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Siebenmorgen T, Menezes F, Benassou S, Merdivan E, Didi K, Mourão ASD, Kitel R, Liò P, Kesselheim S, Piraud M, Theis FJ, Sattler M, Popowicz GM. MISATO: machine learning dataset of protein-ligand complexes for structure-based drug discovery. NATURE COMPUTATIONAL SCIENCE 2024; 4:367-378. [PMID: 38730184 PMCID: PMC11136668 DOI: 10.1038/s43588-024-00627-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 04/11/2024] [Indexed: 05/12/2024]
Abstract
Large language models have greatly enhanced our ability to understand biology and chemistry, yet robust methods for structure-based drug discovery, quantum chemistry and structural biology are still sparse. Precise biomolecule-ligand interaction datasets are urgently needed for large language models. To address this, we present MISATO, a dataset that combines quantum mechanical properties of small molecules and associated molecular dynamics simulations of ~20,000 experimental protein-ligand complexes with extensive validation of experimental data. Starting from the existing experimental structures, semi-empirical quantum mechanics was used to systematically refine these structures. A large collection of molecular dynamics traces of protein-ligand complexes in explicit water is included, accumulating over 170 μs. We give examples of machine learning (ML) baseline models proving an improvement of accuracy by employing our data. An easy entry point for ML experts is provided to enable the next generation of drug discovery artificial intelligence models.
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Affiliation(s)
- Till Siebenmorgen
- Molecular Targets and Therapeutics Center, Institute of Structural Biology, Helmholtz Munich, Neuherberg, Germany
- TUM School of Natural Sciences, Department of Bioscience, Bayerisches NMR Zentrum, Technical University of Munich, Garching, Germany
| | - Filipe Menezes
- Molecular Targets and Therapeutics Center, Institute of Structural Biology, Helmholtz Munich, Neuherberg, Germany
- TUM School of Natural Sciences, Department of Bioscience, Bayerisches NMR Zentrum, Technical University of Munich, Garching, Germany
| | - Sabrina Benassou
- Jülich Supercomputing Centre, Forschungszentrum Jülich, Jülich, Germany
| | | | - Kieran Didi
- Computer Laboratory, Cambridge University, Cambridge, UK
| | - André Santos Dias Mourão
- Molecular Targets and Therapeutics Center, Institute of Structural Biology, Helmholtz Munich, Neuherberg, Germany
- TUM School of Natural Sciences, Department of Bioscience, Bayerisches NMR Zentrum, Technical University of Munich, Garching, Germany
| | - Radosław Kitel
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Pietro Liò
- Computer Laboratory, Cambridge University, Cambridge, UK
| | - Stefan Kesselheim
- Jülich Supercomputing Centre, Forschungszentrum Jülich, Jülich, Germany
| | - Marie Piraud
- Helmholtz AI, Helmholtz Munich, Neuherberg, Germany
| | - Fabian J Theis
- Helmholtz AI, Helmholtz Munich, Neuherberg, Germany
- Computational Health Center, Institute of Computational Biology, Helmholtz Munich, Neuherberg, Germany
- TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Michael Sattler
- Molecular Targets and Therapeutics Center, Institute of Structural Biology, Helmholtz Munich, Neuherberg, Germany
- TUM School of Natural Sciences, Department of Bioscience, Bayerisches NMR Zentrum, Technical University of Munich, Garching, Germany
| | - Grzegorz M Popowicz
- Molecular Targets and Therapeutics Center, Institute of Structural Biology, Helmholtz Munich, Neuherberg, Germany.
- TUM School of Natural Sciences, Department of Bioscience, Bayerisches NMR Zentrum, Technical University of Munich, Garching, Germany.
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2
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Lee H, Lee JY, Jang H, Cho HY, Kang M, Bae SH, Kim S, Kim E, Jang J, Kim JY, Jeon YH. Discovery of proteolysis-targeting chimera targeting undruggable proteins using a covalent ligand screening approach. Eur J Med Chem 2024; 263:115929. [PMID: 37956552 DOI: 10.1016/j.ejmech.2023.115929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/22/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023]
Abstract
Targeted protein degradation (TPD) technology, such as proteolysis-targeting chimera (PROTAC), has become a new therapeutic modality. However, the degradation of undruggable proteins, such as those involved in protein-protein interactions (PPIs), using PROTAC is still limited owing to the difficulties in finding small-molecule binders of these proteins. To identify new chemical moieties that bind to the target sites of the protein of interest (POI), we conducted a site-specific and fragment-based covalent ligand screening using liquid chromatography-tandem mass spectrometry (LC-MS/MS). To apply the selected hits to the PROTAC approach, two-dimensional (2D) nuclear magnetic resonance (NMR) experiments were performed to evaluate the reversible binding of their analogs without covalent warheads. To proof the proposed approach, human mouse double minute (MDM)2 was selected as a model system since it is involved in PPIs and is known to be a degradable target protein. Western blot analysis showed that newly synthesized PROTACs, incorporated reversible analogs of screening hits, affected degradation in a dose- and time-dependent manner. This methodology makes it possible to use PROTAC technology to exploit previously undruggable proteins for TPD.
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Affiliation(s)
- Hyeonjun Lee
- College of Pharmacy, Korea University, 2511 Sejong-ro, Sejong, 30019, South Korea
| | - Ju Yeon Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, South Korea
| | - Hyunsoo Jang
- College of Pharmacy, Korea University, 2511 Sejong-ro, Sejong, 30019, South Korea
| | - Hye Young Cho
- College of Pharmacy, Korea University, 2511 Sejong-ro, Sejong, 30019, South Korea
| | - Minhee Kang
- College of Pharmacy, Korea University, 2511 Sejong-ro, Sejong, 30019, South Korea
| | - Sang Hyun Bae
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, South Korea
| | - Suin Kim
- College of Pharmacy, Korea University, 2511 Sejong-ro, Sejong, 30019, South Korea
| | - Eunji Kim
- Azcuris, Co., Ltd., 2511 Sejong-ro, Sejong, 30019, South Korea
| | - Jaebong Jang
- College of Pharmacy, Korea University, 2511 Sejong-ro, Sejong, 30019, South Korea.
| | - Jin Young Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, South Korea.
| | - Young Ho Jeon
- College of Pharmacy, Korea University, 2511 Sejong-ro, Sejong, 30019, South Korea; Azcuris, Co., Ltd., 2511 Sejong-ro, Sejong, 30019, South Korea.
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3
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Ghafoor N, Yildiz A. Targeting MDM2-p53 Axis through Drug Repurposing for Cancer Therapy: A Multidisciplinary Approach. ACS OMEGA 2023; 8:34583-34596. [PMID: 37779953 PMCID: PMC10536845 DOI: 10.1021/acsomega.3c03471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/01/2023] [Indexed: 10/03/2023]
Abstract
Cancer remains a major cause of morbidity and mortality worldwide, and while current therapies, such as chemotherapy, immunotherapy, and cell therapy, have been effective in many patients, the development of novel therapeutic options remains an urgent priority. Mouse double minute 2 (MDM2) is a key regulator of the tumor suppressor protein p53, which plays a critical role in regulating cellular growth, apoptosis, and DNA repair. Consequently, MDM2 has been the subject of extensive research aimed at developing novel cancer therapies. In this study, we employed a machine learning-based approach to establish a quantitative structure-activity relationship model capable of predicting the potential in vitro efficacy of small molecules as MDM2 inhibitors. Our model was used to screen 5883 FDA-approved drugs, resulting in the identification of promising hits that were subsequently evaluated using molecular docking and molecular dynamics simulations. Two antihistamine drugs, cetirizine (CZ) and rupatadine (RP), exhibited particularly favorable results in the initial in silico analyses. To further assess their potential use as the activators of the p53 pathway, we investigated the antiproliferative capability of the abovementioned drugs on human glioblastoma and neuroblastoma cell lines. Both the compounds exhibited significant antiproliferative effects on the abovementioned cell lines in a dose-dependent manner. The half-maximal inhibitory concentration (IC50) of CZ was found to be 697.87 and 941.37 μM on U87 and SH-SY5Y cell lines, respectively, while the IC50 of RP was found to be 524.28 and 617.07 μM on the same cell lines, respectively. Further investigation by quantitative reverse transcriptase polymerase chain reaction analysis revealed that the CZ-treated cell lines upregulate the expression of the p53-regulated genes involved in cell cycle arrest, apoptosis, and DNA damage response compared to their respective vehicle controls. These findings suggest that CZ activates the p53 pathway by inhibiting MDM2. Our results provide compelling preclinical evidence supporting the potential use of CZ as a modulator of the MDM2-p53 axis and its plausible repurposing for cancer treatment.
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Affiliation(s)
- Naeem
Abdul Ghafoor
- Department
of Molecular Biology and Genetics, Graduate School of Natural and
Applied Sciences, Mugla Sitki Kocman University, 48000 Mugla, Turkey
| | - Aysegul Yildiz
- Department
of Molecular Biology and Genetics, Graduate School of Natural and
Applied Sciences, Mugla Sitki Kocman University, 48000 Mugla, Turkey
- Department
of Molecular Biology and Genetics, Faculty of Science, Mugla Sitki Kocman University, 48000 Mugla, Turkey
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Munisamy M, Mukherjee N, Thomas L, Pham AT, Shakeri A, Zhao Y, Kolesar J, Rao PPN, Rangnekar VM, Rao M. Therapeutic opportunities in cancer therapy: targeting the p53-MDM2/MDMX interactions. Am J Cancer Res 2021; 11:5762-5781. [PMID: 35018225 PMCID: PMC8727821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/22/2021] [Indexed: 06/14/2023] Open
Abstract
Ubiquitination is a key enzymatic post-translational modification that influences p53 stability and function. p53 protein regulates the expression of MDM2 (mouse double-minute 2 protein) E3 ligase and MDMX (double-minute 4 protein), through proteasome-based degradation. Exploration of targeting the ubiquitination pathway offers a potentially promising strategy for precision therapy in a variety of cancers. The p53-MDM2-MDMX pathway provides multiple molecular targets for small molecule screening as potential therapies for wild-type p53. As a result of its effect on molecular carcinogenesis, a personalized therapeutic approach based on the wild-type and mutant p53 protein is desirable. We highlighted the implications of p53 mutations in cancer, p53 ubiquitination mechanistic details, targeting p53-MDM2/MDMX interactions, significant discoveries related to MDM2 inhibitor drug development, MDM2 and MDMX dual target inhibitors, and clinical trials with p53-MDM2/MDMX-targeted drugs. We also investigated potential therapeutic repurposing of selective estrogen receptor modulators (SERMs) in targeting p53-MDM2/MDMX interactions. Molecular docking studies of SERMs were performed utilizing the solved structures of the p53/MDM2/MDMX proteins. These studies identified ormeloxifene as a potential dual inhibitor of p53/MDM2/MDMX interaction, suggesting that repurposing SERMs for dual targeting of p53/MDM2 and p53/MDMX interactions is an attractive strategy for targeting wild-type p53 tumors and warrants further preclinical research.
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Affiliation(s)
- Murali Munisamy
- Department of Translational Medicine Centre, All India Institute of Medical SciencesBhopal, Madhya Pradesh 462020, India
- Department of Pharmacy Practice, Center for Translational Research, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher EducationManipal, Karnataka 576104, India
| | - Nayonika Mukherjee
- Department of Pharmacy Practice, Center for Translational Research, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher EducationManipal, Karnataka 576104, India
| | - Levin Thomas
- Department of Pharmacy Practice, Center for Translational Research, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher EducationManipal, Karnataka 576104, India
| | - Amy Trinh Pham
- Medicinal and Bioorganic Chemistry Lab, School of Pharmacy, Health Sciences Campus, 200 University Avenue West, University of WaterlooWaterloo, ON N2L 3G1, Canada
| | - Arash Shakeri
- Medicinal and Bioorganic Chemistry Lab, School of Pharmacy, Health Sciences Campus, 200 University Avenue West, University of WaterlooWaterloo, ON N2L 3G1, Canada
| | - Yusheng Zhao
- Medicinal and Bioorganic Chemistry Lab, School of Pharmacy, Health Sciences Campus, 200 University Avenue West, University of WaterlooWaterloo, ON N2L 3G1, Canada
| | - Jill Kolesar
- Department of Pharmacy Practice & Science, University of Kentucky567 TODD Building, 789 South Limestone Street, Lexington, Kentucky 40539-0596, USA
| | - Praveen P N Rao
- Medicinal and Bioorganic Chemistry Lab, School of Pharmacy, Health Sciences Campus, 200 University Avenue West, University of WaterlooWaterloo, ON N2L 3G1, Canada
| | - Vivek M Rangnekar
- Markey Cancer Center, University of KentuckyLexington, Kentucky 40536, USA
| | - Mahadev Rao
- Department of Pharmacy Practice, Center for Translational Research, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher EducationManipal, Karnataka 576104, India
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Haronikova L, Bonczek O, Zatloukalova P, Kokas-Zavadil F, Kucerikova M, Coates PJ, Fahraeus R, Vojtesek B. Resistance mechanisms to inhibitors of p53-MDM2 interactions in cancer therapy: can we overcome them? Cell Mol Biol Lett 2021; 26:53. [PMID: 34911439 PMCID: PMC8903693 DOI: 10.1186/s11658-021-00293-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/05/2021] [Indexed: 12/13/2022] Open
Abstract
Since the discovery of the first MDM2 inhibitors, we have gained deeper insights into the cellular roles of MDM2 and p53. In this review, we focus on MDM2 inhibitors that bind to the p53-binding domain of MDM2 and aim to disrupt the binding of MDM2 to p53. We describe the basic mechanism of action of these MDM2 inhibitors, such as nutlin-3a, summarise the determinants of sensitivity to MDM2 inhibition from p53-dependent and p53-independent points of view and discuss the problems with innate and acquired resistance to MDM2 inhibition. Despite progress in MDM2 inhibitor design and ongoing clinical trials, their broad use in cancer treatment is not fulfilling expectations in heterogenous human cancers. We assess the MDM2 inhibitor types in clinical trials and provide an overview of possible sources of resistance to MDM2 inhibition, underlining the need for patient stratification based on these aspects to gain better clinical responses, including the use of combination therapies for personalised medicine.
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Affiliation(s)
- Lucia Haronikova
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53, Brno, Czech Republic.
| | - Ondrej Bonczek
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53, Brno, Czech Republic
- Department of Medical Biosciences, Umea University, 901 87, Umea, Vasterbotten, Sweden
| | - Pavlina Zatloukalova
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Filip Kokas-Zavadil
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Martina Kucerikova
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Philip J Coates
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Robin Fahraeus
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53, Brno, Czech Republic
- Department of Medical Biosciences, Umea University, 901 87, Umea, Vasterbotten, Sweden
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, 75010, Paris, France
| | - Borivoj Vojtesek
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53, Brno, Czech Republic.
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6
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Singh N, Li W. Absolute Binding Free Energy Calculations for Highly Flexible Protein MDM2 and Its Inhibitors. Int J Mol Sci 2020; 21:ijms21134765. [PMID: 32635537 PMCID: PMC7369993 DOI: 10.3390/ijms21134765] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/26/2020] [Accepted: 07/02/2020] [Indexed: 01/16/2023] Open
Abstract
Reliable prediction of binding affinities for ligand-receptor complex has been the primary goal of a structure-based drug design process. In this respect, alchemical methods are evolving as a popular choice to predict the binding affinities for biomolecular complexes. However, the highly flexible protein-ligand systems pose a challenge to the accuracy of binding free energy calculations mostly due to insufficient sampling. Herein, integrated computational protocol combining free energy perturbation based absolute binding free energy calculation with free energy landscape method was proposed for improved prediction of binding free energy for flexible protein-ligand complexes. The proposed method is applied to the dataset of various classes of p53-MDM2 (murine double minute 2) inhibitors. The absolute binding free energy calculations for MDMX (murine double minute X) resulted in a mean absolute error value of 0.816 kcal/mol while it is 3.08 kcal/mol for MDM2, a highly flexible protein compared to MDMX. With the integration of the free energy landscape method, the mean absolute error for MDM2 is improved to 1.95 kcal/mol.
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Affiliation(s)
- Nidhi Singh
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China;
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Wenjin Li
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China;
- Correspondence: ; Tel.: +86-755-2694-2336
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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.
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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
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8
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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.
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9
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Insights into the binding mechanisms of inhibitors of MDM2 based on molecular dynamics simulations and binding free energy calculations. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Muszak D, Łabuzek B, Brela MZ, Twarda-Clapa A, Czub M, Musielak B, Surmiak E, Holak TA. The synthesis and characterization of tetramic acid derivatives as Mdm2-p53 inhibitors. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.03.089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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11
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Mortensen KT, Osberger TJ, King TA, Sore HF, Spring DR. Strategies for the Diversity-Oriented Synthesis of Macrocycles. Chem Rev 2019; 119:10288-10317. [DOI: 10.1021/acs.chemrev.9b00084] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Kim T. Mortensen
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Thomas J. Osberger
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Thomas A. King
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Hannah F. Sore
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - David R. Spring
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
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12
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α-Amino Acids as Synthons in the Ugi-5-Centers-4-Components Reaction: Chemistry and Applications. Symmetry (Basel) 2019. [DOI: 10.3390/sym11060798] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Since the first reports, the Ugi four-component reaction (U-4CR) has been recognized as a keystone transformation enabling the synthesis of peptide mimetics in a single step and with high atom economy. In recent decades, the U-4CR has been a source of inspiration for many chemists fascinated by the possibility of identifying new efficient organic reactions by simply changing one of the components or by coupling in tandem the multicomponent process with a huge variety of organic transformations. Herein we review the synthetic potentialities, the boundaries, and the applications of the U-4CR involving α-amino acids, where the presence of two functional groups—the amino and the carboxylic acids—allowed a 5-center 4-component Ugi-like reaction, a powerful tool to gain access to drug-like multi-functionalized scaffolds.
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13
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Kallen J, Izaac A, Chau S, Wirth E, Schoepfer J, Mah R, Schlapbach A, Stutz S, Vaupel A, Guagnano V, Masuya K, Stachyra TM, Salem B, Chene P, Gessier F, Holzer P, Furet P. Structural States of Hdm2 and HdmX: X-ray Elucidation of Adaptations and Binding Interactions for Different Chemical Compound Classes. ChemMedChem 2019; 14:1305-1314. [PMID: 31066983 DOI: 10.1002/cmdc.201900201] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Indexed: 01/02/2023]
Abstract
Hdm2 (human MDM2, human double minute 2 homologue) counteracts p53 function by direct binding to p53 and by ubiquitin-dependent p53 protein degradation. Activation of p53 by inhibitors of the p53-Hdm2 interaction is being pursued as a therapeutic strategy in p53 wild-type cancers. In addition, HdmX (human MDMX, human MDM4) was also identified as an important therapeutic target to efficiently reactivate p53, and it is likely that dual inhibition of Hdm2 and HdmX is beneficial. Herein we report four new X-ray structures for Hdm2 and five new X-ray structures for HdmX complexes, involving different classes of synthetic compounds (including the worldwide highest resolutions for Hdm2 and HdmX, at 1.13 and 1.20 Å, respectively). We also reveal the key additive 18-crown-ether, which we discovered to enable HdmX crystallization and show its stabilization of various Lys residues. In addition, we report the previously unpublished details of X-ray structure determinations for eight further Hdm2 complexes, including the clinical trial compounds NVP-CGM097 and NVP-HDM201. An analysis of all compound binding modes reveals new and deepened insight into the possible adaptations and structural states of Hdm2 (e.g., flip of F55, flip of Y67, reorientation of H96) and HdmX (e.g., flip of H55, dimer induction), enabling key binding interactions for different compound classes. To facilitate comparisons, we used the same numbering for Hdm2 (as in Q00987) and HdmX (as in O15151, but minus 1). Taken together, these structural insights should prove useful for the design and optimization of further selective and/or dual Hdm2/HdmX inhibitors.
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Affiliation(s)
- Joerg Kallen
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Aude Izaac
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Suzanne Chau
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Emmanuelle Wirth
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Joseph Schoepfer
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Robert Mah
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Achim Schlapbach
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Stefan Stutz
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Andrea Vaupel
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Vito Guagnano
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | | | - Therese-Marie Stachyra
- Disease Area Oncology, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Bahaa Salem
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Patrick Chene
- Disease Area Oncology, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Francois Gessier
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Philipp Holzer
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Pascal Furet
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
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14
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Liu Y, Wang X, Wang G, Yang Y, Yuan Y, Ouyang L. The past, present and future of potential small-molecule drugs targeting p53-MDM2/MDMX for cancer therapy. Eur J Med Chem 2019; 176:92-104. [PMID: 31100649 DOI: 10.1016/j.ejmech.2019.05.018] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/02/2019] [Accepted: 05/06/2019] [Indexed: 02/05/2023]
Abstract
The p53 gene, a well-known tumor suppressor gene, plays a crucial role in cell cycle regulation, DNA repair, cell differentiation, and apoptosis. MDM2 exerts p53-dependent activity mainly by binding to p53 protein to form MDM2-p53 negative feedback loop. In addition, MDM2 is involved in a number of pathways that regulate cell proliferation and apoptosis, playing a p53-independent role. The p53 binding domain of MDMX bind to p53 transcriptional activation domain, inhibiting the transcriptional activity of p53 on its downstream genes, but does not mediate the degradation of p53. The anti-tumor effect is exerted by inhibiting the interaction between the MDM2/MDMX protein and the p53 protein by a small-molecule or by restoring the activity of the p53 protein. This review describes in the structural features, biological functions and mechanisms of p53-MDM2/MDMX, and summarizes small-molecule targeting p53-MDM2/MDMX.
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Affiliation(s)
- Yao Liu
- State Key Laboratory of Biotherapy and Cancer Center, Department of Thoracic Surgery, West China Hospital, Sichuan University, China
| | - Xiaohui Wang
- Department of Pharmacy, Naval Authorities Clinic, Beijing, 100841, China
| | - Guan Wang
- State Key Laboratory of Biotherapy and Cancer Center, Department of Thoracic Surgery, West China Hospital, Sichuan University, China
| | - Yushang Yang
- State Key Laboratory of Biotherapy and Cancer Center, Department of Thoracic Surgery, West China Hospital, Sichuan University, China
| | - Yong Yuan
- State Key Laboratory of Biotherapy and Cancer Center, Department of Thoracic Surgery, West China Hospital, Sichuan University, China.
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, Department of Thoracic Surgery, West China Hospital, Sichuan University, China.
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15
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Levy R, Gregory E, Borcherds W, Daughdrill G. p53 Phosphomimetics Preserve Transient Secondary Structure but Reduce Binding to Mdm2 and MdmX. Biomolecules 2019; 9:biom9030083. [PMID: 30832340 PMCID: PMC6468375 DOI: 10.3390/biom9030083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 02/07/2023] Open
Abstract
The disordered p53 transactivation domain (p53TAD) contains specific levels of transient helical secondary structure that are necessary for its binding to the negative regulators, mouse double minute 2 (Mdm2) and MdmX. The interactions of p53 with Mdm2 and MdmX are also modulated by posttranslational modifications (PTMs) of p53TAD including phosphorylation at S15, T18 and S20 that inhibits p53-Mdm2 binding. It is unclear whether the levels of transient secondary structure in p53TAD are changed by phosphorylation or other PTMs. We used phosphomimetic mutants to determine if adding a negative charge at positions 15 and 18 has any effect on the transient secondary structure of p53TAD and protein-protein binding. Using a combination of biophysical and structural methods, we investigated the effects of single and multisite phosphomimetics on the transient secondary structure of p53TAD and its interaction with Mdm2, MdmX, and the KIX domain. The phosphomimetics reduced Mdm2 and MdmX binding affinity by 3–5-fold, but resulted in minimal changes in transient secondary structure, suggesting that the destabilizing effect of phosphorylation on the p53TAD-Mdm2 interaction is primarily electrostatic. Phosphomimetics had no effect on the p53-KIX interaction, suggesting that increased binding of phosphorylated p53 to KIX may be influenced by decreased competition with its negative regulators.
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Affiliation(s)
- Robin Levy
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA.
- Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL 33612, USA.
| | - Emily Gregory
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA.
- Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL 33612, USA.
| | - Wade Borcherds
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA.
- Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL 33612, USA.
| | - Gary Daughdrill
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA.
- Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL 33612, USA.
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16
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Neochoritis CG, Kazemi Miraki M, Abdelraheem EMM, Surmiak E, Zarganes-Tzitzikas T, Łabuzek B, Holak TA, Dömling A. Design of indole- and MCR-based macrocycles as p53-MDM2 antagonists. Beilstein J Org Chem 2019; 15:513-520. [PMID: 30873235 PMCID: PMC6404402 DOI: 10.3762/bjoc.15.45] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 02/14/2019] [Indexed: 01/02/2023] Open
Abstract
Macrocycles were designed to antagonize the protein–protein interaction p53-MDM2 based on the three-finger pharmacophore F19W23L25. The synthesis was accomplished by a rapid, one-pot synthesis of indole-based macrocycles based on Ugi macrocyclization. The reaction of 12 different α,ω-amino acids and different indole-3-carboxaldehyde derivatives afforded a unique library of macrocycles otherwise difficult to access. Screening of the library for p53-MDM2 inhibition by fluorescence polarization and 1H,15N HSQC NMR measurements confirm MDM2 binding.
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Affiliation(s)
- Constantinos G Neochoritis
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Maryam Kazemi Miraki
- Chemistry Department, Tarbiat Modares University, P.O. Box 14155-4838, Tehran, Iran
| | - Eman M M Abdelraheem
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Ewa Surmiak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Tryfon Zarganes-Tzitzikas
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Beata Łabuzek
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
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17
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Skalniak L, Twarda-Clapa A, Neochoritis CG, Surmiak E, Machula M, Wisniewska A, Labuzek B, Ali AM, Krzanik S, Dubin G, Groves M, Dömling A, Holak TA. A fluorinated indole-based MDM2 antagonist selectively inhibits the growth of p53 wt osteosarcoma cells. FEBS J 2019; 286:1360-1374. [PMID: 30715803 DOI: 10.1111/febs.14774] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 12/15/2018] [Accepted: 01/31/2019] [Indexed: 12/14/2022]
Abstract
The p53 protein is engaged in the repair of DNA mutations and elimination of heavily damaged cells, providing anticancer protection. Dysregulation of p53 activity is a crucial step in carcinogenesis. This dysregulation is often caused by the overexpression of negative regulators of p53, among which MDM2 is the most prominent one. Antagonizing MDM2 with small molecules restores the activity of p53 in p53 wild-type (p53wt ) cells and thus provides positive outcomes in the treatment of p53wt cancers. Previously, we have reported the discovery of a panel of fluoro-substituted indole-based antagonists of MDM2. Here, we demonstrate the biological activity and stereoselectivity of the most active compound from this series. Both enantiomers of the esterified form of the compound, as well as its corresponding carboxylic acids, were found active in fluorescence polarization (FP) assay, nuclear magnetic resonance (NMR) and microscale thermophoresis (MST) assay, with Ki and KD values around 1 μm. From these four compounds, the esterified enantiomer (R)-5a was active in cells, which was evidenced by the increase of p53 levels, the induced expression of p53-target genes (CDKN1A and MDM2), the selective induction of cell cycle arrest, and selective growth inhibition of p53wt U-2 OS and SJSA-1 compared to p53del SAOS-2 cells. The analysis of the crystal structure of human MDM2 in complex with the compound (R)-6a (carboxylic acid of the active (R)-5a compound) revealed the classical three-finger binding mode. Altogether, our data demonstrate the activity of the compound and provide the structural basis for further structure optimization.
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Affiliation(s)
- Lukasz Skalniak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | | | | | - Ewa Surmiak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Monika Machula
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | | | - Beata Labuzek
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Ameena M Ali
- Department of Drug Design, University of Groningen, The Netherlands
| | - Sylwia Krzanik
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grzegorz Dubin
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Matthew Groves
- Department of Drug Design, University of Groningen, The Netherlands
| | | | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
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18
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Parrish RM, Thompson KC, Martínez TJ. Large-Scale Functional Group Symmetry-Adapted Perturbation Theory on Graphical Processing Units. J Chem Theory Comput 2018; 14:1737-1753. [DOI: 10.1021/acs.jctc.7b01053] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Robert M. Parrish
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Keiran C. Thompson
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Todd J. Martínez
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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19
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Qin L, Liu H, Chen R, Zhou J, Cheng X, Chen Y, Huang Y, Su Z. Effect of the Flexible Regions of the Oncoprotein Mouse Double Minute X on Inhibitor Binding Affinity. Biochemistry 2017; 56:5943-5954. [DOI: 10.1021/acs.biochem.7b00903] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Lingyun Qin
- Institute
of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial
Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Huili Liu
- National
Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics
and Mathematics, Chinese Academy of Science, Wuhan 430071, China
| | - Rong Chen
- Institute
of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial
Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Jingjing Zhou
- Institute
of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial
Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Xiyao Cheng
- Institute
of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial
Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Yao Chen
- Institute
of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial
Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Yongqi Huang
- Institute
of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial
Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Zhengding Su
- Institute
of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial
Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
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20
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Estrada-Ortiz N, Neochoritis CG, Twarda-Clapa A, Musielak B, Holak TA, Dömling A. Artificial Macrocycles as Potent p53-MDM2 Inhibitors. ACS Med Chem Lett 2017; 8:1025-1030. [PMID: 29057045 PMCID: PMC5641952 DOI: 10.1021/acsmedchemlett.7b00219] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/20/2017] [Indexed: 11/28/2022] Open
Abstract
Based on a combination of an Ugi four component reaction and a ring closing metathesis, a library of novel artificial macrocyclic inhibitors of the p53-MDM2 interaction was designed and synthesized. These macrocycles, alternatively to stapled peptides, target for the first time the large hydrophobic surface area formed by Tyr67, Gln72, His73, Val93, and Lys94 yielding derivatives with affinity to MDM2 in the nanomolar range. Their binding affinity with MDM2 was evaluated using fluorescence polarization (FP) assay and 1H-15N two-dimensional HSQC nuclear magnetic resonance experiments.
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Affiliation(s)
- Natalia Estrada-Ortiz
- Department of Drug
Design, University of Groningen, A. Deusinglaan 1, Groningen 9700AV, The Netherlands
| | | | - Aleksandra Twarda-Clapa
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
- Malopolska Centre
of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Bogdan Musielak
- Department of Chemistry, Jagiellonian University, Ingardena
3, 30-060 Krakow, Poland
| | - Tad A. Holak
- Malopolska Centre
of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
- Department of Chemistry, Jagiellonian University, Ingardena
3, 30-060 Krakow, Poland
| | - Alexander Dömling
- Department of Drug
Design, University of Groningen, A. Deusinglaan 1, Groningen 9700AV, The Netherlands
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21
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Co-operative intra-protein structural response due to protein–protein complexation revealed through thermodynamic quantification: study of MDM2-p53 binding. J Comput Aided Mol Des 2017; 31:891-903. [DOI: 10.1007/s10822-017-0057-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/30/2017] [Indexed: 12/29/2022]
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22
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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
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23
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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.
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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
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24
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Surmiak E, Twarda-Clapa A, Zak KM, Musielak B, Tomala MD, Kubica K, Grudnik P, Madej M, Jablonski M, Potempa J, Kalinowska-Tluscik J, Dömling A, Dubin G, Holak TA. A Unique Mdm2-Binding Mode of the 3-Pyrrolin-2-one- and 2-Furanone-Based Antagonists of the p53-Mdm2 Interaction. ACS Chem Biol 2016; 11:3310-3318. [PMID: 27709883 DOI: 10.1021/acschembio.6b00596] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The p53 pathway is inactivated in almost all types of cancer by mutations in the p53 encoding gene or overexpression of the p53 negative regulators, Mdm2 and/or Mdmx. Restoration of the p53 function by inhibition of the p53-Mdm2/Mdmx interaction opens up a prospect for a nongenotoxic anticancer therapy. Here, we present the syntheses, activities, and crystal structures of two novel classes of Mdm2-p53 inhibitors that are based on the 3-pyrrolin-2-one and 2-furanone scaffolds. The structures of the complexes formed by these inhibitors and Mdm2 reveal the dimeric protein molecular organization that has not been observed in the small-molecule/Mdm2 complexes described until now. In particular, the 6-chloroindole group does not occupy the usual Trp-23 pocket of Mdm2 but instead is engaged in dimerization. This entirely unique binding mode of the compounds opens new possibilities for optimization of the Mdm2-p53 interaction inhibitors.
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Affiliation(s)
- Ewa Surmiak
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Aleksandra Twarda-Clapa
- Faculty
of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Krzysztof M. Zak
- Faculty
of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Bogdan Musielak
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Marcin D. Tomala
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Katarzyna Kubica
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Przemyslaw Grudnik
- Faculty
of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Mariusz Madej
- Faculty
of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Mateusz Jablonski
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Jan Potempa
- Faculty
of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | | | - Alexander Dömling
- Faculty
of Mathematics and Natural Sciences, Department of Pharmacy, University of Groningen, 9713AV Groningen, The Netherlands
| | - Grzegorz Dubin
- Faculty
of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Tad A. Holak
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
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25
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Ciemny MP, Debinski A, Paczkowska M, Kolinski A, Kurcinski M, Kmiecik S. Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction. Sci Rep 2016; 6:37532. [PMID: 27905468 PMCID: PMC5131342 DOI: 10.1038/srep37532] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/27/2016] [Indexed: 12/27/2022] Open
Abstract
Protein-peptide interactions are often associated with large-scale conformational changes that are difficult to study either by classical molecular modeling or by experiment. Recently, we have developed the CABS-dock method for flexible protein-peptide docking that enables large-scale rearrangements of the protein chain. In this study, we use CABS-dock to investigate the binding of the p53-MDM2 complex, an element of the cell cycle regulation system crucial for anti-cancer drug design. Experimental data suggest that p53-MDM2 binding is affected by significant rearrangements of a lid region - the N-terminal highly flexible MDM2 fragment; however, the details are not clear. The large size of the highly flexible MDM2 fragments makes p53-MDM2 intractable for exhaustive binding dynamics studies using atomistic models. We performed extensive dynamics simulations using the CABS-dock method, including large-scale structural rearrangements of MDM2 flexible regions. Without a priori knowledge of the p53 peptide structure or its binding site, we obtained near-native models of the p53-MDM2 complex. The simulation results match well the experimental data and provide new insights into the possible role of the lid fragment in p53 binding. The presented case study demonstrates that CABS-dock methodology opens up new opportunities for protein-peptide docking with large-scale changes of the protein receptor structure.
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Affiliation(s)
- Maciej Pawel Ciemny
- University of Warsaw, Faculty of Chemistry, Warsaw 02-093, Poland
- University of Warsaw, Faculty of Physics, Warsaw, 02-093, Poland
| | | | - Marta Paczkowska
- University of Warsaw, Faculty of Chemistry, Warsaw 02-093, Poland
| | - Andrzej Kolinski
- University of Warsaw, Faculty of Chemistry, Warsaw 02-093, Poland
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26
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Surmiak E, Neochoritis CG, Musielak B, Twarda-Clapa A, Kurpiewska K, Dubin G, Camacho C, Holak TA, Dömling A. Rational design and synthesis of 1,5-disubstituted tetrazoles as potent inhibitors of the MDM2-p53 interaction. Eur J Med Chem 2016; 126:384-407. [PMID: 27907876 DOI: 10.1016/j.ejmech.2016.11.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/10/2016] [Accepted: 11/12/2016] [Indexed: 11/30/2022]
Abstract
Using the computational pharmacophore-based ANCHOR.QUERY platform a new scaffold was discovered. Potent compounds evolved inhibiting the protein-protein interaction p53-MDM2. An extensive SAR study was performed based on our four-point pharmacophore model, yielding derivatives with affinity to MDM2 in the nanomolar range. Their binding affinity with MDM2 was evaluated using both fluorescence polarization (FP) assay and 2D-NMR-HSQC experiments.
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Affiliation(s)
- Ewa Surmiak
- Department of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Constantinos G Neochoritis
- Department of Pharmacy, Drug Design Department, University of Groningen, 9713AV Groningen, The Netherlands
| | - Bogdan Musielak
- Department of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Aleksandra Twarda-Clapa
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Katarzyna Kurpiewska
- Department of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Grzegorz Dubin
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Carlos Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Avenue, Biomedical Science Tower 3, Pittsburgh, PA 15260, USA
| | - Tad A Holak
- Department of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Alexander Dömling
- Department of Pharmacy, Drug Design Department, University of Groningen, 9713AV Groningen, The Netherlands.
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27
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Joerger AC, Bauer MR, Wilcken R, Baud MGJ, Harbrecht H, Exner TE, Boeckler FM, Spencer J, Fersht AR. Exploiting Transient Protein States for the Design of Small-Molecule Stabilizers of Mutant p53. Structure 2016; 23:2246-2255. [PMID: 26636255 PMCID: PMC4671956 DOI: 10.1016/j.str.2015.10.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/30/2015] [Accepted: 10/04/2015] [Indexed: 12/01/2022]
Abstract
The destabilizing p53 cancer mutation Y220C creates an extended crevice on the surface of the protein that can be targeted by small-molecule stabilizers. Here, we identify different classes of small molecules that bind to this crevice and determine their binding modes by X-ray crystallography. These structures reveal two major conformational states of the pocket and a cryptic, transiently open hydrophobic subpocket that is modulated by Cys220. In one instance, specifically targeting this transient protein state by a pyrrole moiety resulted in a 40-fold increase in binding affinity. Molecular dynamics simulations showed that both open and closed states of this subsite were populated at comparable frequencies along the trajectories. Our data extend the framework for the design of high-affinity Y220C mutant binders for use in personalized anticancer therapy and, more generally, highlight the importance of implementing protein dynamics and hydration patterns in the drug-discovery process.
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Affiliation(s)
- Andreas C Joerger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Matthias R Bauer
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Rainer Wilcken
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Matthias G J Baud
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Hannes Harbrecht
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Thomas E Exner
- Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Frank M Boeckler
- Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - John Spencer
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton, East Sussex BN1 9QJ, UK
| | - Alan R Fersht
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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28
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Mukherjee S, Pantelopulos GA, Voelz VA. Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking. Sci Rep 2016; 6:31631. [PMID: 27538695 PMCID: PMC4990920 DOI: 10.1038/srep31631] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/22/2016] [Indexed: 12/11/2022] Open
Abstract
MDM2 is a negative regulator of p53 activity and an important target for cancer therapeutics. The N-terminal lid region of MDM2 modulates interactions with p53 via competition for its binding cleft, exchanging slowly between docked and undocked conformations in the absence of p53. To better understand these dynamics, we constructed Markov State Models (MSMs) from large collections of unbiased simulation trajectories of apo-MDM2, and find strong evidence for diffuse, yet two-state folding and binding of the N-terminal region to the p53 receptor site. The MSM also identifies holo-like receptor conformations highly suitable for computational docking, despite initiating trajectories from closed-cleft receptor structures unsuitable for docking. Fixed-anchor docking studies using a test set of high-affinity small molecules and peptides show simulated receptor ensembles achieve docking successes comparable to cross-docking studies using crystal structures of receptors bound by alternative ligands. For p53, the best-scoring receptor structures have the N-terminal region lid region bound in a helical conformation mimicking the bound structure of p53, suggesting lid region association induces receptor conformations suitable for binding. These results suggest that MD + MSM approaches can sample binding-competent receptor conformations suitable for computational peptidomimetic design, and that inclusion of disordered regions may be essential to capturing the correct receptor dynamics.
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Affiliation(s)
| | | | - Vincent A Voelz
- Department of Chemistry, Temple University, Philadelphia, PA, USA
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29
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Joerger AC, Fersht AR. The p53 Pathway: Origins, Inactivation in Cancer, and Emerging Therapeutic Approaches. Annu Rev Biochem 2016; 85:375-404. [DOI: 10.1146/annurev-biochem-060815-014710] [Citation(s) in RCA: 363] [Impact Index Per Article: 45.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Andreas C. Joerger
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, 60438 Frankfurt am Main, Germany;
| | - Alan R. Fersht
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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30
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Estrada-Ortiz N, Neochoritis CG, Dömling A. How To Design a Successful p53-MDM2/X Interaction Inhibitor: A Thorough Overview Based on Crystal Structures. ChemMedChem 2016; 11:757-72. [PMID: 26676832 PMCID: PMC4838565 DOI: 10.1002/cmdc.201500487] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/23/2015] [Indexed: 01/10/2023]
Abstract
A recent therapeutic strategy in oncology is based on blocking the protein-protein interaction between the murine double minute (MDM) homologues MDM2/X and the tumor-suppressor protein p53. Inhibiting the binding between wild-type (WT) p53 and its negative regulators MDM2 and/or MDMX has become an important target in oncology to restore the antitumor activity of p53, the so-called guardian of our genome. Interestingly, based on the multiple disclosed compound classes and structural analysis of small-molecule-MDM2 adducts, the p53-MDM2 complex is perhaps the best studied and most targeted protein-protein interaction. Several classes of small molecules have been identified as potent, selective, and efficient inhibitors of the p53-MDM2/X interaction, and many co-crystal structures with the protein are available. Herein we review the properties as well as preclinical and clinical studies of these small molecules and peptides, categorized by scaffold type. A particular emphasis is made on crystallographic structures and the observed binding modes of these compounds, including conserved water molecules present.
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Affiliation(s)
- Natalia Estrada-Ortiz
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD, Groningen, The Netherlands
| | - Constantinos G Neochoritis
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD, Groningen, The Netherlands
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD, Groningen, The Netherlands.
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31
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Angulo J, Goffin SA, Gandhi D, Searcey M, Howell LA. Unveiling the "Three-Finger Pharmacophore" Required for p53-MDM2 Inhibition by Saturation-Transfer Difference (STD) NMR Initial Growth-Rates Approach. Chemistry 2016; 22:5858-62. [PMID: 26864212 DOI: 10.1002/chem.201600114] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Indexed: 02/02/2023]
Abstract
Inhibitors of the p53-MDM2 protein-protein interaction are emerging as a new and validated approach to treating cancer. Herein, we describe the synthesis and inhibitory evaluation of a series of isoquinolin-1-one analogues, and highlight the utility of an initial growth-rates saturation-transfer difference (STD) NMR approach supported by protein-ligand docking to investigate p53-MDM2 inhibition. The approach is illustrated by the study of compound 1, providing key insights into the binding mode of this kind of MDM2 ligands and, more importantly, readily unveiling the previously proposed three-finger pharmacophore requirement for p53-MDM2 inhibition.
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Affiliation(s)
- Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Sarah A Goffin
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Daivik Gandhi
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Mark Searcey
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Lesley A Howell
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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32
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Neochoritis CG, Wang K, Estrada-Ortiz N, Herdtweck E, Kubica K, Twarda A, Zak KM, Holak TA, Dömling A. 2,30-Bis(10H-indole) heterocycles: New p53/MDM2/MDMX antagonists. Bioorg Med Chem Lett 2015; 25:5661-6. [PMID: 26584879 PMCID: PMC4764400 DOI: 10.1016/j.bmcl.2015.11.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 11/05/2015] [Accepted: 11/06/2015] [Indexed: 01/10/2023]
Abstract
The protein–protein interaction of p53 and MDM2/X is a promising non genotoxic anticancer target. A rapid and efficient methodology was developed to synthesize the 2,30-bis(10H-indole) heterocyclic scaffold 2 as ester, acid and amide derivatives. Their binding affinity with MDM2 was evaluated using both fluorescence polarization (FP) assay and HSQC experiments, indicating good inhibition and a perfect starting point for further optimizations.
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Affiliation(s)
| | - Kan Wang
- Department of Chemistry, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA
| | - Natalia Estrada-Ortiz
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Eberhardt Herdtweck
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching bei München, Germany
| | - Katarzyna Kubica
- Department of Organic Chemistry, Jagellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Aleksandra Twarda
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Krzysztof M. Zak
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Tad A. Holak
- Department of Organic Chemistry, Jagellonian University, Ingardena 3, 30-060 Krakow, Poland
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Department of Chemistry, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA
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33
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Kroon E, Schulze JO, Süß E, Camacho CJ, Biondi RM, Dömling A. Discovery of a Potent Allosteric Kinase Modulator by Combining Computational and Synthetic Methods. Angew Chem Int Ed Engl 2015; 54:13933-6. [PMID: 26385475 PMCID: PMC4721676 DOI: 10.1002/anie.201506310] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/12/2015] [Indexed: 12/14/2022]
Abstract
The rational design of allosteric kinase modulators is challenging but rewarding. The protein kinase PDK1, which lies at the center of the growth-factor signaling pathway, possesses an allosteric regulatory site previously validated both in vitro and in cells. ANCHOR.QUERY software was used to discover a potent allosteric PDK1 kinase modulator. Using a recently published PDK1 compound as a template, several new scaffolds that bind to the allosteric target site were generated and one example was validated. The inhibitor can be synthesized in one step by multicomponent reaction (MCR) chemistry when using the ANCHOR.QUERY approach. Our results are significant because the outlined approach allows rapid and efficient scaffold hopping from known molecules into new easily accessible and biologically active ones. Based on increasing interest in allosteric-site drug discovery, we foresee many potential applications for this approach.
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Affiliation(s)
- Edwin Kroon
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen (The Netherlands) http://www.drugdesign.nl
| | - Jörg O Schulze
- Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt (Germany)
| | - Evelyn Süß
- Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt (Germany)
| | - Carlos J Camacho
- University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA 15261 (USA)
| | - Ricardo M Biondi
- Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt (Germany)
| | - Alexander Dömling
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen (The Netherlands) http://www.drugdesign.nl.
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34
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Cheng W, Liang Z, Wang W, Yi C, Li H, Zhang S, Zhang Q. Insight into binding modes of p53 and inhibitors to MDM2 based on molecular dynamic simulations and principal component analysis. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1087598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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35
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Zarganes-Tzitzikas T, Chandgude AL, Dömling A. Multicomponent Reactions, Union of MCRs and Beyond. CHEM REC 2015; 15:981-96. [DOI: 10.1002/tcr.201500201] [Citation(s) in RCA: 172] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Indexed: 11/08/2022]
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36
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Kroon E, Schulze JO, Süß E, Camacho CJ, Biondi RM, Dömling A. Discovery of a Potent Allosteric Kinase Modulator by Combining Computational and Synthetic Methods. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506310] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Edwin Kroon
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen (The Netherlands) http://www.drugdesign.nl
| | - Jörg O. Schulze
- Universitätsklinikum Frankfurt, Theodor‐Stern‐Kai 7, 60590 Frankfurt (Germany)
| | - Evelyn Süß
- Universitätsklinikum Frankfurt, Theodor‐Stern‐Kai 7, 60590 Frankfurt (Germany)
| | - Carlos J. Camacho
- University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA 15261 (USA)
| | - Ricardo M. Biondi
- Universitätsklinikum Frankfurt, Theodor‐Stern‐Kai 7, 60590 Frankfurt (Germany)
| | - Alexander Dömling
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen (The Netherlands) http://www.drugdesign.nl
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37
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Pantelopulos GA, Mukherjee S, Voelz VA. Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics. Proteins 2015; 83:1665-76. [DOI: 10.1002/prot.24852] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 06/08/2015] [Accepted: 06/24/2015] [Indexed: 12/13/2022]
Affiliation(s)
| | - Sudipto Mukherjee
- Department of Chemistry; Temple University; Philadelphia Pennsylvania 19122
| | - Vincent A. Voelz
- Department of Chemistry; Temple University; Philadelphia Pennsylvania 19122
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38
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Bueren-Calabuig JA, Michel J. Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2. PLoS Comput Biol 2015; 11:e1004282. [PMID: 26046940 PMCID: PMC4457491 DOI: 10.1371/journal.pcbi.1004282] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 04/13/2015] [Indexed: 01/16/2023] Open
Abstract
Numerous biomolecular interactions involve unstructured protein regions, but how to exploit such interactions to enhance the affinity of a lead molecule in the context of rational drug design remains uncertain. Here clarification was sought for cases where interactions of different ligands with the same disordered protein region yield qualitatively different results. Specifically, conformational ensembles for the disordered lid region of the N-terminal domain of the oncoprotein MDM2 in the presence of different ligands were computed by means of a novel combination of accelerated molecular dynamics, umbrella sampling, and variational free energy profile methodologies. The resulting conformational ensembles for MDM2, free and bound to p53 TAD (17-29) peptide identify lid states compatible with previous NMR measurements. Remarkably, the MDM2 lid region is shown to adopt distinct conformational states in the presence of different small-molecule ligands. Detailed analyses of small-molecule bound ensembles reveal that the ca. 25-fold affinity improvement of the piperidinone family of inhibitors for MDM2 constructs that include the full lid correlates with interactions between ligand hydrophobic groups and the C-terminal lid region that is already partially ordered in apo MDM2. By contrast, Nutlin or benzodiazepinedione inhibitors, that bind with similar affinity to full lid and lid-truncated MDM2 constructs, interact additionally through their solubilizing groups with N-terminal lid residues that are more disordered in apo MDM2. Life as we know it depends on interactions between proteins. There is substantial evidence that many interactions between proteins involve very flexible protein regions. These disordered regions may undergo disorder/order transitions upon forming an interaction with another protein. Many successful approaches to medicinal chemistry are based on mimicking the interactions of biological molecules with man-made small molecules. However how drug-like small-molecules may modulate protein disorder is currently poorly understood, largely because it is difficult to measure in details this type of interaction with experimental methods. Here we have used computer simulations to resolve with great details the process by which different small-molecules modulate the flexibility of a disordered region of the protein MDM2. This protein is overexpressed in many cancers and small-molecules that recognize MDM2 have been developed over the last decade as possible novel anti-cancer agents. We show that the flexible MDM2 “lid” region adopts different conformational states in the presence of different small-molecules. Our results suggest why some classes of small-molecules form favorable interactions with the lid region, whereas others do not. These findings may prove crucial to develop new and more effective MDM2 inhibitors, and more generally to help drug designers target disordered proteins regions with small-molecules.
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Affiliation(s)
| | - Julien Michel
- EaStCHEM School of Chemistry, the University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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39
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Identification of antipsychotic drug fluspirilene as a potential p53-MDM2 inhibitor: a combined computational and experimental study. J Comput Aided Mol Des 2014; 29:155-63. [DOI: 10.1007/s10822-014-9811-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 10/31/2014] [Indexed: 10/24/2022]
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40
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Patil P, Khoury K, Herdtweck E, Dömling A. A universal isocyanide for diverse heterocycle syntheses. Org Lett 2014; 16:5736-9. [PMID: 25351886 PMCID: PMC4227542 DOI: 10.1021/ol5024882] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
Novel scaffolds are
of uttermost importance for the discovery of
functional material. Three different heterocyclic scaffolds easily
accessible from isocyanoacetaldehyde dimethylacetal 1 by multicomponent reaction (MCR) are described. They can
be efficiently synthesized by a Ugi tetrazole multicomponent reaction
of 1. We discuss the synthesis, 3D structures, and other
physicochemical properties.
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Affiliation(s)
- Pravin Patil
- Department of Drug Design, University of Groningen , Groningen, The Netherlands
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41
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Abstract
In this issue of Structure, Bista and colleagues report that inhibitors of the MDM2/p53 interaction can be designed to interact with a transiently folded α-helical segment of the MDM2 lid region. This suggests that targeting transient protein states in PPI inhibitor design could be a promising strategy to improve affinity and/or selectivity profiles.
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Affiliation(s)
- Matthias R Bauer
- Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard Karls University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
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42
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Boltjes A, Huang Y, van de Velde R, Rijkee L, Wolf S, Gaugler J, Lesniak K, Guzik K, Holak TA, Dömling A. Fragment-based library generation for the discovery of a peptidomimetic p53-Mdm4 inhibitor. ACS COMBINATORIAL SCIENCE 2014; 16:393-6. [PMID: 24983416 PMCID: PMC4130243 DOI: 10.1021/co500026b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/20/2014] [Indexed: 11/29/2022]
Abstract
On the basis of our recently resolved first cocrystal structure of Mdm4 in complex with a small molecule inhibitor (PDB ID 3LBJ ), we devised an approach for the generation of potential Mdm4 selective ligands. We performed the Ugi four-component reaction (Ugi-4CR) in 96-well plates with an indole fragment, which is specially designed to mimic Trp23, a key amino acid for the interaction between p53 and Mdm4. Generally the reaction yielded mostly precipitates collected by 96-well filter plates. The best hit compound was found to be active and selective for Mdm4 (Ki=5 μM, 10-fold stronger than Mdm2). This initial hit may serve as the starting point for designing selective p53-Mdm4 inhibitor with higher affinity.
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Affiliation(s)
- André Boltjes
- Drug
Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, Netherlands
| | - Yijun Huang
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Rob van de Velde
- Drug
Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, Netherlands
| | - Laurie Rijkee
- Drug
Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, Netherlands
| | - Siglinde Wolf
- Max
Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - James Gaugler
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Katarzyna Lesniak
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
| | - Katarzyna Guzik
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
| | - Tad A. Holak
- Max
Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
| | - Alexander Dömling
- Drug
Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, Netherlands
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
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Uversky VN, Davé V, Iakoucheva LM, Malaney P, Metallo SJ, Pathak RR, Joerger AC. Pathological unfoldomics of uncontrolled chaos: intrinsically disordered proteins and human diseases. Chem Rev 2014; 114:6844-79. [PMID: 24830552 PMCID: PMC4100540 DOI: 10.1021/cr400713r] [Citation(s) in RCA: 196] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute University of South Florida, Tampa, Florida 33612, United States
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 22254, Saudi Arabia
| | - Vrushank Davé
- Department of Pathology and Cell Biology , Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - Lilia M. Iakoucheva
- Department of Psychiatry, University of California San Diego, La Jolla, California 92093, United States
| | - Prerna Malaney
- Department of Pathology and Cell Biology , Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Steven J. Metallo
- Department of Chemistry, Georgetown University, Washington, District of Columbia 20057, United States
| | - Ravi Ramesh Pathak
- Department of Pathology and Cell Biology , Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Andreas C. Joerger
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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Tan YS, Spring DR, Abell C, Verma C. The Use of Chlorobenzene as a Probe Molecule in Molecular Dynamics Simulations. J Chem Inf Model 2014; 54:1821-7. [DOI: 10.1021/ci500215x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Yaw Sing Tan
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Bioinformatics
Institute (A*STAR), 30 Biopolis Street,
#07-01 Matrix, Singapore 138671
| | - David R. Spring
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Chris Abell
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Chandra Verma
- Bioinformatics
Institute (A*STAR), 30 Biopolis Street,
#07-01 Matrix, Singapore 138671
- Department
of Biological Sciences, National University of Singapore, 14 Science
Drive 4, Singapore 117543
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, Singapore 637551
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45
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Guo W, Wisniewski JA, Ji H. Hot spot-based design of small-molecule inhibitors for protein-protein interactions. Bioorg Med Chem Lett 2014; 24:2546-54. [PMID: 24751445 DOI: 10.1016/j.bmcl.2014.03.095] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 03/26/2014] [Accepted: 03/28/2014] [Indexed: 12/27/2022]
Abstract
Protein-protein interactions (PPIs) are important targets for the development of chemical probes and therapeutic agents. From the initial discovery of the existence of hot spots at PPI interfaces, it has been proposed that hot spots might provide the key for developing small-molecule PPI inhibitors. However, there has been no review on the ways in which the knowledge of hot spots can be used to achieve inhibitor design, nor critical examination of successful examples. This Digest discusses the characteristics of hot spots and the identification of druggable hot spot pockets. An analysis of four examples of hot spot-based design reveals the importance of this strategy in discovering potent and selective PPI inhibitors. A general procedure for hot spot-based design of PPI inhibitors is outlined.
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Affiliation(s)
- Wenxing Guo
- Department of Chemistry, Center for Cell and Genome Science, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA
| | - John A Wisniewski
- Department of Chemistry, Center for Cell and Genome Science, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA
| | - Haitao Ji
- Department of Chemistry, Center for Cell and Genome Science, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
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46
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Sim AYL, Joseph T, Lane DP, Verma C. Mechanism of Stapled Peptide Binding to MDM2: Possible Consequences for Peptide Design. J Chem Theory Comput 2014; 10:1753-61. [DOI: 10.1021/ct4009238] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Adelene Y. L. Sim
- Bioinformatics
Institute (A*STAR), 30
Biopolis Street #07-01, Matrix, Singapore 138671
| | - Thomas Joseph
- Bioinformatics
Institute (A*STAR), 30
Biopolis Street #07-01, Matrix, Singapore 138671
| | - David P. Lane
- p53
Laboratory (p53Lab, A*STAR), 8A Biomedical Grove, #06-06, Immunos, Singapore 138648
| | - Chandra Verma
- Bioinformatics
Institute (A*STAR), 30
Biopolis Street #07-01, Matrix, Singapore 138671
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, Singapore 637551
- Department
of Biological Sciences, National University of Singapore, 14 Science
Drive 4, Singapore 117543
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