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Queffeulou M, Leprohon P, Fernandez-Prada C, Ouellette M, Mejía-Jaramillo AM. CRISPR-Cas9 high-throughput screening to study drug resistance in Leishmania infantum. mBio 2024:e0047724. [PMID: 38864609 DOI: 10.1128/mbio.00477-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/23/2024] [Indexed: 06/13/2024] Open
Abstract
Parasites of the genus Leishmania pose a global health threat with limited treatment options. New drugs are urgently needed, and genomic screens have the potential to accelerate target discovery, mode of action, and resistance mechanisms against these new drugs. We describe here our effort in developing a genome-wide CRISPR-Cas9 screen in Leishmania, an organism lacking a functional nonhomologous end joining system that must rely on microhomology-mediated end joining, single-strand annealing, or homologous recombination for repairing Cas9-induced double-stranded DNA breaks. A new vector for cloning and expressing single guide RNAs (sgRNAs) was designed and proven to be effective in a small pilot project while enriching specific sgRNAs during drug selection. We then developed a whole-genome library of 49,754 sgRNAs, targeting all the genes of Leishmania infantum. This library was transfected in L. infantum expressing Cas9, and these cells were selected for resistance to two antileishmanials, miltefosine and amphotericin B. The sgRNAs the most enriched in the miltefosine screen targeted the miltefosine transporter gene, but sgRNAs targeting genes coding for a RING-variant protein and a transmembrane protein were also enriched. The sgRNAs the most enriched by amphotericin B targeted the sterol 24 C methyltransferase genes and a hypothetical gene. Through gene disruption experiments, we proved that loss of function of these genes was associated with resistance. This study describes the feasibility of carrying out whole-genome CRISPR-Cas9 screens in Leishmania provided that a strong selective pressure is applied. Such a screen can be used for accelerating the development of urgently needed antileishmanial drugs.IMPORTANCELeishmaniasis, a global health threat, lacks adequate treatment options and drug resistance exacerbates the challenge. This study introduces a CRISPR-Cas9 screening approach in Leishmania infantum, unraveling mechanisms of drug resistance at a genome-wide scale. Our screen was applied against two main antileishmanial drugs, and guides were enriched upon drug selection. These guides targeted known and new targets, hence validating the use of this screen against Leishmania. This strategy provides a powerful tool to expedite drug discovery as well as potential therapeutic targets against this neglected tropical disease.
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Affiliation(s)
- Marine Queffeulou
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU Québec, Université Laval, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Canada
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU Québec, Université Laval, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Canada
| | - Christopher Fernandez-Prada
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU Québec, Université Laval, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU Québec, Université Laval, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Canada
| | - Ana María Mejía-Jaramillo
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU Québec, Université Laval, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Canada
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Nayak A, Chavarria A, Sanders KN, Ghalei H, Khoshnevis S. Sinefungin, a natural nucleoside analog of S-adenosyl methionine, impairs the pathogenicity of Candida albicans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.12.562127. [PMID: 37873365 PMCID: PMC10592816 DOI: 10.1101/2023.10.12.562127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Candida albicans, an opportunistic fungal human pathogen, is a major threat to the healthcare system due to both infections in immunocompromised individuals and the emergence of antifungal resistance. Fungal infection caused by C. albicans, candidiasis, is a life-threatening condition in immunocompromised patients and the current treatments are mostly restricted to polyenes, azoles, and echinocandins. Use of these antifungals is limited by toxicity, drug-drug interactions, and the emergence of resistance, underscoring the importance of identifying novel therapeutic targets and the need for new treatment approaches. C. albicans can undergo a morphological transition from yeast to hyphae and this transition is central to C. albicans virulence. Here, we determine the impact of sinefungin, a natural nucleoside analog of S-adenosyl methionine, on the virulence of C. albicans strain SC5314 by evaluating treatment effects on the morphological transition, human epithelial cell adhesion, and biofilm formation. Our data indicate that sinefungin impairs pathogenic traits of C. albicans including hyphal lengthening, biofilm formation and the adhesion to the human epithelial cell lines, without adversely affecting human cells, therefore highlighting sinefungin as a potential avenue for therapeutic intervention. We determine that the formation of N6-methyladenosine (m6A) is particularly disturbed by sinefungin. More broadly, this study underscores the importance of considering the post-transcriptional control mechanisms of pathogenicity when designing therapeutic solutions to fungal infection.
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Affiliation(s)
- Anushka Nayak
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA
| | - Alejandro Chavarria
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA
| | - Kyla N. Sanders
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA
| | - Homa Ghalei
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA
| | - Sohail Khoshnevis
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA
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3
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Fischer TR, Meidner L, Schwickert M, Weber M, Zimmermann RA, Kersten C, Schirmeister T, Helm M. Chemical biology and medicinal chemistry of RNA methyltransferases. Nucleic Acids Res 2022; 50:4216-4245. [PMID: 35412633 PMCID: PMC9071492 DOI: 10.1093/nar/gkac224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/17/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
RNA methyltransferases (MTases) are ubiquitous enzymes whose hitherto low profile in medicinal chemistry, contrasts with the surging interest in RNA methylation, the arguably most important aspect of the new field of epitranscriptomics. As MTases become validated as drug targets in all major fields of biomedicine, the development of small molecule compounds as tools and inhibitors is picking up considerable momentum, in academia as well as in biotech. Here we discuss the development of small molecules for two related aspects of chemical biology. Firstly, derivates of the ubiquitous cofactor S-adenosyl-l-methionine (SAM) are being developed as bioconjugation tools for targeted transfer of functional groups and labels to increasingly visible targets. Secondly, SAM-derived compounds are being investigated for their ability to act as inhibitors of RNA MTases. Drug development is moving from derivatives of cosubstrates towards higher generation compounds that may address allosteric sites in addition to the catalytic centre. Progress in assay development and screening techniques from medicinal chemistry have led to recent breakthroughs, e.g. in addressing human enzymes targeted for their role in cancer. Spurred by the current pandemic, new inhibitors against coronaviral MTases have emerged at a spectacular rate, including a repurposed drug which is now in clinical trial.
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Affiliation(s)
- Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Laurenz Meidner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marlies Weber
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
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4
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Decreased glutamate transport in acivicin resistant Leishmania tarentolae. PLoS Negl Trop Dis 2021; 15:e0010046. [PMID: 34914690 PMCID: PMC8718007 DOI: 10.1371/journal.pntd.0010046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 12/30/2021] [Accepted: 12/02/2021] [Indexed: 12/24/2022] Open
Abstract
Studies of drug resistance in the protozoan parasites of the genus Leishmania have been helpful in revealing biochemical pathways as potential drug targets. The chlorinated glutamine analogue acivicin has shown good activity against Leishmania cells and was shown to target several enzymes containing amidotransferase domains. We selected a Leishmania tarentolae clone for acivicin resistance. The genome of this resistant strain was sequenced and the gene coding for the amidotransferase domain-containing GMP synthase was found to be amplified. Episomal expression of this gene in wild-type L. tarentolae revealed a modest role in acivicin resistance. The most prominent defect observed in the resistant mutant was reduced uptake of glutamate, and through competition experiments we determined that glutamate and acivicin, but not glutamine, share the same transporter. Several amino acid transporters (AATs) were either deleted or mutated in the resistant cells. Some contributed to the acivicin resistance phenotype although none corresponded to the main glutamate transporter. Through sequence analysis one AAT on chromosome 22 corresponded to the main glutamate transporter. Episomal expression of the gene coding for this transporter in the resistant mutant restored glutamate transport and acivicin susceptibility. Its genetic knockout led to reduced glutamate transport and acivicin resistance. We propose that acivicin binds covalently to this transporter and as such leads to decreased transport of glutamate and acivicin thus leading to acivicin resistance. Studies of drug resistance in the protozoan parasites of the genus Leishmania have been helpful in revealing biochemical pathways as potential drug targets. Here we report on the characterization at the genomics and metabolomics levels of a L. tarentolae strain made resistant to acivicin, an analogue of glutamine with activity against this parasite. We found that resistance to acivicin is accompanied by a reduced uptake and intracellular levels of glutamate and that both are expected to share the same transporter. Through gene overexpression and disruption studies we identified the main amino acid transporter responsible for glutamate uptake.
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Galati A, Scatolini L, Micheli E, Bavasso F, Cicconi A, Maccallini P, Chen L, Roake CM, Schoeftner S, Artandi SE, Gatti M, Cacchione S, Raffa GD. The S-adenosylmethionine analog sinefungin inhibits the trimethylguanosine synthase TGS1 to promote telomerase activity and telomere lengthening. FEBS Lett 2021; 596:42-52. [PMID: 34817067 DOI: 10.1002/1873-3468.14240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 10/16/2021] [Accepted: 11/09/2021] [Indexed: 12/11/2022]
Abstract
Mutations in many genes that control the expression, the function, or the stability of telomerase cause telomere biology disorders (TBDs), such as dyskeratosis congenita, pulmonary fibrosis, and aplastic anemia. Mutations in a subset of the genes associated with TBDs cause reductions of the telomerase RNA moiety hTR, thus limiting telomerase activity. We have recently found that loss of the trimethylguanosine synthase TGS1 increases both hTR abundance and telomerase activity and leads to telomere elongation. Here, we show that treatment with the S-adenosylmethionine analog sinefungin inhibits TGS1 activity, increases the hTR levels, and promotes telomere lengthening in different cell types. Our results hold promise for restoring telomere length in stem and progenitor cells from TBD patients with reduced hTR levels.
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Affiliation(s)
- Alessandra Galati
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Italy
| | - Livia Scatolini
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Italy
| | - Emanuela Micheli
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Italy
| | - Francesca Bavasso
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Italy
| | - Alessandro Cicconi
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Italy
| | - Paolo Maccallini
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Italy
| | - Lu Chen
- Cancer Signaling and Epigenetics Program-Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Caitlin M Roake
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Stefan Schoeftner
- Dipartimento di Scienze della Vita, Università degli studi di Trieste, Italy
| | - Steven E Artandi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Maurizio Gatti
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Italy.,Istituto di Biologia e Patologia Molecolari del CNR, Roma, Italy
| | - Stefano Cacchione
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Italy
| | - Grazia D Raffa
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Italy
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6
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Horn D. Genome-scale RNAi screens in African trypanosomes. Trends Parasitol 2021; 38:160-173. [PMID: 34580035 DOI: 10.1016/j.pt.2021.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 12/11/2022]
Abstract
Genome-scale genetic screens allow researchers to rapidly identify the genes and proteins that impact a particular phenotype of interest. In African trypanosomes, RNA interference (RNAi) knockdown screens have revealed mechanisms underpinning drug resistance, drug transport, prodrug metabolism, quorum sensing, genome replication, and gene expression control. RNAi screening has also been remarkably effective at highlighting promising potential antitrypanosomal drug targets. The first ever RNAi library screen was implemented in African trypanosomes, and genome-scale RNAi screens and other related approaches continue to have a major impact on trypanosomatid research. Here, I review those impacts in terms of both discovery and translation.
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Affiliation(s)
- David Horn
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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7
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Dwivedy A, Mariadasse R, Ahmad M, Chakraborty S, Kar D, Tiwari S, Bhattacharyya S, Sonar S, Mani S, Tailor P, Majumdar T, Jeyakanthan J, Biswal BK. Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2. PLoS Comput Biol 2021; 17:e1009384. [PMID: 34516563 PMCID: PMC8478224 DOI: 10.1371/journal.pcbi.1009384] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 09/28/2021] [Accepted: 08/26/2021] [Indexed: 12/14/2022] Open
Abstract
Apart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, a well-known kinase inhibitor- Sorafenib showed a significant inhibition and dampened viral load in SARS-CoV-2 infected cells. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2. The on-going coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is significantly affecting the world health. Unfortunately, over 180 million cases of COVID-19 resulting in nearly 4 million deaths have been reported till June, 2021. In this study, using a combination of bioinformatics, biochemical and mass spectrometry methods, we show that the Nidovirus RdRp associated Nucleotidyl transferase (NiRAN) domain of the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 exhibits a kinase like activity. Additionally, we also show that few broad spectrum anti-cancer and anti-microbial drugs dampen this kinase like activity. Of note, Sorafenib, an FDA approved anti-cancer kinase inhibiting drug significantly reduces the SARS-CoV-2 load in cell lines. Our study suggests that NiRAN domain of the SARS-CoV-2 RdRp is indispensible for the successful viral life cycle and shows that abolishing this enzymatic function of RdRp by small molecule inhibitors may open novel avenues for COVID-19 therapeutics.
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Affiliation(s)
| | | | | | | | | | | | | | - Sudipta Sonar
- Translational Health Science and Technology Institute, Faridabad, India
| | - Shailendra Mani
- Translational Health Science and Technology Institute, Faridabad, India
| | | | - Tanmay Majumdar
- National Institute of Immunology, New Delhi, India
- * E-mail: (TM); (JJ); (BKB)
| | - Jeyaraman Jeyakanthan
- Department of Bioinformatics, Alagappa University, Tamil Nadu, India
- * E-mail: (TM); (JJ); (BKB)
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8
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Dwivedy A, Mariadasse R, Ahmad M, Chakraborty S, Kar D, Tiwari S, Bhattacharyya S, Sonar S, Mani S, Tailor P, Majumdar T, Jeyakanthan J, Biswal BK. Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2. PLoS Comput Biol 2021. [DOI: https://doi.org/10.1371/journal.pcbi.1009384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Apart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, a well-known kinase inhibitor- Sorafenib showed a significant inhibition and dampened viral load in SARS-CoV-2 infected cells. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2.
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9
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Wang Z, Yang L, Zhao XE. Co-crystallization and structure determination: An effective direction for anti-SARS-CoV-2 drug discovery. Comput Struct Biotechnol J 2021; 19:4684-4701. [PMID: 34426762 PMCID: PMC8373586 DOI: 10.1016/j.csbj.2021.08.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/29/2021] [Accepted: 08/17/2021] [Indexed: 01/18/2023] Open
Abstract
Safer and more-effective drugs are urgently needed to counter infections with the highly pathogenic SARS-CoV-2, cause of the COVID-19 pandemic. Identification of efficient inhibitors to treat and prevent SARS-CoV-2 infection is a predominant focus. Encouragingly, using X-ray crystal structures of therapeutically relevant drug targets (PLpro, Mpro, RdRp, and S glycoprotein) offers a valuable direction for anti-SARS-CoV-2 drug discovery and lead optimization through direct visualization of interactions. Computational analyses based primarily on MMPBSA calculations have also been proposed for assessing the binding stability of biomolecular structures involving the ligand and receptor. In this study, we focused on state-of-the-art X-ray co-crystal structures of the abovementioned targets complexed with newly identified small-molecule inhibitors (natural products, FDA-approved drugs, candidate drugs, and their analogues) with the assistance of computational analyses to support the precision design and screening of anti-SARS-CoV-2 drugs.
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Key Words
- 3CLpro, 3C-Like protease
- ACE2, angiotensin-converting enzyme 2
- COVID-19, coronavirus disease 2019
- Candidate drugs
- Co-crystal structures
- DyKAT, dynamic kinetic asymmetric transformation
- EBOV, Ebola virus
- EC50, half maximal effective concentration
- EMD, Electron Microscopy Data
- FDA, U.S. Food and Drug Administration
- FDA-approved drugs
- HCoV-229E, human coronavirus 229E
- HPLC, high-performance liquid chromatography
- IC50, half maximal inhibitory concentration
- MD, molecular dynamics
- MERS-CoV, Middle East respiratory syndrome coronavirus
- MMPBSA, molecular mechanics Poisson-Boltzmann surface area
- MTase, methyltransferase
- Mpro, main protease
- Natural products
- Nsp, nonstructural protein
- PDB, Protein Data Bank
- PLpro, papain-like protease
- RTP, ribonucleoside triphosphate
- RdRp, RNA-dependent RNA polymerase
- SAM, S-adenosylmethionine
- SARS-CoV, severe acute respiratory syndrome coronavirus
- SARS-CoV-2
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- SI, selectivity index
- Ugi-4CR, Ugi four-component reaction
- cryo-EM, cryo-electron microscopy
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Affiliation(s)
- Zhonglei Wang
- Key Laboratory of Green Natural Products and Pharmaceutical Intermediates in Colleges and Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, PR China
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, PR China
| | - Liyan Yang
- School of Physics and Physical Engineering, Qufu Normal University, Qufu 273165, PR China
| | - Xian-En Zhao
- Key Laboratory of Green Natural Products and Pharmaceutical Intermediates in Colleges and Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, PR China
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Combined gene deletion of dihydrofolate reductase-thymidylate synthase and pteridine reductase in Leishmania infantum. PLoS Negl Trop Dis 2021; 15:e0009377. [PMID: 33905412 PMCID: PMC8104401 DOI: 10.1371/journal.pntd.0009377] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 05/07/2021] [Accepted: 04/11/2021] [Indexed: 12/13/2022] Open
Abstract
Our understanding of folate metabolism in Leishmania has greatly benefited from studies of resistance to the inhibitor methotrexate (MTX). Folates are reduced in Leishmania by the bifunctional dihydrofolate reductase thymidylate synthase (DHFR-TS) and by pteridine reductase (PTR1). To further our understanding of folate metabolism in Leishmania, a Cos-seq genome-wide gain of function screen was performed against MTX and against the two thymidylate synthase (TS) inhibitors 5-fluorouracil and pemetrexed. The screen revealed DHFR-TS and PTR1 but also the nucleoside transporter NT1 and one hypothetical gene derived from chromosome 31. For MTX, the concentration of folate in the culture medium affected the enrichment pattern for genes retrieved by Cos-seq. We generated a L. infantum DHFR-TS null mutant that was thymidine auxotroph, a phenotype that could be rescued by the addition of thymidine or by transfection of the flavin dependent bacterial TS gene ThyX. In these DHFR-TS null mutants it was impossible to obtain a chromosomal null mutant of PTR1 except if DHFR-TS or PTR1 were provided episomally. The transfection of ThyX however did not allow the elimination of PTR1 in a DHFR-TS null mutant. Leishmania can survive without copies of either DHFR-TS or PTR1 but not without both. Provided that our results observed with the insect stage parasites are also replicated with intracellular parasites, it would suggest that antifolate therapy in Leishmania would only work if both DHFR-TS and PTR1 would be targeted simultaneously. The protozoan parasite Leishmania is auxotroph for folate and unconjugated pterins and salvages both from the mammalian host. Two enzymes of the folate metabolism pathway, namely the bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) and the pteridine reductase 1 (PTR1), are being evaluated for drug discovery and repurposing of existing anti-metabolites. Despite their apparent potential, development of DHFR-TS and PTR1 targeted chemotherapy against Leishmania is still awaiting. Here we revisited folate metabolism at the genomic level and report on the identification of known resistance genes alongside some new ones. Through gene disruption studies we found that L. infantum DHFR-TS null mutants are thymidine auxotroph and that these can be rescued by the bacterial flavin dependent thymidylate synthase ThyX. We also found that PTR1 is essential in the absence of a functional DHFR-TS even in the presence of ThyX or thymidine supplementation, indicating the essential role of reduced pterins or folate beyond thymidine synthesis. This study indicates that simultaneous targeting of DHFR-TS and PTR1 will be required for the development of anti-folate chemotherapy against Leishmania.
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Bezerra GA, Holenstein A, Foster WR, Xie B, Hicks KG, Bürer C, Lutz S, Mukherjee A, Sarkar D, Bhattacharya D, Rutter J, Talukdar A, Brown PJ, Luo M, Shi L, Froese DS, Yue WW. Identification of small molecule allosteric modulators of 5,10-methylenetetrahydrofolate reductase (MTHFR) by targeting its unique regulatory domain. Biochimie 2021; 183:100-107. [PMID: 33476699 PMCID: PMC8040968 DOI: 10.1016/j.biochi.2021.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/12/2021] [Accepted: 01/12/2021] [Indexed: 12/26/2022]
Abstract
The folate and methionine cycles, constituting one-carbon metabolism, are critical pathways for cell survival. Intersecting these two cycles, 5,10-methylenetetrahydrofolate reductase (MTHFR) directs one-carbon units from the folate to methionine cycle, to be exclusively used for methionine and S-adenosylmethionine (AdoMet) synthesis. MTHFR deficiency and upregulation result in diverse disease states, rendering it an attractive drug target. The activity of MTHFR is inhibited by the binding of AdoMet to an allosteric regulatory domain distal to the enzyme's active site, which we have previously identified to constitute a novel fold with a druggable pocket. Here, we screened 162 AdoMet mimetics using differential scanning fluorimetry, and identified 4 compounds that stabilized this regulatory domain. Three compounds were sinefungin analogues, closely related to AdoMet and S-adenosylhomocysteine (AdoHcy). The strongest thermal stabilisation was provided by (S)-SKI-72, a potent inhibitor originally developed for protein arginine methyltransferase 4 (PRMT4). Using surface plasmon resonance, we confirmed that (S)-SKI-72 binds MTHFR via its allosteric domain with nanomolar affinity. Assay of MTHFR activity in the presence of (S)-SKI-72 demonstrates inhibition of purified enzyme with sub-micromolar potency and endogenous MTHFR from HEK293 cell lysate in the low micromolar range, both of which are lower than AdoMet. Nevertheless, unlike AdoMet, (S)-SKI-72 is unable to completely abolish MTHFR activity, even at very high concentrations. Combining binding assays, kinetic characterization and compound docking, this work indicates the regulatory domain of MTHFR can be targeted by small molecules and presents (S)-SKI-72 as an excellent candidate for development of MTHFR inhibitors.
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Affiliation(s)
- Gustavo A Bezerra
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, UK
| | - Alexander Holenstein
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Switzerland
| | - William R Foster
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, UK
| | - Bing Xie
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, USA
| | - Kevin G Hicks
- Department of Biochemistry, University of Utah School of Medicine, USA
| | - Céline Bürer
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Switzerland
| | - Seraina Lutz
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Switzerland
| | - Ayan Mukherjee
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - Dipika Sarkar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - Debomita Bhattacharya
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, USA
| | - Arindam Talukdar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Minkui Luo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Program of Pharmacology, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, USA
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Switzerland.
| | - Wyatt W Yue
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, UK.
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Antioxidant Function and Metabolomics Study in Mice after Dietary Supplementation with Methionine. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9494528. [PMID: 33145362 PMCID: PMC7596454 DOI: 10.1155/2020/9494528] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/15/2020] [Indexed: 01/11/2023]
Abstract
The antioxidant function and metabolic profiles in mice after dietary supplementation with methionine were investigated. The results showed that methionine supplementation enhanced liver GSH-Px activity and upregulated Gpx1 expression in the liver and SOD1 and Gpx4 expressions in the jejunum. Nrf2/Keap1 is involved in oxidative stress, and the western blotting data exhibited that dietary methionine markedly increased Keap1 abundance, while failed to influence the Nrf2 signal. Metabolomics investigation showed that methionine administration increased 2-hydroxypyridine, salicin, and asparagine and reduced D-Talose, maltose, aminoisobutyric acid, and inosine 5'-monophosphate in the liver, which are widely reported to involve in oxidative stress, lipid metabolism, and nucleotides generation. In conclusion, our study provides insights into antioxidant function and liver metabolic profiles in response to dietary supplementation with methionine.
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13
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Van den Kerkhof M, Sterckx YGJ, Leprohon P, Maes L, Caljon G. Experimental Strategies to Explore Drug Action and Resistance in Kinetoplastid Parasites. Microorganisms 2020; 8:E950. [PMID: 32599761 PMCID: PMC7356981 DOI: 10.3390/microorganisms8060950] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 06/22/2020] [Indexed: 12/17/2022] Open
Abstract
Kinetoplastids are the causative agents of leishmaniasis, human African trypanosomiasis, and American trypanosomiasis. They are responsible for high mortality and morbidity in (sub)tropical regions. Adequate treatment options are limited and have several drawbacks, such as toxicity, need for parenteral administration, and occurrence of treatment failure and drug resistance. Therefore, there is an urgency for the development of new drugs. Phenotypic screening already allowed the identification of promising new chemical entities with anti-kinetoplastid activity potential, but knowledge on their mode-of-action (MoA) is lacking due to the generally applied whole-cell based approach. However, identification of the drug target is essential to steer further drug discovery and development. Multiple complementary techniques have indeed been used for MoA elucidation. In this review, the different 'omics' approaches employed to define the MoA or mode-of-resistance of current reference drugs and some new anti-kinetoplastid compounds are discussed.
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Affiliation(s)
- Magali Van den Kerkhof
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (M.V.d.K.); (L.M.)
| | - Yann G.-J. Sterckx
- Laboratory of Medical Biochemistry (LMB), University of Antwerp, 2610 Wilrijk, Belgium;
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie du Centre de Recherche du Centre Hospitalier Universitaire de Québec, Université Laval, Québec, QC G1V 0A6, Canada;
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (M.V.d.K.); (L.M.)
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (M.V.d.K.); (L.M.)
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14
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Campagnaro GD, de Koning HP. Purine and pyrimidine transporters of pathogenic protozoa - conduits for therapeutic agents. Med Res Rev 2020; 40:1679-1714. [PMID: 32144812 DOI: 10.1002/med.21667] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/12/2020] [Accepted: 02/18/2020] [Indexed: 02/06/2023]
Abstract
Purines and pyrimidines are essential nutrients for any cell. Most organisms are able to synthesize their own purines and pyrimidines, but this ability was lost in protozoans that adapted to parasitism, leading to a great diversification in transporter activities in these organisms, especially for the acquisition of amino acids and nucleosides from their hosts throughout their life cycles. Many of these transporters have been shown to have sufficiently different substrate affinities from mammalian transporters, making them good carriers for therapeutic agents. In this review, we summarize the knowledge obtained on purine and pyrimidine activities identified in protozoan parasites to date and discuss their importance for the survival of these parasites and as drug carriers, as well as the perspectives of developments in the field.
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Affiliation(s)
- Gustavo D Campagnaro
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 120 University Place, Glasgow, UK
| | - Harry P de Koning
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 120 University Place, Glasgow, UK
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