1
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Chen CY, Elmore S, Lalami I, Neal H, Vadlamudi RK, Raj GV, Ahn JM. Oligo-benzamide-based peptide mimicking tools for modulating biology. Methods Enzymol 2024; 698:221-245. [PMID: 38886033 DOI: 10.1016/bs.mie.2024.04.022] [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] [Indexed: 06/20/2024]
Abstract
The oligo-benzamide scaffold is a rigid organic framework that can hold 2-3 functional groups as O-alkyl substituents on its benzamide units, mirroring their natural arrangement in an α-helix. Oligo-benzamides demonstrated outstanding α-helix mimicry and can be readily synthesized by following high yielding and iterative reaction steps in both solution-phase and solid-phase. A number of oligo-benzamides have been designed to emulate α-helical peptide segments in biologically active proteins and showed strong protein binding, in turn effectively disrupting protein-protein interactions in vitro and in vivo. In this chapter, the design of oligo-benzamides for mimicking α-helices, efficient synthetic routes for producing them, and their biomedical studies showing remarkable potency in inhibiting protein functions are discussed.
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Affiliation(s)
- Chia-Yuan Chen
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, United States
| | - Scott Elmore
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, United States
| | - Ismail Lalami
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, United States
| | - Henry Neal
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, United States
| | - Ratna K Vadlamudi
- Department of Obstetrics and Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Ganesh V Raj
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Jung-Mo Ahn
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, United States.
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2
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Ko S, Kim JY, Park JY, Jung YJ, Choi MJ, Jin KS, Kim Y, Lim YB, Jeong WJ. Modulating the folding and binding of peptides using a stimuli-responsive molecular tweezer. Chem Sci 2023; 14:9600-9607. [PMID: 37712040 PMCID: PMC10498507 DOI: 10.1039/d3sc03758d] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 08/06/2023] [Indexed: 09/16/2023] Open
Abstract
This study presents the development of a β-hairpin (tryptophan zipper, Trpzip)-based molecular tweezer (MT) that can control the folding and binding of α-helical peptides. When an α-helix isolated from the p53 protein was conjugated with Trpzip in an optimized macrocyclic structure, the folded β-hairpin stabilized the helix conformation through the side chain-to-side chain stapling strategy, which notably enhanced target (hDM2) affinity of the peptide. On the other hand, the helicity and binding affinity were significantly reduced when the hairpin was unfolded by a redox stimulus. This stimulus-responsive property was translated into the effective capture and release of model multivalent biomaterials, hDM2-gold nanoparticle conjugates. Since numerous protein interactions are mediated by α-helical peptides, these results suggest that the β-hairpin-based MT holds great potential to be utilized in various biomedical applications, such as protein interaction inhibition and cancer biomarker (e.g., circulating tumor cells and exosomes) detection.
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Affiliation(s)
- Sooho Ko
- Department of Materials Science and Engineering, Yonsei University Seoul 03722 Republic of Korea
| | - Joo-Young Kim
- Department of Biological Sciences and Bioengineering, Inha University Incheon 22212 Republic of Korea
| | - Jung Yeon Park
- KU-KIST Graduate School of Converging Science and Technology, Department of Integrative Energy Engineering, Korea University Seoul 02841 Republic of Korea
| | - You-Jin Jung
- Department of Materials Science and Engineering, Yonsei University Seoul 03722 Republic of Korea
| | - Min-Jae Choi
- Department of Chemical & Biochemical Engineering, Dongguk University Seoul 06420 Republic of Korea
| | - Kyeong Sik Jin
- Pohang Accelerator Laboratory, Pohang University of Science and Technology Pohang 790-784 Republic of Korea
| | - Yongju Kim
- KU-KIST Graduate School of Converging Science and Technology, Department of Integrative Energy Engineering, Korea University Seoul 02841 Republic of Korea
| | - Yong-Beom Lim
- Department of Materials Science and Engineering, Yonsei University Seoul 03722 Republic of Korea
| | - Woo-Jin Jeong
- Department of Biological Sciences and Bioengineering, Inha University Incheon 22212 Republic of Korea
- Department of Biological Engineering, Inha University Incheon 22212 Republic of Korea
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3
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Caramiello A, Bellucci MC, Cristina G, Castellano C, Meneghetti F, Mori M, Secundo F, Viani F, Sacchetti A, Volonterio A. Synthesis and Conformational Analysis of Hydantoin-Based Universal Peptidomimetics. J Org Chem 2023; 88:10381-10402. [PMID: 36226862 PMCID: PMC10407853 DOI: 10.1021/acs.joc.2c01903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Indexed: 11/30/2022]
Abstract
The synthesis of a collection of enantiomerically pure, systematically substituted hydantoins as structural privileged universal mimetic scaffolds is presented. It relies on a chemoselective condensation/cyclization domino process between isocyanates of quaternary or unsubstituted α-amino esters and N-alkyl aspartic acid diesters followed by standard hydrolysis/coupling reactions with amines, using liquid-liquid acid/base extraction protocols for the purification of the intermediates. Besides the nature of the α carbon on the isocyanate moiety, either a quaternary carbon or a more flexible methylene group, conformational studies in silico (molecular modeling), in solution (NMR, circular dichroism (CD), Fourier transform infrared (FTIR)), and in solid state (X-ray) showed that the presented hydantoin-based peptidomimetics are able to project their substituents in positions superimposable to the side chains of common protein secondary structures such as α-helix and β-turn, being the open α-helix conformation slightly favorable according to molecular modeling, while the closed β-turn conformation preferred in solution and in solid state.
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Affiliation(s)
- Alessio
M. Caramiello
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
| | - Maria Cristina Bellucci
- Department
of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133Milano, Italy
| | - Gaetano Cristina
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
| | - Carlo Castellano
- Department
of Chemistry, Università degli Studi
di Milano, via Golgi
19, 20133Milano, Italy
| | - Fiorella Meneghetti
- Department
of Pharmaceutical Sciences, Università
degli Studi di Milano, via Mangiagalli 25, 20133Milano, Italy
| | - Matteo Mori
- Department
of Pharmaceutical Sciences, Università
degli Studi di Milano, via Mangiagalli 25, 20133Milano, Italy
| | - Francesco Secundo
- Consiglio
Nazionale delle Ricerche, Istituto di Scienze
e Tecnologie Chimiche “G. Natta” (SCITEC), via Mario Bianco 9, 20131Milan, Italy
| | - Fiorenza Viani
- Consiglio
Nazionale delle Ricerche, Istituto di Scienze
e Tecnologie Chimiche “G. Natta” (SCITEC), via Mario Bianco 9, 20131Milan, Italy
| | - Alessandro Sacchetti
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
| | - Alessandro Volonterio
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
- Consiglio
Nazionale delle Ricerche, Istituto di Scienze
e Tecnologie Chimiche “G. Natta” (SCITEC), via Mario Bianco 9, 20131Milan, Italy
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4
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Ivanenkov YA, Kukushkin ME, Beloglazkina AA, Shafikov RR, Barashkin AA, Ayginin AA, Serebryakova MS, Majouga AG, Skvortsov DA, Tafeenko VA, Beloglazkina EK. Synthesis and Biological Evaluation of Novel Dispiro-Indolinones with Anticancer Activity. Molecules 2023; 28:molecules28031325. [PMID: 36770991 PMCID: PMC9919490 DOI: 10.3390/molecules28031325] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/19/2023] [Accepted: 01/26/2023] [Indexed: 02/03/2023] Open
Abstract
Novel variously substituted thiohydantoin-based dispiro-indolinones were prepared using a regio- and diastereoselective synthetic route from 5-arylidene-2-thiohydantoins, isatines, and sarcosine. The obtained molecules were subsequently evaluated in vitro against the cancer cell lines LNCaP, PC3, HCTwt, and HCT(-/-). Several compounds demonstrated a relatively high cytotoxic activity vs. LNCaP cells (IC50 = 1.2-3.5 µM) and a reasonable selectivity index (SI = 3-10). Confocal microscopy revealed that the conjugate of propargyl-substituted dispiro-indolinone with the fluorescent dye Sulfo-Cy5-azide was mainly localized in the cytoplasm of HEK293 cells. P388-inoculated mice and HCT116-xenograft BALB/c nude mice were used to evaluate the anticancer activity of compound 29 in vivo. Particularly, the TGRI value for the P388 model was 93% at the final control timepoint. No mortality was registered among the population up to day 31 of the study. In the HCT116 xenograft model, the compound (170 mg/kg, i.p., o.d., 10 days) provided a T/C ratio close to 60% on day 8 after the treatment was completed. The therapeutic index-estimated as LD50/ED50-for compound 29 in mice was ≥2.5. Molecular docking studies were carried out to predict the possible binding modes of the examined molecules towards MDM2 as the feasible biological target. However, such a mechanism was not confirmed by Western blot data and, apparently, the synthesized compounds have a different mechanism of cytotoxic action.
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Affiliation(s)
- Yan A. Ivanenkov
- Chemistry Department, Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
- The Federal State Unitary Enterprise Dukhov Automatics Research Institute (VNIIA), 22. ul. Sushchevskaya, 127055 Moscow, Russia
| | - Maxim E. Kukushkin
- Chemistry Department, Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
| | | | - Radik R. Shafikov
- Chemistry Department, Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, GSP-7, Ulitsa Mklukho-Maklaya 16/10, 17997 Moscow, Russia
- A. N. Belozersky Research Institute of Physico-Chemical Biology MSU, Leninskye Gory, House 1, Building 40, 119992 Moscow, Russia
| | - Alexander A. Barashkin
- Chemistry Department, Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
| | - Andrey A. Ayginin
- Chemistry Department, Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
| | - Marina S. Serebryakova
- Chemistry Department, Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
| | - Alexander G. Majouga
- College of New Materials and Nanotechnologies, National University of Science and Technology MISiS, 119049 Moscow, Russia
| | - Dmitry A. Skvortsov
- Chemistry Department, Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
| | - Viktor A. Tafeenko
- Chemistry Department, Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
| | - Elena K. Beloglazkina
- Chemistry Department, Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
- Correspondence:
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5
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Oyedele AQK, Adelusi TI, Ogunlana AT, Adeyemi RO, Atanda OE, Babalola MO, Ashiru MA, Ayoola IJ, Boyenle ID. Integrated virtual screening and molecular dynamics simulation revealed promising drug candidates of p53-MDM2 interaction. J Mol Model 2022; 28:142. [PMID: 35536362 DOI: 10.1007/s00894-022-05131-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 04/28/2022] [Indexed: 12/13/2022]
Abstract
In the vast majority of malignancies, the p53 tumor suppressor pathway is compromised. In some cancer cells, high levels of MDM2 polyubiquitinate p53 and mark it for destruction, thereby leading to a corresponding downregulation of the protein. MDM2 interacts with p53 via its hydrophobic pocket, and chemical entities that block the dimerization of the protein-protein complex can restore p53 activity. Thus far, only a few chemical compounds have been reported as potent arsenals against p53-MDM2. The Protein Data Bank has crystallogaphic structures of MDM2 in complex with certain compounds. Herein, we have exploited one of the complexes in the identification of new p53-MDM2 antagonists using a hierarchical virtual screening technique. The initial stage was to compile a targeted library of structurally appropriate compounds related to a known effective inhibitor, Nutlin 2, from the PubChem database. The identified 57 compounds were subjected to virtual screening using molecular docking to discover inhibitors with high binding affinity for MDM2. Consequently, five compounds with higher binding affinity than the standard emerged as the most promising therapeutic candidates. When compared to Nutlin 2, four of the drug candidates (CID_140017825, CID_69844501, CID_22721108, and CID_22720965) demonstrated satisfactory pharmacokinetic and pharmacodynamic profiles. Finally, MD simulation of the dynamic behavior of lead-protein complexes reveals the stability of the complexes after a 100,000 ps simulation period. In particular, when compared to the other three leads, overall computational modeling found CID_140017825 to be the best pharmacological candidate. Following thorough experimental trials, it may emerge as a promising chemical entity for cancer therapy.
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Affiliation(s)
- Abdul-Quddus Kehinde Oyedele
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria.,Department of Biochemistry and Nutrition, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Temitope Isaac Adelusi
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
| | - Abdeen Tunde Ogunlana
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
| | - Rofiat Oluwabusola Adeyemi
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria.,Department of Biochemistry and Nutrition, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Opeyemi Emmanuel Atanda
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
| | | | - Mojeed Ayoola Ashiru
- Department of Chemical Sciences, Biochemistry Unit, College of Natural and Applied Science, Fountain University, Osogbo, Nigeria
| | - Isong Josiah Ayoola
- Department of Biochemistry and Nutrition, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Ibrahim Damilare Boyenle
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria. .,College of Health Sciences, Crescent University, Abeokuta, Nigeria.
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6
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Trobe M, Schreiner T, Vareka M, Grimm S, Wölfl B, Breinbauer R. A Modular Synthesis of Teraryl‐based α‐Helix Mimetics, Part 5: A Complete Set of Pyridine Boronic Acid Pinacol Esters Featuring Side Chains of Proteinogenic Amino Acids. European J Org Chem 2022; 2022:e202101280. [PMID: 35910461 PMCID: PMC9304165 DOI: 10.1002/ejoc.202101280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/08/2022] [Indexed: 11/30/2022]
Abstract
Teraryl‐based α‐helix mimetics have proven to be useful compounds for the inhibition of protein‐protein interactions (PPI). We have developed a modular and flexible approach for the synthesis of teraryl‐based α‐helix mimetics using pyridine containing boronic acid building blocks to increase the water solubility. Following our initial publication in which we have introduced the methodology in combination with sequential Pd‐catalyzed cross‐coupling for teraryl assembly, we can now report a complete set of pyridine based boronic acid building blocks decorated with side chains of all proteinogenic amino acids relevant for PPI (Ala, Arg, Asn, Asp, Cys, Gln, Glu, His, Ile, Leu, Lys, Met, Phe, Ser, Thr, Trp, Tyr, Val) to complement the core fragment set. For a representative set of teraryls we have studied the influence of the pyridine rings on the solubility of the assembled oligoarenes.
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Affiliation(s)
- Melanie Trobe
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Till Schreiner
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Martin Vareka
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Sebastian Grimm
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Bernhard Wölfl
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Rolf Breinbauer
- Technische Universitat Graz Institute of Organic Chemistry Stremayrgasse 9 A-8010 Graz AUSTRIA
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7
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Trobe M, Vareka M, Schreiner T, Dobrounig P, Doler C, Holzinger EB, Steinegger A, Breinbauer R. Modular Synthesis of Teraryl‐based alpha ‐Helix Mimetics, Part 3: Iodophenyltriflate Core Fragments Featuring Side Chains of Proteinogenic Amino Acids. European J Org Chem 2022; 2022:e202101278. [PMID: 35910459 PMCID: PMC9306992 DOI: 10.1002/ejoc.202101278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/08/2022] [Indexed: 11/18/2022]
Abstract
Teraryl‐based α‐helix mimetics have proven to be useful compounds for the inhibition of protein‐protein interactions (PPI). We have developed a modular and flexible approach for the synthesis of teraryl‐based α‐helix mimetics using a benzene core unit featuring two leaving groups of differentiated reactivity in the Pd‐catalyzed cross‐coupling used for teraryl assembly. In previous publications we have introduced the methodology of 4‐iodophenyltriflates decorated with the side chains of some of the proteinogenic amino acids. We herein report the core fragments corresponding to the previously missing amino acids Arg, Asn, Asp, Met, Trp and Tyr. Therefore, our set now encompasses all relevant amino acid analogues with the exception of His. In order to be compatible with the triflate moiety, some of the nucleophilic side chains had to be provided in a protected form to serve as stable building blocks. Additionally, cross‐coupling procedures for the assembly of teraryls were investigated.
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Affiliation(s)
- Melanie Trobe
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Martin Vareka
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Till Schreiner
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Patrick Dobrounig
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Carina Doler
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Ella B. Holzinger
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Andreas Steinegger
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Rolf Breinbauer
- Technische Universitat Graz Institute of Organic Chemistry Stremayrgasse 9 A-8010 Graz AUSTRIA
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8
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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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9
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Wu J, Lu G, Wang X. MDM4 alternative splicing and implication in MDM4 targeted cancer therapies. Am J Cancer Res 2021; 11:5864-5880. [PMID: 35018230 PMCID: PMC8727814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/31/2021] [Indexed: 06/14/2023] Open
Abstract
The oncogenic MDM4, initially named MDMX, has been identified as a p53-interacting protein and a key upstream negative regulator of the tumor suppressor p53. Accumulating evidence indicates that MDM4 plays critical roles in the initiation and progression of multiple human cancers. MDM4 is frequently amplified and upregulated in human cancers, contributing to overgrowth and apoptosis inhibition by blocking the expression of downstream target genes of p53 pathway. Disruptors for MDM4-p53 interaction have been shown to restore the anti-tumor activity of p53 in cancer cells. MDM4 possesses multiple splicing isoforms whose expressions are driven by the presence of oncogenes in cancer cells. Some of the MDM4 splicing isoforms lack p53 binding domain and may exhibit p53-independent oncogenic functions. These features render MDM4 to be an attractive therapeutic target for cancer therapy. In the present review, we primarily focus on the detailed molecular structure of MDM4 splicing isoforms, candidate regulators for initiating MDM4 splicing, deregulation of MDM4 isoforms in cancer and potential therapy strategies by targeting splicing isoforms of MDM4.
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Affiliation(s)
- Jin Wu
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer CenterBuffalo, NY, USA
| | - Guanting Lu
- Department of Pathology, Key Laboratory of Tumor Molecular Research, People’s Hospital of Deyang City173 Tai Shan North Road, Deyang 618000, Sichuan, P. R. China
| | - Xinjiang Wang
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer CenterBuffalo, NY, USA
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10
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Fukuda Y, Yokomine M, Kuroda D, Tsumoto K, Morimoto J, Sando S. Peptoid-based reprogrammable template for cell-permeable inhibitors of protein-protein interactions. Chem Sci 2021; 12:13292-13300. [PMID: 34777747 PMCID: PMC8528041 DOI: 10.1039/d1sc01560e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/02/2021] [Indexed: 12/27/2022] Open
Abstract
The development of inhibitors of intracellular protein–protein interactions (PPIs) is of great significance for drug discovery, but the generation of a cell-permeable molecule with high affinity to protein is challenging. Oligo(N-substituted glycines) (oligo-NSGs), referred to as peptoids, are attractive as potential intracellular PPI inhibitors owing to their high membrane permeability. However, their intrinsically flexible backbones make the rational design of inhibitors difficult. Here, we propose a peptoid-based rational approach to develop cell-permeable PPI inhibitors using oligo(N-substituted alanines) (oligo-NSAs). The rigid structures of oligo-NSAs enable independent optimization of each N-substituent to improve binding affinity and membrane permeability, while preserving the backbone shape. A molecule with optimized N-substituents inhibited a target PPI in cells, which demonstrated the utility of oligo-NSA as a reprogrammable template to develop intracellular PPI inhibitors. A peptoid-based modular approach using oligo(N-substituted alanine) as a reprogrammable template enables independent optimization of N-substituents and facile development of cell-permeable inhibitors of protein–protein interactions.![]()
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Affiliation(s)
- Yasuhiro Fukuda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Marin Yokomine
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Daisuke Kuroda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan .,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan .,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan.,Institute of Medical Science, The University of Tokyo 4-6-1, Shirokanedai, Minato-ku Tokyo 108-8639 Japan
| | - Jumpei Morimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan .,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
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11
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Zhang S, Lou J, Li Y, Zhou F, Yan Z, Lyu X, Zhao Y. Recent Progress and Clinical Development of Inhibitors that Block MDM4/p53 Protein-Protein Interactions. J Med Chem 2021; 64:10621-10640. [PMID: 34286973 DOI: 10.1021/acs.jmedchem.1c00940] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
MDM4 is a homologue of MDM2, serving cooperatively as the negative regulator of tumor suppressor p53. Under the shadow of MDM2 inhibitors, limited efforts had been put into the discovery of MDM4 modulators. Recent studies of the experimental drug ALRN-6924, a dual MDM4 and MDM2 inhibitor, suggest that concurrent inhibition of MDM4 and MDM2 might be beneficial over only MDM2 inhibition. In view of the present research progress, we summarized published inhibitors of MDM4/p53 interactions including both peptide-based compounds and small molecules. Cocrystal structures of ligand/MDM4 complexes have been examined, and their structural features were compiled and compared in order to show the molecular basis required for high MDM4 binding affinities. Representative examples of small-molecule MDM4 inhibitors were discussed, followed by clinical results of ALRN-6924, together, providing a consolidated reference for further development of MDM4 inhibitors, either dual or selective.
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Affiliation(s)
- Shiyan Zhang
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China.,State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jianfeng Lou
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China.,State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yafang Li
- Nano Science and Technology Institute, University of Science and Technology of China, Suzhou, Jiangsu 215123, China.,State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Feilong Zhou
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Ziqin Yan
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xilin Lyu
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yujun Zhao
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China.,State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
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12
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Umedera K, Morita T, Yoshimori A, Yamada K, Katoh A, Kouji H, Nakamura H. Synthesis of Three-Dimensional (Di)Azatricyclododecene Scaffold and Its Application to Peptidomimetics. Chemistry 2021; 27:11888-11894. [PMID: 34060167 DOI: 10.1002/chem.202101440] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Indexed: 11/07/2022]
Abstract
A novel sp3 carbon-rich tricyclic 3D scaffold-based peptide mimetic compound library was constructed to target protein-protein interactions. Tricyclic framework 7 was synthesized from 9-azabicyclo[3,3,1]nonan-3-one (11) via a gold(I)-catalyzed Conia-ene reaction. The electron-donating group on the pendant alkyne of cyclization precursor 12 b-e was the key to forming 6-endo-dig cyclized product 7 with complete regioselectivity. Using the synthetic strategy for regioselective construction of bridged tricyclic framework 7, a diazatricyclododecene 3D-scaffold 8 a, which enables the introduction of substituents into the scaffold to mimic amino acid side chains, was designed and synthesized. The peptide mimetics 21 a-u were synthesized via step-by-step installation of three substituents on diazatricyclododecene scaffold 8 a. Compounds 21 a-h were synthesized as α-helix peptide mimics of hydrophobic ZZxxZ and ZxxZZ sequences (Z=Leu or Phe) and subjected to cell-based assays: antiproliferative activity, HIF-1 transcriptional activity which is considered to affect cancer malignancy, and antiviral activity against rabies virus. Compound 21 a showed the strongest inhibitory activity of HIF-1 transcriptional activity (IC50 =4.1±0.8 μM), whereas compounds 21 a-g showed antiviral activity with IC50 values of 4.2-12.4 μM, suggesting that the 3D-scaffold 8 a has potential as a versatile peptide mimic skeleton.
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Affiliation(s)
- Kohei Umedera
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Taiki Morita
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503, Japan.,Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Atsushi Yoshimori
- Institute for Theoretical Medicine, Inc., 26-1, Muraoka-Higashi 2-chome, Fujisawa, 251-0012, Japan
| | - Kentaro Yamada
- Faculty of Agriculture Department of Veterinary Sciences, University of Miyazaki, Miyazaki, 889-2192, Japan.,Faculty of Medicine, Oita University, 1-1, Idaigaoka, Hasama-machi, Yufu-city, Oita, 879-5593, Japan
| | - Akira Katoh
- Faculty of Medicine, Oita University, 1-1, Idaigaoka, Hasama-machi, Yufu-city, Oita, 879-5593, Japan.,Institute of Advanced Medcine, Inc., Oita University, 17-20, Higashi kasuga-machi, Oita-city, Oita, 870-0037, Japan
| | - Hiroyuki Kouji
- Faculty of Medicine, Oita University, 1-1, Idaigaoka, Hasama-machi, Yufu-city, Oita, 879-5593, Japan.,Institute of Advanced Medcine, Inc., Oita University, 17-20, Higashi kasuga-machi, Oita-city, Oita, 870-0037, Japan
| | - Hiroyuki Nakamura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503, Japan.,Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
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13
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Revuelto A, de Lucio H, García-Soriano JC, Sánchez-Murcia PA, Gago F, Jiménez-Ruiz A, Camarasa MJ, Velázquez S. Efficient Dimerization Disruption of Leishmania infantum Trypanothione Reductase by Triazole-phenyl-thiazoles. J Med Chem 2021; 64:6137-6160. [PMID: 33945281 PMCID: PMC8480782 DOI: 10.1021/acs.jmedchem.1c00206] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Indexed: 01/06/2023]
Abstract
Inhibition of Leishmania infantum trypanothione disulfide reductase (LiTryR) by disruption of its homodimeric interface has proved to be an alternative and unexploited strategy in the search for novel antileishmanial agents. Proof of concept was first obtained by peptides and peptidomimetics. Building on previously reported dimerization disruptors containing an imidazole-phenyl-thiazole scaffold, we now report a new 1,2,3-triazole-based chemotype that yields noncompetitive, slow-binding inhibitors of LiTryR. Several compounds bearing (poly)aromatic substituents dramatically improve the ability to disrupt LiTryR dimerization relative to reference imidazoles. Molecular modeling studies identified an almost unexplored hydrophobic region at the interfacial domain as the putative binding site for these compounds. A subsequent structure-based design led to a symmetrical triazole analogue that displayed even more potent inhibitory activity over LiTryR and enhanced leishmanicidal activity. Remarkably, several of these novel triazole-bearing compounds were able to kill both extracellular and intracellular parasites in cell cultures.
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Affiliation(s)
- Alejandro Revuelto
- Instituto
de Química Médica (IQM-CSIC), c/ Juan de la Cierva 3, E-28006 Madrid, Spain
| | - Héctor de Lucio
- Departamento
de Biología de Sistemas, Universidad
de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | | | - Pedro A. Sánchez-Murcia
- Área
de Farmacología, Departamento de Ciencias Biomédicas,
Unidad Asociada al IQM-CSIC, Universidad
de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Federico Gago
- Área
de Farmacología, Departamento de Ciencias Biomédicas,
Unidad Asociada al IQM-CSIC, Universidad
de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Antonio Jiménez-Ruiz
- Departamento
de Biología de Sistemas, Universidad
de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - María-José Camarasa
- Instituto
de Química Médica (IQM-CSIC), c/ Juan de la Cierva 3, E-28006 Madrid, Spain
| | - Sonsoles Velázquez
- Instituto
de Química Médica (IQM-CSIC), c/ Juan de la Cierva 3, E-28006 Madrid, Spain
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14
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Abdildinova A, Kurth MJ, Gong YD. Heterocycles as a Peptidomimetic Scaffold: Solid-Phase Synthesis Strategies. Pharmaceuticals (Basel) 2021; 14:449. [PMID: 34068671 PMCID: PMC8151782 DOI: 10.3390/ph14050449] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 12/04/2022] Open
Abstract
Peptidomimetics are a privileged class of pharmacophores that exhibit improved physicochemical and biological properties. Solid-phase synthesis is a powerful tool for gaining rapid access to libraries of molecules from small molecules to biopolymers and also is widely used for the synthesis of peptidomimetics. Small molecules including heterocycles serve as a core for hundreds of drugs, including peptidomimetic molecules. This review covers solid-phase synthesis strategies for peptidomimetics molecules based on heterocycles.
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Affiliation(s)
- Aizhan Abdildinova
- Innovative Drug Library Research Center, Department of Chemistry, College of Science, Dongguk University, 26, 3-ga, Pil-dong, Jung-gu, Seoul 04620, Korea;
| | - Mark J. Kurth
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Young-Dae Gong
- Innovative Drug Library Research Center, Department of Chemistry, College of Science, Dongguk University, 26, 3-ga, Pil-dong, Jung-gu, Seoul 04620, Korea;
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15
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Park JH, Wang HM, Shin MH, Lim H. Synthesis of a
DNA‐Encoded
Library of Pyrrolo[2,3
‐d
]pyrimidines. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jun Hyung Park
- Department of Chemistry and Division of Advanced Material Science Pohang University of Science and Technology (POSTECH), Pohang 37673 South Korea
| | - Hee Myeong Wang
- Department of Chemistry and Division of Advanced Material Science Pohang University of Science and Technology (POSTECH), Pohang 37673 South Korea
| | - Min Hyeon Shin
- Department of Chemistry and Division of Advanced Material Science Pohang University of Science and Technology (POSTECH), Pohang 37673 South Korea
- POSTECH Biotech Center Pohang 37673 South Korea
| | - Hyun‐Suk Lim
- Department of Chemistry and Division of Advanced Material Science Pohang University of Science and Technology (POSTECH), Pohang 37673 South Korea
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16
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Das A, Gangarde YM, Tomar V, Shinde O, Upadhyay T, Alam S, Ghosh S, Chaudhary V, Saraogi I. Small-Molecule Inhibitor Prevents Insulin Fibrillogenesis and Preserves Activity. Mol Pharm 2020; 17:1827-1834. [PMID: 32347728 DOI: 10.1021/acs.molpharmaceut.9b01080] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Amyloidosis is a well-known but poorly understood phenomenon caused by the aggregation of proteins, often leading to pathological conditions. For example, the aggregation of insulin poses significant challenges during the preparation of pharmaceutical insulin formulations commonly used to treat diabetic patients. Therefore, it is essential to develop inhibitors of insulin aggregation for potential biomedical applications and for important mechanistic insights into amyloidogenic pathways. Here, we have identified a small molecule M1, which causes a dose-dependent reduction in insulin fibril formation. Biophysical analyses and docking results suggest that M1 likely binds to partially unfolded insulin intermediates. Further, M1-treated insulin had lower cytotoxicity and remained functionally active in regulating cell proliferation in cultured Drosophila wing epithelium. Thus, M1 is of great interest as a novel agent for inhibiting insulin aggregation during biopharmaceutical manufacturing.
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17
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Recent Synthetic Approaches towards Small Molecule Reactivators of p53. Biomolecules 2020; 10:biom10040635. [PMID: 32326087 PMCID: PMC7226499 DOI: 10.3390/biom10040635] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/13/2020] [Accepted: 04/15/2020] [Indexed: 12/26/2022] Open
Abstract
The tumor suppressor protein p53 is often called "the genome guardian" and controls the cell cycle and the integrity of DNA, as well as other important cellular functions. Its main function is to trigger the process of apoptosis in tumor cells, and approximately 50% of all cancers are related to the inactivation of the p53 protein through mutations in the TP53 gene. Due to the association of mutant p53 with cancer therapy resistance, different forms of restoration of p53 have been subject of intense research in recent years. In this sense, this review focus on the main currently adopted approaches for activation and reactivation of p53 tumor suppressor function, focusing on the synthetic approaches that are involved in the development and preparation of such small molecules.
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18
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Sirous H, Chemi G, Campiani G, Brogi S. An integrated in silico screening strategy for identifying promising disruptors of p53-MDM2 interaction. Comput Biol Chem 2019; 83:107105. [DOI: 10.1016/j.compbiolchem.2019.107105] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 10/26/2022]
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19
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Wang Z, Ji H. Targeting the Side-Chain Convergence of Hydrophobic α-Helical Hot Spots To Design Small-Molecule Mimetics: Key Binding Features for i, i + 3, and i + 7. J Med Chem 2019; 62:9906-9917. [PMID: 31593458 DOI: 10.1021/acs.jmedchem.9b01324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The conformational convergence of hydrophobic α-helical hot spots was revealed by analyzing α-helix-mediated protein-protein interaction (PPI) complex structures. The pharmacophore models were derived for hydrophobic α-helical hot spots at positions i, i + 3, and i + 7. These provide the foundation for designing generalizable scaffolds that can directly mimic the binding mode of the side chains of α-helical hot spots, offering a new class of small-molecule α-helix mimetics. For the first time, the protocol was developed to identify the PPI targets that have similar binding pockets, allowing evaluation of inhibitor selectivities between α-helix-mediated PPIs. The mimicry efficiency of the previously designed scaffold 1 was disclosed. The close positioning of this small molecule to the additional α-helical hot spots suggests that the decoration of this series of generalizable scaffolds can conveniently reach the binding pockets of additional α-helical hot spots to produce potent small-molecule inhibitors for α-helix-mediated PPIs.
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Affiliation(s)
- Zhen Wang
- Drug Discovery Department , H. Lee Moffitt Cancer Center & Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612-9497 , United States.,Departments of Chemistry and Oncologic Sciences , University of South Florida , Tampa , Florida 33620-9497 , United States
| | - Haitao Ji
- Drug Discovery Department , H. Lee Moffitt Cancer Center & Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612-9497 , United States.,Departments of Chemistry and Oncologic Sciences , University of South Florida , Tampa , Florida 33620-9497 , United States
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20
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Revuelto A, Ruiz-Santaquiteria M, de Lucio H, Gamo A, Carriles AA, Gutiérrez KJ, Sánchez-Murcia PA, Hermoso JA, Gago F, Camarasa MJ, Jiménez-Ruiz A, Velázquez S. Pyrrolopyrimidine vs Imidazole-Phenyl-Thiazole Scaffolds in Nonpeptidic Dimerization Inhibitors of Leishmania infantum Trypanothione Reductase. ACS Infect Dis 2019; 5:873-891. [PMID: 30983322 DOI: 10.1021/acsinfecdis.8b00355] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Disruption of protein-protein interactions of essential oligomeric enzymes by small molecules represents a significant challenge. We recently reported some linear and cyclic peptides derived from an α-helical region present in the homodimeric interface of Leishmania infantum trypanothione reductase ( Li-TryR) that showed potent effects on both dimerization and redox activity of this essential enzyme. Here, we describe our first steps toward the design of nonpeptidic small-molecule Li-TryR dimerization disruptors using a proteomimetic approach. The pyrrolopyrimidine and the 5-6-5 imidazole-phenyl-thiazole α-helix-mimetic scaffolds were suitably decorated with substituents that could mimic three key residues (K, Q, and I) of the linear peptide prototype (PKIIQSVGIS-Nle-K-Nle). Extensive optimization of previously described synthetic methodologies was required. A library of 15 compounds bearing different hydrophobic alkyl and aromatic substituents was synthesized. The imidazole-phenyl-thiazole-based analogues outperformed the pyrrolopyrimidine-based derivatives in both inhibiting the enzyme and killing extracellular and intracellular parasites in cell culture. The most active imidazole-phenyl-thiazole compounds 3e and 3f inhibit Li-TryR and prevent growth of the parasites at low micromolar concentrations similar to those required by the peptide prototype. The intrinsic fluorescence of these compounds inside the parasites visually demonstrates their good permeability in comparison with previous peptide-based Li-TryR dimerization disruptors.
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Affiliation(s)
| | | | - Héctor de Lucio
- Departamento de Biología de Sistemas, Universidad de Alcalá, Alcalá
de Henares, Madrid E-28805, Spain
| | - Ana Gamo
- Instituto de Química Médica (IQM-CSIC), Madrid E-28006, Spain
| | - Alejandra A. Carriles
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry “Rocasolano” (IQFR-CSIC), Madrid E-28006, Spain
| | - Kilian Jesús Gutiérrez
- Departamento de Biología de Sistemas, Universidad de Alcalá, Alcalá
de Henares, Madrid E-28805, Spain
| | - Pedro A. Sánchez-Murcia
- Área de Farmacología, Departamento de Ciencias Biomédicas, Unidad Asociada al IQM-CSIC, Universidad de Alcalá, Alcalá de Henares, Madrid E-28805, Spain
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry “Rocasolano” (IQFR-CSIC), Madrid E-28006, Spain
| | - Federico Gago
- Área de Farmacología, Departamento de Ciencias Biomédicas, Unidad Asociada al IQM-CSIC, Universidad de Alcalá, Alcalá de Henares, Madrid E-28805, Spain
| | | | - Antonio Jiménez-Ruiz
- Departamento de Biología de Sistemas, Universidad de Alcalá, Alcalá
de Henares, Madrid E-28805, Spain
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21
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Synthesis and identification of novel pyridazinylpyrazolone based diazo compounds as inhibitors of human islet amyloid polypeptide aggregation. Bioorg Chem 2019; 84:339-346. [DOI: 10.1016/j.bioorg.2018.11.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 11/17/2018] [Accepted: 11/24/2018] [Indexed: 02/06/2023]
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22
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Peptidomimetics: A Synthetic Tool for Inhibiting Protein–Protein Interactions in Cancer. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09831-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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23
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Lee Y, Im H, Das S, Oh M, Lee JH, Ham S, Lim HS. Bridged α-helix mimetic small molecules. Chem Commun (Camb) 2019; 55:13311-13314. [DOI: 10.1039/c9cc03627j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Herein, we report a strategy for generating conformationally restricted α-helix mimetic small molecules by introducing covalent bridges that limit rotation about the central axis of α-helix mimetics.
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Affiliation(s)
- Yeongju Lee
- Department of Chemistry and Division of Advanced Material Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 37673
- South Korea
| | - Haeri Im
- Department of Chemistry
- Sookmyung Women's University
- Seoul 04310
- South Korea
| | - Sanket Das
- Department of Chemistry and Division of Advanced Material Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 37673
- South Korea
| | - Misook Oh
- Department of Chemistry and Division of Advanced Material Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 37673
- South Korea
| | - Ji Hoon Lee
- New Drug Development Centre
- Daegu Gyeongbuk Medical Innovation Foundation
- Daegu 41061
- South Korea
| | - Sihyun Ham
- Department of Chemistry
- Sookmyung Women's University
- Seoul 04310
- South Korea
| | - Hyun-Suk Lim
- Department of Chemistry and Division of Advanced Material Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 37673
- South Korea
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24
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Jakubkiene V, Vaiciunaite E, Kriukaite K, Didzgalvis J, Tumkevicius S. Efficient synthesis of novel 6-substituted 2-(4-aryl-1,2,3-triazol-1-yl)pyrimidines and 7-deazapurines. SYNTHETIC COMMUN 2018. [DOI: 10.1080/00397911.2018.1474229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- V. Jakubkiene
- Department of Organic Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Vilnius, Lithuania
| | - E. Vaiciunaite
- Department of Organic Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Vilnius, Lithuania
| | - K. Kriukaite
- Department of Organic Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Vilnius, Lithuania
| | - J. Didzgalvis
- Department of Organic Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Vilnius, Lithuania
| | - S. Tumkevicius
- Department of Organic Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Vilnius, Lithuania
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25
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Ran X, Gestwicki JE. Inhibitors of protein-protein interactions (PPIs): an analysis of scaffold choices and buried surface area. Curr Opin Chem Biol 2018; 44:75-86. [PMID: 29908451 DOI: 10.1016/j.cbpa.2018.06.004] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/04/2018] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions (PPI) were once considered 'undruggable', but clinical successes, driven by advanced methods in drug discovery, have challenged that notion. Here, we review the last three years of literature on PPI inhibitors to understand what is working and why. From the 66 recently reported PPI inhibitors, we found that the average molecular weight was significantly greater than 500Da, but that this trend was driven, in large part, by the contribution of peptide-based compounds. Despite differences in average molecular weight, we found that compounds based on small molecules or peptides were almost equally likely to be potent inhibitors (KD<1μM). Finally, we found PPIs with buried surface area (BSA) less than 2000Å2 were more likely to be inhibited by small molecules, while PPIs with larger BSA values were typically inhibited by peptides. PPIs with BSA values over 4000Å2 seemed to create a particular challenge, especially for orthosteric small molecules. Thus, it seems important to choose the inhibitor scaffold based on the properties of the target interaction. Moreover, this survey suggests a (more nuanced) conclusion to the question of whether PPIs are good drug targets; namely, that some PPIs are readily 'druggable' given the right choice of scaffold, while others still seem to deserve the 'undruggable' moniker.
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Affiliation(s)
- Xu Ran
- Institute for Neurodegenerative Diseases and Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, United States
| | - Jason E Gestwicki
- Institute for Neurodegenerative Diseases and Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, United States.
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26
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Soares J, Espadinha M, Raimundo L, Ramos H, Gomes AS, Gomes S, Loureiro JB, Inga A, Reis F, Gomes C, Santos MMM, Saraiva L. DIMP53-1: a novel small-molecule dual inhibitor of p53-MDM2/X interactions with multifunctional p53-dependent anticancer properties. Mol Oncol 2017; 11:612-627. [PMID: 28296148 PMCID: PMC5467495 DOI: 10.1002/1878-0261.12051] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/01/2017] [Accepted: 03/02/2017] [Indexed: 01/07/2023] Open
Abstract
The transcription factor p53 plays a crucial role in cancer development and dissemination, and thus, p53‐targeted therapies are among the most encouraging anticancer strategies. In human cancers with wild‐type (wt) p53, its inactivation by interaction with murine double minute (MDM)2 and MDMX is a common event. Simultaneous inhibition of the p53 interaction with both MDMs is crucial to restore the tumor suppressor activity of p53. Here, we describe the synthesis of the new tryptophanol‐derived oxazoloisoindolinone DIMP53‐1 and identify its activity as a dual inhibitor of the p53–MDM2/X interactions using a yeast‐based assay. DIMP53‐1 caused growth inhibition, mediated by p53 stabilization and upregulation of p53 transcriptional targets involved in cell cycle arrest and apoptosis, in wt p53‐expressing tumor cells, including MDM2‐ or MDMX‐overexpressing cells. Importantly, DIMP53‐1 inhibits the p53–MDM2/X interactions by potentially binding to p53, in human colon adenocarcinoma HCT116 cells. DIMP53‐1 also inhibited the migration and invasion of HCT116 cells, and the migration and tube formation of HMVEC‐D endothelial cells. Notably, in human tumor xenograft mice models, DIMP53‐1 showed a p53‐dependent antitumor activity through induction of apoptosis and inhibition of proliferation and angiogenesis. Finally, no genotoxicity or undesirable toxic effects were observed with DIMP53‐1. In conclusion, DIMP53‐1 is a novel p53 activator, which potentially binds to p53 inhibiting its interaction with MDM2 and MDMX. Although target‐directed, DIMP53‐1 has a multifunctional activity, targeting major hallmarks of cancer through its antiproliferative, proapoptotic, antiangiogenic, anti‐invasive, and antimigratory properties. DIMP53‐1 is a promising anticancer drug candidate and an encouraging starting point to develop improved derivatives for clinical application.
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Affiliation(s)
- Joana Soares
- UCIBIO/REQUIMTE, Universidade do Porto, Portugal.,Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Margarida Espadinha
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - Liliana Raimundo
- UCIBIO/REQUIMTE, Universidade do Porto, Portugal.,Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Helena Ramos
- UCIBIO/REQUIMTE, Universidade do Porto, Portugal.,Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Ana Sara Gomes
- UCIBIO/REQUIMTE, Universidade do Porto, Portugal.,Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Sara Gomes
- UCIBIO/REQUIMTE, Universidade do Porto, Portugal.,Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Joana B Loureiro
- UCIBIO/REQUIMTE, Universidade do Porto, Portugal.,Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Alberto Inga
- CIBIO, Centre for Integrative Biology, Laboratory of Transcriptional Networks, University of Trento, Italy
| | - Flávio Reis
- Laboratory of Pharmacology & Experimental Therapeutics, Institute for Biomedical Imaging and Life Sciences (IBILI), Faculty of Medicine, University of Coimbra, Portugal.,Centre for Neuroscience and Cell Biology - Institute for Biomedical Imaging and Life Sciences (CNC.IBILI) Research Consortium, University of Coimbra, Portugal
| | - Célia Gomes
- Laboratory of Pharmacology & Experimental Therapeutics, Institute for Biomedical Imaging and Life Sciences (IBILI), Faculty of Medicine, University of Coimbra, Portugal.,Centre for Neuroscience and Cell Biology - Institute for Biomedical Imaging and Life Sciences (CNC.IBILI) Research Consortium, University of Coimbra, Portugal
| | - Maria M M Santos
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - Lucília Saraiva
- UCIBIO/REQUIMTE, Universidade do Porto, Portugal.,Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Portugal
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27
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Nguyen D, Liao W, Zeng SX, Lu H. Reviving the guardian of the genome: Small molecule activators of p53. Pharmacol Ther 2017; 178:92-108. [PMID: 28351719 DOI: 10.1016/j.pharmthera.2017.03.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 03/20/2017] [Indexed: 02/07/2023]
Abstract
The tumor suppressor p53 is one of the most important proteins for protection of genomic stability and cancer prevention. Cancers often inactivate it by either mutating its gene or disabling its function. Thus, activating p53 becomes an attractive approach for the development of molecule-based anti-cancer therapy. The past decade and half have witnessed tremendous progress in this area. This essay offers readers with a grand review on this progress with updated information about small molecule activators of p53 either still at bench work or in clinical trials.
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Affiliation(s)
- Daniel Nguyen
- Department of Biochemistry and Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave, LA 70012, United States
| | - Wenjuan Liao
- Department of Biochemistry and Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave, LA 70012, United States
| | - Shelya X Zeng
- Department of Biochemistry and Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave, LA 70012, United States
| | - Hua Lu
- Department of Biochemistry and Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave, LA 70012, United States.
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28
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Kulikov OV, Sevryugina YV, Mehmood A, Saraogi I. Characterization of aggregated morphologies derived from mono- and bis-arylbenzamides – potential alpha-helix mimetics. NEW J CHEM 2017. [DOI: 10.1039/c6nj03775e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report here the synthesis and self-assembly studies of a family of benzamide backbone oligomers bearing various alkyl side chains (e.g., isopropyl, isobutyl, and 2-ethylpentyl), which are potential alpha-helix mimetics capable of disrupting protein–protein interactions.
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Affiliation(s)
- Oleg V. Kulikov
- Department of Chemistry
- Massachusetts Institute of Technology
- Cambridge
- USA
| | | | - Arshad Mehmood
- Department of Chemistry
- Texas Christian University
- Fort Worth
- USA
| | - Ishu Saraogi
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal 462066
- India
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29
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Duan H, Zhu L, Hou J, Peng J, Xie H, Lin Y, Liu C, Li W, Xu H, Wang C, Yang Y. Dual-affinity peptide mediated inter-protein recognition. Org Biomol Chem 2016; 14:11342-11346. [PMID: 27883148 DOI: 10.1039/c6ob02292h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We present for the first time an enhanced interaction affinity between an abundant soluble protein (human serum albumin) and a membrane protein (chemokine receptor 4) mediated by a dual-affinity peptide E5.
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Affiliation(s)
- Hongyang Duan
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.
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30
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Londregan AT, Piotrowski DW, Wei L. Synthesis of Pyridazine-Based α-Helix Mimetics. ACS COMBINATORIAL SCIENCE 2016; 18:651-654. [PMID: 27571162 DOI: 10.1021/acscombsci.6b00111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A versatile synthesis of pyridazine-based small molecule α-helix mimetics (A) is presented. Modular C-C, C-N, and C-O bond-forming reactions allow for the inclusion of a variety of aliphatic, basic, aromatic, and heteroaromatic side chain moieties. This robust synthesis is suitable for the preparation of small pyridazine-based libraries.
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Affiliation(s)
- Allyn T. Londregan
- Pfizer Medicine Design, Eastern
Point Road, Groton, Connecticut 06340, United States
| | - David W. Piotrowski
- Pfizer Medicine Design, Eastern
Point Road, Groton, Connecticut 06340, United States
| | - Liuqing Wei
- Pfizer Medicine Design, Eastern
Point Road, Groton, Connecticut 06340, United States
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31
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Lu S, Jang H, Gu S, Zhang J, Nussinov R. Drugging Ras GTPase: a comprehensive mechanistic and signaling structural view. Chem Soc Rev 2016; 45:4929-52. [PMID: 27396271 PMCID: PMC5021603 DOI: 10.1039/c5cs00911a] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ras proteins are small GTPases, cycling between inactive GDP-bound and active GTP-bound states. Through these switches they regulate signaling that controls cell growth and proliferation. Activating Ras mutations are associated with approximately 30% of human cancers, which are frequently resistant to standard therapies. Over the past few years, structural biology and in silico drug design, coupled with improved screening technology, led to a handful of promising inhibitors, raising the possibility of drugging Ras proteins. At the same time, the invariable emergence of drug resistance argues for the critical importance of additionally honing in on signaling pathways which are likely to be involved. Here we overview current advances in Ras structural knowledge, including the conformational dynamic of full-length Ras in solution and at the membrane, therapeutic inhibition of Ras activity by targeting its active site, allosteric sites, and Ras-effector protein-protein interfaces, Ras dimers, the K-Ras4B/calmodulin/PI3Kα trimer, and targeting Ras with siRNA. To mitigate drug resistance, we propose signaling pathways that can be co-targeted along with Ras and explain why. These include pathways leading to the expression (or activation) of YAP1 and c-Myc. We postulate that these and Ras signaling pathways, MAPK/ERK and PI3K/Akt/mTOR, act independently and in corresponding ways in cell cycle control. The structural data are instrumental in the discovery and development of Ras inhibitors for treating RAS-driven cancers. Together with the signaling blueprints through which drug resistance can evolve, this review provides a comprehensive and innovative master plan for tackling mutant Ras proteins.
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Affiliation(s)
- Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Children’s Medical Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200127, China
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute, Frederick, MD 21702, U.S.A
| | - Shuo Gu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Children’s Medical Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200127, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Children’s Medical Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200127, China
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute, Frederick, MD 21702, U.S.A
- Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Institute of Molecular Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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32
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Avtanski DB, Nagalingam A, Tomaszewski JE, Risbood P, Difillippantonio MJ, Saxena NK, Malhotra SV, Sharma D. Indolo-pyrido-isoquinolin based alkaloid inhibits growth, invasion and migration of breast cancer cells via activation of p53-miR34a axis. Mol Oncol 2016; 10:1118-32. [PMID: 27259808 PMCID: PMC5423185 DOI: 10.1016/j.molonc.2016.04.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/22/2016] [Accepted: 04/13/2016] [Indexed: 12/22/2022] Open
Abstract
The tumor suppressor p53 plays a critical role in suppressing cancer growth and progression and is an attractive target for the development of new targeted therapies. We synthesized several indolo-pyrido-isoquinolin based alkaloids to activate p53 function and examined their therapeutic efficacy using NCI-60 screening. Here, we provide molecular evidence that one of these compounds, 11-methoxy-2,3,4,13-tetrahydro-1H-indolo[2',3':3,4]pyrido[1,2-b]isoquinolin-6-ylium-bromide (termed P18 or NSC-768219) inhibits growth and clonogenic potential of cancer cells. P18 treatment results in downregulation of mesenchymal markers and concurrent upregulation of epithelial markers as well as inhibition of migration and invasion. Experimental epithelial-mesenchymal-transition (EMT) induced by exposure to TGFβ/TNFα is also completely reversed by P18. Importantly, P18 also inhibits mammosphere-formation along with a reduction in the expression of stemness factors, Oct4, Nanog and Sox2. We show that P18 induces expression, phosphorylation and accumulation of p53 in cancer cells. P18-mediated induction of p53 leads to increased nuclear localization and elevated expression of p53 target genes. Using isogenic cancer cells differing only in p53 status, we show that p53 plays an important role in P18-mediated alteration of mesenchymal and epithelial genes, inhibition of migration and invasion of cancer cells. Furthermore, P18 increases miR-34a expression in p53-dependent manner and miR-34a is integral for P18-mediated inhibition of growth, invasion and mammosphere-formation. miR-34a mimics potentiate P18 efficacy while miR-34a antagomirs antagonize P18. Collectively, these data provide evidence that P18 may represent a promising therapeutic strategy for the inhibition of growth and progression of breast cancer and p53-miR-34a axis is important for P18 function.
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Affiliation(s)
- Dimiter B Avtanski
- Department of Oncology, Johns Hopkins University School of Medicine and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA
| | - Arumugam Nagalingam
- Department of Oncology, Johns Hopkins University School of Medicine and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA
| | - Joseph E Tomaszewski
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD 20852, USA
| | - Prabhakar Risbood
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD 20852, USA
| | - Michael J Difillippantonio
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD 20852, USA
| | - Neeraj K Saxena
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 2120, USA.
| | - Sanjay V Malhotra
- Department of Radiation Oncology and Stanford Cancer Institute, Stanford University, Palo Alto, CA, USA.
| | - Dipali Sharma
- Department of Oncology, Johns Hopkins University School of Medicine and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA; Graduate Program in Cellular and Molecular Medicine, Johns Hopkins, Baltimore, MD 21231, USA.
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33
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Krajčovičová S, Soural M. Solid-Phase Synthetic Strategies for the Preparation of Purine Derivatives. ACS COMBINATORIAL SCIENCE 2016; 18:371-86. [PMID: 27248804 DOI: 10.1021/acscombsci.6b00061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This Review summarizes all of the currently described strategies applicable for the solid-phase synthesis of purine derivatives. The individual approaches are classified according to the immobilization procedure used resulting in a linkage of the final scaffold at various positions.
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Affiliation(s)
- Soňa Krajčovičová
- Department
of Organic Chemistry, Faculty of Science, Palacký University, 771 46 Olomouc, Czech Republic
| | - Miroslav Soural
- Department
of Organic Chemistry, Faculty of Science, Palacký University, 771 46 Olomouc, Czech Republic
- Institute
of Molecular and Translation Medicine, Faculty of Medicine and Dentistry, Palacký University, Hněvotínská 5, 779 00, Olomouc, Czech Republic
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34
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Lemos A, Leão M, Soares J, Palmeira A, Pinto M, Saraiva L, Sousa ME. Medicinal Chemistry Strategies to Disrupt the p53-MDM2/MDMX Interaction. Med Res Rev 2016; 36:789-844. [PMID: 27302609 DOI: 10.1002/med.21393] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/16/2016] [Accepted: 03/21/2016] [Indexed: 12/12/2022]
Abstract
The growth inhibitory activity of p53 tumor suppressor is tightly regulated by interaction with two negative regulatory proteins, murine double minute 2 (MDM2) and X (MDMX), which are overexpressed in about half of all human tumors. The elucidation of crystallographic structures of MDM2/MDMX complexes with p53 has been pivotal for the identification of several classes of inhibitors of the p53-MDM2/MDMX interaction. The present review provides in silico strategies and screening approaches used in drug discovery as well as an overview of the most relevant classes of small-molecule inhibitors of the p53-MDM2/MDMX interaction, their progress in pipeline, and highlights particularities of each class of inhibitors. Most of the progress made with high-throughput screening has led to the development of inhibitors belonging to the cis-imidazoline, piperidinone, and spiro-oxindole series. However, novel potent and selective classes of inhibitors of the p53-MDM2 interaction with promising antitumor activity are emerging. Even with the discovery of the 3D structure of complex p53-MDMX, only two small molecules were reported as selective p53-MDMX antagonists, WK298 and SJ-172550. Dual inhibition of the p53-MDM2/MDMX interaction has shown to be an alternative approach since it results in full activation of the p53-dependent pathway. The knowledge of structural requirements crucial to the development of small-molecule inhibitors of the p53-MDMs interactions has enabled the identification of novel antitumor agents with improved in vivo efficacy.
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Affiliation(s)
- Agostinho Lemos
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Mariana Leão
- UCIBIO/REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Joana Soares
- UCIBIO/REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Andreia Palmeira
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Madalena Pinto
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.,CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua de Bragas, 289, 4050-123, Porto, Portugal
| | - Lucília Saraiva
- UCIBIO/REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Maria Emília Sousa
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.,CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua de Bragas, 289, 4050-123, Porto, Portugal
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35
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Kodadek T, McEnaney PJ. Towards vast libraries of scaffold-diverse, conformationally constrained oligomers. Chem Commun (Camb) 2016; 52:6038-59. [PMID: 26996593 PMCID: PMC4846527 DOI: 10.1039/c6cc00617e] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
There is great interest in the development of probe molecules and drug leads that would bind tightly and selectively to protein surfaces that are difficult to target with traditional molecules, such as those involved in protein-protein interactions. The currently available evidence suggests that this will require molecules that are larger and have quite different chemical properties than typical Lipinski-compliant molecules that target enzyme active sites. We describe here efforts to develop vast libraries of conformationally constrained oligomers as a potentially rich source of these molecules.
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Affiliation(s)
- Thomas Kodadek
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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36
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Wang Z, Song T, Feng Y, Guo Z, Fan Y, Xu W, Liu L, Wang A, Zhang Z. Bcl-2/MDM2 Dual Inhibitors Based on Universal Pyramid-Like α-Helical Mimetics. J Med Chem 2016; 59:3152-62. [PMID: 26982372 DOI: 10.1021/acs.jmedchem.5b01913] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
No α-helical mimetic that exhibits Bcl-2/MDM2 dual inhibition has been rationally designed due to the different helicities of the α-helixes at their binding interfaces. Herein, we extracted a one-turn α-helix-mimicking ortho-triarene unit from o-phenylene foldamers. Linking benzamide substrates with a rotatable C-N bond, we constructed a novel semirigid pyramid-like scaffold that could support its two-turn α-helix mimicry without aromatic stacking interactions and could adopt the different dihedral angles of the key residues of p53 and BH3-only peptides. On the basis of this universal scaffold, a series of substituent groups were installed to capture the key residues of both p53TAD and BimBH3 and balance the differences of the bulks between them. Identified by FP, ITC, and NMR spectroscopy, a compound 6e (zq-1) that directly binds to Mcl-1, Bcl-2, and MDM2 with balanced submicromolar affinities was obtained. Cell-based experiments demonstrated its antitumor ability through Bcl-2/MDM2 dual inhibition simultaneously.
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Affiliation(s)
- Ziqian Wang
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology , No. 158-89, Zhongshan Road, Dalian 116012, People's Republic of China
| | - Ting Song
- School of Life Science and Technology, Dalian University of Technology , Dalian 116024, People's Republic of China
| | - Yingang Feng
- Shandong Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao 266101, People's Republic of China
| | - Zongwei Guo
- School of Life Science and Technology, Dalian University of Technology , Dalian 116024, People's Republic of China
| | - Yudan Fan
- School of Life Science and Technology, Dalian University of Technology , Dalian 116024, People's Republic of China
| | - Wenjie Xu
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology , No. 158-89, Zhongshan Road, Dalian 116012, People's Republic of China
| | - Lu Liu
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology , No. 158-89, Zhongshan Road, Dalian 116012, People's Republic of China
| | - Anhui Wang
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology , No. 158-89, Zhongshan Road, Dalian 116012, People's Republic of China
| | - Zhichao Zhang
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology , No. 158-89, Zhongshan Road, Dalian 116012, People's Republic of China
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37
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Lee JH, Oh M, Kim HS, Lee H, Im W, Lim HS. Converting One-Face α-Helix Mimetics into Amphiphilic α-Helix Mimetics as Potent Inhibitors of Protein-Protein Interactions. ACS COMBINATORIAL SCIENCE 2016; 18:36-42. [PMID: 26651509 DOI: 10.1021/acscombsci.5b00080] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Many biologically active α-helical peptides adopt amphiphilic helical structures that contain hydrophobic residues on one side and hydrophilic residues on the other side. Therefore, α-helix mimetics capable of mimicking such amphiphilic helical peptides should possess higher binding affinity and specificity to target proteins. Here we describe an efficient method for generating amphiphilic α-helix mimetics. One-face α-helix mimetics having hydrophobic side chains on one side was readily converted into amphiphilic α-helix mimetics by introducing appropriate charged residues on the opposite side. We also demonstrate that such two-face amphiphilic α-helix mimetics indeed show remarkably improved binding affinity to a target protein, compared to one-face hydrophobic α-helix mimetics. We believe that generating a large combinatorial library of these amphiphilic α-helix mimetics can be valuable for rapid discovery of highly potent and specific modulators of protein-protein interactions.
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Affiliation(s)
- Ji Hoon Lee
- New
Drug Development Center, Daegu Gyeongbuk Medical Innovation Foundation, Daegu 701-310, South Korea
| | - Misook Oh
- Department
of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 790-784, South Korea
- Department
of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Hyun Soo Kim
- Department
of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 790-784, South Korea
| | - Huisun Lee
- Department
of Molecular Biosciences and Centre for Computational Biology, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Wonpil Im
- Department
of Molecular Biosciences and Centre for Computational Biology, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Hyun-Suk Lim
- Department
of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 790-784, South Korea
- Department
of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
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38
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Trobe M, Breinbauer R. Improved and scalable synthesis of building blocks for the modular synthesis of teraryl-based alpha-helix mimetics. MONATSHEFTE FUR CHEMIE 2015. [DOI: 10.1007/s00706-015-1599-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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39
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Pettersson M, Quant M, Min J, Iconaru L, Kriwacki RW, Waddell MB, Guy RK, Luthman K, Grøtli M. Design, Synthesis and Evaluation of 2,5-Diketopiperazines as Inhibitors of the MDM2-p53 Interaction. PLoS One 2015; 10:e0137867. [PMID: 26427060 PMCID: PMC4591261 DOI: 10.1371/journal.pone.0137867] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 08/23/2015] [Indexed: 11/19/2022] Open
Abstract
The transcription factor p53 is the main tumour suppressor in cells and many cancer types have p53 mutations resulting in a loss of its function. In tumours that retain wild-type p53 function, p53 activity is down-regulated by MDM2 (human murine double minute 2) via a direct protein-protein interaction. We have designed and synthesised two series of 2,5-diketopiperazines as inhibitors of the MDM2-p53 interaction. The first set was designed to directly mimic the α-helical region of the p53 peptide, containing key residues in the i, i+4 and i+7 positions of a natural α-helix. Conformational analysis indicated that 1,3,6-trisubstituted 2,5-diketopiperazines were able to place substituents in the same spatial orientation as an α-helix template. The key step of the synthesis involved the cyclisation of substituted dipeptides. The other set of tetrasubstituted 2,5-diketopiperazines were designed based on structure-based docking studies and the Ugi multicomponent reaction was used for the synthesis. This latter set comprised the most potent inhibitors which displayed micromolar IC50-values in a biochemical fluorescence polarisation assay.
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Affiliation(s)
- Mariell Pettersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Maria Quant
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Jaeki Min
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, 38105, United States of America
| | - Luigi Iconaru
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, 38105, United States of America
| | - Richard W. Kriwacki
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, 38105, United States of America
| | - M. Brett Waddell
- Molecular Interaction Analysis Shared Resource, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, 38105, United States of America
| | - R. Kiplin Guy
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, 38105, United States of America
| | - Kristina Luthman
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
- * E-mail:
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40
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Wilson AJ. Helix mimetics: Recent developments. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:33-40. [DOI: 10.1016/j.pbiomolbio.2015.05.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 12/19/2022]
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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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42
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Hoggard LR, Zhang Y, Zhang M, Panic V, Wisniewski JA, Ji H. Rational design of selective small-molecule inhibitors for β-catenin/B-cell lymphoma 9 protein-protein interactions. J Am Chem Soc 2015; 137:12249-60. [PMID: 26352795 DOI: 10.1021/jacs.5b04988] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Selective inhibition of α-helix-mediated protein-protein interactions (PPIs) with small organic molecules provides great potential for the discovery of chemical probes and therapeutic agents. Protein Data Bank data mining using the HippDB database indicated that (1) the side chains of hydrophobic projecting hot spots at positions i, i + 3, and i + 7 of an α-helix had few orientations when interacting with the second protein and (2) the hot spot pockets of PPI complexes had different sizes, shapes, and chemical groups when interacting with the same hydrophobic projecting hot spots of α-helix. On the basis of these observations, a small organic molecule, 4'-fluoro-N-phenyl-[1,1'-biphenyl]-3-carboxamide, was designed as a generic scaffold that itself directly mimics the binding mode of the side chains of hydrophobic projecting hot spots at positions i, i + 3, and i + 7 of an α-helix. Convenient decoration of this generic scaffold led to the selective disruption of α-helix-mediated PPIs. A series of small-molecule inhibitors selective for β-catenin/B-cell lymphoma 9 (BCL9) over β-catenin/cadherin PPIs was designed and synthesized. The binding mode of new inhibitors was characterized by site-directed mutagenesis and structure-activity relationship studies. This new class of inhibitors can selectively disrupt β-catenin/BCL9 over β-catenin/cadherin PPIs, suppress the transactivation of canonical Wnt signaling, downregulate the expression of Wnt target genes, and inhibit the growth of Wnt/β-catenin-dependent cancer cells.
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Affiliation(s)
- Logan R Hoggard
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Yongqiang Zhang
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Min Zhang
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Vanja Panic
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - John A Wisniewski
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Haitao Ji
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
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43
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Lanning ME, Fletcher S. Multi-Facial, Non-Peptidic α-Helix Mimetics. BIOLOGY 2015; 4:540-55. [PMID: 26404384 PMCID: PMC4588149 DOI: 10.3390/biology4030540] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/11/2015] [Accepted: 08/14/2015] [Indexed: 01/13/2023]
Abstract
α-Helices often recognize their target proteins at protein–protein interfaces through more than one recognition face. This review describes the state-of-the-art in the design of non-peptidic α-helix mimetics that reproduce functionality from multiple faces of an α-helix.
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Affiliation(s)
- Maryanna E Lanning
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA.
| | - Steven Fletcher
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA.
- University of Maryland Greenebaum Cancer Center, 22 S. Greene St., Baltimore, MD 21201, USA.
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44
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Prieur V, Pujol MD, Guillaumet G. A Strategy for the Triarylation of Pyrrolopyrimidines by Using Microwave-Promoted Cross-Coupling Reactions. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500625] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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45
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Sheng C, Dong G, Miao Z, Zhang W, Wang W. State-of-the-art strategies for targeting protein-protein interactions by small-molecule inhibitors. Chem Soc Rev 2015; 44:8238-59. [PMID: 26248294 DOI: 10.1039/c5cs00252d] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Targeting protein-protein interactions (PPIs) has emerged as a viable approach in modern drug discovery. However, the identification of small molecules enabling us to effectively interrupt their interactions presents significant challenges. In the recent past, significant advances have been made in the development of new biological and chemical strategies to facilitate the discovery process of small-molecule PPI inhibitors. This review aims to highlight the state-of-the-art technologies and the achievements made recently in this field. The "hot spots" of PPIs have been proved to be critical for small molecules to bind. Three strategies including screening, designing, and synthetic approaches have been explored for discovering PPI inhibitors by targeting the "hot spots". Although the classic high throughput screening approach can be used, fragment screening, fragment-based drug design and newly improved virtual screening are demonstrated to be more effective in the discovery of PPI inhibitors. In addition to screening approaches, design strategies including anchor-based and small molecule mimetics of secondary structures involved in PPIs have become powerful tools as well. Finally, constructing new chemically spaced libraries with high diversity and complexity is becoming an important area of interest for PPI inhibitors. The successful cases from the recent five year studies are used to illustrate how these approaches are implemented to uncover and optimize small molecule PPI inhibitors and notably some of them have become promising therapeutics.
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Affiliation(s)
- Chunquan Sheng
- Department of Medicinal Chemistry, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, P. R. China.
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46
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes. Angew Chem Int Ed Engl 2015; 54:8896-927. [PMID: 26119925 PMCID: PMC4557054 DOI: 10.1002/anie.201412070] [Citation(s) in RCA: 496] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) are involved at all levels of cellular organization, thus making the development of PPI inhibitors extremely valuable. The identification of selective inhibitors is challenging because of the shallow and extended nature of PPI interfaces. Inhibitors can be obtained by mimicking peptide binding epitopes in their bioactive conformation. For this purpose, several strategies have been evolved to enable a projection of side chain functionalities in analogy to peptide secondary structures, thereby yielding molecules that are generally referred to as peptidomimetics. Herein, we introduce a new classification of peptidomimetics (classes A-D) that enables a clear assignment of available approaches. Based on this classification, the Review summarizes strategies that have been applied for the structure-based design of PPI inhibitors through stabilizing or mimicking turns, β-sheets, and helices.
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Affiliation(s)
- Marta Pelay-Gimeno
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Adrian Glas
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Oliver Koch
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
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47
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Lanning ME, Wilder PT, Bailey H, Drennen B, Cavalier M, Chen L, Yap JL, Raje M, Fletcher S. Towards more drug-like proteomimetics: two-faced, synthetic α-helix mimetics based on a purine scaffold. Org Biomol Chem 2015. [PMID: 26204921 DOI: 10.1039/c5ob00478k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Mimicry of two faces of an α-helix might yield more potent and more selective inhibitors of aberrant, helix-mediated protein-protein interactions (PPI). Herein, we demonstrate that a 2,6,9-tri-substituted purine is capable of disrupting the Mcl-1-Bak-BH3 PPI through effective mimicry of key residues on opposing faces of the Bak-BH3 α-helix.
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Affiliation(s)
- M E Lanning
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA.
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48
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Strukturbasierte Entwicklung von Protein-Protein-Interaktionsinhibitoren: Stabilisierung und Nachahmung von Peptidliganden. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412070] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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49
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Laraia L, McKenzie G, Spring DR, Venkitaraman AR, Huggins DJ. Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions. CHEMISTRY & BIOLOGY 2015; 22:689-703. [PMID: 26091166 PMCID: PMC4518475 DOI: 10.1016/j.chembiol.2015.04.019] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/01/2015] [Accepted: 04/08/2015] [Indexed: 01/19/2023]
Abstract
Protein-protein interactions (PPIs) underlie the majority of biological processes, signaling, and disease. Approaches to modulate PPIs with small molecules have therefore attracted increasing interest over the past decade. However, there are a number of challenges inherent in developing small-molecule PPI inhibitors that have prevented these approaches from reaching their full potential. From target validation to small-molecule screening and lead optimization, identifying therapeutically relevant PPIs that can be successfully modulated by small molecules is not a simple task. Following the recent review by Arkin et al., which summarized the lessons learnt from prior successes, we focus in this article on the specific challenges of developing PPI inhibitors and detail the recent advances in chemistry, biology, and computation that facilitate overcoming them. We conclude by providing a perspective on the field and outlining four innovations that we see as key enabling steps for successful development of small-molecule inhibitors targeting PPIs.
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Affiliation(s)
- Luca Laraia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Grahame McKenzie
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Ashok R Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - David J Huggins
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK; Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, 19 JJ Thomson Avenue, Cambridge CB3 0HE, UK.
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50
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Pettersson M, Bliman D, Jacobsson J, Nilsson JR, Min J, Iconaru L, Guy RK, Kriwacki RW, Andréasson J, Grøtli M. 8-Triazolylpurines: Towards Fluorescent Inhibitors of the MDM2/p53 Interaction. PLoS One 2015; 10:e0124423. [PMID: 25942498 PMCID: PMC4420247 DOI: 10.1371/journal.pone.0124423] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 03/02/2015] [Indexed: 11/18/2022] Open
Abstract
Small molecule nonpeptidic mimics of α-helices are widely recognised as protein-protein interaction (PPIs) inhibitors. Protein-protein interactions mediate virtually all important regulatory pathways in a cell, and the ability to control and modulate PPIs is therefore of great significance to basic biology, where controlled disruption of protein networks is key to understanding network connectivity and function. We have designed and synthesised two series of 2,6,9-substituted 8-triazolylpurines as α-helix mimetics. The first series was designed based on low energy conformations but did not display any biological activity in a biochemical fluorescence polarisation assay targeting MDM2/p53. Although solution NMR conformation studies demonstrated that such molecules could mimic the topography of an α-helix, docking studies indicated that the same compounds were not optimal as inhibitors for the MDM2/p53 interaction. A new series of 8-triazolylpurines was designed based on a combination of docking studies and analysis of recently published inhibitors. The best compound displayed low micromolar inhibitory activity towards MDM2/p53 in a biochemical fluorescence polarisation assay. In order to evaluate the applicability of these compounds as biologically active and intrinsically fluorescent probes, their absorption/emission properties were measured. The compounds display fluorescent properties with quantum yields up to 50%.
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Affiliation(s)
- Mariell Pettersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - David Bliman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jimmy Jacobsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jesper R. Nilsson
- Department of Chemical and Biological Engineering/Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, Sweden
| | - Jaeki Min
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, United States of America
| | - Luigi Iconaru
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, United States of America
| | - R. Kiplin Guy
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, United States of America
| | - Richard W. Kriwacki
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, United States of America
| | - Joakim Andréasson
- Department of Chemical and Biological Engineering/Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- * E-mail:
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