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Sherpa C, Rausch JW, Le Grice SFJ. HIV Genetic Diversity - Superpower of a Formidable Virus. Curr HIV Res 2021; 18:69-73. [PMID: 32223727 DOI: 10.2174/1570162x1802200311104204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Chringma Sherpa
- Basic Research Laboratory Center for Cancer Research National Cancer Institute National Institute of Health Frederick, Maryland, 21702, United States
| | - Jason W Rausch
- Basic Research Laboratory Center for Cancer Research National Cancer Institute National Institute of Health Frederick, MD, 21702, United States
| | - Stuart F J Le Grice
- Basic Research Laboratory Center for Cancer Research National Cancer Institute National Institute of Health Frederick, MD, 21702, United States
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Sherpa C, Le Grice SFJ. Adeno-Associated Viral Vector Mediated Expression of Broadly- Neutralizing Antibodies Against HIV-Hitting a Fast-Moving Target. Curr HIV Res 2021; 18:114-131. [PMID: 32039686 DOI: 10.2174/1570162x18666200210121339] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/05/2020] [Accepted: 01/16/2020] [Indexed: 12/12/2022]
Abstract
The vast genetic variability of HIV has impeded efforts towards a cure for HIV. Lifelong administration of combined antiretroviral therapy (cART) is highly effective against HIV and has markedly increased the life expectancy of HIV infected individuals. However, the long-term usage of cART is associated with co-morbidities and the emergence of multidrug-resistant escape mutants necessitating the development of alternative approaches to combat HIV/AIDS. In the past decade, the development of single-cell antibody cloning methods has facilitated the characterization of a diverse array of highly potent neutralizing antibodies against a broad range of HIV strains. Although the passive transfer of these broadly neutralizing antibodies (bnAbs) in both animal models and humans has been shown to elicit significant antiviral effects, long term virologic suppression requires repeated administration of these antibodies. Adeno-associated virus (AAV) mediated antibody gene transfer provides a long-term expression of these antibodies from a single administration of the recombinant vector. Therefore, this vectored approach holds promises in the treatment and prevention of a chronic disease like HIV infection. Here, we provide an overview of HIV genetic diversity, AAV vectorology, and anti-HIV bnAbs and summarize the promises and challenges of the application of AAV in the delivery of bnAbs for HIV prevention and therapy.
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Affiliation(s)
- Chringma Sherpa
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, Maryland, 21702, United States
| | - Stuart F J Le Grice
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, Maryland, 21702, United States
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Rausch JW, Heinz WF, Payea MJ, Sherpa C, Gorospe M, Le Grice SFJ. Characterizing and circumventing sequence restrictions for synthesis of circular RNA in vitro. Nucleic Acids Res 2021; 49:e35. [PMID: 33406226 DOI: 10.1093/nar/gkaa1256] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/27/2020] [Accepted: 12/18/2020] [Indexed: 01/10/2023] Open
Abstract
Just as eukaryotic circular RNA (circRNA) is a product of intracellular backsplicing, custom circRNA can be synthesized in vitro using a transcription template in which transposed halves of a split group I intron flank the sequence of the RNA to be circularized. Such permuted intron-exon (PIE) constructs have been used to produce circRNA versions of ribozymes, mimics of viral RNA motifs, a streptavidin aptamer, and protein expression vectors for genetic engineering and vaccine development. One limitation of this approach is the obligatory incorporation of small RNA segments (E1 and E2) into nascent circRNA at the site of end-joining. This restriction may preclude synthesis of small circRNA therapeutics and RNA nanoparticles that are sensitive to extraneous sequence, as well as larger circRNA mimics whose sequences must precisely match those of the native species on which they are modelled. In this work, we used serial mutagenesis and in vitro selection to determine how varying E1 and E2 sequences in a thymidylate synthase (td) group I intron PIE transcription template construct affects circRNA synthesis yield. Based on our collective findings, we present guidelines for the design of custom-tailored PIE transcription templates from which synthetic circRNAs of almost any sequence may be efficiently synthesized.
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Affiliation(s)
- Jason W Rausch
- Basic Research Laboratory, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Matthew J Payea
- Laboratory of Genetics and Genomics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Chringma Sherpa
- Basic Research Laboratory, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Stuart F J Le Grice
- Basic Research Laboratory, National Cancer Institute, NIH, Frederick, MD 21702, USA
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Sherpa C, Grice SFJL. Structural Fluidity of the Human Immunodeficiency Virus Rev Response Element. Viruses 2020; 12:v12010086. [PMID: 31940828 PMCID: PMC7019801 DOI: 10.3390/v12010086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 12/03/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 01/22/2023] Open
Abstract
Nucleocytoplasmic transport of unspliced and partially spliced human immunodeficiency virus (HIV) RNA is mediated in part by the Rev response element (RRE), a ~350 nt cis-acting element located in the envelope coding region of the viral genome. Understanding the interaction of the RRE with the viral Rev protein, cellular co-factors, and its therapeutic potential has been the subject of almost three decades of structural studies, throughout which a recurring discussion theme has been RRE topology, i.e., whether it comprises 4 or 5 stem-loops (SLs) and whether this has biological significance. Moreover, while in vitro mutagenesis allows the construction of 4 SL and 5 SL RRE conformers and testing of their roles in cell culture, it has not been immediately clear if such findings can be translated to a clinical setting. Herein, we review several articles demonstrating remarkable flexibility of the HIV-1 and HIV-2 RREs following initial observations that HIV-1 resistance to trans-dominant Rev therapy was founded in structural rearrangement of its RRE. These observations can be extended not only to cell culture studies demonstrating a growth advantage for the 5 SL RRE conformer but also to evolution in RRE topology in patient isolates. Finally, RRE conformational flexibility provides a target for therapeutic intervention, and we describe high throughput screening approaches to exploit this property.
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Sherpa C, Rausch JW, Le Grice SF. Structural characterization of maternally expressed gene 3 RNA reveals conserved motifs and potential sites of interaction with polycomb repressive complex 2. Nucleic Acids Res 2019; 46:10432-10447. [PMID: 30102382 PMCID: PMC6212721 DOI: 10.1093/nar/gky722] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/30/2018] [Indexed: 12/15/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as key players in gene regulation. However, our incomplete understanding of the structure of lncRNAs has hindered molecular characterization of their function. Maternally expressed gene 3 (Meg3) lncRNA is a tumor suppressor that is downregulated in various types of cancer. Mechanistic studies have reported a role for Meg3 in epigenetic regulation by interacting with chromatin-modifying complexes such as the polycomb repressive complex 2 (PRC2), guiding them to genomic sites via DNA-RNA triplex formation. Resolving the structure of Meg3 RNA and characterizing its interactions with cellular binding partners will deepen our understanding of tumorigenesis and provide a framework for RNA-based anti-cancer therapies. Herein, we characterize the architectural landscape of Meg3 RNA and its interactions with PRC2 from a functional standpoint.
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Affiliation(s)
- Chringma Sherpa
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD 21702, USA
| | - Jason W Rausch
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD 21702, USA
| | - Stuart Fj Le Grice
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD 21702, USA
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Abstract
Targeting RNA offers the potential in many diseases of a therapeutic treatment. Due to its large surface area and ability to adopt different conformations, targeting RNA has proven challenging. Medium-sized branched peptides are of the size to competitively bind RNA while remaining cell permeable, stable in vivo, and non-toxic. Additionally, the ease in generating a large library followed by high-throughput screening provides a way to suggest a scaffold with high diversity that is capable of targeting the structure and sequence of RNA. The ability to select various types of amino acid modifications in the branched peptide allows for variable structures and interactions of the branched peptide but can result in too large a task if not approached properly. In this chapter, we discuss a strategy to selectively recognize RNAs of interest through high throughput screening of branched peptides, validation of hits and biophysical characterization, leading by example with our experience in targeting HIV-1 RNAs with branched peptides.
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Affiliation(s)
- Ashley N Peralta
- Department of Chemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, VA, United States
| | - Yumin Dai
- Department of Chemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, VA, United States
| | - Chringma Sherpa
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, United States
| | - Stuart F J Le Grice
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, United States
| | - Webster L Santos
- Department of Chemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, VA, United States.
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Dai Y, Peralta AN, Wynn JE, Sherpa C, Li H, Verma A, Le Grice SFJ, Santos WL. Molecular recognition of a branched peptide with HIV-1 Rev Response Element (RRE) RNA. Bioorg Med Chem 2019; 27:1759-1765. [PMID: 30879859 PMCID: PMC6476629 DOI: 10.1016/j.bmc.2019.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/01/2019] [Accepted: 03/06/2019] [Indexed: 01/27/2023]
Abstract
Interaction of HIV-1 rev response element (RRE) RNA with its cognate protein, Rev, is critical for HIV-1 replication. Understanding the mode of interaction between RRE RNA and ligands at the binding site can facilitate RNA molecular recognition as well as provide a strategy for developing anti-HIV therapeutics. Our approach utilizes branched peptides as a scaffold for multivalent binding to RRE IIB (high affinity rev binding site) with incorporation of unnatural amino acids to increase affinity via non-canonical interactions with the RNA. Previous high throughput screening of a 46,656-member library revealed several hits that bound RRE IIB RNA in the sub-micromolar range. In particular, the lead compound, 4B3, displayed a Kd value of 410 nM and demonstrated selectivity towards RRE. A ribonuclease protection assay revealed that 4B3 binds to the stem-loop structure of RRE IIB RNA, which was confirmed by SHAPE analysis with 234 nt long NL4-3 RRE RNA. Our studies further indicated interaction of 4B3 with both primary and secondary Rev binding sites.
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Affiliation(s)
- Yumin Dai
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Ashley N Peralta
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Jessica E Wynn
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Chringma Sherpa
- Basic Research Laboratory, National Cancer Institute, Frederick, MD 21702, United States
| | - Hao Li
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Astha Verma
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Stuart F J Le Grice
- Basic Research Laboratory, National Cancer Institute, Frederick, MD 21702, United States
| | - Webster L Santos
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States.
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Dai Y, Wynn JE, Peralta AN, Sherpa C, Jayaraman B, Li H, Verma A, Frankel AD, Le Grice SF, Santos WL. Discovery of a Branched Peptide That Recognizes the Rev Response Element (RRE) RNA and Blocks HIV-1 Replication. J Med Chem 2018; 61:9611-9620. [PMID: 30289719 PMCID: PMC6557124 DOI: 10.1021/acs.jmedchem.8b01076] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We synthesized and screened a unique 46 656-member library composed of unnatural amino acids that revealed several hits against RRE IIB RNA. Among the hit peptides identified, peptide 4A5 was found to be selective against competitor RNAs and inhibited HIV-1 Rev-RRE RNA interaction in cell culture in a p24 ELISA assay. Biophysical characterization in a ribonuclease protection assay suggested that 4A5 bound to the stem-loop region in RRE IIB while SHAPE MaP probing with 234 nt RRE RNA indicated additional interaction with secondary Rev binding sites. Taken together, our investigation suggests that HIV replication is inhibited by 4A5 blocking binding of Rev and subsequent multimerization.
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Affiliation(s)
- Yumin Dai
- Department of Chemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia, 24060, United States
| | - Jessica E. Wynn
- Department of Chemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia, 24060, United States
| | - Ashley N. Peralta
- Department of Chemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia, 24060, United States
| | - Chringma Sherpa
- Basic Research Laboratory, National Cancer Institute, Frederick, Maryland, 21702, United States
| | - Bhargavi Jayaraman
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, 94158, United States
| | - Hao Li
- Department of Chemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia, 24060, United States
| | - Astha Verma
- Department of Chemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia, 24060, United States
| | - Alan D. Frankel
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, 94158, United States
| | - Stuart F. Le Grice
- Basic Research Laboratory, National Cancer Institute, Frederick, Maryland, 21702, United States
| | - Webster L. Santos
- Department of Chemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia, 24060, United States
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Crawford DW, Blakeley BD, Chen PH, Sherpa C, Le Grice SF, Laird-Offringa IA, McNaughton BR. An Evolved RNA Recognition Motif That Suppresses HIV-1 Tat/TAR-Dependent Transcription. ACS Chem Biol 2016; 11:2206-15. [PMID: 27253715 DOI: 10.1021/acschembio.6b00145] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Potent and selective recognition and modulation of disease-relevant RNAs remain a daunting challenge. We previously examined the utility of the U1A N-terminal RNA recognition motif as a scaffold for tailoring new RNA hairpin recognition and showed that as few as one or two mutations can result in moderate affinity (low μM dissociation constant) for the human immunodeficiency virus (HIV) trans-activation response element (TAR) RNA, an RNA hairpin controlling transcription of the human immunodeficiency virus (HIV) genome. Here, we use yeast display and saturation mutagenesis of established RNA-binding regions in U1A to identify new synthetic proteins that potently and selectively bind TAR RNA. Our best candidate has truly altered, not simply broadened, RNA-binding selectivity; it binds TAR with subnanomolar affinity (apparent dissociation constant of ∼0.5 nM) but does not appreciably bind the original U1A RNA target (U1hpII). It specifically recognizes the TAR RNA hairpin in the context of the HIV-1 5'-untranslated region, inhibits the interaction between TAR RNA and an HIV trans-activator of transcription (Tat)-derived peptide, and suppresses Tat/TAR-dependent transcription. Proteins described in this work are among the tightest TAR RNA-binding reagents-small molecule, nucleic acid, or protein-reported to date and thus have potential utility as therapeutics and basic research tools. Moreover, our findings demonstrate how a naturally occurring RNA recognition motif can be dramatically resurfaced through mutation, leading to potent and selective recognition-and modulation-of disease-relevant RNA.
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Affiliation(s)
| | | | - Po-Han Chen
- Department of Surgery and Department of Biochemistry & Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90033, United States
| | - Chringma Sherpa
- Basic
Research Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Stuart F.J. Le Grice
- Basic
Research Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ite A. Laird-Offringa
- Department of Surgery and Department of Biochemistry & Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90033, United States
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Sherpa C, Rausch JW, Le Grice SFJ, Hammarskjold ML, Rekosh D. The HIV-1 Rev response element (RRE) adopts alternative conformations that promote different rates of virus replication. Nucleic Acids Res 2015; 43:4676-86. [PMID: 25855816 PMCID: PMC4482075 DOI: 10.1093/nar/gkv313] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/27/2015] [Indexed: 01/03/2023] Open
Abstract
The HIV Rev protein forms a complex with a 351 nucleotide sequence present in unspliced and incompletely spliced human immunodeficiency virus (HIV) mRNAs, the Rev response element (RRE), to recruit the cellular nuclear export receptor Crm1 and Ran-GTP. This complex facilitates nucleo-cytoplasmic export of these mRNAs. The precise secondary structure of the HIV-1 RRE has been controversial, since studies have reported alternative structures comprising either four or five stem-loops. The published structures differ only in regions that lie outside of the primary Rev binding site. Using in-gel SHAPE, we have now determined that the wt NL4-3 RRE exists as a mixture of both structures. To assess functional differences between these RRE ‘conformers’, we created conformationally locked mutants by site-directed mutagenesis. Using subgenomic reporters, as well as HIV replication assays, we demonstrate that the five stem-loop form of the RRE promotes greater functional Rev/RRE activity compared to the four stem-loop counterpart.
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Affiliation(s)
- Chringma Sherpa
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Jason W Rausch
- Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Stuart F J Le Grice
- Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Marie-Louise Hammarskjold
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - David Rekosh
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
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Gurung TD, Sherpa C, Agrawal VP, Lekhak B. Isolation and Characterization of Antibacterial Actinomycetes from Soil Samples of Kalapatthar, Mount Everest Region. ACTA ACUST UNITED AC 1970. [DOI: 10.3126/njst.v10i0.2957] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Seventy-nine Actinomycetes were isolated from soils of Kalapatthar (5545m), Mount Everest region. Twenty seven (34.18%) of the isolates showed an antibacterial activity against at least one test-bacteria among two Gram positive and nine Gram negative bacteria in primary screening by perpendicular streak method. Thirteen (48.15%) showed antibacterial activity in secondary screening. The result showed that three of the isolates, K.6.3, K.14.2, and K.58.5 were highly active with an inhibition zone e"20mm and broad spectrum antibacterial activity including two methicillin resistant Staphylococcus aureus (MRSA) strains. Minimum inhibitory concentration (MIC) of antibacterial metabolites of the isolate K.6.3 was 1mg/ml, and that of isolates K.14.2 and K.58.5 was 2mg/ml. Two spots were detected on thin layer chromatography plate from each of the metabolites which was completely different from the spot produced by vancomycin. The active isolates from primary screening were heterogeneous in their overall macroscopic, biochemical, and physiological characteristics through unweighted pair group method using average (UPGMA) cluster analysis. Delineation of the three active isolates showing potent broad spectrum antibacterial activity revealed that they belonged to distinct taxonomic groups.Key words: Antibacterial activity; Minimum inhibitory concentration; Thin layer chromatographyDOI: 10.3126/njst.v10i0.2957Nepal Journal of Science and Technology Vol. 10, 2009 Page: 173-182
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