1
|
Tantak M, Rayala R, Deng Z, Bunnell A, Wang T, Chaudhari P, Leng F, Nefzi A. Polyheterocyclic peptidomimetics: Parallel solid phase synthesis of oligo cyclic guanidines and their inhibition activity against Mycobacterium tuberculosis DNA gyrase. Bioorg Med Chem Lett 2023; 93:129439. [PMID: 37557925 PMCID: PMC10993493 DOI: 10.1016/j.bmcl.2023.129439] [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: 07/11/2023] [Revised: 08/01/2023] [Accepted: 08/06/2023] [Indexed: 08/11/2023]
Abstract
Polyheterocycles are one of the most desired synthetic targets due to their numerous and valuable applications in various fields. We report the design and the parallel synthesis of novel linear oligocyclic guanidine peptidomimetics from predesigned reduced polyamides. A screening of these compounds identified active Mycobacterium tuberculosis DNA gyrase inhibitors which do not inhibit human DNA topoisomerase IIα and topoisomerase I.
Collapse
Affiliation(s)
- Mukund Tantak
- Center for Translational Science, Florida International University, 11350 SW Village Parkway, Port Saint Lucie, FL 34987, USA
| | - Ramanjaneyulu Rayala
- Center for Translational Science, Florida International University, 11350 SW Village Parkway, Port Saint Lucie, FL 34987, USA
| | - Zifang Deng
- Department of Chemistry & Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Ashley Bunnell
- Center for Translational Science, Florida International University, 11350 SW Village Parkway, Port Saint Lucie, FL 34987, USA
| | - Ting Wang
- Center for Translational Science, Florida International University, 11350 SW Village Parkway, Port Saint Lucie, FL 34987, USA
| | - Prakash Chaudhari
- Center for Translational Science, Florida International University, 11350 SW Village Parkway, Port Saint Lucie, FL 34987, USA
| | - Fenfei Leng
- Department of Chemistry & Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Adel Nefzi
- Center for Translational Science, Florida International University, 11350 SW Village Parkway, Port Saint Lucie, FL 34987, USA; Herbert Wertheim College of Medicine, FIU, 11200 SW 8th St, Miami, FL 33199, USA.
| |
Collapse
|
2
|
McQuaid K, Pipier A, Cardin C, Monchaud D. Interactions of small molecules with DNA junctions. Nucleic Acids Res 2022; 50:12636-12656. [PMID: 36382400 PMCID: PMC9825177 DOI: 10.1093/nar/gkac1043] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/13/2022] [Accepted: 10/23/2022] [Indexed: 11/17/2022] Open
Abstract
The four natural DNA bases (A, T, G and C) associate in base pairs (A=T and G≡C), allowing the attached DNA strands to assemble into the canonical double helix of DNA (or duplex-DNA, also known as B-DNA). The intrinsic supramolecular properties of nucleobases make other associations possible (such as base triplets or quartets), which thus translates into a diversity of DNA structures beyond B-DNA. To date, the alphabet of DNA structures is ripe with approximately 20 letters (from A- to Z-DNA); however, only a few of them are being considered as key players in cell biology and, by extension, valuable targets for chemical biology intervention. In the present review, we summarise what is known about alternative DNA structures (what are they? When, where and how do they fold?) and proceed to discuss further about those considered nowadays as valuable therapeutic targets. We discuss in more detail the molecular tools (ligands) that have been recently developed to target these structures, particularly the three- and four-way DNA junctions, in order to intervene in the biological processes where they are involved. This new and stimulating chemical biology playground allows for devising innovative strategies to fight against genetic diseases.
Collapse
Affiliation(s)
- Kane T McQuaid
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Angélique Pipier
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| | - Christine J Cardin
- Correspondence may also be addressed to Christine J. Cardin. Tel: +44 118 378 8215;
| | - David Monchaud
- To whom correspondence should be addressed. Tel: +33 380 399 043;
| |
Collapse
|
3
|
Ivens E, Cominetti MM, Searcey M. Junctions in DNA: underexplored targets for therapeutic intervention. Bioorg Med Chem 2022; 69:116897. [DOI: 10.1016/j.bmc.2022.116897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 11/02/2022]
|
4
|
Doering SR, Freeman K, Debevec G, Geer P, Santos RG, Lavoi TM, Giulianotti MA, Pinilla C, Appel JR, Houghten RA, Ericson MD, Haskell-Luevano C. Discovery of Nanomolar Melanocortin-3 Receptor (MC3R)-Selective Small Molecule Pyrrolidine Bis-Cyclic Guanidine Agonist Compounds Via a High-Throughput "Unbiased" Screening Campaign. J Med Chem 2021; 64:5577-5592. [PMID: 33886285 PMCID: PMC8552302 DOI: 10.1021/acs.jmedchem.0c02041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The central melanocortin-3 and melanocortin-4 receptors (MC3R, MC4R) are key regulators of body weight and energy homeostasis. Herein, the discovery and characterization of first-in-class small molecule melanocortin agonists with selectivity for the melanocortin-3 receptor over the melanocortin-4 receptor are reported. Identified via "unbiased" mixture-based high-throughput screening approaches, pharmacological evaluation of these pyrrolidine bis-cyclic guanidines resulted in nanomolar agonist activity at the melanocortin-3 receptor. The pharmacological profiles at the remaining melanocortin receptor subtypes tested indicated similar agonist potencies at both the melanocortin-1 and melanocortin-5 receptors and antagonist or micromolar agonist activities at the melanocortin-4 receptor. This group of small molecules represents a new area of chemical space for the melanocortin receptors with mixed receptor pharmacology profiles that may serve as novel lead compounds to modulate states of dysregulated energy balance.
Collapse
Affiliation(s)
- Skye R Doering
- Department of Medicinal Chemistry and Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Katie Freeman
- Department of Medicinal Chemistry and Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Ginamarie Debevec
- Florida International University, Port St. Lucie, Florida 34987, United States
| | - Phaedra Geer
- Florida International University, Port St. Lucie, Florida 34987, United States
| | - Radleigh G Santos
- Nova Southeastern University, 3301 College Avenue, Fort Lauderdale, Florida 33314, United States
| | - Travis M Lavoi
- Florida International University, Port St. Lucie, Florida 34987, United States
| | - Marc A Giulianotti
- Florida International University, Port St. Lucie, Florida 34987, United States
| | - Clemencia Pinilla
- Florida International University, Port St. Lucie, Florida 34987, United States
| | - Jon R Appel
- Florida International University, Port St. Lucie, Florida 34987, United States
| | - Richard A Houghten
- Florida International University, Port St. Lucie, Florida 34987, United States
| | - Mark D Ericson
- Department of Medicinal Chemistry and Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Carrie Haskell-Luevano
- Department of Medicinal Chemistry and Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
5
|
Seddek A, Annamalai T, Tse-Dinh YC. Type IA Topoisomerases as Targets for Infectious Disease Treatments. Microorganisms 2021; 9:E86. [PMID: 33401386 PMCID: PMC7823277 DOI: 10.3390/microorganisms9010086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/13/2020] [Accepted: 12/17/2020] [Indexed: 12/19/2022] Open
Abstract
Infectious diseases are one of the main causes of death all over the world, with antimicrobial resistance presenting a great challenge. New antibiotics need to be developed to provide therapeutic treatment options, requiring novel drug targets to be identified and pursued. DNA topoisomerases control the topology of DNA via DNA cleavage-rejoining coupled to DNA strand passage. The change in DNA topological features must be controlled in vital processes including DNA replication, transcription, and DNA repair. Type IIA topoisomerases are well established targets for antibiotics. In this review, type IA topoisomerases in bacteria are discussed as potential targets for new antibiotics. In certain bacterial pathogens, topoisomerase I is the only type IA topoisomerase present, which makes it a valuable antibiotic target. This review will summarize recent attempts that have been made to identify inhibitors of bacterial topoisomerase I as potential leads for antibiotics and use of these inhibitors as molecular probes in cellular studies. Crystal structures of inhibitor-enzyme complexes and more in-depth knowledge of their mechanisms of actions will help to establish the structure-activity relationship of potential drug leads and develop potent and selective therapeutics that can aid in combating the drug resistant bacterial infections that threaten public health.
Collapse
Affiliation(s)
- Ahmed Seddek
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (A.S.); (T.A.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Thirunavukkarasu Annamalai
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (A.S.); (T.A.)
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (A.S.); (T.A.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| |
Collapse
|
6
|
Magana M, Pushpanathan M, Santos AL, Leanse L, Fernandez M, Ioannidis A, Giulianotti MA, Apidianakis Y, Bradfute S, Ferguson AL, Cherkasov A, Seleem MN, Pinilla C, de la Fuente-Nunez C, Lazaridis T, Dai T, Houghten RA, Hancock REW, Tegos GP. The value of antimicrobial peptides in the age of resistance. THE LANCET. INFECTIOUS DISEASES 2020; 20:e216-e230. [PMID: 32653070 DOI: 10.1016/s1473-3099(20)30327-3] [Citation(s) in RCA: 514] [Impact Index Per Article: 128.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/29/2020] [Accepted: 04/16/2020] [Indexed: 12/20/2022]
Abstract
Accelerating growth and global expansion of antimicrobial resistance has deepened the need for discovery of novel antimicrobial agents. Antimicrobial peptides have clear advantages over conventional antibiotics which include slower emergence of resistance, broad-spectrum antibiofilm activity, and the ability to favourably modulate the host immune response. Broad bacterial susceptibility to antimicrobial peptides offers an additional tool to expand knowledge about the evolution of antimicrobial resistance. Structural and functional limitations, combined with a stricter regulatory environment, have hampered the clinical translation of antimicrobial peptides as potential therapeutic agents. Existing computational and experimental tools attempt to ease the preclinical and clinical development of antimicrobial peptides as novel therapeutics. This Review identifies the benefits, challenges, and opportunities of using antimicrobial peptides against multidrug-resistant pathogens, highlights advances in the deployment of novel promising antimicrobial peptides, and underlines the needs and priorities in designing focused development strategies taking into account the most advanced tools available.
Collapse
Affiliation(s)
- Maria Magana
- Department of Biopathology and Clinical Microbiology, Aeginition Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Ana L Santos
- Department of Chemistry, Rice University, Houston, TX, USA; Investigación Sanitaria de las Islas Baleares, Palma, Spain
| | - Leon Leanse
- Department of Dermatology, Harvard Medical School, Boston, MA, USA; Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michael Fernandez
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | | | | | | | - Steven Bradfute
- Department of Internal Medicine, Center for Global Health, University of New Mexico, Albuquerque, NM, USA
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Artem Cherkasov
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Mohamed N Seleem
- Department of Comparative Pathobiology, Purdue University College of Veterinary Medicine, West Lafayette, IN, USA
| | - Clemencia Pinilla
- Torrey Pines Institute for Molecular Studies, Port St Lucie, FL, USA
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Themis Lazaridis
- Department of Chemistry, The City College of New York, New York, NY, USA; Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, NY, USA
| | - Tianhong Dai
- Department of Dermatology, Harvard Medical School, Boston, MA, USA; Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Robert E W Hancock
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - George P Tegos
- Reading Hospital, Tower Health, West Reading, PA, USA; Micromoria, Venture X Marlborough, Marlborough, MA, USA.
| |
Collapse
|
7
|
Identification of Bis-Cyclic Guanidines as Antiplasmodial Compounds from Positional Scanning Mixture-Based Libraries. Molecules 2019; 24:molecules24061100. [PMID: 30897744 PMCID: PMC6471430 DOI: 10.3390/molecules24061100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/05/2019] [Accepted: 03/13/2019] [Indexed: 01/23/2023] Open
Abstract
The screening of more than 30 million compounds derived from 81 small molecule libraries built on 81 distinct scaffolds identified pyrrolidine bis-cyclic guanidine library (TPI-1955) to be one of the most active and selective antiplasmodial libraries. The screening of the positional scanning library TPI-1955 arranged on four sets of sublibraries (26 + 26 + 26 + 40), totaling 120 samples for testing provided information about the most important groups of each variable position in the TPI-1955 library containing 738,192 unique compounds. The parallel synthesis of the individual compounds derived from the deconvolution of the positional scanning library led to the identification of active selective antiplasmodial pyrrolidine bis-cyclic guanidines.
Collapse
|
8
|
Tran T, Chiem K, Jani S, Arivett BA, Lin DL, Lad R, Jimenez V, Farone MB, Debevec G, Santos R, Giulianotti M, Pinilla C, Tolmasky ME. Identification of a small molecule inhibitor of the aminoglycoside 6'-N-acetyltransferase type Ib [AAC(6')-Ib] using mixture-based combinatorial libraries. Int J Antimicrob Agents 2018; 51:752-761. [PMID: 29410367 DOI: 10.1016/j.ijantimicag.2018.01.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/13/2018] [Accepted: 01/24/2018] [Indexed: 11/28/2022]
Abstract
The aminoglycoside, 6'-N-acetyltransferase type Ib [AAC(6')-Ib] is the most widely distributed enzyme among AAC(6')-I-producing Gram-negative pathogens and confers resistance to clinically relevant aminoglycosides, including amikacin. This enzyme is therefore an ideal target for enzymatic inhibitors that could overcome resistance to aminoglycosides. The search for inhibitors was carried out using mixture-based combinatorial libraries, the scaffold ranking approach, and the positional scanning strategy. A library with high inhibitory activity had pyrrolidine pentamine scaffold and was selected for further analysis. This library contained 738,192 compounds with functionalities derived from 26 different amino acids (R1, R2 and R3) and 42 different carboxylic acids (R4) in four R-group functionalities. The most active compounds all contained S-phenyl (R1 and R3) and S-hydromethyl (R2) functionalities at three locations and differed at the R4 position. The compound containing 3-phenylbutyl at R4 (compound 206) was a robust enzymatic inhibitor in vitro, in combination with amikacin it potentiated the inhibition of growth of three resistant bacteria in culture, and it improved survival when used as treatment of Galleria mellonella infected with aac(6')-Ib-harboring Klebsiella pneumoniae and Acinetobacter baumannii strains.
Collapse
Affiliation(s)
- Tung Tran
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA
| | - Kevin Chiem
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA
| | - Saumya Jani
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA
| | - Brock A Arivett
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN; Department of Chemistry, Middle Tennessee State University, Murfreesboro, TN
| | - David L Lin
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA
| | - Rupali Lad
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA
| | - Verónica Jimenez
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA
| | - Mary B Farone
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN
| | | | - Radleigh Santos
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, FL
| | - Marc Giulianotti
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, FL
| | | | - Marcelo E Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA.
| |
Collapse
|
9
|
Giulianotti MA, Vesely BA, Azhari A, Souza A, LaVoi T, Houghten RA, Kyle DE, Leahy JW. Identification of a Hit Series of Antileishmanial Compounds through the Use of Mixture-Based Libraries. ACS Med Chem Lett 2017; 8:802-807. [PMID: 28835792 DOI: 10.1021/acsmedchemlett.7b00045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/10/2017] [Indexed: 11/28/2022] Open
Abstract
From a screening campaign that included mixture-based libraries containing more than 6 million compounds, a lead series of bis-cyclic guanidines was identified as the most promising. Lead optimization resulted in the identification of potent (IC50 < 500 nM) and selective compounds within this series as well as potent and selective monoguanidines.
Collapse
Affiliation(s)
- Marc A. Giulianotti
- Department of Chemistry, University of South Florida, CHE 205, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Brian A. Vesely
- Department
of Global Health, College of Public Health, University of South Florida, 3720 Spectrum Boulevard, Suite 304, Tampa, Florida 33612, United States
| | - Ala Azhari
- Department
of Global Health, College of Public Health, University of South Florida, 3720 Spectrum Boulevard, Suite 304, Tampa, Florida 33612, United States
| | - Ashley Souza
- Department
of Global Health, College of Public Health, University of South Florida, 3720 Spectrum Boulevard, Suite 304, Tampa, Florida 33612, United States
| | - Travis LaVoi
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Richard A. Houghten
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Dennis E. Kyle
- Department
of Global Health, College of Public Health, University of South Florida, 3720 Spectrum Boulevard, Suite 304, Tampa, Florida 33612, United States
| | - James W. Leahy
- Department of Chemistry, University of South Florida, CHE 205, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
- Florida Center of Excellence for Drug Discovery
and Innovation, University of South Florida, 3720 Spectrum Boulevard, Suite 303, Tampa, Florida 33612, United States
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, MDC 7, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| |
Collapse
|
10
|
Juliano SA, Pierce S, deMayo JA, Balunas MJ, Angeles-Boza AM. Exploration of the Innate Immune System of Styela clava: Zn2+ Binding Enhances the Antimicrobial Activity of the Tunicate Peptide Clavanin A. Biochemistry 2017; 56:1403-1414. [DOI: 10.1021/acs.biochem.6b01046] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Samuel A. Juliano
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - Scott Pierce
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - James A. deMayo
- Division
of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Marcy J. Balunas
- Division
of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Alfredo M. Angeles-Boza
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| |
Collapse
|
11
|
Small-Molecule Inhibitors Targeting Topoisomerase I as Novel Antituberculosis Agents. Antimicrob Agents Chemother 2016; 60:4028-36. [PMID: 27114277 DOI: 10.1128/aac.00288-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/15/2016] [Indexed: 01/30/2023] Open
Abstract
Bacterial topoisomerase functions are required for regulation of DNA supercoiling and overcoming the DNA topological barriers that are encountered during many vital cellular processes. DNA gyrase and topoisomerase IV of the type IIA bacterial topoisomerase family are important clinical targets for antibacterial therapy. Topoisomerase I, belonging to the type IA topoisomerase family, has recently been validated as a potential antitubercular target. The topoisomerase I activity has been shown to be essential for bacterial viability and infection in a murine model of tuberculosis. Mixture-based combinatorial libraries were screened in this study to identify novel bacterial topoisomerase I inhibitors. Using positional-scanning deconvolution, selective small-molecule inhibitors of bacterial topoisomerase I were identified starting from a polyamine scaffold. Antibacterial assays demonstrated that four of these small-molecule inhibitors of bacterial topoisomerase I are bactericidal against Mycobacterium smegmatis and Mycobacterium tuberculosis The MICs for growth inhibition of M. smegmatis increased with overexpression of recombinant M. tuberculosis topoisomerase I, consistent with inhibition of intracellular topoisomerase I activity being involved in the antimycobacterial mode of action.
Collapse
|
12
|
Fleeman R, LaVoi TM, Santos RG, Morales A, Nefzi A, Welmaker GS, Medina-Franco JL, Giulianotti MA, Houghten RA, Shaw LN. Combinatorial Libraries As a Tool for the Discovery of Novel, Broad-Spectrum Antibacterial Agents Targeting the ESKAPE Pathogens. J Med Chem 2015; 58:3340-55. [PMID: 25780985 DOI: 10.1021/jm501628s] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Mixture based synthetic combinatorial libraries offer a tremendous enhancement for the rate of drug discovery, allowing the activity of millions of compounds to be assessed through the testing of exponentially fewer samples. In this study, we used a scaffold-ranking library to screen 37 different libraries for antibacterial activity against the ESKAPE pathogens. Each library contained between 10000 and 750000 structural analogues for a total of >6 million compounds. From this, we identified a bis-cyclic guanidine library that displayed strong antibacterial activity. A positional scanning library for these compounds was developed and used to identify the most effective functional groups at each variant position. Individual compounds were synthesized that were broadly active against all ESKAPE organisms at concentrations <2 μM. In addition, these compounds were bactericidal, had antibiofilm effects, showed limited potential for the development of resistance, and displayed almost no toxicity when tested against human lung cells and erythrocytes. Using a murine model of peritonitis, we also demonstrate that these agents are highly efficacious in vivo.
Collapse
Affiliation(s)
| | - Travis M LaVoi
- ∥Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987, United States
| | - Radleigh G Santos
- ∥Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987, United States
| | - Angela Morales
- ∥Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987, United States
| | - Adel Nefzi
- ∥Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987, United States
| | - Gregory S Welmaker
- ∥Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987, United States
| | - José L Medina-Franco
- ⊥Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico
| | - Marc A Giulianotti
- ∥Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987, United States
| | - Richard A Houghten
- ∥Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987, United States
| | | |
Collapse
|
13
|
Onwuha-Ekpete L, Tack L, Knapinska A, Smith L, Kaushik G, Lavoi T, Giulianotti M, Houghten RA, Fields GB, Minond D. Novel pyrrolidine diketopiperazines selectively inhibit melanoma cells via induction of late-onset apoptosis. J Med Chem 2014; 57:1599-608. [PMID: 24471466 PMCID: PMC3983399 DOI: 10.1021/jm4019542] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A common liability of cancer drugs is toxicity to noncancerous cells. Thus, molecules are needed that are potent toward cancer cells while sparing healthy cells. The cost of traditional cell-based HTS is dictated by the library size, which is typically in the hundreds of thousands of individual compounds. Mixture-based combinatorial libraries offer a cost-effective alternative to single-compound libraries while eliminating the need for molecular target validation. Presently, lung cancer and melanoma cells were screened in parallel with healthy cells using a mixture-based library. A novel class of compounds was discovered that selectively inhibited melanoma cell growth via apoptosis with submicromolar potency while sparing healthy cells. Additionally, the cost of screening and biological follow-up experiments was significantly lower than in typical HTS. Our findings suggest that mixture-based phenotypic HTS can significantly reduce cost and hit-to-lead time while yielding novel compounds with promising pharmacology.
Collapse
Affiliation(s)
- Lillian Onwuha-Ekpete
- Torrey Pines Institute for Molecular Studies , 11350 South West Village Parkway, Port St. Lucie, Florida 34987, United States
| | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Scaffold ranking and positional scanning utilized in the discovery of nAChR-selective compounds suitable for optimization studies. J Med Chem 2013; 56:10103-17. [PMID: 24274400 DOI: 10.1021/jm401543h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Nicotine binds to nicotinic acetylcholine receptors (nAChR), which can exist as many different subtypes. The α4β2 nAChR is the most prevalent subtype in the brain and possesses the most evidence linking it to nicotine seeking behavior. Herein we report the use of mixture based combinatorial libraries for the rapid discovery of a series of α4β2 nAChR selective compounds. Further chemistry optimization provided compound 301, which was characterized as a selective α4β2 nAChR antagonist. This compound displayed no agonist activity but blocked nicotine-induced depolarization of HEK cells with an IC50 of approximately 430 nM. 301 demonstrated nearly 500-fold selectivity for binding and 40-fold functional selectivity for α4β2 over α3β4 nAChR. In total over 5 million compounds were assessed through the use of just 170 samples in order to identify a series of structural analogues suitable for future optimization toward the goal of developing clinically relevant smoking cessation medications.
Collapse
|
15
|
Dey M, Patra S, Su LY, Segall AM. Tumor cell death mediated by peptides that recognize branched intermediates of DNA replication and repair. PLoS One 2013; 8:e78751. [PMID: 24244353 PMCID: PMC3828334 DOI: 10.1371/journal.pone.0078751] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 09/20/2013] [Indexed: 12/15/2022] Open
Abstract
Effective treatments for cancer are still needed, both for cancers that do not respond well to current therapeutics and for cancers that become resistant to available treatments. Herein we investigated the effect of a structure-selective d-amino acid peptide wrwycr that binds replication fork mimics and Holliday Junction (HJs) intermediates of homologous recombination (HR) in vitro, and inhibits their resolution by HJ-processing enzymes. We predicted that treating cells with HJ-binding compounds would lead to accumulation of DNA damage. As cells repair endogenous or exogenous DNA damage, collapsed replication forks and HJ intermediates will accumulate and serve as targets for the HJ-binding peptides. Inhibiting junction resolution will lead to further accumulation of DNA breaks, eventually resulting in amplification of the damage and causing cell death. Both peptide wrwycr and the related wrwyrggrywrw entered cancer cells and reduced cell survival in a dose- and time-dependent manner. Early markers for DNA damage, γH2AX foci and 53BP1 foci, increased with dose and/or time exposure to the peptides. DNA breaks persisted at least 48 h, and both checkpoint proteins Chk1 and Chk2 were activated. The passage of the cells from S to G2/M was blocked even after 72 h. Apoptosis, however, was not induced in either HeLa or PC3 cells. Based on colony-forming assays, about 35% peptide-induced cytotoxicity was irreversible. Finally, sublethal doses of peptide wrwycr (50–100 µM) in conjunction with sublethal doses of several DNA damaging agents (etoposide, doxorubicin, and HU) reduced cell survival at least additively and sometimes synergistically. Taken together, the results suggest that the peptides merit further investigation as proof-of-principle molecules for a new class of anti-cancer therapeutics, in particular in combination with other DNA damaging therapies.
Collapse
Affiliation(s)
- Mamon Dey
- Department of Biology and Center for Microbial Sciences, San Diego State University, San Diego, California, United States of America
| | - Sukanya Patra
- Department of Biology and Center for Microbial Sciences, San Diego State University, San Diego, California, United States of America
| | - Leo Y. Su
- Department of Biology and Center for Microbial Sciences, San Diego State University, San Diego, California, United States of America
| | - Anca M. Segall
- Department of Biology and Center for Microbial Sciences, San Diego State University, San Diego, California, United States of America
- * E-mail:
| |
Collapse
|
16
|
Zavesky BP, Babij NR, Fritz JA, Wolfe JP. Synthesis of cyclic guanidines via Pd-catalyzed alkene carboamination. Org Lett 2013; 15:5420-3. [PMID: 24147839 DOI: 10.1021/ol402377y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A new approach to the synthesis of substituted 5-membered cyclic guanidines is described. Palladium-catalyzed alkene carboamination reactions between acyclic N-allyl guanidines and aryl or alkenyl halides provide these products in good yield. This method allows access to a number of different cyclic guanidine derivatives in only two steps from readily available allylic amines.
Collapse
Affiliation(s)
- Blane P Zavesky
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | | | | | | |
Collapse
|
17
|
Wu B, Zhang Z, Noberini R, Barile E, Giulianotti M, Pinilla C, Houghten RA, Pasquale EB, Pellecchia M. HTS by NMR of combinatorial libraries: a fragment-based approach to ligand discovery. ACTA ACUST UNITED AC 2013; 20:19-33. [PMID: 23352136 DOI: 10.1016/j.chembiol.2012.10.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 10/17/2012] [Accepted: 10/19/2012] [Indexed: 11/29/2022]
Abstract
Fragment-based ligand design (FBLD) approaches have become more widely used in drug discovery projects from both academia and industry, and are even often preferred to traditional high-throughput screening (HTS) of large collection of compounds (>10(5)). A key advantage of FBLD approaches is that these often rely on robust biophysical methods such as NMR spectroscopy for detection of ligand binding, hence are less prone to artifacts that too often plague the results from HTS campaigns. In this article, we introduce a screening strategy that takes advantage of both the robustness of protein NMR spectroscopy as the detection method, and the basic principles of combinatorial chemistry to enable the screening of large libraries of fragments (>10(5) compounds) preassembled on a common backbone. We used the method to identify compounds that target protein-protein interactions.
Collapse
Affiliation(s)
- Bainan Wu
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
18
|
The mathematics of a successful deconvolution: a quantitative assessment of mixture-based combinatorial libraries screened against two formylpeptide receptors. Molecules 2013; 18:6408-24. [PMID: 23722730 PMCID: PMC4106117 DOI: 10.3390/molecules18066408] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 05/20/2013] [Accepted: 05/24/2013] [Indexed: 01/04/2023] Open
Abstract
In the past 20 years, synthetic combinatorial methods have fundamentally advanced the ability to synthesize and screen large numbers of compounds for drug discovery and basic research. Mixture-based libraries and positional scanning deconvolution combine two approaches for the rapid identification of specific scaffolds and active ligands. Here we present a quantitative assessment of the screening of 32 positional scanning libraries in the identification of highly specific and selective ligands for two formylpeptide receptors. We also compare and contrast two mixture-based library approaches using a mathematical model to facilitate the selection of active scaffolds and libraries to be pursued for further evaluation. The flexibility demonstrated in the differently formatted mixture-based libraries allows for their screening in a wide range of assays.
Collapse
|
19
|
Rideout MC, Naili I, Boldt JL, Flores-Fujimoto A, Patra S, Rostron JE, Segall AM. wrwyrggrywrw is a single-chain functional analog of the Holliday junction-binding homodimer, (wrwycr)2. Peptides 2013; 40:112-22. [PMID: 23291222 PMCID: PMC3646928 DOI: 10.1016/j.peptides.2012.12.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 12/23/2012] [Accepted: 12/26/2012] [Indexed: 11/22/2022]
Abstract
DNA repair pathways in bacteria that use homologous recombination involve the formation and subsequent resolution of Holliday junction (HJ) intermediates. We have previously identified several hexameric peptides that bind to HJs and interfere with HJ processing enzymes in vitro. The peptide WRWYCR and its D-amino acid stereoisomer wrwycr, are potent antibacterial agents. These hexapeptides must form homodimers in order to interact stably with HJs, and inhibit bacterial growth, and this represents a potential limitation. Herein we describe a disulfide bond-independent inhibitor, WRWYRGGRYWRW and its D-stereoisomer wrwyrggrywrw. We have characterized these single-chain, linear analogs of the hexapeptides, and show that in addition to effectively binding to HJs, and inhibiting the activity of DNA repair enzymes that process HJs, they have equal or greater potency against Gram-positive and Gram-negative bacterial growth. The analogs were also shown to cause DNA damage in bacteria, and disrupt the integrity of the bacterial cytoplasmic membrane. Finally, we found that they have little toxicity toward several eukaryotic cell types at concentrations needed to inhibit bacterial growth.
Collapse
Affiliation(s)
- Marc C. Rideout
- Department of Biology and Center for Microbial Sciences, San Diego State University, San Diego, California 92182
| | - Ilham Naili
- Department of Biology and Center for Microbial Sciences, San Diego State University, San Diego, California 92182
| | - Jeffrey L. Boldt
- Department of Biology and Center for Microbial Sciences, San Diego State University, San Diego, California 92182
| | - America Flores-Fujimoto
- Department of Biology and Center for Microbial Sciences, San Diego State University, San Diego, California 92182
| | - Sukanya Patra
- Department of Biology and Center for Microbial Sciences, San Diego State University, San Diego, California 92182
| | - Jason E. Rostron
- Department of Biology and Center for Microbial Sciences, San Diego State University, San Diego, California 92182
| | - Anca M. Segall
- Department of Biology and Center for Microbial Sciences, San Diego State University, San Diego, California 92182
- To whom correspondence should be addressed: , Phone: (619) 594-6528, Fax: (619) 594-5676
| |
Collapse
|
20
|
Yitzhaki S, Rostron JE, Xu Y, Rideout MC, Authement RN, Barlow SB, Segall AM. Similarities between exogenously- and endogenously-induced envelope stress: the effects of a new antibacterial molecule, TPI1609-10. PLoS One 2012; 7:e44896. [PMID: 23071502 PMCID: PMC3469575 DOI: 10.1371/journal.pone.0044896] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 08/15/2012] [Indexed: 11/19/2022] Open
Abstract
Antibiotics with novel and/or multiple targets are highly desirable in the face of the steady rise of clinical antibiotic resistance. We have screened and identified small molecules, typified by the compound TPI1609-10 (aka SM10), with antibiotic activity against both gram-positive and gram-negative bacteria. SM10 was screened in vitro to bind branched Holliday junction intermediates of homologous recombination and tyrosine recombinase-mediated recombination; thus, the cellular targets of the small molecules were expected to include the RuvABC Holliday junction resolvasome and the XerCD complex involved in proper segregation of replicated chromosomes to daughter cells. SM10 indeed induces DNA damage and filamentation in E. coli. However, SM10 also induces envelope stress and causes increased production of intracellular reactive oxygen species. In addition, SM10 has similar effects to endogenously-induced envelope stress via overproducing outer membrane proteins (OmpC and OmpF), which also induces the SOS response, chromosome fragmentation, and production of reactive oxygen species. The synergy between SM10, and cerulenin, a fatty acid synthesis inhibitor, together with the SM10 hypersensitivity of cpx and rpoE mutants, further support that SM10's mode of action damages membrane damage. The lethality of SM10 treatment and of OmpC overproduction are observed in both aerobically- and anaerobically-grown cells, and is accompanied by substantial DNA damage even anaerobically. Thus, only some DNA damage is due to reactive oxygen. We propose that membrane depolarization and the potential reduction in intracellular pH, leading to abasic site formation, cause a substantial amount of the DNA damage associated with both SM10 treatment and endogenous envelope stress. While it is difficult to completely exclude effects related to envelope damage as the sources of DNA damage, trapping intermediates associated with DNA repair and chromosome segregation pathways remains very likely. Thus SM10 may have distinct but synergistic modes of action.
Collapse
Affiliation(s)
- Shmuel Yitzhaki
- Department of Biology and Center for Microbial Sciences, San Diego State University, San Diego, California, United States of America
| | - Jason E. Rostron
- Department of Biology and Center for Microbial Sciences, San Diego State University, San Diego, California, United States of America
| | - Yan Xu
- Department of Biology and Center for Microbial Sciences, San Diego State University, San Diego, California, United States of America
| | - Marc C. Rideout
- Department of Biology and Center for Microbial Sciences, San Diego State University, San Diego, California, United States of America
| | - R. Nathan Authement
- Department of Biology and Center for Microbial Sciences, San Diego State University, San Diego, California, United States of America
| | - Steven B. Barlow
- Department of Biology and Center for Microbial Sciences, San Diego State University, San Diego, California, United States of America
- Electron Microscopy Facility, San Diego State University, San Diego, California, United States of America
| | - Anca M. Segall
- Department of Biology and Center for Microbial Sciences, San Diego State University, San Diego, California, United States of America
- * E-mail:
| |
Collapse
|