1
|
Uppuladinne MVN, Achalere A, Sonavane U, Joshi R. Probing the structure of human tRNA 3Lys in the presence of ligands using docking, MD simulations and MSM analysis. RSC Adv 2023; 13:25778-25796. [PMID: 37655355 PMCID: PMC10467029 DOI: 10.1039/d3ra03694d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/14/2023] [Indexed: 09/02/2023] Open
Abstract
The tRNA3Lys, which acts as a primer for human immunodeficiency virus type 1 (HIV-1) reverse transcription, undergoes structural changes required for the formation of a primer-template complex. Small molecules have been targeted against tRNA3Lys to inhibit the primer-template complex formation. The present study aims to understand the kinetics of the conformational landscape spanned by tRNA3Lys in apo form using molecular dynamics simulations and Markov state modeling. The study is taken further to investigate the effect of small molecules like 1,4T and 1,5T on structural conformations and kinetics of tRNA3Lys, and comparative analysis is presented. Markov state modeling of tRNA3Lys apo resulted in three metastable states where the conformations have shown the non-canonical structures of the anticodon loop. Based on analyses of ligand-tRNA3Lys interactions, crucial ion and water mediated H-bonds and free energy calculations, it was observed that the 1,4-triazole more strongly binds to the tRNA3Lys compared to 1,5-triazole. However, the MSM analysis suggest that the 1,5-triazole binding to tRNA3Lys has brought rigidity not only in the binding pocket (TΨC arm, D-TΨC loop) but also in the whole structure of tRNA3Lys. This may affect the easy opening of primer tRNA3Lys required for HIV-1 reverse transcription.
Collapse
Affiliation(s)
- Mallikarjunachari V N Uppuladinne
- High Performance Computing - Medical and Bioinformatics Applications, Centre for Development of Advanced Computing (C-DAC) Panchavati, Pashan Pune India
| | - Archana Achalere
- High Performance Computing - Medical and Bioinformatics Applications, Centre for Development of Advanced Computing (C-DAC) Panchavati, Pashan Pune India
| | - Uddhavesh Sonavane
- High Performance Computing - Medical and Bioinformatics Applications, Centre for Development of Advanced Computing (C-DAC) Panchavati, Pashan Pune India
| | - Rajendra Joshi
- High Performance Computing - Medical and Bioinformatics Applications, Centre for Development of Advanced Computing (C-DAC) Panchavati, Pashan Pune India
| |
Collapse
|
2
|
Benedetti E, Micouin L, Fleurisson C. Cyclic cis-1,3-Diamines Derived from Bicyclic Hydrazines: Synthesis and Applications. Synlett 2021. [DOI: 10.1055/s-0040-1707324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractCyclic cis-1,3-diamines are versatile building blocks frequently found in natural molecules or biologically active compounds. In comparison with widely studied 1,2-diamines, and despite their chemical similarity, 1,3-diamines have been investigated less intensively probably because of a lack of general synthetic procedures giving access to these compounds with good levels of chemo-, regio-, and stereocontrol. In this Account we will give a general overview of the biological interest of cyclic cis-1,3-diamines. We will then describe the synthesis and potential applications of these compounds with a particular focus on the work realized in our laboratory.1 Introduction2 Biological Relevance of the cis-1,3-Diamine Motif3 Classical Synthetic Strategies towards cis-1,3-Diamines4 N–N Bond Cleavage of Bicyclic Hydrazines: A Versatile Method to Access cis-1,3-Diamines4.1 Preparation of Five-Membered Cyclic cis-1,3-Diamino Alcohols4.2 Access to Fluorinated 1,3-cis-Diaminocyclopentanes4.3 Synthesis of cis-1,3-Diaminocyclohexitols4.4 Formation of Cyclic cis-3,5-Diaminopiperidines5 Applications of Cyclic cis-1,3-Diamines5.1 Small-Molecular RNA Binders5.2 Fluorinated 1,3-Diamino Cyclopentanes as NMR Probes6 Concluding Remarks
Collapse
Affiliation(s)
| | - Laurent Micouin
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques – UMR8601 CNRS Université de Paris
| | | |
Collapse
|
3
|
Blond A, Ennifar E, Tisné C, Micouin L. The design of RNA binders: targeting the HIV replication cycle as a case study. ChemMedChem 2014; 9:1982-96. [PMID: 25100137 DOI: 10.1002/cmdc.201402259] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Indexed: 01/08/2023]
Abstract
The human immunodeficiency virus 1 (HIV-1) replication cycle is finely tuned with many important steps involving RNA-RNA or protein-RNA interactions, all of them being potential targets for the development of new antiviral compounds. This cycle can also be considered as a good benchmark for the evaluation of early-stage strategies aiming at designing drugs that bind to RNA, with the possibility to correlate in vitro activities with antiviral properties. In this review, we highlight different approaches developed to interfere with four important steps of the HIV-1 replication cycle: the early stage of reverse transcription, the transactivation of viral transcription, the nuclear export of partially spliced transcripts and the dimerization step.
Collapse
Affiliation(s)
- Aurélie Blond
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601, CNRS, Université Paris Descartes, Sorbonne Paris Cité, Faculté des Sciences Fondamentales et Biomédicales, 45 Rue des Saints Pères, 75006 Paris (France)
| | | | | | | |
Collapse
|
4
|
|
5
|
Moumné R, Catala M, Larue V, Micouin L, Tisné C. Fragment-based design of small RNA binders: Promising developments and contribution of NMR. Biochimie 2012; 94:1607-19. [DOI: 10.1016/j.biochi.2012.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 02/01/2012] [Indexed: 02/06/2023]
|
6
|
Isel C, Ehresmann C, Marquet R. Initiation of HIV Reverse Transcription. Viruses 2010; 2:213-243. [PMID: 21994608 PMCID: PMC3185550 DOI: 10.3390/v2010213] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 01/08/2010] [Accepted: 01/13/2010] [Indexed: 12/01/2022] Open
Abstract
Reverse transcription of retroviral genomes into double stranded DNA is a key event for viral replication. The very first stage of HIV reverse transcription, the initiation step, involves viral and cellular partners that are selectively packaged into the viral particle, leading to an RNA/protein complex with very specific structural and functional features, some of which being, in the case of HIV-1, linked to particular isolates. Recent understanding of the tight spatio-temporal regulation of reverse transcription and its importance for viral infectivity further points toward reverse transcription and potentially its initiation step as an important drug target.
Collapse
Affiliation(s)
- Catherine Isel
- Authors to whom correspondence should be addressed; E-Mail: ; Tel.: +33-388-417-040; Fax: +33-388-602-218 (C.I.); E-Mail: ; Tel.: +33-388-417-054; Fax: +33-388-602-218 (R.M.)
| | | | - Roland Marquet
- Authors to whom correspondence should be addressed; E-Mail: ; Tel.: +33-388-417-040; Fax: +33-388-602-218 (C.I.); E-Mail: ; Tel.: +33-388-417-054; Fax: +33-388-602-218 (R.M.)
| |
Collapse
|
7
|
Chung F, Tisné C, Lecourt T, Seijo B, Dardel F, Micouin L. Design of tRNALys3Ligands: Fragment Evolution and Linker Selection Guided by NMR Spectroscopy. Chemistry 2009; 15:7109-16. [DOI: 10.1002/chem.200802451] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
8
|
Kaushik-Basu N, Basu A, Harris D. Peptide inhibition of HIV-1: current status and future potential. BioDrugs 2008; 22:161-75. [PMID: 18481899 DOI: 10.2165/00063030-200822030-00003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
More than 2 decades of intensive research has focused on defining replication mechanisms of HIV type 1 (HIV-1), the etiologic agent of AIDS. The delineation of strategies for combating this viral infection has yielded many innovative approaches toward this end. HIV-1 is a lentivirus in the family retroviridae that is relatively small with regard to both structure and genome size, having a diploid RNA genome of approximately 9 kb, with only three major genes and several gene products resulting from alternate splicing and translational frameshifting. Most marketed drugs for treating AIDS are inhibitors of HIV-1 reverse transcriptase or protease enzymes, but new targets include the integrase enzyme, cell surface interactions that facilitate viral entry, and also virus particle maturation and assembly. The emergence of drug-resistant variants of HIV-1 has been the main impediment to successful treatment of AIDS. Thus, there is a pressing need to develop novel treatment strategies targeting multiple stages of the virus life-cycle. Research efforts aimed at developing successful means for combating HIV-1 infection have included development of peptide inhibitors of HIV-1. This article summarizes past and current endeavors in the development of peptides that inhibit replication of HIV-1 and the role of peptide inhibitors in the search for new anti-HIV drugs.
Collapse
Affiliation(s)
- Neerja Kaushik-Basu
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, Newark, NJ 07103, USA.
| | | | | |
Collapse
|
9
|
Chung F, Tisné C, Lecourt T, Dardel F, Micouin L. NMR-guided fragment-based approach for the design of tRNA(Lys3) ligands. Angew Chem Int Ed Engl 2007; 46:4489-91. [PMID: 17486554 DOI: 10.1002/anie.200605201] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Florence Chung
- Chimie Thérapeutique, Université Paris Descartes, CNRS, 4 avenue de l'Observatoire, 75006 Paris, France
| | | | | | | | | |
Collapse
|
10
|
Chung F, Tisné C, Lecourt T, Dardel F, Micouin L. NMR-Guided Fragment-Based Approach for the Design of tRNALys3 Ligands. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200605201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
11
|
Eshete M, Marchbank MT, Deutscher SL, Sproat B, Leszczynska G, Malkiewicz A, Agris PF. Specificity of Phage Display Selected Peptides for Modified Anticodon Stem and Loop Domains of tRNA. Protein J 2007; 26:61-73. [PMID: 17237992 DOI: 10.1007/s10930-006-9046-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein recognition of RNA has been studied using Peptide Phage Display Libraries, but in the absence of RNA modifications. Peptides from two libraries, selected for binding the modified anticodon stem and loop (ASL) of human tRNA(LyS3) having 2-thiouridine (s(2)U34) and pseudouridine (psi39), bound the modified human ASL(Lys3)(s(2)U34;psi39) preferentially and had significant homology with RNA binding proteins. Selected peptides were narrowed to a manageable number using a less sensitive, but inexpensive assay before conducting intensive characterization. The affinity and specificity of the best binding peptide (with an N-terminal fluorescein) were characterized by fluorescence spectrophotometry. The peptide exhibited the highest binding affinity for ASL(LYS3)(s(2)U34; psi39), followed by the hypermodified ASL(Lys3) (mcm(5)s(2) U34; ms(2)t(6)A37) and the unmodified ASL(Lys3), but bound poorly to singly modified ASL(Lys3) constructs (psi39, ms(2)t(6)A37, s(2)34), ASL(Lys1,2) (t(6)A37) and Escherichia coli ASL(Glu) (s(2)U34). Thus, RNA modifications are potentially important recognition elements for proteins and can be targets for selective recognition by peptides.
Collapse
Affiliation(s)
- Matthewos Eshete
- Department of Molecular and Structural Biochemistry, North Carolina State University, 128 Polk Hall, Campus Box 7622, Raleigh, NC, 27695-7622, USA
| | | | | | | | | | | | | |
Collapse
|