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Fragment-Based Lead Discovery Strategies in Antimicrobial Drug Discovery. Antibiotics (Basel) 2023; 12:antibiotics12020315. [PMID: 36830226 PMCID: PMC9951956 DOI: 10.3390/antibiotics12020315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Fragment-based lead discovery (FBLD) is a powerful application for developing ligands as modulators of disease targets. This approach strategy involves identification of interactions between low-molecular weight compounds (100-300 Da) and their putative targets, often with low affinity (KD ~0.1-1 mM) interactions. The focus of this screening methodology is to optimize and streamline identification of fragments with higher ligand efficiency (LE) than typical high-throughput screening. The focus of this review is on the last half decade of fragment-based drug discovery strategies that have been used for antimicrobial drug discovery.
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Joaquim AR, Gionbelli MP, Gosmann G, Fuentefria AM, Lopes MS, Fernandes de Andrade S. Novel Antimicrobial 8-Hydroxyquinoline-Based Agents: Current Development, Structure-Activity Relationships, and Perspectives. J Med Chem 2021; 64:16349-16379. [PMID: 34779640 DOI: 10.1021/acs.jmedchem.1c01318] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The search for new antimicrobials is imperative due to the emergent resistance of new microorganism strains. In this context, revisiting known classes like 8-hydroxyquinolines could be an interesting strategy to discover new agents. The 8-hydroxyquinoline derivatives nitroxoline and clioquinol are used to treat microbial infections; however, these drugs are underused, being available in few countries or limited to topical use. After years of few advances, in the last two decades, the potent activity of clioquinol and nitroxoline against several targets and the privileged structure of 8-hydroxyquinoline nucleus have prompted an increased interest in the design of novel antimicrobial, anticancer, and anti-Alzheimer agents based on this class. Herein, we discuss the current development and antimicrobial structure-activity relationships of this class in the perspective of using the 8-hydroxyquinoline nucleus for the search for novel antimicrobial agents. Furthermore, the most investigated molecular targets concerning 8-hydroxyquinoline derivatives are explored in the final section.
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Affiliation(s)
- Angélica Rocha Joaquim
- Pharmaceutical Synthesis Group (PHARSG), Universidade Federal do Rio Grande do Sul, Av. Ipiranga, 2752, Azenha, Porto Alegre, RS 90610-000, Brazil.,Programa de Pós-graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Av. Ipiranga, 2752, Azenha, Porto Alegre, RS 90610-000, Brazil
| | - Mariana Pies Gionbelli
- Pharmaceutical Synthesis Group (PHARSG), Universidade Federal do Rio Grande do Sul, Av. Ipiranga, 2752, Azenha, Porto Alegre, RS 90610-000, Brazil.,Programa de Pós-graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Av. Ipiranga, 2752, Azenha, Porto Alegre, RS 90610-000, Brazil
| | - Grace Gosmann
- Programa de Pós-graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Av. Ipiranga, 2752, Azenha, Porto Alegre, RS 90610-000, Brazil
| | - Alexandre Meneghello Fuentefria
- Programa de Pós-graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Av. Ipiranga, 2752, Azenha, Porto Alegre, RS 90610-000, Brazil.,Programa de Pós-graduação em Microbiologia Agrícola e do Ambiente, Universidade Federal do Rio Grande do Sul, Sarmento Leite, 500, Farroupilha, Porto Alegre, RS 90050-170, Brazil
| | - Marcela Silva Lopes
- Programa de Pós-graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Av. Ipiranga, 2752, Azenha, Porto Alegre, RS 90610-000, Brazil
| | - Saulo Fernandes de Andrade
- Pharmaceutical Synthesis Group (PHARSG), Universidade Federal do Rio Grande do Sul, Av. Ipiranga, 2752, Azenha, Porto Alegre, RS 90610-000, Brazil.,Programa de Pós-graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Av. Ipiranga, 2752, Azenha, Porto Alegre, RS 90610-000, Brazil.,Programa de Pós-graduação em Microbiologia Agrícola e do Ambiente, Universidade Federal do Rio Grande do Sul, Sarmento Leite, 500, Farroupilha, Porto Alegre, RS 90050-170, Brazil
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Patel KB, Kononova O, Cai S, Barsegov V, Parmar VS, Kumar R, Singh BR. Botulinum neurotoxin inhibitor binding dynamics and kinetics relevant for drug design. Biochim Biophys Acta Gen Subj 2021; 1865:129933. [PMID: 34023445 DOI: 10.1016/j.bbagen.2021.129933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/05/2021] [Accepted: 05/17/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND A natural product analog, 3-(4-nitrophenyl)-7H-furo[3,2-g]chromen-7-one, which is a nitrophenyl psoralen (NPP) was found to be an effective inhibitor of botulinum neurotoxin type A (BoNT/A). METHODS In this work, we performed enzyme inhibition kinetics and employed biochemical techniques such as isothermal calorimetry (ITC) and fluorescence spectroscopy as well as molecular modeling to examine the kinetics and binding mechanism of NPP inhibitor with BoNT/A LC. RESULTS Studies of inhibition mechanism and binding dynamics of NPP to BoNT/A light chain (BoNT/A LC) showed that NPP is a mixed type inhibitor for the zinc endopeptidase activity, implying that at least part of the inhibitor-enzyme binding site may be different from the substrate-enzyme binding site. By using biochemical techniques, we demonstrated NPP forms a stable complex with BoNT/A LC. These observations were confirmed by Molecular Dynamics (MD) simulation, which demonstrates that NPP binds to the site near the active site. CONCLUSION The NPP binding interferes with BoNT/A LC binding to the SNAP-25, hence, inhibits its cleavage. Based on these results, we propose a modified strategy for designing a molecule to enhance the efficiency of the inhibition against the neurotoxic effect of BoNT. GENERAL SIGNIFICANCE Insights into the interactions of NPP with BoNT/A LC using biochemical and computational approaches will aid in the future development of effective countermeasures and better pharmacological strategies against botulism.
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Affiliation(s)
- Kruti B Patel
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA, USA; Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, North Dartmouth, MA, USA
| | - Olga Kononova
- Department of Chemistry and Biochemistry, University of Massachusetts Lowell, Lowell, MA, USA
| | - Shuowei Cai
- Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, North Dartmouth, MA, USA
| | - Valeri Barsegov
- Department of Chemistry and Biochemistry, University of Massachusetts Lowell, Lowell, MA, USA
| | - Virinder S Parmar
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA, USA; Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Raj Kumar
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA, USA
| | - Bal Ram Singh
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA, USA; Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, North Dartmouth, MA, USA; Prime Bio Inc., Dartmouth, MA, USA.
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Chauhan R, Chauhan V, Sonkar P, Vimal M, Dhaked RK. Targeted 8-hydroxyquinoline fragment based small molecule drug discovery against neglected botulinum neurotoxin type F. Bioorg Chem 2019; 92:103297. [PMID: 31557621 DOI: 10.1016/j.bioorg.2019.103297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 11/24/2022]
Abstract
OBJECTIVES Botulinum neurotoxins are highly potent biological warfare agents. The unavailability of countermeasures against these neurotoxins has been a matter of extensive research. However, no clinical therapeutics has come to existence till date. The 8-hydroxyquinoline (8-HQ) scaffold is established privileged compound and its potential as drug candidate against BoNTs is recently being explored. METHODS In present work, three course studies were performed involving in silico, in vitro and in vivo cascade to screen 8-HQ small molecule inhibitors against BoNT/F intoxication. ~800 molecules obtained from open repositories were screened in silico and commercially obtained twenty-four 8-HQ derived small molecule inhibitors were evaluated against rBoNT/F light chain through fluorescence thermal shift (FTS) assay. Selected compounds were further evaluated through endopeptidase assay. Further binding affinity analysis was done through surface plasmon resonance (SPR) based Proteon™ XPR 36 system. Finally, the in vivo efficacy of these compounds was evaluated in mice model. RESULTS Three compounds NSC1011, NSC1014 and NSC84094 were found to be highly inhibitory after screening of 8-HQ compounds through FTS assay and endopeptidase assay. SPR based protein-small molecule interaction studies showed highest affinity binding of NSC1014 (KD: 5.58E-06) with BoNT/F-LC. NSC1011, NSC1014, and NSC84094 displayed IC50 of 30.47 ± 6.24, 14.91 ± 2.49 and 17.39 ± 2.74 μM, respectively, in endopeptidase assay. NSC1011 and NSC1014 displayed marked extension of survival time in mice model. CONCLUSION NSC1011 and NSC1014 have emerged as promising drug candidate against BoNT/F intoxication displaying higher potential than previously reported compounds.
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Affiliation(s)
- Ritika Chauhan
- Biotechnology Division, Defence Research & Development Establishment, Jhansi Road, Gwalior 474002, MP, India
| | - Vinita Chauhan
- Biotechnology Division, Defence Research & Development Establishment, Jhansi Road, Gwalior 474002, MP, India
| | - Priyanka Sonkar
- Biotechnology Division, Defence Research & Development Establishment, Jhansi Road, Gwalior 474002, MP, India
| | - Manorama Vimal
- Synthetic Chemistry Division, Defence Research & Development Establishment, Jhansi Road, Gwalior 474002, MP, India
| | - Ram Kumar Dhaked
- Biotechnology Division, Defence Research & Development Establishment, Jhansi Road, Gwalior 474002, MP, India.
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Chauhan R, Chauhan V, Sonkar P, Dhaked RK. Identification of Inhibitors against Botulinum Neurotoxins: 8-Hydroxyquinolines Hold Promise. Mini Rev Med Chem 2019; 19:1694-1706. [PMID: 31490749 DOI: 10.2174/1389557519666190906120228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 12/13/2018] [Accepted: 08/20/2019] [Indexed: 11/22/2022]
Abstract
Botulinum neurotoxins (BoNTs) are the most toxic category A biological warfare agents. There is no therapeutics available for BoNT intoxication yet, necessitating the development of a medical countermeasure against these neurotoxins. The discovery of small molecule-based drugs has revolutionized in the last two decades resulting in the identification of several small molecule inhibitors of BoNTs. However, none progressed to clinical trials. 8-Hydroxyquinolines scaffold-based molecules are important 'privileged structures' that can be exploited as inhibitors of a diverse range of targets. In this review, our study of recent reports suggests the development of 8-hydroxyquinoline derived molecules as a potential drug may be on the horizon.
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Affiliation(s)
- Ritika Chauhan
- Biotechnology Division, Defence Research & Development Establishment, Jhansi Road, Gwalior-474002, MP, India
| | - Vinita Chauhan
- Biotechnology Division, Defence Research & Development Establishment, Jhansi Road, Gwalior-474002, MP, India
| | - Priyanka Sonkar
- Biotechnology Division, Defence Research & Development Establishment, Jhansi Road, Gwalior-474002, MP, India
| | - Ram Kumar Dhaked
- Biotechnology Division, Defence Research & Development Establishment, Jhansi Road, Gwalior-474002, MP, India
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Pitard I, Malliavin TE. Structural Biology and Molecular Modeling to Analyze the Entry of Bacterial Toxins and Virulence Factors into Host Cells. Toxins (Basel) 2019; 11:toxins11060369. [PMID: 31238550 PMCID: PMC6628625 DOI: 10.3390/toxins11060369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 12/26/2022] Open
Abstract
Understanding the functions and mechanisms of biological systems is an outstanding challenge. One way to overcome it is to combine together several approaches such as molecular modeling and experimental structural biology techniques. Indeed, the interplay between structural and dynamical properties of the system is crucial to unravel the function of molecular machinery’s. In this review, we focus on how molecular simulations along with structural information can aid in interpreting biological data. Here, we examine two different cases: (i) the endosomal translocation toxins (diphtheria, tetanus, botulinum toxins) and (ii) the activation of adenylyl cyclase inside the cytoplasm (edema factor, CyA, ExoY).
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Affiliation(s)
- Irène Pitard
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR3528, 75015 Paris, France.
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR3756, 75015 Paris, France.
- Sorbonne Université, Collège Doctoral, Ecole Doctorale Complexité du Vivant, 75005 Paris, France.
| | - Thérèse E Malliavin
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR3528, 75015 Paris, France.
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR3756, 75015 Paris, France.
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Feltrup TM, Patel K, Kumar R, Cai S, Singh BR. A novel role of C-terminus in introducing a functionally flexible structure critical for the biological activity of botulinum neurotoxin. Sci Rep 2018; 8:8884. [PMID: 29891845 PMCID: PMC5995822 DOI: 10.1038/s41598-018-26764-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 05/17/2018] [Indexed: 02/06/2023] Open
Abstract
Botulinum neurotoxin (BoNT) is responsible for botulism, a clinical condition resulting in flaccid muscle paralysis and potentially death. The light chain is responsible for its intracellular toxicity through its endopeptidase activity. Available crystal structures of BoNT/A light chains (LCA) are based on various truncated versions (tLCA) of the full-length LCA (fLCA) and do not necessarily reflect the true structure of LCA in solution. The understanding of the mechanism of action, longevity of intoxication, and an improved development of endopeptidase inhibitors are dependent on first having a better insight into the structure of LCA in solution. Using an array of biophysical techniques, we report that the fLCA structure is significantly more flexible than tLCA in solution, which may be responsible for its dramatically higher enzymatic activity. This seems to be achieved by a much stronger, more rapid binding to substrate (SNAP-25) of the fLCA compared to tLCA. These results suggest that the C-terminus of LCA plays a critical role in introducing a flexible structure, which is essential for its biological function. This is the first report of such a massive structural role of the C-terminus of a protein being critical for maintaining a functional state.
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Affiliation(s)
- Thomas M Feltrup
- Department of Chemistry & Biochemistry, University of Massachusetts Dartmouth, North Dartmouth, MA, 02747, USA
| | - Kruti Patel
- Department of Chemistry & Biochemistry, University of Massachusetts Dartmouth, North Dartmouth, MA, 02747, USA
| | - Raj Kumar
- Botulinum Research Center, Institute of Advanced Sciences, North Dartmouth, MA, 02747, USA
| | - Shuowei Cai
- Department of Chemistry & Biochemistry, University of Massachusetts Dartmouth, North Dartmouth, MA, 02747, USA
| | - Bal Ram Singh
- Botulinum Research Center, Institute of Advanced Sciences, North Dartmouth, MA, 02747, USA.
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