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Khamitova А, Berillo D, Lozynskyi A, Konechnyi Y, Mural D, Georgiyants V, Lesyk R. Thiadiazole and Thiazole Derivatives as Potential Antimicrobial Agents. Mini Rev Med Chem 2024; 24:531-545. [PMID: 37448365 DOI: 10.2174/1389557523666230713115947] [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: 04/24/2023] [Revised: 05/17/2023] [Accepted: 06/09/2023] [Indexed: 07/15/2023]
Abstract
BACKGROUND This review summarizes data on heterocyclic systems with thiadiazole and thiazole fragments in molecules as promising antimicrobial agents. INTRODUCTION Thiadiazole and thiazole backbones are the most favored and well-known heterocycles, a common and essential feature of various drugs. These scaffolds occupy a central position and are the main structural components of numerous drugs with a wide spectrum of action. These include antimicrobial, antituberculous, anti-inflammatory, analgesic, antiepileptic, antiviral, and anticancer agents. METHOD The research is based on bibliosemantic and analytical methods using bibliographic and abstract databases, as well as databases of chemical compounds. RESULT This review reports on thiadiazole and thiazole derivatives, which have important pharmacological properties. We are reviewing the structural modifications of various thiadiazole and thiazole derivatives, more specifically, the antimicrobial activity reported over the last years, as we have taken this as our main research area. 80 compounds were illustrated, and various derivatives containing hydrazone bridged thiazole and pyrrole rings, 2-pyridine and 4-pyridine substituted thiazole derivatives, compounds containing di-, tri- and tetrathiazole moieties, spiro-substituted 4- thiazolidinone-imidazoline-pyridines were analyzed. Derivatives of 5-heteroarylidene-2,4- thiazolidinediones, fluoroquinolone-thiadiazole hybrids, and others. CONCLUSION 1,3,4-thiadiazoles and thiazoles are valuable resource for researchers engaged in rational drug design and development in this area.
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Affiliation(s)
- Аkzhonas Khamitova
- Department of Pharmaceutical and Toxicological Chemistry, Pharmacognosy and Botany, NJSC «Asfendiyarov Kazakh National Medical University», 94 Tole Bi, Almaty, 050000, Kazakhstan
| | - Dmitriy Berillo
- Department of Pharmaceutical and Toxicological Chemistry, Pharmacognosy and Botany, NJSC «Asfendiyarov Kazakh National Medical University», 94 Tole Bi, Almaty, 050000, Kazakhstan
- Department of Chemistry and Biochemical Engineering, Institute of Chemical and Biological Technologies (IHBT), Satbayev University 22 Satbaev, Almaty, 050013, Kazakhstan
| | - Andrii Lozynskyi
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, 69 Pekarska, Lviv, 79010, Ukraine
| | - Yulian Konechnyi
- Department of Microbiology, Danylo Halytsky Lviv National Medical University, 69 Pekarska, Lviv, 79010, Ukraine
| | - Dmytro Mural
- Department of Pharmaceutical Chemistry, National University of Pharmacy, 4 Valentynivska, Kharkiv, 61168, Ukraine
| | - Victoriya Georgiyants
- Department of Pharmaceutical Chemistry, National University of Pharmacy, 4 Valentynivska, Kharkiv, 61168, Ukraine
| | - Roman Lesyk
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, 69 Pekarska, Lviv, 79010, Ukraine
- Department of Biotechnology and Cell Biology, University of Information Technology and Management in Rzeszow, 2 Sucharskiego, Rzeszow, 35-225, Poland
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2
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Ayon NJ. High-Throughput Screening of Natural Product and Synthetic Molecule Libraries for Antibacterial Drug Discovery. Metabolites 2023; 13:625. [PMID: 37233666 PMCID: PMC10220967 DOI: 10.3390/metabo13050625] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 05/27/2023] Open
Abstract
Due to the continued emergence of resistance and a lack of new and promising antibiotics, bacterial infection has become a major public threat. High-throughput screening (HTS) allows rapid screening of a large collection of molecules for bioactivity testing and holds promise in antibacterial drug discovery. More than 50% of the antibiotics that are currently available on the market are derived from natural products. However, with the easily discoverable antibiotics being found, finding new antibiotics from natural sources has seen limited success. Finding new natural sources for antibacterial activity testing has also proven to be challenging. In addition to exploring new sources of natural products and synthetic biology, omics technology helped to study the biosynthetic machinery of existing natural sources enabling the construction of unnatural synthesizers of bioactive molecules and the identification of molecular targets of antibacterial agents. On the other hand, newer and smarter strategies have been continuously pursued to screen synthetic molecule libraries for new antibiotics and new druggable targets. Biomimetic conditions are explored to mimic the real infection model to better study the ligand-target interaction to enable the designing of more effective antibacterial drugs. This narrative review describes various traditional and contemporaneous approaches of high-throughput screening of natural products and synthetic molecule libraries for antibacterial drug discovery. It further discusses critical factors for HTS assay design, makes a general recommendation, and discusses possible alternatives to traditional HTS of natural products and synthetic molecule libraries for antibacterial drug discovery.
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Affiliation(s)
- Navid J Ayon
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
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3
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Kumari M, Subbarao N. Convolutional neural network-based quantitative structure-activity relationship and fingerprint analysis against inhibitors of anthrax lethal factor. Future Med Chem 2023; 15:853-866. [PMID: 37248697 DOI: 10.4155/fmc-2023-0093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/10/2023] [Indexed: 05/31/2023] Open
Abstract
Aim: To develop a one-dimensional convolutional neural network-based quantitative structure-activity relationship (1D-CNN-QSAR) model to identify novel anthrax inhibitors and analyze chemical space. Methods: We developed a 1D-CNN-QSAR model to identify novel anthrax inhibitors. Results: The statistical results of the 1D-CNN-QSAR model showed a mean square error of 0.045 and a predicted correlation coefficient of 0.79 for the test set. Further, chemical space analysis showed more than 80% fragment pair similarity, with activity cliffs associated with carboxylic acid, 2-phenylfurans, N-phenyldihydropyrazole, N-phenylpyrrole, furan, 4-methylene-1H-pyrazol-5-one, phenylimidazole, phenylpyrrole and phenylpyrazolidine. Conclusion: These fragments may serve as the basis for developing potent novel drug candidates for anthrax. Finally, we concluded that our proposed 1D-CNN-QSAR model and fingerprint analysis might be used to discover potential anthrax drug candidates.
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Affiliation(s)
- Madhulata Kumari
- Amity Institute of Biotechnology, Amity University, Rajasthan, Jaipur, India
| | - Naidu Subbarao
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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4
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Xu Y, Cuccui J, Denman C, Maharjan T, Wren BW, Wagner GK. Structure-activity relationships in a new class of non-substrate-like covalent inhibitors of the bacterial glycosyltransferase LgtC. Bioorg Med Chem 2018; 26:2973-2983. [PMID: 29602676 DOI: 10.1016/j.bmc.2018.03.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/03/2018] [Accepted: 03/04/2018] [Indexed: 02/07/2023]
Abstract
Lipooligosaccharide (LOS) structures in the outer core of Gram-negative mucosal pathogens such as Neisseria meningitidis and Haemophilus influenzae contain characteristic glycoepitopes that contribute significantly to bacterial virulence. An important example is the digalactoside epitope generated by the retaining α-1,4-galactosyltransferase LgtC. These digalactosides camouflage the pathogen from the host immune system and increase its serum resistance. Small molecular inhibitors of LgtC are therefore sought after as chemical tools to study bacterial virulence, and as potential candidates for anti-virulence drug discovery. We have recently discovered a new class of non-substrate-like inhibitors of LgtC. The new inhibitors act via a covalent mode of action, targeting a non-catalytic cysteine residue in the LgtC active site. Here, we describe, for the first time, structure-activity relationships for this new class of glycosyltransferase inhibitors. We have carried out a detailed analysis of the inhibition kinetics to establish the relative contribution of the non-covalent binding and the covalent inactivation steps for overall inhibitory activity. Selected inhibitors were also evaluated against a serum-resistant strain of Haemophilus influenzae, but did not enhance the killing effect of human serum.
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Affiliation(s)
- Yong Xu
- King's College London, Department of Chemistry, Faculty of Natural & Mathematical Sciences, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Jon Cuccui
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, UK
| | - Carmen Denman
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, UK
| | - Tripty Maharjan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, UK
| | - Brendan W Wren
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, UK
| | - Gerd K Wagner
- King's College London, Department of Chemistry, Faculty of Natural & Mathematical Sciences, Britannia House, 7 Trinity Street, London SE1 1DB, UK.
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5
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Kaminskyy D, Kryshchyshyn A, Lesyk R. 5-Ene-4-thiazolidinones - An efficient tool in medicinal chemistry. Eur J Med Chem 2017; 140:542-594. [PMID: 28987611 PMCID: PMC7111298 DOI: 10.1016/j.ejmech.2017.09.031] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 07/14/2017] [Accepted: 09/17/2017] [Indexed: 02/02/2023]
Abstract
The presented review is an attempt to summarize a huge volume of data on 5-ene-4-thiazolidinones being a widely studied class of small molecules used in modern organic and medicinal chemistry. The manuscript covers approaches to the synthesis of 5-ene-4-thiazolidinone derivatives: modification of the C5 position of the basic core; synthesis of the target compounds in the one-pot or multistage reactions or transformation of other related heterocycles. The most prominent pharmacological profiles of 5-ene derivatives of different 4-thiazolidinone subtypes belonging to hit-, lead-compounds, drug-candidates and drugs as well as the most studied targets have been discussed. Currently target compounds (especially 5-en-rhodanines) are assigned as frequent hitters or pan-assay interference compounds (PAINS) within high-throughput screening campaigns. Nevertheless, the crucial impact of the presence/nature of C5 substituent (namely 5-ene) on the pharmacological effects of 5-ene-4-thiazolidinones was confirmed by the numerous listed findings from the original articles. The main directions for active 5-ene-4-thiazolidinones optimization have been shown: i) complication of the fragment in the C5 position; ii) introduction of the substituents in the N3 position (especially fragments with carboxylic group or its derivatives); iii) annealing in complex heterocyclic systems; iv) combination with other pharmacologically attractive fragments within hybrid pharmacophore approach. Moreover, the utilization of 5-ene-4-thiazolidinones in the synthesis of complex compounds with potent pharmacological application is described. The chemical transformations cover mainly the reactions which involve the exocyclic double bond in C5 position of the main core and correspond to the abovementioned direction of the 5-ene-4-thiazolidinone modification.
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Affiliation(s)
- Danylo Kaminskyy
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, Lviv-10, 79010, Ukraine
| | - Anna Kryshchyshyn
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, Lviv-10, 79010, Ukraine
| | - Roman Lesyk
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, Lviv-10, 79010, Ukraine.
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6
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Nagy B, Galla Z, Bencze LC, Toșa MI, Paizs C, Forró E, Fülöp F. Covalently Immobilized Lipases are Efficient Stereoselective Catalysts for the Kinetic Resolution of rac-(5-Phenylfuran-2-yl)-β-alanine Ethyl Ester Hydrochlorides. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700174] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Botond Nagy
- Institute of Pharmaceutical Chemistry; University of Szeged; Eötvös u. 6 6701 Szeged Hungary
- Faculty of Chemistry and Chemical Engineering; Biocatalysis and Biotransformation Research Centre; Arany János str. 11 400028 Cluj-Napoca Romania
| | - Zsolt Galla
- Institute of Pharmaceutical Chemistry; University of Szeged; Eötvös u. 6 6701 Szeged Hungary
| | - László Csaba Bencze
- Faculty of Chemistry and Chemical Engineering; Biocatalysis and Biotransformation Research Centre; Arany János str. 11 400028 Cluj-Napoca Romania
| | - Monica Ioana Toșa
- Faculty of Chemistry and Chemical Engineering; Biocatalysis and Biotransformation Research Centre; Arany János str. 11 400028 Cluj-Napoca Romania
| | - Csaba Paizs
- Faculty of Chemistry and Chemical Engineering; Biocatalysis and Biotransformation Research Centre; Arany János str. 11 400028 Cluj-Napoca Romania
| | - Enikő Forró
- Institute of Pharmaceutical Chemistry; University of Szeged; Eötvös u. 6 6701 Szeged Hungary
| | - Ferenc Fülöp
- Institute of Pharmaceutical Chemistry; University of Szeged; Eötvös u. 6 6701 Szeged Hungary
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7
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Affiliation(s)
- Megan Garland
- Cancer
Biology Program, ‡Department of Pathology, §Department of Microbiology and Immunology, and ∥Department of
Chemical and Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Sebastian Loscher
- Cancer
Biology Program, ‡Department of Pathology, §Department of Microbiology and Immunology, and ∥Department of
Chemical and Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Matthew Bogyo
- Cancer
Biology Program, ‡Department of Pathology, §Department of Microbiology and Immunology, and ∥Department of
Chemical and Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
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8
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Head BM, Rubinstein E, Meyers AFA. Alternative pre-approved and novel therapies for the treatment of anthrax. BMC Infect Dis 2016; 16:621. [PMID: 27809794 PMCID: PMC5094018 DOI: 10.1186/s12879-016-1951-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 10/22/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacillus anthracis, the causative agent of anthrax, is a spore forming and toxin producing rod-shaped bacterium that is classified as a category A bioterror agent. This pathogenic microbe can be transmitted to both animals and humans. Clinical presentation depends on the route of entry (direct contact, ingestion, injection or aerosolization) with symptoms ranging from isolated skin infections to more severe manifestations such as cardiac or pulmonary shock, meningitis, and death. To date, anthrax is treatable if antibiotics are administered promptly and continued for 60 days. However, if treatment is delayed or administered improperly, the patient's chances of survival are decreased drastically. In addition, antibiotics are ineffective against the harmful anthrax toxins and spores. Therefore, alternative therapeutics are essential. In this review article, we explore and discuss advances that have been made in anthrax therapy with a primary focus on alternative pre-approved and novel antibiotics as well as anti-toxin therapies. METHODS A literature search was conducted using the University of Manitoba search engine. Using this search engine allowed access to a greater variety of journals/articles that would have otherwise been restricted for general use. In order to be considered for discussion for this review, all articles must have been published later than 2009. RESULTS The alternative pre-approved antibiotics demonstrated high efficacy against B. anthracis both in vitro and in vivo. In addition, the safety profile and clinical pharmacology of these drugs were already known. Compounds that targeted underexploited bacterial processes (DNA replication, RNA synthesis, and cell division) were also very effective in combatting B. anthracis. In addition, these novel compounds prevented bacterial resistance. Targeting B. anthracis virulence, more specifically the anthrax toxins, increased the length of which treatment could be administered. CONCLUSIONS Several novel and pre-existing antibiotics, as well as toxin inhibitors, have shown increasing promise. A combination treatment that targets both bacterial growth and toxin production would be ideal and probably necessary for effectively combatting this armed bacterium.
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Affiliation(s)
- Breanne M. Head
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9 Canada
| | - Ethan Rubinstein
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9 Canada
| | - Adrienne F. A. Meyers
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9 Canada
- National Laboratory for HIV Immunology, JC Wilt Infectious Disease Research Centre, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
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9
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Ambrose EA. Botulinum Neurotoxin, Tetanus Toxin, and Anthrax Lethal Factor Countermeasures. TOPICS IN MEDICINAL CHEMISTRY 2016. [DOI: 10.1007/7355_2016_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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10
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Zhang X, Amin EA. Highly predictive support vector machine (SVM) models for anthrax toxin lethal factor (LF) inhibitors. J Mol Graph Model 2016; 63:22-8. [PMID: 26615468 PMCID: PMC4713341 DOI: 10.1016/j.jmgm.2015.11.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 10/07/2015] [Accepted: 11/06/2015] [Indexed: 01/08/2023]
Abstract
Anthrax is a highly lethal, acute infectious disease caused by the rod-shaped, Gram-positive bacterium Bacillus anthracis. The anthrax toxin lethal factor (LF), a zinc metalloprotease secreted by the bacilli, plays a key role in anthrax pathogenesis and is chiefly responsible for anthrax-related toxemia and host death, partly via inactivation of mitogen-activated protein kinase kinase (MAPKK) enzymes and consequent disruption of key cellular signaling pathways. Antibiotics such as fluoroquinolones are capable of clearing the bacilli but have no effect on LF-mediated toxemia; LF itself therefore remains the preferred target for toxin inactivation. However, currently no LF inhibitor is available on the market as a therapeutic, partly due to the insufficiency of existing LF inhibitor scaffolds in terms of efficacy, selectivity, and toxicity. In the current work, we present novel support vector machine (SVM) models with high prediction accuracy that are designed to rapidly identify potential novel, structurally diverse LF inhibitor chemical matter from compound libraries. These SVM models were trained and validated using 508 compounds with published LF biological activity data and 847 inactive compounds deposited in the Pub Chem BioAssay database. One model, M1, demonstrated particularly favorable selectivity toward highly active compounds by correctly predicting 39 (95.12%) out of 41 nanomolar-level LF inhibitors, 46 (93.88%) out of 49 inactives, and 844 (99.65%) out of 847 Pub Chem inactives in external, unbiased test sets. These models are expected to facilitate the prediction of LF inhibitory activity for existing molecules, as well as identification of novel potential LF inhibitors from large datasets.
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Affiliation(s)
- Xia Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN 55414-2959, United States
| | - Elizabeth Ambrose Amin
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN 55414-2959, United States; Minnesota Supercomputing Institute for Advanced Computational Research, 117 Pleasant St SE, Minneapolis, MN, United States.
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11
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Kurbanov EK, Chiu TL, Solberg J, Francis S, Maize KM, Fernandez J, Johnson RL, Hawkinson JE, Walters MA, Finzel BC, Amin EA. Probing the S2′ Subsite of the Anthrax Toxin Lethal Factor Using Novel N-Alkylated Hydroxamates. J Med Chem 2015; 58:8723-33. [DOI: 10.1021/acs.jmedchem.5b01446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elbek K. Kurbanov
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Ting-Lan Chiu
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Jonathan Solberg
- Institute
for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Subhashree Francis
- Institute
for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Kimberly M. Maize
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Jenna Fernandez
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Rodney L. Johnson
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Jon E. Hawkinson
- Institute
for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Michael A. Walters
- Institute
for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Barry C. Finzel
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Elizabeth Ambrose Amin
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
- Minnesota
Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota 55455, United States
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12
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Dahlin JL, Walters MA. The essential roles of chemistry in high-throughput screening triage. Future Med Chem 2014; 6:1265-90. [PMID: 25163000 PMCID: PMC4465542 DOI: 10.4155/fmc.14.60] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
It is increasingly clear that academic high-throughput screening (HTS) and virtual HTS triage suffers from a lack of scientists trained in the art and science of early drug discovery chemistry. Many recent publications report the discovery of compounds by screening that are most likely artifacts or promiscuous bioactive compounds, and these results are not placed into the context of previous studies. For HTS to be most successful, it is our contention that there must exist an early partnership between biologists and medicinal chemists. Their combined skill sets are necessary to design robust assays and efficient workflows that will weed out assay artifacts, false positives, promiscuous bioactive compounds and intractable screening hits, efforts that ultimately give projects a better chance at identifying truly useful chemical matter. Expertise in medicinal chemistry, cheminformatics and purification sciences (analytical chemistry) can enhance the post-HTS triage process by quickly removing these problematic chemotypes from consideration, while simultaneously prioritizing the more promising chemical matter for follow-up testing. It is only when biologists and chemists collaborate effectively that HTS can manifest its full promise.
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Affiliation(s)
- Jayme L Dahlin
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
- Medical Scientist Training Program, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Michael A Walters
- Institute for Therapeutics Discovery & Development, University of Minnesota, Minneapolis, MN 55414, USA
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13
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Identification of exosite-targeting inhibitors of anthrax lethal factor by high-throughput screening. ACTA ACUST UNITED AC 2014; 19:875-82. [PMID: 22840775 DOI: 10.1016/j.chembiol.2012.05.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 05/10/2012] [Accepted: 05/17/2012] [Indexed: 12/24/2022]
Abstract
Protease inhibitor discovery has focused almost exclusively on compounds that bind to the active site. Inhibitors targeting protease exosites, regions outside of the active site that influence catalysis, offer potential advantages of increased specificity but are difficult to systematically discover. Here, we describe an assay suitable for detecting exosite-targeting inhibitors of the metalloproteinase anthrax lethal factor (LF) based on cleavage of a full-length mitogen-activated protein kinase kinase (MKK) substrate. We used this assay to screen a small-molecule library and then subjected hits to a secondary screen to exclude compounds that efficiently blocked cleavage of a peptide substrate. We identified a compound that preferentially inhibited cleavage of MKKs compared with peptide substrates and could suppress LF-induced macrophage cytolysis. This approach should be generally applicable to the discovery of exosite-targeting inhibitors of many additional proteases.
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14
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Structure-based pharmacophore modeling and virtual screening to identify novel inhibitors for anthrax lethal factor. Med Chem Res 2014. [DOI: 10.1007/s00044-014-0947-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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15
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Bouzianas DG. Potential biological targets ofBacillus anthracisin anti-infective approaches against the threat of bioterrorism. Expert Rev Anti Infect Ther 2014; 5:665-84. [PMID: 17678429 DOI: 10.1586/14787210.5.4.665] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The terrorist attacks of 2001 involving anthrax underscore the imperative that safe and effective medical countermeasures should be readily available. Vaccination appears to be the most effective form of mass protection against a biological attack, but the current vaccines have drawbacks that justify the enormous amount of effort currently being put into developing more effective vaccines and other treatment modalities. After providing a comprehensive overview of the organism Bacillus anthracis as a biological weapon and its pathogenicity, this review briefly summarizes the current knowledge vital to the management of anthrax disease. This knowledge has been acquired since 2001 as a result of the progress on anthrax research and focuses on the possible development of improved human anti-infective strategies targeting B. anthracis spore components, as well as strategies based on host-pathogen interactions.
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Affiliation(s)
- Dimitrios G Bouzianas
- Department of Medical Laboratories, Faculty of Health and Care Professions, University-level Technological Educational Institute of Thessaloniki, Greece.
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16
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Williams JD, Khan AR, Cardinale SC, Butler MM, Bowlin TL, Peet NP. Small molecule inhibitors of anthrax lethal factor toxin. Bioorg Med Chem 2013; 22:419-34. [PMID: 24290062 DOI: 10.1016/j.bmc.2013.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 10/29/2013] [Accepted: 11/05/2013] [Indexed: 10/26/2022]
Abstract
This manuscript describes the preparation of new small molecule inhibitors of Bacillus anthracis lethal factor. Our starting point was the symmetrical, bis-quinolinyl compound 1 (NSC 12155). Optimization of one half of this molecule led to new LF inhibitors that were desymmetrized to afford more drug-like compounds.
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Affiliation(s)
- John D Williams
- Microbiotix, Inc., Department of Medicinal Chemistry, One Innovation Drive, Worcester, MA 01605, United States; Microbiotix, Inc., Department of Molecular Biology, One Innovation Drive, Worcester, MA 01605, United States
| | - Atiyya R Khan
- Microbiotix, Inc., Department of Medicinal Chemistry, One Innovation Drive, Worcester, MA 01605, United States; Microbiotix, Inc., Department of Molecular Biology, One Innovation Drive, Worcester, MA 01605, United States
| | - Steven C Cardinale
- Microbiotix, Inc., Department of Medicinal Chemistry, One Innovation Drive, Worcester, MA 01605, United States; Microbiotix, Inc., Department of Molecular Biology, One Innovation Drive, Worcester, MA 01605, United States
| | - Michelle M Butler
- Microbiotix, Inc., Department of Medicinal Chemistry, One Innovation Drive, Worcester, MA 01605, United States; Microbiotix, Inc., Department of Molecular Biology, One Innovation Drive, Worcester, MA 01605, United States
| | - Terry L Bowlin
- Microbiotix, Inc., Department of Medicinal Chemistry, One Innovation Drive, Worcester, MA 01605, United States; Microbiotix, Inc., Department of Molecular Biology, One Innovation Drive, Worcester, MA 01605, United States
| | - Norton P Peet
- Microbiotix, Inc., Department of Medicinal Chemistry, One Innovation Drive, Worcester, MA 01605, United States; Microbiotix, Inc., Department of Molecular Biology, One Innovation Drive, Worcester, MA 01605, United States.
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17
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Calugi C, Trabocchi A, Lalli C, Guarna A. d-Proline-based peptidomimetic inhibitors of anthrax lethal factor. Eur J Med Chem 2012; 56:96-107. [DOI: 10.1016/j.ejmech.2012.08.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 08/17/2012] [Accepted: 08/20/2012] [Indexed: 11/27/2022]
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18
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Chiu TL, Amin EA. Development of a comprehensive, validated pharmacophore hypothesis for anthrax toxin lethal factor (LF) inhibitors using genetic algorithms, Pareto scoring, and structural biology. J Chem Inf Model 2012; 52:1886-97. [PMID: 22697455 PMCID: PMC3477282 DOI: 10.1021/ci300121p] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Anthrax is an acute infectious disease caused by the spore-forming bacterium Bacillus anthracis. The anthrax toxin lethal factor (LF), an 89-kDa zinc hydrolase secreted by the bacilli, is the toxin component chiefly responsible for pathogenesis and has been a popular target for rational and structure-based drug design. Although hundreds of small-molecule compounds have been designed to target the LF active site, relatively few reported inhibitors have exhibited activity in cell-based assays, and no LF inhibitor is currently available to treat or prevent anthrax. This study presents a new pharmacophore map assembly, validated by experiment, designed to rapidly identify and prioritize promising LF inhibitor scaffolds from virtual compound libraries. The new hypothesis incorporates structural information from all five available LF enzyme-inhibitor complexes deposited in the Protein Data Bank (PDB) and is the first LF pharmacophore map reported to date that includes features representing interactions involving all three key subsites of the LF catalytic binding region. In a wide-ranging validation study on all 546 compounds for which published LF biological activity data exist, this model displayed strong selectivity toward nanomolar-level LF inhibitors, successfully identifying 72.1% of existing nanomolar-level compounds in an unbiased test set, while rejecting 100% of weakly active (>100 μM) compounds. In addition to its capabilities as a database searching tool, this comprehensive model points to a number of key design principles and previously unidentified ligand-receptor interactions that are likely to influence compound potency.
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Affiliation(s)
- Ting-Lan Chiu
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Elizabeth A. Amin
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
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19
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Schepetkin IA, Kirpotina LN, Khlebnikov AI, Hanks TS, Kochetkova I, Pascual DW, Jutila MA, Quinn MT. Identification and characterization of a novel class of c-Jun N-terminal kinase inhibitors. Mol Pharmacol 2012; 81:832-45. [PMID: 22434859 DOI: 10.1124/mol.111.077446] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In efforts to identify novel small molecules with anti-inflammatory properties, we discovered a unique series of tetracyclic indenoquinoxaline derivatives that inhibited lipopolysaccharide (LPS)-induced nuclear factor-κB/activating protein 1 activation. Compound IQ-1 (11H-indeno[1,2-b]quinoxalin-11-one oxime) was found to be a potent, noncytotoxic inhibitor of pro-inflammatory cytokine [interleukin (IL)-1α, IL-1β, IL-6, IL-10, tumor necrosis factor (TNF)-α, interferon-γ, and granulocyte-macrophage colony-stimulating factor] and nitric oxide production by human and murine monocyte/macrophages. Three additional potent inhibitors of cytokine production were identified through further screening of IQ-1 analogs. The sodium salt of IQ-1 inhibited LPS-induced TNF-α and IL-6 production in MonoMac-6 cells with IC(50) values of 0.25 and 0.61 μM, respectively. Screening of 131 protein kinases revealed that derivative IQ-3 [11H-indeno[1,2-b]quinoxalin-11-one-O-(2-furoyl)oxime]was a specific inhibitor of the c-Jun N-terminal kinase (JNK) family, with preference for JNK3. This compound, as well as IQ-1 and three additional oxime indenoquinoxalines, were found to be high-affinity JNK inhibitors with nanomolar binding affinity and ability to inhibit c-Jun phosphorylation. Furthermore, docking studies showed that hydrogen bonding interactions of the active indenoquinoxalines with Asn152, Gln155, and Met149 of JNK3 played an important role in enzyme binding activity. Finally, we showed that the sodium salt of IQ-1 had favorable pharmacokinetics and inhibited the ovalbumin-induced CD4(+) T-cell immune response in a murine delayed-type hypersensitivity model in vivo. We conclude that compounds with an indenoquinoxaline nucleus can serve as specific small-molecule modulators for mechanistic studies of JNKs as well as a potential leads for the development of anti-inflammatory drugs.
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Affiliation(s)
- Igor A Schepetkin
- Department of Immunology and Infectious Diseases, Montana State University, Bozeman, MT 59717, USA
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20
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Inhibition of anthrax lethal factor: lability of hydroxamate as a chelating group. Appl Microbiol Biotechnol 2012; 94:1041-9. [PMID: 22270239 DOI: 10.1007/s00253-012-3893-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 01/02/2012] [Accepted: 01/05/2012] [Indexed: 12/24/2022]
Abstract
The metalloprotease activity of lethal factor (LF) from Bacillus anthracis (B. anthracis) is a main source of toxicity in the lethality of anthrax infection. Thus, the understanding of the enzymatic activity and inhibition of B. anthracis LF is of scientific and clinical interests. We have designed, synthesized, and studied a peptide inhibitor of LF, R9LF-1, with the structure NH(2)-(D: -Arg)(9)-Val-Leu-Arg-CO-NHOH in which the C-terminal hydroxamic acid is commonly used in the inhibitors of metalloproteases to chelate the active-site zinc. This inhibitor was shown to be very stable in solution and effectively inhibited LF in kinetic assays. However, its protection on murine macrophages against lethal toxin's lysis activity was relatively weak in longer assays. We further observed that the hydroxamic acid group in R9LF-1 was hydrolyzed by LF, and the hydrolytic product of this inhibitor is considerably weaker in inhibition of potency. To resist this unique hydrolytic activity of LF, we further designed a new inhibitor R9LF-2 which contained the same structure as R9LF-1 except replacing the hydroxamic acid group with N,O-dimethyl hydroxamic acid (DMHA), -N(CH(3))-O-CH(3). R9LF-2 was not hydrolyzed by LF in long-term incubation. It has a high inhibitory potency vs. LF with an inhibition constant of 6.4 nM had a better protection of macrophages against LF toxicity than R9LF-1. These results suggest that in the development of new LF inhibitors, the stability of the chelating group should be carefully examined and that DMHA is a potentially useful moiety to be used in new LF inhibitors.
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21
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Green KD, Chen W, Garneau-Tsodikova S. Identification and characterization of inhibitors of the aminoglycoside resistance acetyltransferase Eis from Mycobacterium tuberculosis. ChemMedChem 2012; 7:73-7. [PMID: 21898832 PMCID: PMC3401626 DOI: 10.1002/cmdc.201100332] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 08/18/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Keith D. Green
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109 (USA) Fax: (+ 1)734-615-5521
| | - Wenjing Chen
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109 (USA) Fax: (+ 1)734-615-5521
- Chemical Biology Doctoral Program, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109 (USA)
| | - Sylvie Garneau-Tsodikova
- Chemical Biology Doctoral Program, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109 (USA)
- Department of Medicinal Chemistry in the College of Pharmacy, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109 (USA)
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22
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Wei D, Bu Z, Yu A, Li F. Identification of a lead small-molecule inhibitor of anthrax lethal toxin by using fluorescence-based high-throughput screening. BMB Rep 2011; 44:811-5. [DOI: 10.5483/bmbrep.2011.44.12.811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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23
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Johnson S, Barile E, Farina B, Purves A, Wei J, Chen LH, Shiryaev S, Zhang Z, Rodionova I, Agrawal A, Cohen SM, Osterman A, Strongin A, Pellecchia M. Targeting metalloproteins by fragment-based lead discovery. Chem Biol Drug Des 2011; 78:211-23. [PMID: 21564556 DOI: 10.1111/j.1747-0285.2011.01136.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
It has been estimated that nearly one-third of functional proteins contain a metal ion. These constitute a wide variety of possible drug targets including metalloproteinases, dehydrogenases, oxidoreductases, hydrolases, deacetylases, or many others in which the metal ion is either of catalytic or of structural nature. Despite the predominant role of a metal ion in so many classes of drug targets, current high-throughput screening techniques do not usually produce viable hits against these proteins, likely due to the lack of proper metal-binding pharmacophores in the current screening libraries. Herein, we describe a novel fragment-based drug discovery approach using a metal-targeting fragment library that is based on a variety of distinct classes of metal-binding groups designed to reliably anchor the fragments at the target's metal ions. We show that the approach can effectively identify novel, potent and selective agents that can be readily developed into metalloprotein-targeted therapeutics.
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Affiliation(s)
- Sherida Johnson
- Sanford-Burnham Medical Research Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA
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24
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Jiao GS, Kim S, Moayeri M, Cregar-Hernandez L, McKasson L, Margosiak SA, Leppla SH, Johnson AT. Antidotes to anthrax lethal factor intoxication. Part 1: Discovery of potent lethal factor inhibitors with in vivo efficacy. Bioorg Med Chem Lett 2010; 20:6850-3. [PMID: 20864339 PMCID: PMC2965585 DOI: 10.1016/j.bmcl.2010.08.058] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 08/10/2010] [Accepted: 08/12/2010] [Indexed: 10/19/2022]
Abstract
Sub-nanomolar small molecule inhibitors of anthrax lethal factor have been identified using SAR and Merck L915 (4) as a model compound. One of these compounds (16) provided 100% protection in a rat lethal toxin model of anthrax disease.
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25
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Bouzianas DG. Current and future medical approaches to combat the anthrax threat. J Med Chem 2010; 53:4305-31. [PMID: 20102155 DOI: 10.1021/jm901024b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Dimitrios G Bouzianas
- Laboratory of Molecular Endocrinology, Division of Endocrinology and Metabolism, AHEPA University Hospital, 1 S. Kyriakidi Street, P.C. 54636, Thessaloniki, Macedonia, Greece.
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26
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Yuan H, Johnson SL, Chen LH, Wei J, Pellecchia M. A novel pharmacophore model for the design of anthrax lethal factor inhibitors. Chem Biol Drug Des 2010; 76:263-8. [PMID: 20572812 DOI: 10.1111/j.1747-0285.2010.01000.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This study aims at the identification of novel structural features on the surface of the Zn-dependent metalloprotease lethal factor (LF) from anthrax onto which to design novel and selective inhibitors. We report that by targeting an unexplored region of LF that exhibits ligand-induced conformational changes, we could obtain inhibitors with at least 30-fold LF selectivity compared to two other most related human metalloproteases, MMP-2 and MMP-9. Based on these results, we propose a novel pharmacophore model that, together with the preliminarily identified compounds, should help the design of more potent and selective inhibitors against anthrax.
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Affiliation(s)
- Hongbin Yuan
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
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27
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Agrawal A, Johnson SL, Jacobsen JA, Miller MT, Chen LH, Pellecchia M, Cohen SM. Chelator fragment libraries for targeting metalloproteinases. ChemMedChem 2010; 5:195-9. [PMID: 20058293 DOI: 10.1002/cmdc.200900516] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Arpita Agrawal
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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28
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Vovk MV, Pinchuk OM, Tolmachov AO, Gakh AA. Synthesis of 1-(4-trifluoromethoxyphenyl)-2,5-dimethyl-3-(2-R-thiazol-4-yl)-1H-pyrroles via chain heterocyclization. Molecules 2010; 15:997-1006. [PMID: 20335958 PMCID: PMC6263183 DOI: 10.3390/molecules15020997] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2009] [Revised: 02/22/2010] [Accepted: 02/22/2010] [Indexed: 11/17/2022] Open
Abstract
The title compounds, (4-trifluoromethoxyphenyl)-2,5-dimethyl-3-(2-R-thiazol-4-yl)-1H-pyrroles, were prepared in four steps starting from commercially available 4-trifluoromethoxyaniline. The pyrrole (second ring) was added in one step using the Paal-Knorr method. The thiazole (third ring) was added in three steps using chloroacylation with chloroacetonitrile followed by heterocyclization with thioamides/thioureas.
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Affiliation(s)
- Mykhaylo V. Vovk
- Institute of Organic Chemistry, NAS of Ukraine, Murmanska 5, 02094 Kyiv, Ukraine
- Authors to whom correspondence should be addressed; E-Mails: (M.V.V.); (A.A.G.)
| | - Oleksandr M. Pinchuk
- Institute of Organic Chemistry, NAS of Ukraine, Murmanska 5, 02094 Kyiv, Ukraine
| | | | - Andrei A. Gakh
- Oak Ridge National Laboratory, Oak Ridge, TN 37831-6242, USA
- Authors to whom correspondence should be addressed; E-Mails: (M.V.V.); (A.A.G.)
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29
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Chiu TL, Solberg J, Patil S, Geders TW, Zhang X, Rangarajan S, Francis R, Finzel BC, Walters MA, Hook DJ, Amin EA. Identification of novel non-hydroxamate anthrax toxin lethal factor inhibitors by topomeric searching, docking and scoring, and in vitro screening. J Chem Inf Model 2009; 49:2726-34. [PMID: 19928768 PMCID: PMC2805240 DOI: 10.1021/ci900186w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Anthrax is an infectious disease caused by Bacillus anthracis, a Gram-positive, rod-shaped, anaerobic bacterium. The lethal factor (LF) enzyme is secreted by B. anthracis as part of a tripartite exotoxin and is chiefly responsible for anthrax-related cytotoxicity. As LF can remain in the system long after antibiotics have eradicated B. anthracis from the body, the preferred therapeutic modality would be the administration of antibiotics together with an effective LF inhibitor. Although LF has garnered a great deal of attention as an attractive target for rational drug design, relatively few published inhibitors have demonstrated activity in cell-based assays and, to date, no LF inhibitor is available as a therapeutic or preventive agent. Here we present a novel in silico high-throughput virtual screening protocol that successfully identified 5 non-hydroxamic acid small molecules as new, preliminary LF inhibitor scaffolds with low micromolar inhibition against that target, resulting in a 12.8% experimental hit rate. This protocol screened approximately 35 million nonredundant compounds for potential activity against LF and comprised topomeric searching, docking and scoring, and drug-like filtering. Among these 5 hit compounds, none of which has previously been identified as a LF inhibitor, three exhibited experimental IC(50) values less than 100 microM. These three preliminary hits may potentially serve as scaffolds for lead optimization as well as templates for probe compounds to be used in mechanistic studies. Notably, our docking simulations predicted that these novel hits are likely to engage in critical ligand-receptor interactions with nearby residues in at least two of the three (S1', S1-S2, and S2') subsites in the LF substrate binding area. Further experimental characterization of these compounds is in process. We found that micromolar-level LF inhibition can be attained by compounds with non-hydroxamate zinc-binding groups that exhibit monodentate zinc chelation as long as key hydrophobic interactions with at least two LF subsites are retained.
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Affiliation(s)
- Ting-Lan Chiu
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Jonathan Solberg
- Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Satish Patil
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455-0431
| | - Todd W. Geders
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Xia Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Subhashree Rangarajan
- Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Rawle Francis
- Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Barry C. Finzel
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Michael A. Walters
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
- Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Derek J. Hook
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
- Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Elizabeth A. Amin
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
- Minnesota Supercomputing Institute for Advanced Computational Research, 117 Pleasant St. SE, Minneapolis, MN 55455
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30
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Bouzianas DG. Medical countermeasures to protect humans from anthrax bioterrorism. Trends Microbiol 2009; 17:522-8. [PMID: 19781945 DOI: 10.1016/j.tim.2009.08.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Revised: 07/25/2009] [Accepted: 08/24/2009] [Indexed: 12/27/2022]
Abstract
The deliberate dissemination of Bacillus anthracis spores via the US mail system in 2001 confirmed their potential use as a biological weapon for mass human casualties. This dramatically highlighted the need for specific medical countermeasures to enable the authorities to protect individuals from a future bioterrorism attack. Although vaccination appears to be the most effective and economical form of mass protection, current vaccines have significant drawbacks that justify the immense research effort to develop improved treatment modalities. After eight years and an expenditure of more than $50 billion, only marginal progress has been made in developing effective therapeutics. This article summarizes the most important medical countermeasures that have mostly been developed since the 2001 events, and highlights current problems and possible avenues for future research.
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Affiliation(s)
- Dimitrios G Bouzianas
- Technological Educational Institute of Thessaloniki, Department of Medical Laboratories, Laboratory of Immunology and Microbiology, PO Box 145-61, Thessaloniki 541-01, Macedonia, Greece.
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31
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Aiello D, Barnes MH, Biswas EE, Biswas SB, Gu S, Williams JD, Bowlin TL, Moir DT. Discovery, characterization and comparison of inhibitors of Bacillus anthracis and Staphylococcus aureus replicative DNA helicases. Bioorg Med Chem 2009; 17:4466-76. [PMID: 19477652 DOI: 10.1016/j.bmc.2009.05.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2008] [Revised: 05/01/2009] [Accepted: 05/07/2009] [Indexed: 12/19/2022]
Abstract
Antibacterial compounds with new mechanisms of action are needed for effective therapy against drug-resistant pathogens in the clinic and in biodefense. Screens for inhibitors of the essential replicative helicases of Bacillus anthracis and Staphylococcus aureus yielded 18 confirmed hits (IC(50)25 microM). Several (5 of 18) of the inhibitors were also shown to inhibit DNA replication in permeabilized polA-deficient B. anthracis cells. One of the most potent inhibitors also displayed antibacterial activity (MIC approximately 5 microg/ml against a range of Gram-positive species including bacilli and staphylococci) together with good selectivity for bacterial versus mammalian cells (CC(50)/MIC>16) suitable for further optimization. This compound shares the bicyclic ring of the clinically proven aminocoumarin scaffold, but is not a gyrase inhibitor. It exhibits a mixed mode of helicase inhibition including a component of competitive inhibition with the DNA substrate (K(i)=8 microM) and is rapidly bactericidal at 4 x MIC.
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32
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Johnson SL, Chen LH, Barille E, Emdadi A, Sabet M, Yuan H, Wei J, Guiney D, Pellecchia M. Structure-activity relationship studies of a novel series of anthrax lethal factor inhibitors. Bioorg Med Chem 2009; 17:3352-68. [PMID: 19359184 PMCID: PMC2730741 DOI: 10.1016/j.bmc.2009.03.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Revised: 03/13/2009] [Accepted: 03/20/2009] [Indexed: 10/21/2022]
Abstract
We report on the identification of a novel small molecule inhibitor of anthrax lethal factor using a high-throughput screening approach. Guided by molecular docking studies, we carried out structure-activity relationship (SAR) studies and evaluated activity and selectivity of most promising compounds in in vitro enzyme inhibition assays and cellular assays. Selected compounds were further analyzed for their in vitro ADME properties, which allowed us to select two compounds for further preliminary in vivo efficacy studies. The data provided represents the basis for further pharmacology and medicinal chemistry optimizations that could result in novel anti-anthrax therapies.
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Affiliation(s)
- Sherida L. Johnson
- Burnham Institute for Medical Research, Cancer Research Center and Infectious and Inflammatory Disease Center, 10901 North Torrey Pines Rd, La Jolla, CA 92037
| | - Li-Hsing Chen
- Burnham Institute for Medical Research, Cancer Research Center and Infectious and Inflammatory Disease Center, 10901 North Torrey Pines Rd, La Jolla, CA 92037
| | - Elisa Barille
- Burnham Institute for Medical Research, Cancer Research Center and Infectious and Inflammatory Disease Center, 10901 North Torrey Pines Rd, La Jolla, CA 92037
| | - Aras Emdadi
- Burnham Institute for Medical Research, Cancer Research Center and Infectious and Inflammatory Disease Center, 10901 North Torrey Pines Rd, La Jolla, CA 92037
| | - Mojgan Sabet
- Department of Medicine, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Hongbin Yuan
- Burnham Institute for Medical Research, Cancer Research Center and Infectious and Inflammatory Disease Center, 10901 North Torrey Pines Rd, La Jolla, CA 92037
| | - Jun Wei
- Burnham Institute for Medical Research, Cancer Research Center and Infectious and Inflammatory Disease Center, 10901 North Torrey Pines Rd, La Jolla, CA 92037
| | - Donald Guiney
- Department of Medicine, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Maurizio Pellecchia
- Burnham Institute for Medical Research, Cancer Research Center and Infectious and Inflammatory Disease Center, 10901 North Torrey Pines Rd, La Jolla, CA 92037
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33
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Agrawal A, de Oliveira CAF, Cheng Y, Jacobsen JA, McCammon JA, Cohen SM. Thioamide hydroxypyrothiones supersede amide hydroxypyrothiones in potency against anthrax lethal factor. J Med Chem 2009; 52:1063-74. [PMID: 19170530 PMCID: PMC2698031 DOI: 10.1021/jm8013212] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Anthrax lethal factor (LF) is a critical virulence factor in the pathogenesis of anthrax. A structure-activity relationship (SAR) of potential lethal factor inhibitors (LFi) is presented in which the zinc-binding group (ZBG), linker, and backbone moieties for a series of hydroxypyrone-based compounds were systematically varied. It was found that hydroxypyrothione ZBGs generate more potent inhibitors than hydroxypyrone ZBGs. Furthermore, coupling the hydroxypyrothione to a backbone group via a thioamide bond improves potency when compared to an amide linker. QM/MM studies show that the thioamide bond in these inhibitors allows for the formation of two additional hydrogen bonds with the protein active site. In both types of hydroxypyrothione compounds, ligand efficiencies of 0.29-0.54 kcal mol(-1) per heavy atom were achieved. The results highlight the need for a better understanding to optimize the interplay between the ZBG, linker, and backbone to get improved LFi.
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Affiliation(s)
- Arpita Agrawal
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
| | - César Augusto F. de Oliveira
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
- Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, Department of Pharmacology, University of California at San Diego, La Jolla, California 92093
| | - Yuhui Cheng
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
- Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, Department of Pharmacology, University of California at San Diego, La Jolla, California 92093
| | - Jennifer A. Jacobsen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
- Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, Department of Pharmacology, University of California at San Diego, La Jolla, California 92093
| | - Seth M. Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
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Zavodszky MI, Rohatgi A, Van Voorst JR, Yan H, Kuhn LA. Scoring ligand similarity in structure-based virtual screening. J Mol Recognit 2009; 22:280-92. [DOI: 10.1002/jmr.942] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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35
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Pogány P, Kovács A, Szécsényi KM, Leovac VM. FT-IR and theoretical study of 3,5-dimethyl-1H-pyrazole-1-carboxamidine (L) and the complexes CoL2(H2O)2(NO3)2, NiL2(H2O)2(NO3)2. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2008; 71:1466-1473. [PMID: 18562246 DOI: 10.1016/j.saa.2008.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Accepted: 05/05/2008] [Indexed: 05/26/2023]
Abstract
In the paper a joint experimental and theoretical study of 3,5-dimethyl-1H-pyrazole-1-carboxamidine (L) as well as its complexes CoL2(H2O)2(NO3)2 and NiL2(H2O)2(NO3)2 is reported. On the basis of FT-IR experiments and a DFT-derived scaled quantum mechanical force field the normal coordinate analysis of L was carried out. The FT-IR spectra of the two complexes were interpreted using the present assignment of L and computed vibrational data of the complexes. The ionic and charge transfer interactions in the complexes were assessed by means of natural bond orbital (NBO) analysis.
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Affiliation(s)
- Peter Pogány
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, H-1111 Budapest, Szt. Gellért tér 4, Hungary
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Gaddis BD, Rubert Pérez CM, Chmielewski J. Inhibitors of anthrax lethal factor based upon N-oleoyldopamine. Bioorg Med Chem Lett 2008; 18:2467-70. [DOI: 10.1016/j.bmcl.2008.02.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Revised: 02/12/2008] [Accepted: 02/14/2008] [Indexed: 11/30/2022]
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37
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Schepetkin IA, Khlebnikov AI, Quinn MT. N-Benzoylpyrazoles Are Novel Small-Molecule Inhibitors of Human Neutrophil Elastase. J Med Chem 2007; 50:4928-38. [PMID: 17850059 DOI: 10.1021/jm070600+] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human neutrophil elastase (NE) plays an important role in the pathogenesis of pulmonary disease. Using high-throughput chemolibrary screening, we identified 10 N-benzoylpyrazole derivatives that were potent NE inhibitors. Nine additional NE inhibitors were identified through further screening of N-benzoylpyrazole analogues. Evaluation of inhibitory activity against a range of proteases showed high specificity for NE, although several derivatives were also potent inhibitors of chymotrypsin. Analysis of reaction kinetics and inhibitor stability revealed that N-benzoylpyrazoles were pseudoirreversible competitive inhibitors of NE. Structure-activity relationship (SAR) analysis demonstrated that modification of N-benzoylpyrazole ring substituents modulated enzyme selectivity and potency. Furthermore, molecular modeling of the binding of selected active and inactive compounds to the NE active site revealed that active compounds fit well into the catalytic site, whereas inactive derivatives contained substituents or conformations that hindered binding or accessibility to the catalytic residues. Thus, N-benzoylpyrazole derivatives represent novel structural templates that can be utilized for further development of efficacious NE inhibitors.
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Affiliation(s)
- Igor A Schepetkin
- Department of Veterinary Molecular Biology, Montana State University, Bozeman, Montana 59717, USA
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38
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Gaddis BD, Avramova LV, Chmielewski J. Inhibitors of anthrax lethal factor. Bioorg Med Chem Lett 2007; 17:4575-8. [PMID: 17574849 DOI: 10.1016/j.bmcl.2007.05.089] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Revised: 05/24/2007] [Accepted: 05/30/2007] [Indexed: 10/23/2022]
Abstract
An inhibitor of anthrax lethal toxin mediated cell death (1) was identified by a medium throughput cell-based screen. This compound was determined to specifically inhibit anthrax lethal factor (LF), and subsequent SAR studies produced an even more potent inhibitor (4). Mechanistic studies identified these agents as uncompetitive inhibitors of LF with Ki values of 3.0 and 1.7 microM, respectively, with good cell potency and low cytotoxicity.
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Affiliation(s)
- Brandon D Gaddis
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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Kimura RH, Steenblock ER, Camarero JA. Development of a cell-based fluorescence resonance energy transfer reporter for Bacillus anthracis lethal factor protease. Anal Biochem 2007; 369:60-70. [PMID: 17586456 DOI: 10.1016/j.ab.2007.05.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2007] [Revised: 04/23/2007] [Accepted: 05/14/2007] [Indexed: 11/23/2022]
Abstract
We report the construction of a cell-based fluorescent reporter for anthrax lethal factor (LF) protease activity using the principle of fluorescence resonance energy transfer (FRET). This was accomplished by engineering an Escherichia coli cell line to express a genetically encoded FRET reporter and LF protease. Both proteins were encoded in two different expression plasmids under the control of different tightly controlled inducible promoters. The FRET-based reporter was designed to contain a LF recognition sequence flanked by the FRET pair formed by CyPet and YPet fluorescent proteins. The length of the linker between both fluorescent proteins was optimized using a flexible peptide linker containing several Gly-Gly-Ser repeats. Our results indicate that this FRET-based LF reporter was readily expressed in E. coli cells showing high levels of FRET in vivo in the absence of LF. The FRET signal, however, decreased five times after inducing LF expression in the same cell. These results suggest that this cell-based LF FRET reporter may be used to screen genetically encoded libraries in vivo against LF.
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Affiliation(s)
- Richard H Kimura
- Biosciences and Biotechnology Division, Livermore National Laboratory, University of California, Livermore, CA 94550, USA
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Kumar G, Parasuraman P, Sharma SK, Banerjee T, Karmodiya K, Surolia N, Surolia A. Discovery of a rhodanine class of compounds as inhibitors of Plasmodium falciparum enoyl-acyl carrier protein reductase. J Med Chem 2007; 50:2665-75. [PMID: 17477517 DOI: 10.1021/jm061257w] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enoyl acyl carrier protein (ACP) reductase, one of the enzymes of the type II fatty acid biosynthesis pathway, has been established as a promising target for the development of new drugs for malaria. Here we present the discovery of a rhodanine (2-thioxothiazolidin-4-one) class of compounds as inhibitors of this enzyme using a combined approach of rational selection of compounds for screening, analogue search, docking studies, and lead optimization. The most potent inhibitor exhibits an IC(50) of 35.6 nM against Plasmodium falciparum enoyl ACP reductase (PfENR) and inhibits growth of the parasite in red blood cell cultures at an IC(50) value of 750 nM. Many more compounds of this class were found to inhibit PfENR at low nanomolar to low micromolar concentrations, expanding the scope for developing new antimalarial drugs. The structure-activity relationship of these rhodanine compounds is discussed.
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Affiliation(s)
- Gyanendra Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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Johnson SL, Chen LH, Pellecchia M. A high-throughput screening approach to anthrax lethal factor inhibition. Bioorg Chem 2007; 35:306-12. [PMID: 17320146 PMCID: PMC2020844 DOI: 10.1016/j.bioorg.2006.12.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Revised: 12/27/2006] [Accepted: 12/29/2006] [Indexed: 11/22/2022]
Abstract
A high-throughput screening approach was used to identify new inhibitors of the metallo-protease lethal factor from Bacillus anthracis. A library of approximately 14,000 compounds was screened using a fluorescence-based in vitro assay and hits were further characterized enzymatically via measurements of IC50 and Ki values against a small panel of metallo-proteases. This study led to the identification of new scaffolds that inhibit LF and the Botulinum Neurotoxin Type A in the low micromolar range, while sparing the human metallo-proteases MMP-2 and MMP-9. Therefore, these scaffolds could be further exploited for the development of potent and selective anti-toxin agents.
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Affiliation(s)
| | | | - Maurizio Pellecchia
- * To whom correspondence should be addressed: Tel. 858.646.3159 Fax. 858.795.5225
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