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Kassu M, Parvatkar PT, Milanes J, Monaghan NP, Kim C, Dowgiallo M, Zhao Y, Asakawa AH, Huang L, Wagner A, Miller B, Carter K, Barrett KF, Tillery LM, Barrett LK, Phan IQ, Subramanian S, Myler PJ, Van Voorhis WC, Leahy JW, Rice CA, Kyle DE, Morris J, Manetsch R. Shotgun Kinetic Target-Guided Synthesis Approach Enables the Discovery of Small-Molecule Inhibitors against Pathogenic Free-Living Amoeba Glucokinases. ACS Infect Dis 2023; 9:2190-2201. [PMID: 37820055 PMCID: PMC10644346 DOI: 10.1021/acsinfecdis.3c00284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Indexed: 10/13/2023]
Abstract
Pathogenic free-living amoebae (pFLA) can cause life-threatening central nervous system (CNS) infections and warrant the investigation of new chemical agents to combat the rise of infection from these pathogens. Naegleria fowleri glucokinase (NfGlck), a key metabolic enzyme involved in generating glucose-6-phosphate, was previously identified as a potential target due to its limited sequence similarity with human Glck (HsGlck). Herein, we used our previously demonstrated multifragment kinetic target-guided synthesis (KTGS) screening strategy to identify inhibitors against pFLA glucokinases. Unlike the majority of previous KTGS reports, our current study implements a "shotgun" approach, where fragments were not biased by predetermined binding potentials. The study resulted in the identification of 12 inhibitors against 3 pFLA glucokinase enzymes─NfGlck, Balamuthia mandrillaris Glck (BmGlck), and Acanthamoeba castellanii Glck (AcGlck). This work demonstrates the utility of KTGS to identify small-molecule binders for biological targets where resolved X-ray crystal structures are not readily accessible.
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Affiliation(s)
- Mintesinot Kassu
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Prakash T. Parvatkar
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Jillian Milanes
- Eukaryotic
Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Neil P. Monaghan
- Eukaryotic
Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Chungsik Kim
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Matthew Dowgiallo
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Yingzhao Zhao
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Ami H. Asakawa
- Department
of Pharmaceutical Sciences, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Lili Huang
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Alicia Wagner
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Brandon Miller
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Karissa Carter
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Kayleigh F. Barrett
- Center
for Emerging and Re-emerging Infectious Diseases (CERID), Division
of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, Washington 98109, United States
| | - Logan M. Tillery
- Center
for Emerging and Re-emerging Infectious Diseases (CERID), Division
of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, Washington 98109, United States
| | - Lynn K. Barrett
- Center
for Emerging and Re-emerging Infectious Diseases (CERID), Division
of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, Washington 98109, United States
| | - Isabelle Q. Phan
- Center for Global Infectious Diseases Research, Seattle Children’s Research Center, Seattle, Washington 98109, United States
| | - Sandhya Subramanian
- Center for Global Infectious Diseases Research, Seattle Children’s Research Center, Seattle, Washington 98109, United States
| | - Peter J. Myler
- Center for Global Infectious Diseases Research, Seattle Children’s Research Center, Seattle, Washington 98109, United States
| | - Wesley C. Van Voorhis
- Center
for Emerging and Re-emerging Infectious Diseases (CERID), Division
of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, Washington 98109, United States
| | - James W. Leahy
- Department of Chemistry, University
of
South Florida, Tampa, Florida 33620, United States
| | - Christopher A. Rice
- Department
of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue
Institute for Drug Discovery (PIDD), Purdue
University, West Lafayette, Indiana 47907, United States
- Purdue Institute
of Inflammation, Immunology and Infectious Disease (PI4D), Purdue University, West Lafayette, Indiana 47907, United States
- Department
of Cellular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Dennis E. Kyle
- Department
of Cellular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - James Morris
- Eukaryotic
Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Roman Manetsch
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
- Department
of Pharmaceutical Sciences, Northeastern
University, Boston, Massachusetts 02115, United States
- Center
for Drug Discovery, Northeastern University, Boston, Massachusetts 02115, United States
- Barnett
Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts 02115, United States
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Sundaramoorthy R, Vadivelu M, Karthikeyan K, Praveen C. Mechanosynthesis of Triazolyl-bis(indolyl)methane Pharmacophores via Gold Catalysis: A Prelude to Their Molecular Electronic Properties and Biological Potency. ChemMedChem 2023; 18:e202200529. [PMID: 36529707 DOI: 10.1002/cmdc.202200529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/26/2022] [Accepted: 12/17/2022] [Indexed: 12/23/2022]
Abstract
Chemical structures possessing both 1,2,3-triazole and bis(indolyl)methane fragments gained considerable interest in drug synthesis owing to their established biological efficacies. However, 1,2,3-triazoles linked at the bridging position of bis(indolyl)methane is a logical and unexplored design approach. In this regard, nine new triazolyl-bis(indolyl)methane conjugates under AuCl catalyzed ball-milling conditions were accomplished. Comparative evaluation on absorptive and emissive properties of the synthesized dyads were also analyzed. To unravel the influence of different peripheral substituents on the electronic structure and π-orbital properties, theoretical investigations were performed. Screening of molecules for free radical scavenging, anti-inflammatory and antidiabetic showed comparable potency against reference drugs. In particular, compounds 7 h, 7 d and 7 a displayed good efficiency of α-amylase inhibition. The DNA gyrase inhibitory potential of all compounds were assessed in silico which revealed high binding affinity (ΔG=-8.99 Kcal/mol) for 7 i followed by 7 h (ΔG=-7.80 Kcal/mol) with the targeted protein.
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Affiliation(s)
- Ramachandran Sundaramoorthy
- Department of Chemistry, B. S. Abdur Rahman Crescent Institute of Science and Technology, Chennai, 600048, Tamil Nadu, India
| | - Murugan Vadivelu
- Department of Chemistry, B. S. Abdur Rahman Crescent Institute of Science and Technology, Chennai, 600048, Tamil Nadu, India
| | - Kesavan Karthikeyan
- Department of Chemistry, B. S. Abdur Rahman Crescent Institute of Science and Technology, Chennai, 600048, Tamil Nadu, India
| | - Chandrasekar Praveen
- Electrochemical Power Sources Division, CSIR-Central Electrochemical Research Institute, Karaikudi, 630003, Tamil Nadu, India
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3
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Liu Q, Sheng L, Liu YY, Gao T, Wang H, Liu Y, Cao A. A potential inhibitor of MDM2 by restoring the native conformation of the p53 α-helical peptide on gold nanoparticles. ChemMedChem 2022; 17:e202100623. [PMID: 35037401 DOI: 10.1002/cmdc.202100623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/14/2021] [Indexed: 11/11/2022]
Abstract
Many efforts have been made to develop inhibitors of MDM2 as potential drugs for cancer therapy. In this work, we use our previous developed conformational engineering technique to stabilize the binding conformation of the p53 transcription activation domain (TAD) peptide on gold NPs (AuNPs), and create an AuNP-based anti-MDM2 artificial antibody, denoted as Goldbody, that specifically binds MDM2. Though the free TAD peptide is unstructured, circular dichroism spectra confirm that its α-helical conformation in the original p53 protein is restored on the anti-MDM2 Goldbody, and surface plasmon resonance (SPR) experiments confirm that there is strong specific interaction between the anti-MDM2 Goldbody and MDM2, demonstrating the anti-MDM2 Goldbody as a potential inhibitor of MDM2. This work demonstrates that the conformational engineering technique is not limited to the antigen-antibody systems, but can also be applied more widely in other protein-protein interfaces to create more and more artificial proteins for various biomedical applications.
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Affiliation(s)
- Qi Liu
- Shanghai University, Institute of Nanochemistry and Nanobiology, CHINA
| | - Lingjie Sheng
- Shanghai University, Institute of Nanochemistry and Nanobiology, CHINA
| | - Yuan-Yuan Liu
- Shanghai University, Institute of Nanochemistry and Nanobiology, CHINA
| | - Tiange Gao
- Shanghai University, Institute of Nanochemistry and Nanobiology, CHINA
| | - Haifang Wang
- Shanghai University, Institute of Nanochemistry and Nanobiology, CHINA
| | - Yuanfang Liu
- Peking University, College of Chemistry and Molecular Engineering, CHINA
| | - Aoneng Cao
- Shanghai University, Institute of Nanochemistry and Nanobiology, No.99 Shangda Rd. Rm201, Bldg. E, 200444, Shanghai, CHINA
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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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5
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van der Vlag R, Yagiz Unver M, Felicetti T, Twarda‐Clapa A, Kassim F, Ermis C, Neochoritis CG, Musielak B, Labuzek B, Dömling A, Holak TA, Hirsch AKH. Optimized Inhibitors of MDM2 via an Attempted Protein-Templated Reductive Amination. ChemMedChem 2020; 15:370-375. [PMID: 31774938 PMCID: PMC7064911 DOI: 10.1002/cmdc.201900574] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/21/2019] [Indexed: 12/17/2022]
Abstract
Innovative and efficient hit-identification techniques are required to accelerate drug discovery. Protein-templated fragment ligations represent a promising strategy in early drug discovery, enabling the target to assemble and select its binders from a pool of building blocks. Development of new protein-templated reactions to access a larger structural diversity and expansion of the variety of targets to demonstrate the scope of the technique are of prime interest for medicinal chemists. Herein, we present our attempts to use a protein-templated reductive amination to target protein-protein interactions (PPIs), a challenging class of drug targets. We address a flexible pocket, which is difficult to achieve by structure-based drug design. After careful analysis we did not find one of the possible products in the kinetic target-guided synthesis (KTGS) approach, however subsequent synthesis and biochemical evaluation of each library member demonstrated that all the obtained molecules inhibit MDM2. The most potent library member (Ki =0.095 μm) identified is almost as active as Nutlin-3, a potent inhibitor of the p53-MDM2 PPI.
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Affiliation(s)
- Ramon van der Vlag
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - M. Yagiz Unver
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - Tommaso Felicetti
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
- Department of Pharmaceutical SciencesUniversity of PerugiaVia del Liceo 106123PerugiaItaly
| | | | - Fatima Kassim
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - Cagdas Ermis
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - Constantinos G. Neochoritis
- Department of Pharmacy, Drug Design groupUniversity of GroningenA. Deusinglaan 1GroningenThe Netherlands
- Chemistry departmentUniversity of Crete70013HeraklionGreece
| | - Bogdan Musielak
- Faculty of ChemistryJagiellonian UniversityGronostajowa 230-387KrakowPoland
| | - Beata Labuzek
- Faculty of ChemistryJagiellonian UniversityGronostajowa 230-387KrakowPoland
| | - Alexander Dömling
- Department of Pharmacy, Drug Design groupUniversity of GroningenA. Deusinglaan 1GroningenThe Netherlands
| | - Tad A. Holak
- Faculty of ChemistryJagiellonian UniversityGronostajowa 230-387KrakowPoland
| | - Anna K. H. Hirsch
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus Building E8.166123SaarbrückenGermany
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