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Bernacchia L, Paris A, Gupta A, Charman RJ, McGreig J, Wass MN, Kad NM. Identification of a novel DNA repair inhibitor using an in silico driven approach shows effective combinatorial activity with genotoxic agents against multidrug-resistant Escherichia coli. Protein Sci 2024; 33:e4948. [PMID: 38501485 PMCID: PMC10949335 DOI: 10.1002/pro.4948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/30/2024] [Accepted: 02/12/2024] [Indexed: 03/20/2024]
Abstract
Increasing antimicrobial drug resistance represents a global existential threat. Infection is a particular problem in immunocompromised individuals, such as patients undergoing cancer chemotherapy, due to the targeting of rapidly dividing cells by antineoplastic agents. We recently developed a strategy that targets bacterial nucleotide excision DNA repair (NER) to identify compounds that act as antimicrobial sensitizers specific for patients undergoing cancer chemotherapy. Building on this, we performed a virtual drug screening of a ~120,000 compound library against the key NER protein UvrA. From this, numerous target compounds were identified and of those a candidate compound, Bemcentinib (R428), showed a strong affinity toward UvrA. This NER protein possesses four ATPase sites in its dimeric state, and we found that Bemcentinib could inhibit UvrA's ATPase activity by ~90% and also impair its ability to bind DNA. As a result, Bemcentinib strongly diminishes NER's ability to repair DNA in vitro. To provide a measure of in vivo activity we discovered that the growth of Escherichia coli MG1655 was significantly inhibited when Bemcentinib was combined with the DNA damaging agent 4-NQO, which is analogous to UV. Using the clinically relevant DNA-damaging antineoplastic cisplatin in combination with Bemcentinib against the urological sepsis-causing E. coli strain EC958 caused complete growth inhibition. This study offers a novel approach for the potential development of new compounds for use as adjuvants in antineoplastic therapy.
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Affiliation(s)
| | - Antoine Paris
- School of Biological SciencesUniversity of KentCanterburyUK
| | - Arya Gupta
- School of Biological SciencesUniversity of KentCanterburyUK
| | | | - Jake McGreig
- School of Biological SciencesUniversity of KentCanterburyUK
| | - Mark N. Wass
- School of Biological SciencesUniversity of KentCanterburyUK
| | - Neil M. Kad
- School of Biological SciencesUniversity of KentCanterburyUK
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Wu Y, Liu C, Hu L. Fragment-Based Dynamic Combinatorial Chemistry for Identification of Selective α-Glucosidase Inhibitors. ACS Med Chem Lett 2022; 13:1791-1796. [PMID: 36385930 PMCID: PMC9661702 DOI: 10.1021/acsmedchemlett.2c00405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 10/13/2022] [Indexed: 11/28/2022] Open
Abstract
Efforts to combine advantages of fragment-based drug design (FBDD) and dynamic combinatorial chemistry (DCC) for the development of selective α-glucosidase inhibitors were described. Starting from 5 rationally designed fragments, two iterative dynamic combinatorial libraries (DCLs) comprising 29 acylhydrazone products were generated and screened using α-glucosidase and α-amylase as the templates. The optimal ligand identified showed substantial α-glucosidase inhibition with high selectivity over α-amylase as well as low cytotoxicity. Furthermore, inhibition type and detailed ligand/enzyme binding interactions were elucidated by the binding kinetic study and docking simulation, respectively.
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Affiliation(s)
- Yao Wu
- School of Pharmacy, Jiangsu
University, 301 Xuefu Road, 212013 Zhenjiang, China
| | - Changming Liu
- School of Pharmacy, Jiangsu
University, 301 Xuefu Road, 212013 Zhenjiang, China
| | - Lei Hu
- School of Pharmacy, Jiangsu
University, 301 Xuefu Road, 212013 Zhenjiang, China
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Verma N, Srivastava S, Malik R, Goyal P, Pandey J. Inhibition and disintegration of Bacillus subtilis biofilm with small molecule inhibitors identified through virtual screening for targeting TasA (28-261), the major protein component of ECM. J Biomol Struct Dyn 2022; 41:2431-2447. [PMID: 35098894 DOI: 10.1080/07391102.2022.2033135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Microbial biofilms have been recognized for a vital role in antibiotic resistance and chronic microbial infections for 2-3 decades; still, there are no 'anti-biofilm drugs' available for human applications. There is an urgent need to develop novel 'anti-biofilms' therapeutics to manage biofilm-associated infectious diseases. Several reports have suggested that targeting molecules involved in quorum sensing or biofilm-specific transcription may inhibit biofilm formation. However, the possibility of targeting other vital components of microbial biofilms, especially the extracellular matrix (ECM) components, has remained largely unexplored. Here we report targeting TasA(28-261), the major proteinaceous component of Bacillus subtilis ECM with two small molecule inhibitors (lovastatin and simvastatin) identified through virtual screening and drug repurposing, resulted in complete inhibition of biofilm. In molecular docking and dynamics simulation studies, lovastatin was observed to make stable interactions with TasA(28-261), whereas the simvastatin - TasA(28-261) interactions were relatively less stable. However, in subsequent in vitro studies, both lovastatin and simvastatin successfully inhibited B. subtilis biofilm formation at MIC values of < 10 µg/ml. Besides, these potential inhibitors also caused the disintegration of pre-formed biofilms. Results presented here provide 'proof of concept' for the hypothesis that targeting the extracellular matrix's vital component(s) could be one of the most efficient approaches for inhibiting microbial biofilms and disintegrating the pre-formed biofilms. We propose that a similar approach targeting ECM-associated proteins with FDA-approved drugs could be implemented to develop novel anti-biofilm therapeutic strategies against biofilm-forming chronic microbial pathogens.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nidhi Verma
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Shubham Srivastava
- Department of Pharmacy, School of Chemistry & Pharmacy, Central University fo Rajasthan, Ajmer, Rajasthan, India
| | - Ruchi Malik
- Department of Pharmacy, School of Chemistry & Pharmacy, Central University fo Rajasthan, Ajmer, Rajasthan, India
| | - Pankaj Goyal
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Janmejay Pandey
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
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Abstract
We developed a new approach to selectively modify native proteins in their biological environment using electrophilic covalent aptamers. These aptamers are generated through introduction of a proximity-driven electrophile at specific nucleotide sites. Using thrombin as a proof-of-concept, we demonstrate that covalent aptamers can selectively transfer a variety of functional handles and/or irreversibly crosslink to the target protein. This approach offers broad programmability and high target specificity. Furthermore, it addresses issues common to aptamers such as instability towards endogenous nucleases and residence times during target engagement. Covalent aptamers are new tools that enable specific protein modification and sensitive protein detection. Moreover, they provide prolonged, nuclease-resistant enzyme inhibition.
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Affiliation(s)
- Yaniv Tivon
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Gianna Falcone
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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5
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Hernández ÁP, Díez P, García PA, Pérez-Andrés M, Ortega P, Jambrina PG, Díez D, Castro MÁ, Fuentes M. A Novel Cytotoxic Conjugate Derived from the Natural Product Podophyllotoxin as a Direct-Target Protein Dual Inhibitor. Molecules 2020; 25:molecules25184258. [PMID: 32957517 PMCID: PMC7571232 DOI: 10.3390/molecules25184258] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 12/11/2022] Open
Abstract
Natural products are the ideal basis for the design of novel efficient molecular entities. Podophyllotoxin, a naturally occurring cyclolignan, is an example of natural product which displays a high versatility from a biological activity point of view. Based on its unique chemical structure, different derivatives have been synthesized presenting the original antitumoral properties associated with the compound, i.e., the tubulin polymerization inhibition and arising anti-topoisomerase II activity from structural modifications on the cyclolignan skeleton. In this report, we present a novel conjugate or hybrid which chemically combines both biological activities in one single molecule. Chemical design has been planned based in our lead compound, podophyllic aldehyde, as an inhibitor of tubulin polymerization, and in etoposide, an approved antitumoral drug targeting topoisomerase II. The cytotoxicity and selectivity of the novel synthetized hybrid has been evaluated in several cell lines of different solid tumors. In addition, these dual functional effects of the novel compound have been also evaluated by molecular docking approaches.
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Affiliation(s)
- Ángela-Patricia Hernández
- Departamento de Ciencias Farmacéuticas, Área de Química Farmacéutica, Facultad de Farmacia, CIETUS/IBSAL, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain; (Á.-P.H.); (P.A.G.)
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (P.D.); (M.P.-A.)
| | - Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (P.D.); (M.P.-A.)
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Pablo A. García
- Departamento de Ciencias Farmacéuticas, Área de Química Farmacéutica, Facultad de Farmacia, CIETUS/IBSAL, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain; (Á.-P.H.); (P.A.G.)
| | - Martín Pérez-Andrés
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (P.D.); (M.P.-A.)
| | - Pablo Ortega
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad de, 37008 Salamanca, Spain; (P.O.); (P.G.J.)
| | - Pablo G. Jambrina
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad de, 37008 Salamanca, Spain; (P.O.); (P.G.J.)
| | - David Díez
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad de, 37008 Salamanca, Spain;
| | - María Ángeles Castro
- Departamento de Ciencias Farmacéuticas, Área de Química Farmacéutica, Facultad de Farmacia, CIETUS/IBSAL, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain; (Á.-P.H.); (P.A.G.)
- Correspondence: (M.Á.C.); (M.F.)
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (P.D.); (M.P.-A.)
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
- Correspondence: (M.Á.C.); (M.F.)
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Bosken YK, Cholko T, Lou YC, Wu KP, Chang CEA. Insights Into Dynamics of Inhibitor and Ubiquitin-Like Protein Binding in SARS-CoV-2 Papain-Like Protease. Front Mol Biosci 2020; 7:174. [PMID: 32850963 PMCID: PMC7417481 DOI: 10.3389/fmolb.2020.00174] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/06/2020] [Indexed: 11/28/2022] Open
Abstract
Covid-19 is caused by a novel form of coronavirus for which there are currently no vaccines or anti-viral drugs. This virus, termed SARS-CoV-2 (CoV2), contains Papain-like protease (PLpro) involved in viral replication and immune response evasion. Drugs targeting this protease therefore have great potential for inhibiting the virus, and have proven successful in older coronaviruses. Here, we introduce two effective inhibitors of SARS-CoV-1 (CoV1) and MERS-CoV to assess their potential for inhibiting CoV2 PLpro. We ran 1 μs molecular dynamics (MD) simulations of CoV2, CoV1, and MERS-CoV ligand-free PLpro to characterize the dynamics of CoV2 PLpro, and made comparisons between the three to elucidate important similarities and differences relevant to drug design and ubiquitin-like protein binding for deubiquitinating and deISGylating activity of CoV2. Next, we simulated the inhibitors bound to CoV1 and CoV2 PLpro in various poses and at different known binding sites to analyze their binding modes. We found that the naphthalene-based ligand shows strong potential as an inhibitor of CoV2 PLpro by binding at the putative naphthalene inhibitor binding site in both computational predictions and experimental assays. Our modeling work suggested strategies to improve naphthalene-based compounds, and our results from molecular docking showed that the newly designed compounds exhibited improved binding affinity. The other ligand, chemotherapy drug 6-mercaptopurine (6MP), showed little to no stable intermolecular interaction with PLpro and quickly dissociated or remained highly mobile. We demonstrate multiple ways to improve the binding affinity of the naphthalene-based inhibitor scaffold by engaging new residues in the unused space of the binding site. Analysis of CoV2 PLpro also brings insights into recognition of ubiquitin-like proteins that may alter innate immune response.
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Affiliation(s)
- Yuliana K Bosken
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Timothy Cholko
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Yuan-Chao Lou
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Kuen-Phon Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States
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