1
|
Umehara E, Teixeira TR, Cajás RA, Amaro MC, de Moraes J, Lago JHG. EDBD-3,6-Epidioxy-1,10-Bisaboladiene-An Endoperoxide Sesquiterpene Obtained from Drimys brasiliensis (Winteraceae) Exhibited Potent Preclinical Efficacy against Schistosoma mansoni Infection. Antibiotics (Basel) 2024; 13:779. [PMID: 39200079 PMCID: PMC11350924 DOI: 10.3390/antibiotics13080779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/07/2024] [Accepted: 08/15/2024] [Indexed: 09/01/2024] Open
Abstract
Schistosomiasis, a neglected tropical disease impacting over 250 million individuals globally, remains a major public health challenge due to its prevalence and significant impact on affected communities. Praziquantel, the sole available treatment, highlights the urgency of the need for novel anthelmintic agents to achieve the World Health Organization (WHO) goal of schistosomiasis elimination. Previous studies reported the promising antiparasitic activity of different terpenoids against Schistosoma mansoni Sambon (Diplostomida: Schistosomatidae). In the present work, the hexane extract from branches of Drimys brasiliensis afforded a diastereomeric mixture of endoperoxide sesquiterpenes, including 3,6-epidioxy-bisabola-1,10-diene (EDBD). This compound was evaluated in vitro and in vivo against S. mansoni. EDBD exhibited a significant reduction in S. mansoni viability in vitro, with an effective concentration (EC50) value of 4.1 µM. Additionally, EDBD demonstrated no toxicity to mammalian cells. In silico analysis predicted good drug-likeness properties, adhering to pharmaceutical industry standards, including favorable ADME profiles. Furthermore, oral treatment of S. mansoni-infected mice with EDBD (400 mg/kg) resulted in a remarkable egg burden reduction (98% and 99% in tissues and feces, respectively) surpassing praziquantel's efficacy. These findings suggest the promising potential of EDBD as a lead molecule for developing a novel schistosomiasis treatment.
Collapse
Affiliation(s)
- Eric Umehara
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André 09280-560, SP, Brazil;
| | - Thainá R. Teixeira
- Centro de Pesquisas de Doenças Negligenciadas, Universidade Guarulhos, Guarulhos 07023-070, SP, Brazil; (T.R.T.); (M.C.A.)
| | - Rayssa A. Cajás
- Centro de Pesquisas de Doenças Negligenciadas, Universidade Guarulhos, Guarulhos 07023-070, SP, Brazil; (T.R.T.); (M.C.A.)
| | - Monique C. Amaro
- Centro de Pesquisas de Doenças Negligenciadas, Universidade Guarulhos, Guarulhos 07023-070, SP, Brazil; (T.R.T.); (M.C.A.)
| | - Josué de Moraes
- Centro de Pesquisas de Doenças Negligenciadas, Universidade Guarulhos, Guarulhos 07023-070, SP, Brazil; (T.R.T.); (M.C.A.)
- Núcleo de Pesquisas em Doenças Negligenciadas, Instituto Científico e Tecnológico, Universidade Brasil, São Paulo 08230-030, SP, Brazil
| | - João Henrique G. Lago
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André 09280-560, SP, Brazil;
| |
Collapse
|
2
|
Godinez-Macias KP, Winzeler EA. CACTI: an in silico chemical analysis tool through the integration of chemogenomic data and clustering analysis. J Cheminform 2024; 16:84. [PMID: 39049122 PMCID: PMC11270953 DOI: 10.1186/s13321-024-00885-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 07/14/2024] [Indexed: 07/27/2024] Open
Abstract
It is well-accepted that knowledge of a small molecule's target can accelerate optimization. Although chemogenomic databases are helpful resources for predicting or finding compound interaction partners, they tend to be limited and poorly annotated. Furthermore, unlike genes, compound identifiers are often not standardized, and many synonyms may exist, especially in the biological literature, making batch analysis of compounds difficult. Here, we constructed an open-source annotation and target hypothesis prediction tool that explores some of the largest chemical and biological databases, mining these for both common name, synonyms, and structurally similar molecules. We used this Chemical Analysis and Clustering for Target Identification (CACTI) tool to analyze the Pathogen Box collection, an open-source set of 400 drug-like compounds active against a variety of microbial pathogens. Our analysis resulted in 4,315 new synonyms, 35,963 pieces of new information and target prediction hints for 58 members.Scientific contributionsWith the employment of this tool, a comprehensive report with known evidence, close analogs and drug-target prediction can be obtained for large-scale chemical libraries that will facilitate their evaluation and future target validation and optimization efforts.
Collapse
Affiliation(s)
- Karla P Godinez-Macias
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA.
| |
Collapse
|
3
|
Moreira-Filho JT, Neves BJ, Cajas RA, Moraes JD, Andrade CH. Artificial intelligence-guided approach for efficient virtual screening of hits against Schistosoma mansoni. Future Med Chem 2023; 15:2033-2050. [PMID: 37937522 DOI: 10.4155/fmc-2023-0152] [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: 05/25/2023] [Accepted: 10/06/2023] [Indexed: 11/09/2023] Open
Abstract
Background: The impact of schistosomiasis, which affects over 230 million people, emphasizes the urgency of developing new antischistosomal drugs. Artificial intelligence is vital in accelerating the drug discovery process. Methodology & results: We developed classification and regression machine learning models to predict the schistosomicidal activity of compounds not experimentally tested. The prioritized compounds were tested on schistosomula and adult stages of Schistosoma mansoni. Four compounds demonstrated significant activity against schistosomula, with 50% effective concentration values ranging from 9.8 to 32.5 μM, while exhibiting no toxicity in animal and human cell lines. Conclusion: These findings represent a significant step forward in the discovery of antischistosomal drugs. Further optimization of these active compounds can pave the way for their progression into preclinical studies.
Collapse
Affiliation(s)
- José Teófilo Moreira-Filho
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, 74605-170, Brazil
| | - Bruno Junior Neves
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, 74605-170, Brazil
| | - Rayssa Araujo Cajas
- Research Center on Neglected Diseases (NPDN), Universidade Guarulhos, Guarulhos, 07023-070, Brazil
| | - Josué de Moraes
- Research Center on Neglected Diseases (NPDN), Universidade Guarulhos, Guarulhos, 07023-070, Brazil
| | - Carolina Horta Andrade
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, 74605-170, Brazil
- Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| |
Collapse
|
4
|
Rocha V, Cajas RA, Andrade-de-Siqueira AI, Almeida RBP, Godoy-Silva J, Gonçalves MM, Lago JHG, de Moraes J. Evaluating the Antischistosomal Activity of Dehydrodieugenol B and Its Methyl Ether Isolated from Nectandra leucantha-A Preclinical Study against Schistosoma mansoni Infection. ACS OMEGA 2023; 8:40890-40897. [PMID: 37929107 PMCID: PMC10620922 DOI: 10.1021/acsomega.3c06111] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/06/2023] [Indexed: 11/07/2023]
Abstract
Schistosomiasis, a parasitic disease affecting nearly 250 million individuals globally, poses a significant health challenge. With praziquantel being the sole available treatment and its limited efficacy in early stage infections, the identification of novel bioactive compounds becomes imperative. This study examines the potential of dehydrodieugenol B (1) and its methyl ether (2), derived from the leaves of the Brazilian Nectandra leucantha plant (Lauraceae), in combatting Schistosoma mansoni infections through a preclinical approach. Initially, compound 1 displayed noteworthy in vitro antiparasitic activity with an EC50 of 31.9 μM, showcasing low toxicity in mammalian cells and an in vivo animal model (Caenorhabditis elegans). Conversely, compound 2 exhibited no activity. In silico predictions pointed to favorable oral bioavailability and the absence of PAINS similarities. Subsequently, a single oral dose of 400 mg/kg of compound 1 or praziquantel was administered to mice infected with adult (patent infection) or immature parasites (prepatent infection). Remarkably, in prepatent infections, 1 resulted in a significant reduction (approximately 50%) in both worm and egg burden, while praziquantel reduced worm and egg numbers by 30%. The superior efficacy of dehydrodieugenol B (1) compared to praziquantel in premature infections holds the potential to advance the development of new molecular prototypes for schistosomiasis treatment.
Collapse
Affiliation(s)
- Vinicius
C. Rocha
- Instituto
de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema 09972-270, Brazil
| | - Rayssa A. Cajas
- Núcleo
de Pesquisa em Doenças Negligenciadas, Universidade Guarulhos, Guarulhos, São Paulo 07023-070, Brazil
| | | | - Roberto B. P. Almeida
- Departamento
de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Julia Godoy-Silva
- Núcleo
de Pesquisa em Doenças Negligenciadas, Universidade Guarulhos, Guarulhos, São Paulo 07023-070, Brazil
| | - Marina M. Gonçalves
- Centro
de Ciências Naturais e Humanas, Universidade
Federal do ABC, Santo
André, São Paulo 09210-180, Brazil
| | - João Henrique G. Lago
- Centro
de Ciências Naturais e Humanas, Universidade
Federal do ABC, Santo
André, São Paulo 09210-180, Brazil
| | - Josué de Moraes
- Núcleo
de Pesquisa em Doenças Negligenciadas, Universidade Guarulhos, Guarulhos, São Paulo 07023-070, Brazil
| |
Collapse
|
5
|
Padalino G, Coghlan A, Pagliuca G, Forde-Thomas JE, Berriman M, Hoffmann KF. Using ChEMBL to Complement Schistosome Drug Discovery. Pharmaceutics 2023; 15:1359. [PMID: 37242601 PMCID: PMC10220823 DOI: 10.3390/pharmaceutics15051359] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Schistosomiasis is one of the most important neglected tropical diseases. Until an effective vaccine is registered for use, the cornerstone of schistosomiasis control remains chemotherapy with praziquantel. The sustainability of this strategy is at substantial risk due to the possibility of praziquantel insensitive/resistant schistosomes developing. Considerable time and effort could be saved in the schistosome drug discovery pipeline if available functional genomics, bioinformatics, cheminformatics and phenotypic resources are systematically leveraged. Our approach, described here, outlines how schistosome-specific resources/methodologies, coupled to the open-access drug discovery database ChEMBL, can be cooperatively used to accelerate early-stage, schistosome drug discovery efforts. Our process identified seven compounds (fimepinostat, trichostatin A, NVP-BEP800, luminespib, epoxomicin, CGP60474 and staurosporine) with ex vivo anti-schistosomula potencies in the sub-micromolar range. Three of those compounds (epoxomicin, CGP60474 and staurosporine) also demonstrated potent and fast-acting ex vivo effects on adult schistosomes and completely inhibited egg production. ChEMBL toxicity data were also leveraged to provide further support for progressing CGP60474 (as well as luminespib and TAE684) as a novel anti-schistosomal compound. As very few compounds are currently at the advanced stages of the anti-schistosomal pipeline, our approaches highlight a strategy by which new chemical matter can be identified and quickly progressed through preclinical development.
Collapse
Affiliation(s)
- Gilda Padalino
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, King Edward VII Avenue, Cardiff CF10 3NB, UK
| | - Avril Coghlan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK;
| | | | | | - Matthew Berriman
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, 120 University Place, Glasgow G12 8TA, UK;
| | - Karl F. Hoffmann
- The Department of Life Sciences (DLS), Aberystwyth University, Aberystwyth SY23 3DA, UK;
| |
Collapse
|
6
|
Molecular Dynamic Analysis of Carbapenem-Resistant Klebsiella pneumonia’s Porin Proteins with Beta Lactam Antibiotics and Zinc Oxide Nanoparticles. Molecules 2023; 28:molecules28062510. [PMID: 36985482 PMCID: PMC10055515 DOI: 10.3390/molecules28062510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 03/12/2023] Open
Abstract
To prevent the rapidly increasing prevalence of bacterial resistance, it is crucial to discover new antibacterial agents. The emergence of Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae has been associated with a higher mortality rate in gulf union countries and worldwide. Compared to physical and chemical approaches, green zinc oxide nanoparticle (ZnO-NP) synthesis is thought to be significantly safer and more ecofriendly. The present study used molecular dynamics (MD) to examine how ZnO-NPs interact with porin protein (GLO21), a target of β-lactam antibiotics, and then tested this interaction in vitro by determining the zone of inhibition (IZ), minimum inhibitory concentration (MIC), and minimum bactericidal concentration (MBC), as well as the alteration of KPC’s cell surface. The nanoparticles produced were characterized by UV-Vis spectroscopy, zetasizer, Fourier-transform infrared spectroscopy (FTIR), and scanning electron microscopy (SEM). In silico investigation was conducted using a variety of computational techniques, including Autodock Vina for protein and ligand docking and Desmond for MD simulation. The candidate ligands that interact with the GLO21 protein were biosynthesized ZnO-NPs, meropenem, imipenem, and cefepime. Analysis of MD revealed that the ZnO-NPs had the highest log P value (−9.1 kcal/mol), which indicates higher permeability through the bacterial surface, followed by cefepime (−7.9 kcal/mol), meropenem (−7.5 kcal/mol), and imipenem (−6.4 kcal/mol). All tested compounds and ZnO-NPs possess similar binding sites of porin proteins. An MD simulation study showed a stable system for ZnO-NPs and cefepime, as confirmed by RMSD and RMSF values during 100 ns trajectories. The test compounds were further inspected for their intersection with porin in terms of hydrophobic, hydrogen, and ionic levels. In addition, the stability of these bonds were measured by observing the protein–ligand contact within 100 ns trajectories. ZnO-NPs showed promising results for fighting KPC, represented in MIC (0.2 mg/mL), MBC (0.5 mg/mL), and ZI (24 mm diameter). To draw the conclusion that ZnO-NP is a potent antibacterial agent and in order to identify potent antibacterial drugs that do not harm human cells, further in vivo studies are required.
Collapse
|
7
|
Dokla EME, Abutaleb NS, Milik SN, Kandil EAEA, Qassem OM, Elgammal Y, Nasr M, McPhillie MJ, Abouzid KAM, Seleem MN, Imming P, Adel M. SAR investigation and optimization of benzimidazole-based derivatives as antimicrobial agents against Gram-negative bacteria. Eur J Med Chem 2023; 247:115040. [PMID: 36584632 DOI: 10.1016/j.ejmech.2022.115040] [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: 09/09/2022] [Revised: 12/03/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Antibiotic-resistant bacteria represent a serious threat to modern medicine and human life. Only a minority of antibacterial agents are active against Gram-negative bacteria. Hence, the development of novel antimicrobial agents will always be a vital need. In an effort to discover new therapeutics against Gram-negative bacteria, we previously reported a structure-activity-relationship (SAR) study on 1,2-disubstituted benzimidazole derivatives. Compound III showed a potent activity against tolC-mutant Escherichia coli with an MIC value of 2 μg/mL, representing a promising lead for further optimization. Building upon this study, herein, 49 novel benzimidazole compounds were synthesized to investigate their antibacterial activity against Gram-negative bacteria. Our design focused on three main goals, to address the low permeability of our compounds and improve their cellular accumulation, to expand the SAR study to the unexplored ring C, and to optimize the lead compound (III) by modification of the methanesulfonamide moiety. Compounds (25a-d, 25f-h, 25k, 25l, 25p, 25r, 25s, and 26b) exhibited potent activity against tolC-mutant E. coli with MIC values ranging from 0.125 to 4 μg/mL, with compound 25d displaying the highest potency among the tested compounds with an MIC value of 0.125 μg/mL. As its predecessor, III, compound 25d exhibited an excellent safety profile without any significant cytotoxicity to mammalian cells. Time-kill kinetics assay indicated that 25d exhibited a bacteriostatic activity and significantly reduced E. coli JW55031 burden as compared to DMSO. Additionally, combination of 25d with colistin partially restored its antibacterial activity against Gram-negative bacterial strains (MIC values ranging from 4 to 16 μg/mL against E. coli BW25113, K. pneumoniae, A. baumannii, and P. aeruginosa). Furthermore, formulation of III and 25d as lipidic nanoparticles (nanocapsules) resulted in moderate enhancement of their antibacterial activity against Gram-negative bacterial strains (A. Baumannii, N. gonorrhoeae) and compound 25d demonstrated superior activity to the lead compound III. These findings establish compound 25d as a promising candidate for treatment of Gram-negative bacterial infections and emphasize the potential of nano-formulations in overcoming poor cellular accumulation in Gram-negative bacteria where further optimization and investigation are warranted to improve the potency and broaden the spectrum of our compounds.
Collapse
Affiliation(s)
- Eman M E Dokla
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo, 11566, Egypt; Institute für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, Halle (Saale), 06120, Germany.
| | - Nader S Abutaleb
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA; Department of Microbiology and Immunology, Zagazig University, Zagazig, 44519, Egypt
| | - Sandra N Milik
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo, 11566, Egypt; School of Chemistry, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Ezzat A E A Kandil
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo, 11566, Egypt
| | - Omar M Qassem
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo, 11566, Egypt; Purdue University Institute of Drug Discovery, Purdue University, West Lafayette, IN, 47907, USA
| | - Yehia Elgammal
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Maha Nasr
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo, 11566, Egypt
| | - Martin J McPhillie
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Khaled A M Abouzid
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo, 11566, Egypt
| | - Mohamed N Seleem
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA; Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Peter Imming
- Institute für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, Halle (Saale), 06120, Germany
| | - Mai Adel
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo, 11566, Egypt.
| |
Collapse
|
8
|
Zhu D, Johannsen S, Masini T, Simonin C, Haupenthal J, Illarionov B, Andreas A, Awale M, Gierse RM, van der Laan T, van der Vlag R, Nasti R, Poizat M, Buhler E, Reiling N, Müller R, Fischer M, Reymond JL, Hirsch AKH. Discovery of novel drug-like antitubercular hits targeting the MEP pathway enzyme DXPS by strategic application of ligand-based virtual screening. Chem Sci 2022; 13:10686-10698. [PMID: 36320685 PMCID: PMC9491098 DOI: 10.1039/d2sc02371g] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/07/2022] [Indexed: 12/04/2022] Open
Abstract
In the present manuscript, we describe how we successfully used ligand-based virtual screening (LBVS) to identify two small-molecule, drug-like hit classes with excellent ADMET profiles against the difficult to address microbial enzyme 1-deoxy-d-xylulose-5-phosphate synthase (DXPS). In the fight against antimicrobial resistance (AMR), it has become increasingly important to address novel targets such as DXPS, the first enzyme of the 2-C-methyl-d-erythritol-4-phosphate (MEP) pathway, which affords the universal isoprenoid precursors. This pathway is absent in humans but essential for pathogens such as Mycobacterium tuberculosis, making it a rich source of drug targets for the development of novel anti-infectives. Standard computer-aided drug-design tools, frequently applied in other areas of drug development, often fail for targets with large, hydrophilic binding sites such as DXPS. Therefore, we introduce the concept of pseudo-inhibitors, combining the benefits of pseudo-ligands (defining a pharmacophore) and pseudo-receptors (defining anchor points in the binding site), for providing the basis to perform a LBVS against M. tuberculosis DXPS. Starting from a diverse set of reference ligands showing weak inhibition of the orthologue from Deinococcus radiodurans DXPS, we identified three structurally unrelated classes with promising in vitro (against M. tuberculosis DXPS) and whole-cell activity including extensively drug-resistant strains of M. tuberculosis. The hits were validated to be specific inhibitors of DXPS and to have a unique mechanism of inhibition. Furthermore, two of the hits have a balanced profile in terms of metabolic and plasma stability and display a low frequency of resistance development, making them ideal starting points for hit-to-lead optimization of antibiotics with an unprecedented mode of action. We identified two drug-like antitubercular hits with submicromolar inhibition constants against the target 1-deoxy-d-xylulose-5-phosphate synthase (DXPS) with a new mode of action and promising activity against drug-resistant tuberculosis.![]()
Collapse
Affiliation(s)
- Di Zhu
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Sandra Johannsen
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1 66123 Saarbrücken Germany
| | - Tiziana Masini
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Céline Simonin
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1 66123 Saarbrücken Germany
| | - Boris Illarionov
- Hamburg School of Food Science, Institute of Food Chemistry Grindelallee 117 20146 Hamburg Germany
| | - Anastasia Andreas
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1 66123 Saarbrücken Germany
| | - Mahendra Awale
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Robin M Gierse
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Tridia van der Laan
- Department of Mycobacteria, National Institute of Public Health and the Environment (RIVM), Diagnostics and Laboratory Surveillance (IDS) Infectious Diseases Research Antonie van Leeuwenhoeklaan 9 3721 MA Bilthoven The Netherlands
| | - Ramon van der Vlag
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Rita Nasti
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Mael Poizat
- Symeres Kadijk 3 9747 AT Groningen The Netherlands
| | - Eric Buhler
- Laboratoire Matière et Systèmes Complexes (MSC), UMR CNRS 7057, Université Paris Cité Bâtiment Condorcet 75205 Paris Cedex 13 France
| | - Norbert Reiling
- RG Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center Borstel Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems Borstel Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1 66123 Saarbrücken Germany
- Helmholtz International Lab for Anti-infectives Campus Building E8.1 66123 Saarbrücken Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry Grindelallee 117 20146 Hamburg Germany
| | - Jean-Louis Reymond
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
- Helmholtz International Lab for Anti-infectives Campus Building E8.1 66123 Saarbrücken Germany
| |
Collapse
|
9
|
Novel antimicrobial ciprofloxacin-pyridinium quaternary ammonium salts with improved physicochemical properties and DNA gyrase inhibitory activity. Med Chem Res 2021. [DOI: 10.1007/s00044-021-02798-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
10
|
Deblais L, Rajashekara G. Compound Prioritization through Meta-Analysis Enhances the Discovery of Antimicrobial Hits against Bacterial Pathogens. Antibiotics (Basel) 2021; 10:antibiotics10091065. [PMID: 34572646 PMCID: PMC8471430 DOI: 10.3390/antibiotics10091065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022] Open
Abstract
The development of informatic tools to improve the identification of novel antimicrobials would significantly reduce the cost and time of drug discovery. We previously screened several plant (Xanthomonas sp., Clavibacter sp., Acidovorax sp., and Erwinia sp.), animal (Avian pathogenic Escherichia coli and Mycoplasma sp.), and human (Salmonella sp. and Campylobacter sp.) pathogens against a pre-selected small molecule library (n = 4182 SM) to identify novel SM (hits) that completely inhibited the bacterial growth or attenuated at least 75% of the virulence (quorum sensing or biofilm). Our meta-analysis of the primary screens (n = 11) using the pre-selected library (approx. 10.2 ± 9.3% hit rate per screen) demonstrated that the antimicrobial activity and spectrum of activity, and type of inhibition (growth versus virulence inhibitors) correlated with several physico-chemical properties (PCP; e.g., molecular weight, molar refraction, Zagreb group indexes, Kiers shape, lipophilicity, and hydrogen bond donors and acceptors). Based on these correlations, we build an in silico model that accurately classified 80.8% of the hits (n = 1676/2073). Therefore, the pre-selected SM library of 4182 SM was narrowed down to 1676 active SM with predictable PCP. Further, 926 hits affected only one species and 1254 hits were active against specific type of pathogens; however, no correlation was detected between PCP and the type of pathogen (29%, 34%, and 46% were specific for animal, human foodborne and plant pathogens, respectively). In conclusion, our in silico model allowed rational identification of SM with potential antimicrobial activity against bacterial pathogens. Therefore, the model developed in this study may facilitate future drug discovery efforts by accelerating the identification of uncharacterized antimicrobial molecules and predict their spectrum of activity.
Collapse
|
11
|
Synthesis of novel thiophene fused pyrazoline-thiocyanatoethanone derivative: Spectral, DFT, pharmacological, docking and in vitro antibacterial studies. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
12
|
Ma Z, Hu X, Li Y, Liang D, Dong Y, Wang B, Li W. Electrochemical oxidative synthesis of 1,3,4-thiadiazoles from isothiocyanates and hydrazones. Org Chem Front 2021. [DOI: 10.1039/d1qo00168j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A metal- and oxidant-free electrosynthesis of 2-amino-1,3,4-thiadiazoles through tandem addition/chemoselective C–S coupling.
Collapse
Affiliation(s)
- Zhongxiao Ma
- School of Chemistry and Chemical Engineering
- Kunming University
- Kunming 650214
- China
| | - Xiao Hu
- School of Chemistry and Chemical Engineering
- Kunming University
- Kunming 650214
- China
| | - Yanni Li
- School of Chemistry and Chemical Engineering
- Kunming University
- Kunming 650214
- China
| | - Deqiang Liang
- School of Chemistry and Chemical Engineering
- Kunming University
- Kunming 650214
- China
| | - Ying Dong
- College of Chemistry
- Chemical Engineering and Materials Science
- Shandong Normal University
- Jinan 250014
- China
| | - Baoling Wang
- School of Chemistry and Chemical Engineering
- Kunming University
- Kunming 650214
- China
| | - Weili Li
- School of Chemistry and Chemical Engineering
- Kunming University
- Kunming 650214
- China
| |
Collapse
|
13
|
Fullam E, Young RJ. Physicochemical properties and Mycobacterium tuberculosis transporters: keys to efficacious antitubercular drugs? RSC Med Chem 2020; 12:43-56. [PMID: 34041481 PMCID: PMC8130550 DOI: 10.1039/d0md00265h] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/15/2020] [Indexed: 12/14/2022] Open
Abstract
Securing novel, safe, and effective medicines to treat Mycobacterium tuberculosis remains an elusive goal, particularly influenced by the largely impervious Mtb envelope that limits exposure and thus efficacy of inhibitors at their cellular and periplasmic targets. The impact of physicochemical properties on pharmacokinetic parameters that govern oral absorption and exposure at sites of infection is considered alongside how these properties influence penetration of the Mtb envelope, with the likely influence of transporter proteins. The findings are discussed to benchmark current drugs and the emerging pipeline, whilst considering tactics for future rational and targeted design strategies, based around emerging data on Mtb transporters and their structures and functions.
Collapse
Affiliation(s)
- Elizabeth Fullam
- School of Life Sciences, University of Warwick Coventry CV4 7AL UK
| | | |
Collapse
|
14
|
Jian Y, Merceron R, De Munck S, Forbes HE, Hulpia F, Risseeuw MDP, Van Hecke K, Savvides SN, Munier-Lehmann H, Boshoff HIM, Van Calenbergh S. Endeavors towards transformation of M. tuberculosis thymidylate kinase (MtbTMPK) inhibitors into potential antimycobacterial agents. Eur J Med Chem 2020; 206:112659. [PMID: 32823003 PMCID: PMC11000207 DOI: 10.1016/j.ejmech.2020.112659] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/08/2020] [Accepted: 07/08/2020] [Indexed: 01/30/2023]
Abstract
As the last enzyme in nucleotide synthesis as precursors for DNA replication, thymidylate kinase of M. tuberculosis (MtbTMPK) attracts significant interest as a target in the discovery of new anti-tuberculosis agents. Earlier, we discovered potent MtbTMPK inhibitors, but these generally suffered from poor antimycobacterial activity, which we hypothesize is due to poor bacterial uptake. To address this, we herein describe our efforts to equip previously reported MtbTMPK inhibitors with targeting moieties to increase the whole cell activity of the hybrid analogues. Introduction of a simplified Fe-chelating siderophore motif gave rise to analogue 17 that combined favorable enzyme inhibitory activity with significant activity against M. tuberculosis (MIC of 12.5 μM). Conjugation of MtbTMPK inhibitors with an imidazo[1,2-a]pyridine or 3,5-dinitrobenzamide scaffold afforded analogues 26, 27 and 28, with moderate MtbTMPK enzyme inhibitory potency, but sub-micromolar activity against mycobacteria without significant cytotoxicity. These results indicate that conjugation with structural motifs known to favor mycobacterial uptake may be a valid approach for discovering new antimycobacterial agents.
Collapse
Affiliation(s)
- Yanlin Jian
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Ottergemsesteenweg 460, B-9000, Ghent, Belgium
| | - Romain Merceron
- VIB Center for Inflammation Research, Zwijnaarde, Ghent, 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent, 9052, Belgium
| | - Steven De Munck
- VIB Center for Inflammation Research, Zwijnaarde, Ghent, 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent, 9052, Belgium
| | - He Eun Forbes
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, United States
| | - Fabian Hulpia
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Ottergemsesteenweg 460, B-9000, Ghent, Belgium
| | - Martijn D P Risseeuw
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Ottergemsesteenweg 460, B-9000, Ghent, Belgium
| | - Kristof Van Hecke
- XStruct, Department of Chemistry, Ghent University, Krijgslaan 281 S3, Gent, B-9000, Belgium
| | - Savvas N Savvides
- VIB Center for Inflammation Research, Zwijnaarde, Ghent, 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent, 9052, Belgium
| | - Hélène Munier-Lehmann
- Unit of Chemistry and Biocatalysis, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28 Rue du Dr. Roux, Cedex, 15 75724, Paris, France
| | - Helena I M Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, United States
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Ottergemsesteenweg 460, B-9000, Ghent, Belgium.
| |
Collapse
|
15
|
McDowell LL, Quinn CL, Leeds JA, Silverman JA, Silver LL. Perspective on Antibacterial Lead Identification Challenges and the Role of Hypothesis-Driven Strategies. SLAS DISCOVERY 2020; 24:440-456. [PMID: 30890054 DOI: 10.1177/2472555218818786] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
For the past three decades, the pharmaceutical industry has undertaken many diverse approaches to discover novel antibiotics, with limited success. We have witnessed and personally experienced many mistakes, hurdles, and dead ends that have derailed projects and discouraged scientists and business leaders. Of the many factors that affect the outcomes of screening campaigns, a lack of understanding of the properties that drive efflux and permeability requirements across species has been a major barrier for advancing hits to leads. Hits that possess bacterial spectrum have seldom also possessed druglike properties required for developability and safety. Persistence in solving these two key barriers is necessary for the reinvestment into discovering antibacterial agents. This perspective narrates our experience in antibacterial discovery-our lessons learned about antibacterial challenges as well as best practices for screening strategies. One of the tenets that guides us is that drug discovery is a hypothesis-driven science. Application of this principle, at all steps in the antibacterial discovery process, should improve decision making and possibly the odds of what has become, in recent decades, an increasingly challenging endeavor with dwindling success rates.
Collapse
Affiliation(s)
- Laura L McDowell
- 1 Novartis Institutes for Biomedical Research, Emeryville, CA, USA
| | | | - Jennifer A Leeds
- 1 Novartis Institutes for Biomedical Research, Emeryville, CA, USA
| | | | | |
Collapse
|
16
|
De Rycker M, Horn D, Aldridge B, Amewu RK, Barry CE, Buckner FS, Cook S, Ferguson MAJ, Gobeau N, Herrmann J, Herrling P, Hope W, Keiser J, Lafuente-Monasterio MJ, Leeson PD, Leroy D, Manjunatha UH, McCarthy J, Miles TJ, Mizrahi V, Moshynets O, Niles J, Overington JP, Pottage J, Rao SPS, Read KD, Ribeiro I, Silver LL, Southern J, Spangenberg T, Sundar S, Taylor C, Van Voorhis W, White NJ, Wyllie S, Wyatt PG, Gilbert IH. Setting Our Sights on Infectious Diseases. ACS Infect Dis 2020; 6:3-13. [PMID: 31808676 PMCID: PMC6958537 DOI: 10.1021/acsinfecdis.9b00371] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In
May 2019, the Wellcome Centre for Anti-Infectives Research (WCAIR) at the University of Dundee, UK, held an international
conference with the aim of discussing some key questions around discovering
new medicines for infectious diseases and a particular focus on diseases
affecting Low and Middle Income Countries. There is an urgent need
for new drugs to treat most infectious diseases. We were keen to see
if there were lessons that we could learn across different disease
areas and between the preclinical and clinical phases with the aim
of exploring how we can improve and speed up the drug discovery, translational,
and clinical development processes. We started with an introductory
session on the current situation and then worked backward from clinical
development to combination therapy, pharmacokinetic/pharmacodynamic
(PK/PD) studies, drug discovery pathways, and new starting points
and targets. This Viewpoint aims to capture some of the learnings.
Collapse
Affiliation(s)
- Manu De Rycker
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - David Horn
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Bree Aldridge
- Tufts University School of Medicine, 136 Harrison Avenue, Boston, Massachusetts 02111, United States
| | - Richard K. Amewu
- Department of Chemistry, University of Ghana, P.O. Box LG56, Legon, Accra, Ghana
| | - Clifton E. Barry
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Frederick S. Buckner
- Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, MS 358061, 750 Republican Street, Rm E-606, Seattle, Washington 98109-4766, United States
| | - Sarah Cook
- School of Humanities, University of Glasgow, 1 University Gardens, Glasgow G12 8QQ, United Kingdom
| | - Michael A. J. Ferguson
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Nathalie Gobeau
- Medicines for Malaria Venture (MMV), PO Box 1826, 20 Route de Pré-Bois, 1215 Geneva 15, Switzerland
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland, Department Microbial Natural Products, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Centre for Infection Research, partner
site Hannover-Braunschweig, Germany
| | | | - William Hope
- Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - Jennifer Keiser
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, CH-4051 Basel, Switzerland
- University of Basel, CH-4001 Basel, Switzerland
| | | | | | - Didier Leroy
- Medicines for Malaria Venture (MMV), PO Box 1826, 20 Route de Pré-Bois, 1215 Geneva 15, Switzerland
| | - Ujjini H. Manjunatha
- Novartis Institute for Tropical Diseases (NITD), Novartis Institutes for BioMedical Research (NIBR), 5300 Chiron Way, Emeryville, California 94608, United States
| | - James McCarthy
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Hertson, Queensland 4006, Australia
| | - Timothy J. Miles
- Tres Cantos Medicines Development Campus, Diseases of the Developing World (DDW), GlaxoSmithKline, Tres Cantos, Spain
| | - Valerie Mizrahi
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine and Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town, Observatory, Cape Town 7925, South Africa
| | - Olena Moshynets
- Biofilm Study Group, Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, 150 Zabolotnoho Street, Kiev 03143, Ukraine
| | - Jacquin Niles
- School of Engineering, Massachusetts Institute of Technology, Building 1-206, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, United States
| | - John P. Overington
- Medicines Discovery Catapult, Alderley
Park, Alderley Edge, Cheshire SK10 4TG, United Kingdom
| | - John Pottage
- ViiV Healthcare, 980 Great West Road, Brentford, Middlesex TW8 9GS, United Kingdom
| | - Srinivasa P. S. Rao
- Novartis Institute for Tropical Diseases (NITD), Novartis Institutes for BioMedical Research (NIBR), 5300 Chiron Way, Emeryville, California 94608, United States
| | - Kevin D. Read
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Isabela Ribeiro
- Drugs for Neglected Diseases Initiative (DNDi), Chemin Louis-Dunant 15, 1202 Genève, Switzerland
| | | | - Jen Southern
- Lancaster Institute for the Contemporary Arts (LICA), The LICA Building, Lancaster University, Lancaster LA1 4YW, United Kingdom
| | - Thomas Spangenberg
- Global Health Institute of Merck, Ares Trading S.A., a subsidiary
of Merck KGaA Darmstadt Germany, Route de Crassier 1, 1262 Eysins, Switzerland
| | - Shyam Sundar
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Caitlin Taylor
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine and Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town, Observatory, Cape Town 7925, South Africa
| | - Wes Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, MS 358061, 750 Republican Street, Rm E-606, Seattle, Washington 98109-4766, United States
| | - Nicholas J. White
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, 3/F, 60th Anniversary Chalermprakiat Building, 420/6 Rajvithi Road, Bangkok 10400, Thailand
| | - Susan Wyllie
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Paul G. Wyatt
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Ian H. Gilbert
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| |
Collapse
|
17
|
Lim AT, Vincent IM, Barrett MP, Gilbert IH. Small Polar Hits against S. aureus: Screening, Initial Hit Optimization, and Metabolomic Studies. ACS OMEGA 2019; 4:19199-19215. [PMID: 31763544 PMCID: PMC6869403 DOI: 10.1021/acsomega.9b02507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/03/2019] [Indexed: 06/10/2023]
Abstract
The global prevalence of antibacterial resistance requires new antibacterial drugs with novel chemical scaffolds and modes of action. It is also vital to design compounds with optimal physicochemical properties to permeate the bacterial cell envelope. We described an approach of combining and integrating whole cell screening and metabolomics into early antibacterial drug discovery using a library of small polar compounds. Whole cell screening of a diverse library of small polar compounds against Staphylococcus aureus gave compound 2. Hit expansion was carried out to determine structure-activity relationships. A selection of compounds from this series, together with other screened active compounds, was subjected to an initial metabolomics study to provide a metabolic fingerprint of the mode of action. It was found that compound 2 and its analogues have a different mode of action from some of the known antibacterial compounds tested. This early study highlighted the potential of whole cell screening and metabolomics in early antibacterial drug discovery. Future works will require improving potency and performing orthogonal studies to confirm the modes of action.
Collapse
Affiliation(s)
- Andrew
S. T. Lim
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, U.K.
| | - Isabel M. Vincent
- Glasgow
Polyomics, University of Glasgow, Wolfson
Wohl Cancer Research Centre, Garscube Campus, Bearsden G61 1QH, U.K.
| | - Michael P. Barrett
- Glasgow
Polyomics, University of Glasgow, Wolfson
Wohl Cancer Research Centre, Garscube Campus, Bearsden G61 1QH, U.K.
- Wellcome
Centre for Molecular Parasitology, Institute of Infection, Immunity
and Inflammation, University of Glasgow, Glasgow G12 8TA, U.K.
| | - Ian H. Gilbert
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, U.K.
| |
Collapse
|
18
|
Synthesis and Biological Evaluation of Lipophilic Nucleoside Analogues as Inhibitors of Aminoacyl-tRNA Synthetases. Antibiotics (Basel) 2019; 8:antibiotics8040180. [PMID: 31600972 PMCID: PMC6963541 DOI: 10.3390/antibiotics8040180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/02/2019] [Accepted: 10/04/2019] [Indexed: 11/16/2022] Open
Abstract
Emerging antibiotic resistance in pathogenic bacteria and reduction of compounds in the existing antibiotics discovery pipeline is the most critical concern for healthcare professionals. A potential solution aims to explore new or existing targets/compounds. Inhibition of bacterial aminoacyl-tRNA synthetase (aaRSs) could be one such target for the development of antibiotics. The aaRSs are a group of enzymes that catalyze the transfer of an amino acid to their cognate tRNA and therefore play a pivotal role in translation. Thus, selective inhibition of these enzymes could be detrimental to microbes. The 5′-O-(N-(L-aminoacyl)) sulfamoyladenosines (aaSAs) are potent inhibitors of the respective aaRSs, however due to their polarity and charged nature they cannot cross the bacterial membranes. In this work, we increased the lipophilicity of these existing aaSAs in an effort to promote their penetration through the bacterial membrane. Two strategies were followed, either attaching a (permanent) alkyl moiety at the adenine ring via alkylation of the N6-position or introducing a lipophilic biodegradable prodrug moiety at the alpha-terminal amine, totaling eight new aaSA analogues. All synthesized compounds were evaluated in vitro using either a purified Escherichiacoli aaRS enzyme or in presence of total cellular extract obtained from E. coli. The prodrugs showed comparable inhibitory activity to the parent aaSA analogues, indicating metabolic activation in cellular extracts, but had little effect on bacteria. During evaluation of the N6-alkylated compounds against different microbes, the N6-octyl containing congener 6b showed minimum inhibitory concentration (MIC) of 12.5 µM against Sarcina lutea while the dodecyl analogue 6c displayed MIC of 6.25 µM against Candidaalbicans.
Collapse
|
19
|
Andrews LD, Kane TR, Dozzo P, Haglund CM, Hilderbrandt DJ, Linsell MS, Machajewski T, McEnroe G, Serio AW, Wlasichuk KB, Neau DB, Pakhomova S, Waldrop GL, Sharp M, Pogliano J, Cirz RT, Cohen F. Optimization and Mechanistic Characterization of Pyridopyrimidine Inhibitors of Bacterial Biotin Carboxylase. J Med Chem 2019; 62:7489-7505. [PMID: 31306011 DOI: 10.1021/acs.jmedchem.9b00625] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A major challenge for new antibiotic discovery is predicting the physicochemical properties that enable small molecules to permeate Gram-negative bacterial membranes. We have applied physicochemical lessons from previous work to redesign and improve the antibacterial potency of pyridopyrimidine inhibitors of biotin carboxylase (BC) by up to 64-fold and 16-fold against Escherichia coli and Pseudomonas aeruginosa, respectively. Antibacterial and enzyme potency assessments in the presence of an outer membrane-permeabilizing agent or in efflux-compromised strains indicate that penetration and efflux properties of many redesigned BC inhibitors could be improved to various extents. Spontaneous resistance to the improved pyridopyrimidine inhibitors in P. aeruginosa occurs at very low frequencies between 10-8 and 10-9. However, resistant isolates had alarmingly high minimum inhibitory concentration shifts (16- to >128-fold) compared to the parent strain. Whole-genome sequencing of resistant isolates revealed that either BC target mutations or efflux pump overexpression can lead to the development of high-level resistance.
Collapse
Affiliation(s)
- Logan D Andrews
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Timothy R Kane
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Paola Dozzo
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Cat M Haglund
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Darin J Hilderbrandt
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Martin S Linsell
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Timothy Machajewski
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Glen McEnroe
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Alisa W Serio
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Kenneth B Wlasichuk
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - David B Neau
- Northeastern Collaborative Access Team , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Svetlana Pakhomova
- Department of Biological Sciences , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Grover L Waldrop
- Department of Biological Sciences , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Marc Sharp
- Linnaeus Bioscience Inc. , 3210 Merryfield Row , San Diego , California 92121 , United States
| | - Joe Pogliano
- Linnaeus Bioscience Inc. , 3210 Merryfield Row , San Diego , California 92121 , United States.,University of California, San Diego , 9500 Gilman Drive , La Jolla, San Diego , California 92093 , United States
| | - Ryan T Cirz
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Frederick Cohen
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| |
Collapse
|
20
|
Panduwawala TD, Iqbal S, Thompson AL, Genov M, Pretsch A, Pretsch D, Liu S, Ebright RH, Howells A, Maxwell A, Moloney MG. Functionalised bicyclic tetramates derived from cysteine as antibacterial agents. Org Biomol Chem 2019; 17:5615-5632. [PMID: 31120090 PMCID: PMC6686852 DOI: 10.1039/c9ob01076a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Routes to bicyclic tetramates derived from cysteine permitting ready incorporation of functionality at two different points around the periphery of a heterocyclic skeleton are reported. This has enabled the identification of systems active against Gram-positive bacteria, some of which show gyrase and RNA polymerase inhibitory activity. In particular, tetramates substituted with glycosyl side chains, chosen to impart polarity and aqueous solubility, show high antibacterial activity coupled with modest gyrase/polymerase activity in two cases. An analysis of physicochemical properties indicates that the antibacterially active tetramates generally occupy physicochemical space with MW of 300-600, clog D7.4 of -2.5 to 4 and rel. PSA of 11-22%. This work demonstrates that biologically active 3D libraries are readily available by manipulation of a tetramate skeleton.
Collapse
Affiliation(s)
- Tharindi D Panduwawala
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, UK.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Exploring the Chemical Space of Cytochrome P450 Inhibitors Using Integrated Physicochemical Parameters, Drug Efficiency Metrics and Decision Tree Models. COMPUTATION 2019. [DOI: 10.3390/computation7020026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The cytochrome P450s (CYPs) play a central role in the metabolism of various endogenous and exogenous compounds including drugs. CYPs are vulnerable to inhibition and induction which can lead to adverse drug reactions. Therefore, insights into the underlying mechanism of CYP450 inhibition and the estimation of overall CYP inhibitor properties might serve as valuable tools during the early phases of drug discovery. Herein, we present a large data set of inhibitors against five major metabolic CYPs (CYP1A2, CYP2C9, CYP2C19, CYP2D6 and CYP3A4) for the evaluation of important physicochemical properties and ligand efficiency metrics to define property trends across various activity levels (active, efficient and inactive). Decision tree models for CYP inhibition were developed with an accuracy >90% for both the training set and 10-folds cross validation. Overall, molecular weight (MW), hydrogen bond acceptors/donors (HBA/HBD) and lipophilicity (clogP/logPo/w) represent important physicochemical descriptors for CYP450 inhibitors. However, highly efficient CYP inhibitors show mean MW, HBA, HBD and logP values between 294.18–482.40,5.0–8.2,1–7.29 and 1.68–2.57, respectively. Our results might help in optimization of toxicological profiles associated with new chemical entities (NCEs), through a better understanding of inhibitor properties leading to CYP-mediated interactions.
Collapse
|
22
|
Synthesis, spectral characterization, docking studies and biological activity of urea, thiourea, sulfonamide and carbamate derivatives of imatinib intermediate. Mol Divers 2018; 23:723-738. [DOI: 10.1007/s11030-018-9906-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/11/2018] [Indexed: 10/27/2022]
|
23
|
Dougan G, Dowson C, Overington J. Meeting the discovery challenge of drug-resistant infections: progress and focusing resources. Drug Discov Today 2018; 24:452-461. [PMID: 30476550 DOI: 10.1016/j.drudis.2018.11.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/12/2018] [Accepted: 11/20/2018] [Indexed: 01/10/2023]
Abstract
Following multiple warnings from governments and health organisations, there has been renewed investment, led by the public sector, in the discovery of novel antimicrobials to meet the challenge of rising levels of drug-resistant infection, particularly in the case of resistance to antibiotics. Initiatives have also been announced to support and enable the antibiotic discovery process. In January 2018, the Medicines Discovery Catapult, UK, hosted a symposium: Next Generation Antibiotics Discovery, to consider the latest initiatives and any remaining challenges to inform and guide the international research community and better focus resources to yield a novel class of antibiotic.
Collapse
Affiliation(s)
- Gordon Dougan
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK; The Department of Medicine, University of Cambridge, UK.
| | | | - John Overington
- Medicine Discovery Catapult, Mereside, Alderly Park, Alderly Edge, Cheshire, UK
| | | |
Collapse
|
24
|
Wlodarchak N, Teachout N, Beczkiewicz J, Procknow R, Schaenzer AJ, Satyshur K, Pavelka M, Zuercher W, Drewry D, Sauer JD, Striker R. In Silico Screen and Structural Analysis Identifies Bacterial Kinase Inhibitors which Act with β-Lactams To Inhibit Mycobacterial Growth. Mol Pharm 2018; 15:5410-5426. [PMID: 30285456 PMCID: PMC6648700 DOI: 10.1021/acs.molpharmaceut.8b00905] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
New tools and concepts are needed to combat antimicrobial resistance. Actinomycetes and firmicutes share several eukaryotic-like Ser/Thr kinases (eSTK) that offer antibiotic development opportunities, including PknB, an essential mycobacterial eSTK. Despite successful development of potent biochemical PknB inhibitors by many groups, clinically useful microbiologic activity has been elusive. Additionally, PknB kinetics are not fully described, nor are structures with specific inhibitors available to inform inhibitor design. We used computational modeling with available structural information to identify human kinase inhibitors predicted to bind PknB, and we selected hits based on drug-like characteristics intended to increase the likelihood of cell entry. The computational model suggested a family of inhibitors, the imidazopyridine aminofurazans (IPAs), bind PknB with high affinity. We performed an in-depth characterization of PknB and found that these inhibitors biochemically inhibit PknB, with potency roughly following the predicted models. A novel X-ray structure confirmed that the inhibitors bound as predicted and made favorable protein contacts with the target. These inhibitors also have antimicrobial activity toward mycobacteria and nocardia. We demonstrated that the inhibitors are uniquely potentiated by β-lactams but not antibiotics traditionally used to treat mycobacteria, consistent with PknB's role in sensing cell wall stress. This is the first demonstration in the phylum actinobacteria that some β-lactam antibiotics could be more effective if paired with a PknB inhibitor. Collectively, our data show that in silico modeling can be used as a tool to discover promising drug leads, and the inhibitors we discovered can act with clinically relevant antibiotics to restore their efficacy against bacteria with limited treatment options.
Collapse
Affiliation(s)
- Nathan Wlodarchak
- Department of Medicine, University of Wisconsin-Madison, 3341 Microbial Sciences Building, 1550 Linden Dr., Madison, WI 53706
| | - Nathan Teachout
- Department of Medicine, University of Wisconsin-Madison, 3341 Microbial Sciences Building, 1550 Linden Dr., Madison, WI 53706
| | - Jeffrey Beczkiewicz
- Department of Medicine, University of Wisconsin-Madison, 3341 Microbial Sciences Building, 1550 Linden Dr., Madison, WI 53706
| | - Rebecca Procknow
- Department of Medicine, University of Wisconsin-Madison, 3341 Microbial Sciences Building, 1550 Linden Dr., Madison, WI 53706
| | - Adam J. Schaenzer
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, 4203 Microbial Sciences Building, 1550 Linden Dr., Madison, WI 53706
| | - Kenneth Satyshur
- Small Molecule Screening Facility, Carbone Cancer Center, University of Wisconsin-Madison, 1111Highland Ave., Madison, WI 53705
| | - Martin Pavelka
- School of Medicine and Dentistry, University of Rochester Medical Center, 601 Elmwood Ave., Rochester, NY 14620
| | - William Zuercher
- Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, SGC Center for Chemical Biology, 120 Mason Farm Rd., Chapel Hill, NC 27599
| | - David Drewry
- Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, SGC Center for Chemical Biology, 120 Mason Farm Rd., Chapel Hill, NC 27599
| | - John-Demian Sauer
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, 4203 Microbial Sciences Building, 1550 Linden Dr., Madison, WI 53706
| | - Rob Striker
- Department of Medicine, University of Wisconsin-Madison, 3341 Microbial Sciences Building, 1550 Linden Dr., Madison, WI 53706,William S. Middleton Memorial Veterans Hospital, 2500 Overlook Terr., Madison, WI 53705,To whom correspondence should be addressed Rob Striker, Department of Medicine, University of Wisconsin-Madison, 3301 Microbial Sciences Building, 1550 Linden Dr., Madison, WI 53706, 608-263-2994,
| |
Collapse
|
25
|
Ullah A, Iftikhar F, Arfan M, Batool Kazmi ST, Anjum MN, Haq IU, Ayaz M, Farooq S, Rashid U. Amino acid conjugated antimicrobial drugs: Synthesis, lipophilicity- activity relationship, antibacterial and urease inhibition activity. Eur J Med Chem 2018; 145:140-153. [DOI: 10.1016/j.ejmech.2017.12.089] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/14/2017] [Accepted: 12/27/2017] [Indexed: 11/28/2022]
|
26
|
Malhotra S, Mugumbate G, Blundell TL, Higueruelo AP. TIBLE: a web-based, freely accessible resource for small-molecule binding data for mycobacterial species. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2017:3866794. [PMID: 29220433 PMCID: PMC5502366 DOI: 10.1093/database/bax041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/25/2017] [Indexed: 02/03/2023]
Abstract
Database URL http://www-cryst.bioc.cam.ac.uk/tible/.
Collapse
Affiliation(s)
- Sony Malhotra
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Grace Mugumbate
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Alicia P Higueruelo
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| |
Collapse
|
27
|
Abstract
Natural products (NPs) have been used as traditional medicines since antiquity. With more than 1060 estimated compounds with molecular weights less than 500 Da representing chemical space, NPs occupy a very small percentage; however, they are significantly overrepresented in biologically relevant chemical space. The classical approach concentrates on identifying one or more NPs with biological activity from a source organism. There is much more to be learned from NPs than we can discover this narrow view. In this review, we discuss ways to harness the global properties of NPs.
Collapse
Affiliation(s)
- Asmaa Boufridi
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; ,
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; ,
| |
Collapse
|
28
|
McKerrow JH, Lipinski CA. The rule of five should not impede anti-parasitic drug development. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2017. [PMID: 28623818 PMCID: PMC5473536 DOI: 10.1016/j.ijpddr.2017.05.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The “rule of 5” has become a mainstay of decision-making in the pharmaceutical industry as well as in nonindustrial (academic and institutional) drug development. However the authors of the original paper never intended for “double cutoffs” to preclude development of new drug leads for parasitic diseases. “rule of 5” is a mainstay of decision-making in drug screening efforts. Acts as an absorption-permeability alert procedure to guide medicinal chemists. Never intended to apply to parasitic infectious diseases. Should not impede anti-parasitic drug development.
Collapse
Affiliation(s)
- James H McKerrow
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, United States.
| | - Christopher A Lipinski
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, United States
| |
Collapse
|
29
|
Structure-Based Discovery of Small Molecules Binding to RNA. TOPICS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1007/7355_2016_29] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
30
|
Moloney MG. Natural Products as a Source for Novel Antibiotics. Trends Pharmacol Sci 2016; 37:689-701. [DOI: 10.1016/j.tips.2016.05.001] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/02/2016] [Accepted: 05/02/2016] [Indexed: 01/04/2023]
|
31
|
Ebejer JP, Charlton MH, Finn PW. Are the physicochemical properties of antibacterial compounds really different from other drugs? J Cheminform 2016; 8:30. [PMID: 27274770 PMCID: PMC4891840 DOI: 10.1186/s13321-016-0143-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/25/2016] [Indexed: 01/12/2023] Open
Abstract
Background It is now widely recognized that there is an urgent need for new antibacterial drugs, with novel mechanisms of action, to combat the rise of multi-drug resistant bacteria. However, few new compounds are reaching the market. Antibacterial drug discovery projects often succeed in identifying potent molecules in biochemical assays but have been beset by difficulties in obtaining antibacterial activity. A commonly held view, based on analysis of marketed antibacterial compounds, is that antibacterial drugs possess very different physicochemical properties to other drugs, and that this profile is required for antibacterial activity. Results We have re-examined this issue by performing a cheminformatics analysis of the literature data available in the ChEMBL database. The physicochemical properties of compounds with a recorded activity in an antibacterial assay were calculated and compared to two other datasets extracted from ChEMBL, marketed antibacterials and drugs marketed for other therapeutic indications. The chemical class of the compounds and Gram-negative/Gram-positive profile were also investigated. This analysis shows that compounds with antibacterial activity have physicochemical property profiles very similar to other drug classes. Conclusions The observation that many current antibacterial drugs lie in regions of physicochemical property space far from conventional small molecule therapeutics is correct. However, the inference that a compound must lie in one of these “outlier” regions in order to possess antibacterial activity is not supported by our analysis. Electronic supplementary material The online version of this article (doi:10.1186/s13321-016-0143-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jean-Paul Ebejer
- InhibOx Limited, Oxford Centre for Innovation, New Road, Oxford, OX1 1BY UK ; Centre for Molecular Medicine and Biobanking, University of Malta, Msida, MSD 2080 Malta
| | - Michael H Charlton
- InhibOx Limited, Oxford Centre for Innovation, New Road, Oxford, OX1 1BY UK
| | - Paul W Finn
- InhibOx Limited, Oxford Centre for Innovation, New Road, Oxford, OX1 1BY UK ; University of Buckingham, Hunter Street, Buckingham, MK18 1EG UK
| |
Collapse
|
32
|
Abstract
The practice of medicine was profoundly transformed by the introduction of the antibiotics (compounds isolated from Nature) and the antibacterials (compounds prepared by synthesis) for the control of bacterial infection. As a result of the extraordinary success of these compounds over decades of time, a timeless biological activity for these compounds has been presumed. This presumption is no longer. The inexorable acquisition of resistance mechanisms by bacteria is retransforming medical practice. Credible answers to this dilemma are far better recognized than they are being implemented. In this perspective we examine (and in key respects, reiterate) the chemical and biological strategies being used to address the challenge of bacterial resistance.
Collapse
Affiliation(s)
- Jed F. Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame IN 46556–5670, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame IN 46556–5670, USA
| |
Collapse
|