,Department of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Hendrik Luesch
- Department of Medicinal Chemistry, University of Florida, Gainesville, FL, 32610, USA.,Center for Natural Product Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL, 32610, USA
| | - Robert W Huigens
- Department of Medicinal Chemistry, University of Florida, Gainesville, FL, 32610, USA.,Center for Natural Product Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL, 32610, USA
| |
Collapse
|
19
|
Xu H, Liu L, Fan X, Zhang G, Li Y, Jiang B. Identification of a diverse synthetic abietane diterpenoid library for anticancer activity. Bioorg Med Chem Lett 2016; 27:505-510. [PMID: 28011223 DOI: 10.1016/j.bmcl.2016.12.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 12/06/2016] [Accepted: 12/09/2016] [Indexed: 10/20/2022]
Abstract
A diverse natural-product-like synthetic abietane diterpenoid library contains about 56 compounds were obtained, and evaluated for their potential in vitro cytotoxic or antitumor activity against A549, PC-3 and SKOV-3 tumor cell lines by SRB assay. Treatment of A549 cells with the most potent compound ketone 19 showed induction of apoptosis, as revealed by JC-1 mitochondrial membrane potential staining, TUNNEL assay, western blotting analysis and flow cytometry assay.
Collapse
Affiliation(s)
- Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, PR China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
| | - Lili Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, PR China
| | - Xiaoting Fan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, PR China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, PR China
| | - Guanjun Zhang
- College of Chemical Engineering and Materials Science, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Yuanchao Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, PR China.
| |
Collapse
|
20
|
Kim J, Jung J, Koo J, Cho W, Lee WS, Kim C, Park W, Park SB. Diversity-oriented synthetic strategy for developing a chemical modulator of protein-protein interaction. Nat Commun 2016; 7:13196. [PMID: 27774980 PMCID: PMC5078997 DOI: 10.1038/ncomms13196] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 09/09/2016] [Indexed: 12/24/2022] Open
Abstract
Diversity-oriented synthesis (DOS) can provide a collection of diverse and complex drug-like small molecules, which is critical in the development of new chemical probes for biological research of undruggable targets. However, the design and synthesis of small-molecule libraries with improved biological relevance as well as maximized molecular diversity represent a key challenge. Herein, we employ functional group-pairing strategy for the DOS of a chemical library containing privileged substructures, pyrimidodiazepine or pyrimidine moieties, as chemical navigators towards unexplored bioactive chemical space. To validate the utility of this DOS library, we identify a new small-molecule inhibitor of leucyl-tRNA synthetase-RagD protein-protein interaction, which regulates the amino acid-dependent activation of mechanistic target of rapamycin complex 1 signalling pathway. This work highlights that privileged substructure-based DOS strategy can be a powerful research tool for the construction of drug-like compounds to address challenging biological targets.
Collapse
Affiliation(s)
- Jonghoon Kim
- Department of Biophysics and Chemical Biology, CRI Center for Chemical Proteomics, Seoul National University, Seoul 151-747, Korea
| | - Jinjoo Jung
- Department of Biophysics and Chemical Biology, CRI Center for Chemical Proteomics, Seoul National University, Seoul 151-747, Korea
| | - Jaeyoung Koo
- Department of Biophysics and Chemical Biology, CRI Center for Chemical Proteomics, Seoul National University, Seoul 151-747, Korea
| | - Wansang Cho
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Won Seok Lee
- Department of Biophysics and Chemical Biology, CRI Center for Chemical Proteomics, Seoul National University, Seoul 151-747, Korea
| | - Chanwoo Kim
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Wonwoo Park
- Department of Biophysics and Chemical Biology, CRI Center for Chemical Proteomics, Seoul National University, Seoul 151-747, Korea
| | - Seung Bum Park
- Department of Biophysics and Chemical Biology, CRI Center for Chemical Proteomics, Seoul National University, Seoul 151-747, Korea
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| |
Collapse
|
21
|
Mapping Protein-Protein Interactions of the Resistance-Related Bacterial Zeta Toxin-Epsilon Antitoxin Complex (ε₂ζ₂) with High Affinity Peptide Ligands Using Fluorescence Polarization. Toxins (Basel) 2016; 8:toxins8070222. [PMID: 27438853 PMCID: PMC4963854 DOI: 10.3390/toxins8070222] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 06/29/2016] [Accepted: 07/05/2016] [Indexed: 01/01/2023] Open
Abstract
Toxin–antitoxin systems constitute a native survival strategy of pathogenic bacteria and thus are potential targets of antibiotic drugs. Here, we target the Zeta–Epsilon toxin–antitoxin system, which is responsible for the stable maintenance of certain multiresistance plasmids in Gram-positive bacteria. Peptide ligands were designed on the basis of the ε2ζ2 complex. Three α helices of Zeta forming the protein–protein interaction (PPI) site were selected and peptides were designed conserving the residues interacting with Epsilon antitoxin while substituting residues binding intramolecularly to other parts of Zeta. Designed peptides were synthesized with an N-terminal fluoresceinyl-carboxy-residue for binding assays and provided active ligands, which were used to define the hot spots of the ε2ζ2 complex. Further shortening and modification of the binding peptides provided ligands with affinities <100 nM, allowing us to determine the most relevant PPIs and implement a robust competition binding assay.
Collapse
|
22
|
Suć J, Tumir LM, Glavaš-Obrovac L, Jukić M, Piantanida I, Jerić I. The impact of α-hydrazino acids embedded in short fluorescent peptides on peptide interactions with DNA and RNA. Org Biomol Chem 2016; 14:4865-74. [PMID: 27161341 DOI: 10.1039/c6ob00425c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of novel hydrazino-based peptidomimetics and analogues comprising N-terminal lysine and C-terminal phenanthridinyl-l-alanine were prepared. The presented results demonstrate the up to now unknown possibility to finely modulate peptide interactions with DNA/RNA by α-hydrazino group insertion and how the different positioning of two α-hydrazino groups in peptides controls binding to various double stranded and single stranded DNA and RNA. All peptidomimetics bind with 1-10 micromolar affinity to ds-DNA/RNA, whereby the binding mode is a combination of electrostatic interactions and hydrophobic interactions within DNA/RNA grooves. Insertion of the α-hydrazino group into the peptide systematically decreased its fluorimetric response to DNA/RNA binding in the order: mono-hydrazino < alternating-hydrazino < sequential-hydrazino group. Binding studies of ss-polynucleotides suggest intercalation of phenanthridine between polynucleotide bases, whereby affinity and fluorimetric response decrease with the number of α-hydrazino groups in the peptide sequence. Particularly interesting was the interaction of two sequential α-hydrazino acids-peptidomimetic with poly rG, characterised by a specific strong increase of CD bands, while all other peptide/ssRNA combinations gave only a CD-band decrease. All mentioned interactions could also be reversibly controlled by adjusting the pH, due to the protonation of the fluorophore.
Collapse
Affiliation(s)
- Josipa Suć
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | | | | | | | | | | |
Collapse
|
23
|
Discovery of new low-molecular-weight p53–Mdmx disruptors and their anti-cancer activities. Bioorg Med Chem 2016; 24:1919-26. [DOI: 10.1016/j.bmc.2016.03.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 11/16/2022]
|
24
|
Corbi-Verge C, Kim PM. Motif mediated protein-protein interactions as drug targets. Cell Commun Signal 2016; 14:8. [PMID: 26936767 PMCID: PMC4776425 DOI: 10.1186/s12964-016-0131-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/25/2016] [Indexed: 12/17/2022] Open
Abstract
Protein-protein interactions (PPI) are involved in virtually every cellular process and thus represent an attractive target for therapeutic interventions. A significant number of protein interactions are frequently formed between globular domains and short linear peptide motifs (DMI). Targeting these DMIs has proven challenging and classical approaches to inhibiting such interactions with small molecules have had limited success. However, recent new approaches have led to the discovery of potent inhibitors, some of them, such as Obatoclax, ABT-199, AEG-40826 and SAH-p53-8 are likely to become approved drugs. These novel inhibitors belong to a wide range of different molecule classes, ranging from small molecules to peptidomimetics and biologicals. This article reviews the main reasons for limited success in targeting PPIs, discusses how successful approaches overcome these obstacles to discovery promising inhibitors for human protein double minute 2 (HDM2), B-cell lymphoma 2 (Bcl-2), X-linked inhibitor of apoptosis protein (XIAP), and provides a summary of the promising approaches currently in development that indicate the future potential of PPI inhibitors in drug discovery.
Collapse
Affiliation(s)
- Carles Corbi-Verge
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.
| | - Philip M Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, M5S 3E1, Canada.
| |
Collapse
|
25
|
Developing structure-activity relationships from an HTS hit for inhibition of the Cks1-Skp2 protein-protein interaction. Bioorg Med Chem Lett 2015; 25:5199-202. [PMID: 26463131 DOI: 10.1016/j.bmcl.2015.09.067] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 09/25/2015] [Accepted: 09/28/2015] [Indexed: 11/21/2022]
Abstract
Structure-activity relationships have been developed around 5-bromo-8-toluylsulfonamidoquinoline 1 a hit compound in an assay for the interaction of the E3 ligase Skp2 with Cks1, part of the SCF ligase complex. Disruption of this protein-protein interaction results in higher levels of CDK inhibitor p27, which can act as a tumor suppressor. The results of the SAR developed highlight the relationship between the sulfonamide and quinoline nitrogen, while also suggesting that an aryl substituent at the 5-position of the quinoline ring contributes to the potency in the interaction assay. Compounds showing potency in the interaction assay result in greater levels of p27 and have been shown to inhibit cell growth of two p27 sensitive tumor cell lines.
Collapse
|
26
|
Peptide and small molecule inhibitors of the Keap1-Nrf2 protein-protein interaction. Biochem Soc Trans 2015; 43:674-9. [PMID: 26551711 DOI: 10.1042/bst20150051] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Indexed: 01/07/2023]
Abstract
The transcription factor nuclear factor erythroid-2-related factor 2 (Nrf2) up-regulates the expression of a range of cytoprotective enzymes with antioxidant response elements in their promoter regions and thus can protect cells against oxidative damage. Increasing Nrf2 activity has been proposed as a therapeutic intervention in a range of chronic neurodegenerative conditions and cancer chemoprevention. One of the main mechanisms by which Nrf2 is negatively regulated involves an interaction with the ubiquitination facilitator protein, Kelch-like ECH-associated protein 1 (Keap1) that facilitates degradation of Nrf2. Inhibition of this process underlies the mode of action of a broad group of compounds that increase Nrf2 activity. A number of natural products, including the isothiocyanate sulforaphane, up-regulate Nrf2 by interacting with Keap1 in a covalent manner to stall its activity. Recently, a number of peptide and small molecule inhibitors of the protein-protein interaction (PPI) between Keap1 and Nrf2 have been described. These classes of compound have contrasting modes of action at the molecular level and there is emerging evidence that their biological activities have similarities and differences. This review describes the various classes of PPI inhibitor that have been described in the literature and the biological evaluations that have been performed.
Collapse
|
27
|
Gowthaman R, Miller SA, Rogers S, Khowsathit J, Lan L, Bai N, Johnson DK, Liu C, Xu L, Anbanandam A, Aubé J, Roy A, Karanicolas J. DARC: Mapping Surface Topography by Ray-Casting for Effective Virtual Screening at Protein Interaction Sites. J Med Chem 2015; 59:4152-70. [PMID: 26126123 DOI: 10.1021/acs.jmedchem.5b00150] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions represent an exciting and challenging target class for therapeutic intervention using small molecules. Protein interaction sites are often devoid of the deep surface pockets presented by "traditional" drug targets, and crystal structures reveal that inhibitors typically engage these sites using very shallow binding modes. As a consequence, modern virtual screening tools developed to identify inhibitors of traditional drug targets do not perform as well when they are instead deployed at protein interaction sites. To address the need for novel inhibitors of important protein interactions, here we introduce an alternate docking strategy specifically designed for this regime. Our method, termed DARC (Docking Approach using Ray-Casting), matches the topography of a surface pocket "observed" from within the protein to the topography "observed" when viewing a potential ligand from the same vantage point. We applied DARC to carry out a virtual screen against the protein interaction site of human antiapoptotic protein Mcl-1 and found that four of the top-scoring 21 compounds showed clear inhibition in a biochemical assay. The Ki values for these compounds ranged from 1.2 to 21 μM, and each had ligand efficiency comparable to promising small-molecule inhibitors of other protein-protein interactions. These hit compounds do not resemble the natural (protein) binding partner of Mcl-1, nor do they resemble any known inhibitors of Mcl-1. Our results thus demonstrate the utility of DARC for identifying novel inhibitors of protein-protein interactions.
Collapse
Affiliation(s)
- Ragul Gowthaman
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Sven A Miller
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Steven Rogers
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Jittasak Khowsathit
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Lan Lan
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Nan Bai
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - David K Johnson
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Chunjing Liu
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Liang Xu
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Asokan Anbanandam
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Jeffrey Aubé
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Anuradha Roy
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - John Karanicolas
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| |
Collapse
|
28
|
Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors. Molecules 2015; 20:11569-603. [PMID: 26111183 PMCID: PMC6272567 DOI: 10.3390/molecules200611569] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 06/02/2015] [Accepted: 06/15/2015] [Indexed: 02/06/2023] Open
Abstract
Blocking protein-protein interactions (PPI) using small molecules or peptides modulates biochemical pathways and has therapeutic significance. PPI inhibition for designing drug-like molecules is a new area that has been explored extensively during the last decade. Considering the number of available PPI inhibitor databases and the limited number of 3D structures available for proteins, docking and scoring methods play a major role in designing PPI inhibitors as well as stabilizers. Docking methods are used in the design of PPI inhibitors at several stages of finding a lead compound, including modeling the protein complex, screening for hot spots on the protein-protein interaction interface and screening small molecules or peptides that bind to the PPI interface. There are three major challenges to the use of docking on the relatively flat surfaces of PPI. In this review we will provide some examples of the use of docking in PPI inhibitor design as well as its limitations. The combination of experimental and docking methods with improved scoring function has thus far resulted in few success stories of PPI inhibitors for therapeutic purposes. Docking algorithms used for PPI are in the early stages, however, and as more data are available docking will become a highly promising area in the design of PPI inhibitors or stabilizers.
Collapse
|
29
|
Laraia L, McKenzie G, Spring DR, Venkitaraman AR, Huggins DJ. Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions. CHEMISTRY & BIOLOGY 2015; 22:689-703. [PMID: 26091166 PMCID: PMC4518475 DOI: 10.1016/j.chembiol.2015.04.019] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/01/2015] [Accepted: 04/08/2015] [Indexed: 01/19/2023]
Abstract
Protein-protein interactions (PPIs) underlie the majority of biological processes, signaling, and disease. Approaches to modulate PPIs with small molecules have therefore attracted increasing interest over the past decade. However, there are a number of challenges inherent in developing small-molecule PPI inhibitors that have prevented these approaches from reaching their full potential. From target validation to small-molecule screening and lead optimization, identifying therapeutically relevant PPIs that can be successfully modulated by small molecules is not a simple task. Following the recent review by Arkin et al., which summarized the lessons learnt from prior successes, we focus in this article on the specific challenges of developing PPI inhibitors and detail the recent advances in chemistry, biology, and computation that facilitate overcoming them. We conclude by providing a perspective on the field and outlining four innovations that we see as key enabling steps for successful development of small-molecule inhibitors targeting PPIs.
Collapse
Affiliation(s)
- Luca Laraia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Grahame McKenzie
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Ashok R Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - David J Huggins
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK; Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, 19 JJ Thomson Avenue, Cambridge CB3 0HE, UK.
| |
Collapse
|
30
|
Structure- and ligand-based virtual screening identifies new scaffolds for inhibitors of the oncoprotein MDM2. PLoS One 2015; 10:e0121424. [PMID: 25884407 PMCID: PMC4401541 DOI: 10.1371/journal.pone.0121424] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 02/13/2015] [Indexed: 11/19/2022] Open
Abstract
A major challenge in the field of ligand discovery is to identify chemically useful fragments that can be developed into inhibitors of specific protein-protein interactions. Low molecular weight fragments (with molecular weight less than 250 Da) are likely to bind weakly to a protein’s surface. Here we use a new virtual screening procedure which uses a combination of similarity searching and docking to identify chemically tractable scaffolds that bind to the p53-interaction site of MDM2. The binding has been verified using capillary electrophoresis which has proven to be an excellent screening method for such small, weakly binding ligands.
Collapse
|
31
|
Harvey AL, Edrada-Ebel R, Quinn RJ. The re-emergence of natural products for drug discovery in the genomics era. Nat Rev Drug Discov 2015; 14:111-29. [PMID: 25614221 DOI: 10.1038/nrd4510] [Citation(s) in RCA: 1556] [Impact Index Per Article: 172.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Natural products have been a rich source of compounds for drug discovery. However, their use has diminished in the past two decades, in part because of technical barriers to screening natural products in high-throughput assays against molecular targets. Here, we review strategies for natural product screening that harness the recent technical advances that have reduced these barriers. We also assess the use of genomic and metabolomic approaches to augment traditional methods of studying natural products, and highlight recent examples of natural products in antimicrobial drug discovery and as inhibitors of protein-protein interactions. The growing appreciation of functional assays and phenotypic screens may further contribute to a revival of interest in natural products for drug discovery.
Collapse
Affiliation(s)
- Alan L Harvey
- 1] Research and Innovation Support, Dublin City University, Dublin 9, Ireland. [2] Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow G4 0NR, UK
| | - RuAngelie Edrada-Ebel
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow G4 0NR, UK
| | - Ronald J Quinn
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia
| |
Collapse
|
32
|
Abstract
Protein-protein interactions are associated with key activities and pathways in the cell, and in that regard are promising targets for drug discovery. However, in terms of small molecule drugs, this promise has not been realized. The physical nature of many protein-protein interaction surfaces renders them unable to support binding of small drug-like molecules. In addition, there are other unique hurdles presented by this class that make the drug development process difficult and risky. Nevertheless, success stories have begun to steadily appear in this field. These experiences are starting to provide general strategies and tools to help overcome the problems inherent in pursuing protein-protein interaction targets. These lessons should improve the rate of success as these systems are pursued in the future.
Collapse
Affiliation(s)
- David C Fry
- Roche Research Center, 340 Kingsland Street, Nutley, NJ, 07110, USA,
| |
Collapse
|
33
|
Cukuroglu E, Engin HB, Gursoy A, Keskin O. Hot spots in protein–protein interfaces: Towards drug discovery. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 116:165-73. [DOI: 10.1016/j.pbiomolbio.2014.06.003] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/30/2014] [Accepted: 06/12/2014] [Indexed: 11/16/2022]
|
34
|
Villoutreix BO, Kuenemann MA, Poyet JL, Bruzzoni-Giovanelli H, Labbé C, Lagorce D, Sperandio O, Miteva MA. Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology. Mol Inform 2014; 33:414-437. [PMID: 25254076 PMCID: PMC4160817 DOI: 10.1002/minf.201400040] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 04/21/2014] [Indexed: 12/13/2022]
Abstract
[Formula: see text] Fundamental processes in living cells are largely controlled by macromolecular interactions and among them, protein-protein interactions (PPIs) have a critical role while their dysregulations can contribute to the pathogenesis of numerous diseases. Although PPIs were considered as attractive pharmaceutical targets already some years ago, they have been thus far largely unexploited for therapeutic interventions with low molecular weight compounds. Several limiting factors, from technological hurdles to conceptual barriers, are known, which, taken together, explain why research in this area has been relatively slow. However, this last decade, the scientific community has challenged the dogma and became more enthusiastic about the modulation of PPIs with small drug-like molecules. In fact, several success stories were reported both, at the preclinical and clinical stages. In this review article, written for the 2014 International Summer School in Chemoinformatics (Strasbourg, France), we discuss in silico tools (essentially post 2012) and databases that can assist the design of low molecular weight PPI modulators (these tools can be found at www.vls3d.com). We first introduce the field of protein-protein interaction research, discuss key challenges and comment recently reported in silico packages, protocols and databases dedicated to PPIs. Then, we illustrate how in silico methods can be used and combined with experimental work to identify PPI modulators.
Collapse
Affiliation(s)
- Bruno O Villoutreix
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
- CDithem, Faculté de Pharmacie, 1 rue du Prof Laguesse59000 Lille, France
| | - Melaine A Kuenemann
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
| | - Jean-Luc Poyet
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
- IUH, Hôpital Saint-LouisParis, France
- CDithem, Faculté de Pharmacie, 1 rue du Prof Laguesse59000 Lille, France
| | - Heriberto Bruzzoni-Giovanelli
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
- CIC, Clinical investigation center, Hôpital Saint-LouisParis, France
| | - Céline Labbé
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
| | - David Lagorce
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
| | - Olivier Sperandio
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
- CDithem, Faculté de Pharmacie, 1 rue du Prof Laguesse59000 Lille, France
| | - Maria A Miteva
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
| |
Collapse
|
35
|
Bonache MÁ, Balsera B, López-Méndez B, Millet O, Brancaccio D, Gómez-Monterrey I, Carotenuto A, Pavone LM, Reille-Seroussi M, Gagey-Eilstein N, Vidal M, de la Torre-Martı́nez R, Fernández-Carvajal A, Ferrer-Montiel A, García-López MT, Martín-Martínez M, de Vega MJP, González-Muñiz R. De novo designed library of linear helical peptides: an exploratory tool in the discovery of protein-protein interaction modulators. ACS COMBINATORIAL SCIENCE 2014; 16:250-8. [PMID: 24725184 DOI: 10.1021/co500005x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) have emerged as important targets for pharmaceutical intervention because of their essential role in numerous physiological and pathological processes, but screening efforts using small-molecules have led to very low hit rates. Linear peptides could represent a quick and effective approach to discover initial PPI hits, particularly if they have inherent ability to adopt specific peptide secondary structures. Here, we address this hypothesis through a linear helical peptide library, composed of four sublibraries, which was designed by theoretical predictions of helicity (Agadir software). The 13-mer peptides of this collection fixes either a combination of three aromatic or two aromatic and one aliphatic residues on one face of the helix (Ac-SSEEX(5)ARNX(9)AAX(12)N-NH2), since these are structural features quite common at PPIs interfaces. The 81 designed peptides were conveniently synthesized by parallel solid-phase methodologies, and the tendency of some representative library components to adopt the intended secondary structure was corroborated through CD and NMR experiments. As proof of concept in the search for PPI modulators, the usefulness of this library was verified on the widely studied p53-MDM2 interaction and on the communication between VEGF and its receptor Flt-1, two PPIs for which a hydrophobic α-helix is essential for the interaction. We have demonstrated here that, in both cases, selected peptides from the library, containing the right hydrophobic sequence of the hot-spot in one of the protein partners, are able to interact with the complementary protein. Moreover, we have discover some new, quite potent inhibitors of the VEGF-Flt-1 interaction, just by replacing one of the aromatic residues of the initial F(5)Y(9)Y(12) peptide by W, in agreement with previous results on related antiangiogenic peptides. Finally, the HTS evaluation of the full collection on thermoTRPs has led to a few antagonists of TRPV1 and TRPA1 channels, which open new avenues on the way to innovative modulators of these channels.
Collapse
Affiliation(s)
- M. Ángeles Bonache
- Instituto de Química-Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Beatriz Balsera
- Instituto de Química-Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Oscar Millet
- CICbioGUNE, Structural Biology Unit, 48160 Bilbao, Spain
| | - Diego Brancaccio
- Department
of Pharmacy, University of Naples “Federico II”, Via D. Montesano
49, 80131 Naples, Italy
| | - Isabel Gómez-Monterrey
- Department
of Pharmacy, University of Naples “Federico II”, Via D. Montesano
49, 80131 Naples, Italy
| | - Alfonso Carotenuto
- Department
of Pharmacy, University of Naples “Federico II”, Via D. Montesano
49, 80131 Naples, Italy
| | - Luigi M. Pavone
- Department
of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Via S. Pansini 5, 80131, Naples, Italy
| | - Marie Reille-Seroussi
- UMR
8638
CNRS, UFR de Pharmacie, Université Paris Descartes, PRES
Sorbonne Paris Cité, 4 avenue de l’Observatoire, 75006 Paris, France
| | - Nathalie Gagey-Eilstein
- UMR
8638
CNRS, UFR de Pharmacie, Université Paris Descartes, PRES
Sorbonne Paris Cité, 4 avenue de l’Observatoire, 75006 Paris, France
| | - Michel Vidal
- UMR
8638
CNRS, UFR de Pharmacie, Université Paris Descartes, PRES
Sorbonne Paris Cité, 4 avenue de l’Observatoire, 75006 Paris, France
- UF
“Pharmacocinétique et pharmacochimie”, Hôpital Cochin, , AP-HP, 27 rue du Faubourg Saint Jacques, 75014 Paris, France
| | - Roberto de la Torre-Martı́nez
- Instituto
de Biología Molecular y Celular, Universidad Miguel Hernández, Avenida de la Universidad s/n, 03202 Elche (Alicante), Spain
| | - Asia Fernández-Carvajal
- Instituto
de Biología Molecular y Celular, Universidad Miguel Hernández, Avenida de la Universidad s/n, 03202 Elche (Alicante), Spain
| | - Antonio Ferrer-Montiel
- Instituto
de Biología Molecular y Celular, Universidad Miguel Hernández, Avenida de la Universidad s/n, 03202 Elche (Alicante), Spain
| | | | | | | | | |
Collapse
|
36
|
Chen K, Michelsen K, Kurzeja RJM, Han J, Vazir M, St Jean DJ, Hale C, Wahl RC. Discovery of Small-Molecule Glucokinase Regulatory Protein Modulators That Restore Glucokinase Activity. ACTA ACUST UNITED AC 2014; 19:1014-23. [PMID: 24717911 DOI: 10.1177/1087057114530468] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 03/01/2014] [Indexed: 11/16/2022]
Abstract
In the nuclei of hepatocytes, glucokinase regulatory protein (GKRP) modulates the activity of glucokinase (GK), a key regulator of glucose homeostasis. Currently, direct activators of GK (GKAs) are in development for the treatment of type 2 diabetes. However, this approach is generally associated with a risk of hypoglycemia. To mitigate such risk, we target the GKRP regulation, which indirectly restores GK activity. Here we describe a screening strategy to look specifically for GKRP modulators, in addition to traditional GKAs. Two high-throughput screening campaigns were performed with our compound libraries using a luminescence assay format, one with GK alone and the other with a GK/GKRP complex in the presence of sorbitol-6-phosphate (S6P). By a subtraction method in the hit triage process of these campaigns, we discovered two close analogs that bind GKRP specifically with sub-µM potency to a site distinct from where fructose-1-phosphate binds. These small molecules are first-in-class allosteric modulators of the GK/GKRP interaction and are fully active even in the presence of S6P. Activation of GK by this particular mechanism, without altering the enzymatic profile, represents a novel pharmacologic modality of intervention in the GK/GKRP pathway.
Collapse
Affiliation(s)
- Kui Chen
- Amgen, Inc, Molecular Structure and Characterization, Thousand Oaks, CA, USA
| | - Klaus Michelsen
- Amgen, Inc, Molecular Structure and Characterization, Cambridge, MA, USA
| | | | - Joon Han
- Amgen, Inc, Biologic Discovery, Thousand Oaks, CA, USA
| | - Mukta Vazir
- Amgen, Inc, Protein Technologies, Thousand Oaks, CA, USA
| | | | - Clarence Hale
- Amgen, Inc, Metabolic Disorders, Thousand Oaks, CA, USA
| | - Robert C Wahl
- Amgen, Inc, Molecular Structure and Characterization, Thousand Oaks, CA, USA
| |
Collapse
|
37
|
Rafferty RJ, Hicklin RW, Maloof KA, Hergenrother PJ. Synthesis of complex and diverse compounds through ring distortion of abietic acid. Angew Chem Int Ed Engl 2013; 53:220-4. [PMID: 24273016 DOI: 10.1002/anie.201308743] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Indexed: 11/11/2022]
Abstract
Many compound screening collections are populated by members that possess a low degree of structural complexity. In an effort to generate compounds that are both complex and diverse, we have developed a strategy that uses natural products as a starting point for complex molecule synthesis. Herein we apply this complexity-to-diversity approach to abietic acid, an abundant natural product used commercially in paints, varnishes, and lacquers. From abietic acid we synthesize a collection of complex (as assessed by fraction of sp(3) -hybridized carbons and number of stereogenic centers) and diverse (as assessed by Tanimoto analysis) small molecules. The 84 compounds constructed herein, and those created through similar efforts, should find utility in a variety of biological screens.
Collapse
Affiliation(s)
- Ryan J Rafferty
- Department of Chemistry, University of Illinois at Urbana-Champaign, 261 RAL, Box 36-5, 600 S. Mathews, Urbana, IL 61801 (USA)
| | | | | | | |
Collapse
|
38
|
Rafferty RJ, Hicklin RW, Maloof KA, Hergenrother PJ. Synthesis of Complex and Diverse Compounds through Ring Distortion of Abietic Acid. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201308743] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
|
39
|
Bista M, Wolf S, Khoury K, Kowalska K, Huang Y, Wrona E, Arciniega M, Popowicz GM, Holak TA, Dömling A. Transient protein states in designing inhibitors of the MDM2-p53 interaction. Structure 2013; 21:2143-51. [PMID: 24207125 DOI: 10.1016/j.str.2013.09.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 09/10/2013] [Accepted: 09/13/2013] [Indexed: 11/28/2022]
Abstract
Reactivation of p53 by release of the functional protein from its inhibition by MDM2 provides an efficient, nongenotoxic approach to a wide variety of cancers. We present the cocrystal structures of two complexes of MDM2 with inhibitors based on 6-chloroindole scaffolds. Both molecules bound to a distinct conformational state of MDM2 with nM-μM affinities. In contrast to other structurally characterized antagonists, which mimic three amino acids of p53 (Phe19, Trp23, and Leu26), the compounds induced an additional hydrophobic pocket on the MDM2 surface and unveiled a four-point binding mode. The enlarged interaction interface of the inhibitors resulted in extension of small molecules binding toward the "lid" segment of MDM2 (residues 19-23)--a nascent element that interferes with p53 binding. As supported by protein engineering and molecular dynamics studies, employing these unstable elements of MDM2 provides an efficient and yet unexplored alternative in development of MDM2-p53 association inhibitors.
Collapse
Affiliation(s)
- Michal Bista
- Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Wang W, Cao H, Wolf S, Camacho-Horvitz MS, Holak TA, Dömling A. Benzimidazole-2-one: a novel anchoring principle for antagonizing p53-Mdm2. Bioorg Med Chem 2013; 21:3982-95. [PMID: 22789708 PMCID: PMC3716288 DOI: 10.1016/j.bmc.2012.06.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 06/05/2012] [Accepted: 06/11/2012] [Indexed: 12/11/2022]
Abstract
Herein we propose the benzimidazole-2-one substructure as a suitable tryptophan mimic and thus a reasonable starting point for the design of p53 Mdm2 antagonists. We devise a short multicomponent reaction route to hitherto unknown 2-(2-oxo-2,3-dihydro-1H-benzo[d]imidazol-1-yl)acetamides by reacting mono N-carbamate protected phenylenediamine in a Ugi-3CR followed by base induced cyclisation. Our preliminary synthesis and screening results are presented here. The finding of the benzimidazolone moiety as a tryptophan replacement in mdm2 is significant as it offers access to novel scaffolds with potentially higher selectivity and potency and improved biological activities. Observing low μM affinities to mdm2 by NMR and fluorescence polarization we conclude that the 2-(2-oxo-2,3-dihydro-1H-benzo[d]imidazol-1-yl)acetamide scaffold might be a good starting point to further optimize the affinities to Mdm2.
Collapse
Affiliation(s)
- Wei Wang
- University of Pittsburgh, 3501 Fifth Avenue, BST3 11019, Pittsburgh, PA 1526, USA
| | | | | | | | | | | |
Collapse
|
41
|
Inhibition and stabilization of protein–protein interactions. Bioorg Med Chem 2013; 21:3981. [DOI: 10.1016/j.bmc.2013.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
42
|
Florent JC. [Small compounds libraries: a research tool for chemical biology]. Biol Aujourdhui 2013; 207:39-54. [PMID: 23694724 DOI: 10.1051/jbio/2013006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Indexed: 06/02/2023]
Abstract
Obtaining and screening collections of small molecules remain a challenge for biologists. Recent advances in analytical techniques and instrumentation now make screening possible in academia. The history of the creation of such public or commercial collections and their accessibility is related. It shows that there is interest for an academic laboratory involved in medicinal chemistry, chemogenomics or "chemical biology" to organize its own collection and make it available through existing networks such as the French National chimiothèque or the European partner network "European Infrastructure of open screening platforms for Chemical Biology" EU-OpenScreen under construction.
Collapse
Affiliation(s)
- Jean-Claude Florent
- Laboratoire de Conception, Synthèse et Vectorisation de Biomolécules (CSVB), UMR 176 CNRS-Institut Curie, Institut Curie Centre de Recherche, 75248 Paris Cedex, France.
| |
Collapse
|
43
|
Golden MS, Cote SM, Sayeg M, Zerbe BS, Villar EA, Beglov D, Sazinsky SL, Georgiadis RM, Vajda S, Kozakov D, Whitty A. Comprehensive experimental and computational analysis of binding energy hot spots at the NF-κB essential modulator/IKKβ protein-protein interface. J Am Chem Soc 2013; 135:6242-56. [PMID: 23506214 PMCID: PMC3680600 DOI: 10.1021/ja400914z] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report a comprehensive analysis of binding energy hot spots at the protein-protein interaction (PPI) interface between nuclear factor kappa B (NF-κB) essential modulator (NEMO) and IκB kinase subunit β (IKKβ), an interaction that is critical for NF-κB pathway signaling, using experimental alanine scanning mutagenesis and also the FTMap method for computational fragment screening. The experimental results confirm that the previously identified NEMO binding domain (NBD) region of IKKβ contains the highest concentration of hot-spot residues, the strongest of which are W739, W741, and L742 (ΔΔG = 4.3, 3.5, and 3.2 kcal/mol, respectively). The region occupied by these residues defines a potentially druggable binding site on NEMO that extends for ~16 Å to additionally include the regions that bind IKKβ L737 and F734. NBD residues D738 and S740 are also important for binding but do not make direct contact with NEMO, instead likely acting to stabilize the active conformation of surrounding residues. We additionally found two previously unknown hot-spot regions centered on IKKβ residues L708/V709 and L719/I723. The computational approach successfully identified all three hot-spot regions on IKKβ. Moreover, the method was able to accurately quantify the energetic importance of all hot-spot residues involving direct contact with NEMO. Our results provide new information to guide the discovery of small-molecule inhibitors that target the NEMO/IKKβ interaction. They additionally clarify the structural and energetic complementarity between "pocket-forming" and "pocket-occupying" hot-spot residues, and further validate computational fragment mapping as a method for identifying hot spots at PPI interfaces.
Collapse
Affiliation(s)
- Mary S. Golden
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Shaun M. Cote
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Marianna Sayeg
- Department of Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Brandon S. Zerbe
- Department of Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Elizabeth A. Villar
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Dmitri Beglov
- Department of Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Stephen L. Sazinsky
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Rosina M. Georgiadis
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Sandor Vajda
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Dima Kozakov
- Department of Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Adrian Whitty
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| |
Collapse
|
44
|
Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface. PLoS Comput Biol 2013; 9:e1002951. [PMID: 23505360 PMCID: PMC3591273 DOI: 10.1371/journal.pcbi.1002951] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 01/11/2013] [Indexed: 01/22/2023] Open
Abstract
Despite intense interest and considerable effort via high-throughput screening, there are few examples of small molecules that directly inhibit protein-protein interactions. This suggests that many protein interaction surfaces may not be intrinsically “druggable” by small molecules, and elevates in importance the few successful examples as model systems for improving our fundamental understanding of druggability. Here we describe an approach for exploring protein fluctuations enriched in conformations containing surface pockets suitable for small molecule binding. Starting from a set of seven unbound protein structures, we find that the presence of low-energy pocket-containing conformations is indeed a signature of druggable protein interaction sites and that analogous surface pockets are not formed elsewhere on the protein. We further find that ensembles of conformations generated with this biased approach structurally resemble known inhibitor-bound structures more closely than equivalent ensembles of unbiased conformations. Collectively these results suggest that “druggability” is a property encoded on a protein surface through its propensity to form pockets, and inspire a model in which the crude features of the predisposed pocket(s) restrict the range of complementary ligands; additional smaller conformational changes then respond to details of a particular ligand. We anticipate that the insights described here will prove useful in selecting protein targets for therapeutic intervention. Identifying small-molecule inhibitors of protein interactions has traditionally presented a challenge for modern screening methods, despite interest stemming from the fact that such interactions comprise the underlying mechanisms for cell proliferation, differentiation, and survival. This suggests that many protein interaction surfaces may not be intrinsically “druggable” by small molecules, and elevates in importance the few successful examples as model systems for improving our understanding of factors contributing to druggability. Here we describe a new approach for exploring protein fluctuations leading to surface pockets suitable for small molecule binding. We find that the presence of such pockets is indeed a signature of druggable protein interaction sites, suggesting that “druggability” is a property encoded on a protein surface through its propensity to form pockets. We anticipate that the insights described here will prove useful in selecting protein targets for therapeutic intervention.
Collapse
|
45
|
Learning a peptide-protein binding affinity predictor with kernel ridge regression. BMC Bioinformatics 2013; 14:82. [PMID: 23497081 PMCID: PMC3651388 DOI: 10.1186/1471-2105-14-82] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 02/21/2013] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The cellular function of a vast majority of proteins is performed through physical interactions with other biomolecules, which, most of the time, are other proteins. Peptides represent templates of choice for mimicking a secondary structure in order to modulate protein-protein interaction. They are thus an interesting class of therapeutics since they also display strong activity, high selectivity, low toxicity and few drug-drug interactions. Furthermore, predicting peptides that would bind to a specific MHC alleles would be of tremendous benefit to improve vaccine based therapy and possibly generate antibodies with greater affinity. Modern computational methods have the potential to accelerate and lower the cost of drug and vaccine discovery by selecting potential compounds for testing in silico prior to biological validation. RESULTS We propose a specialized string kernel for small bio-molecules, peptides and pseudo-sequences of binding interfaces. The kernel incorporates physico-chemical properties of amino acids and elegantly generalizes eight kernels, comprised of the Oligo, the Weighted Degree, the Blended Spectrum, and the Radial Basis Function. We provide a low complexity dynamic programming algorithm for the exact computation of the kernel and a linear time algorithm for it's approximation. Combined with kernel ridge regression and SupCK, a novel binding pocket kernel, the proposed kernel yields biologically relevant and good prediction accuracy on the PepX database. For the first time, a machine learning predictor is capable of predicting the binding affinity of any peptide to any protein with reasonable accuracy. The method was also applied to both single-target and pan-specific Major Histocompatibility Complex class II benchmark datasets and three Quantitative Structure Affinity Model benchmark datasets. CONCLUSION On all benchmarks, our method significantly (p-value ≤ 0.057) outperforms the current state-of-the-art methods at predicting peptide-protein binding affinities. The proposed approach is flexible and can be applied to predict any quantitative biological activity. Moreover, generating reliable peptide-protein binding affinities will also improve system biology modelling of interaction pathways. Lastly, the method should be of value to a large segment of the research community with the potential to accelerate the discovery of peptide-based drugs and facilitate vaccine development. The proposed kernel is freely available at http://graal.ift.ulaval.ca/downloads/gs-kernel/.
Collapse
|
46
|
Fry D, Huang KS, Di Lello P, Mohr P, Müller K, So SS, Harada T, Stahl M, Vu B, Mauser H. Design of Libraries Targeting Protein-Protein Interfaces. ChemMedChem 2013; 8:726-32. [DOI: 10.1002/cmdc.201200540] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Indexed: 11/10/2022]
|
47
|
Zak K, Pecak A, Rys B, Wladyka B, Dömling A, Weber L, Holak TA, Dubin G. Mdm2 and MdmX inhibitors for the treatment of cancer: a patent review (2011-present). Expert Opin Ther Pat 2013; 23:425-48. [PMID: 23374098 DOI: 10.1517/13543776.2013.765405] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION One of the hallmarks of cancer cells is the inactivation of the p53 pathway either due to mutations in the p53 gene or over-expression of negative regulators, Mdm2 and/or MdmX. Pharmacological disruption of the Mdm2/X-p53 interaction to restore p53 activity is an attractive concept, aiming at a targeted and non-toxic cancer treatment. AREAS COVERED The introduction covers the biological role of p53 pathway and its regulation by Mdm2 and MdmX in normal and cancer cells and the current repertoire and development status of inhibitors of the Mdm2/X-p53 interaction for the treatment of cancer. The main part of the article covers patents and patent applications describing small molecule inhibitors of the Mdm2/X-p53 interaction published from 2011 until 2012. EXPERT OPINION The area of small molecule Mdm2/X-p53 interaction inhibitor development is progressing fast. Several Phase I clinical studies and preclinical programs are now in progress, however, the clinical proof concept has yet to be demonstrated. Multiple available compounds inhibit Mdm2-p53 interaction with nanomolar affinities, but MdmX is still missing such potent binders. Since research points to a complementary mode of Mdm2 and MdmX action, the future compound classes will possibly want to include dual actions versus Mdm2 and MdmX.
Collapse
Affiliation(s)
- Krzysztof Zak
- Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Kraków, Poland
| | | | | | | | | | | | | | | |
Collapse
|
48
|
A ring-distortion strategy to construct stereochemically complex and structurally diverse compounds from natural products. Nat Chem 2013; 5:195-202. [PMID: 23422561 DOI: 10.1038/nchem.1549] [Citation(s) in RCA: 254] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 12/06/2012] [Indexed: 12/18/2022]
Abstract
High-throughput screening is the dominant method used to identify lead compounds in drug discovery. As such, the makeup of screening libraries largely dictates the biological targets that can be modulated and the therapeutics that can be developed. Unfortunately, most compound-screening collections consist principally of planar molecules with little structural or stereochemical complexity, compounds that do not offer the arrangement of chemical functionality necessary for the modulation of many drug targets. Here we describe a novel, general and facile strategy for the creation of diverse compounds with high structural and stereochemical complexity using readily available natural products as synthetic starting points. We show through the evaluation of chemical properties (which include fraction of sp(3) carbons, ClogP and the number of stereogenic centres) that these compounds are significantly more complex and diverse than those in standard screening collections, and we give guidelines for the application of this strategy to any suitable natural product.
Collapse
|
49
|
Computational study and peptide inhibitors design for the CDK9 - cyclin T1 complex. J Mol Model 2013; 19:1711-25. [PMID: 23296566 DOI: 10.1007/s00894-012-1735-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 12/13/2012] [Indexed: 01/08/2023]
Abstract
Cyclin dependent kinase 9 (CDK9) is a protein that belongs to the cyclin-dependent kinases family, and its main role is in the regulation of the cell transcription processes. Since the increased activity of CDK9 is connected with the development of pathological processes such as tumor growth and survival and HIV-1 replication, inhibition of the CDK9 could be of particular interest for treating such diseases. The activation of CDK9 is initiated by the formation of CDK9/cyclin T1 complex, therefore disruption of its formation could be a promising strategy for the design of CDK9 inhibitors. In order to assist in the design of potential inhibitors of CDK9/cyclin T1 complex formation, a computational study of the CDK9/cyclin T1 interface was conducted. Ten peptides were designed using the information from the analysis of the complex, hot spot residues and fragment based design. The designed peptides were docked to CDK9 structures obtained by molecular dynamics simulations of CDK9/cyclin T1 complex and the CDK9 alone and their binding affinities were evaluated using molecular mechanics Poisson Boltzman surface area (MM-PBSA) method and steered molecular dynamics (SMD). Designed peptide sequences LQTLGF and ESIILQ, both derived from the surface of cyclin T1, as well as the peptide sequence PRWPE, derived from fragment based design, showed the most favorable binding properties and were selected for our further studies.
Collapse
|
50
|
Kastritis PL, Bonvin AMJJ. On the binding affinity of macromolecular interactions: daring to ask why proteins interact. J R Soc Interface 2012; 10:20120835. [PMID: 23235262 PMCID: PMC3565702 DOI: 10.1098/rsif.2012.0835] [Citation(s) in RCA: 299] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Interactions between proteins are orchestrated in a precise and time-dependent manner, underlying cellular function. The binding affinity, defined as the strength of these interactions, is translated into physico-chemical terms in the dissociation constant (Kd), the latter being an experimental measure that determines whether an interaction will be formed in solution or not. Predicting binding affinity from structural models has been a matter of active research for more than 40 years because of its fundamental role in drug development. However, all available approaches are incapable of predicting the binding affinity of protein–protein complexes from coordinates alone. Here, we examine both theoretical and experimental limitations that complicate the derivation of structure–affinity relationships. Most work so far has concentrated on binary interactions. Systems of increased complexity are far from being understood. The main physico-chemical measure that relates to binding affinity is the buried surface area, but it does not hold for flexible complexes. For the latter, there must be a significant entropic contribution that will have to be approximated in the future. We foresee that any theoretical modelling of these interactions will have to follow an integrative approach considering the biology, chemistry and physics that underlie protein–protein recognition.
Collapse
Affiliation(s)
- Panagiotis L Kastritis
- Bijvoet Center for Biomolecular Research, Faculty of Science, Chemistry, Utrecht University, , Padualaan 8, Utrecht, The Netherlands
| | | |
Collapse
|