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Structural and computational studies of HIV-1 RNA.

ABSTRACT: Viruses remain a global threat to animals, plants, and humans. The type 1 human immunodeficiency virus (HIV-1) is a member of the retrovirus family and carries an RNA genome, which is reverse transcribed into viral DNA and further integrated into the host-cell DNA for viral replication and proliferation. The RNA structures from the HIV-1 genome provide valuable insights into the mechanisms underlying the viral replication cycle. Moreover, these structures serve as models for designing novel therapeutic approaches. Here, we review structural data on RNA from the HIV-1 genome as well as computational studies based on these structural data. The review is organized according to the type of structured RNA element which contributes to different steps in the viral replication cycle. This is followed by an overview of the HIV-1 transactivation response element (TAR) RNA as a model system for understanding dynamics and interactions in the viral RNA systems. The review concludes with a description of computational studies, highlighting the impact of biomolecular simulations in elucidating the mechanistic details of various steps in the HIV-1's replication cycle.

SUBMITTER: Levintov L

PROVIDER: S-EPMC10730233 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature

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Structural and computational studies of HIV-1 RNA.

Levintov Lev L Vashisth Harish H

RNA biology 20231215 1

Viruses remain a global threat to animals, plants, and humans. The type 1 human immunodeficiency virus (HIV-1) is a member of the retrovirus family and carries an RNA genome, which is reverse transcribed into viral DNA and further integrated into the host-cell DNA for viral replication and proliferation. The RNA structures from the HIV-1 genome provide valuable insights into the mechanisms underlying the viral replication cycle. Moreover, these structures serve as models for designing novel ther ...[more]

PMID: 38100535

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Project description:We report herein on the solid-state structures of three closely related triphenylamine derivatives endowed with tricyanovinyl (TCV) and dicyanovinyl (DCV) groups. The molecules described contain structural features commonly found in the design of functional organic materials, especially donor-acceptor molecular and polymeric architectures. The common feature noticeable in these structures is the impact of these exceptionally strong electron-accepting groups in forcing partial planarity of the portion of the molecule carrying these groups and directing the molecular packing in the solid state, resulting in the formation of π-stacks of dimers within the unit cell of each. Stacks are formed between phenyl groups bearing electron-accepting groups on two adjacent molecules. Short π-π stack distances ranging from 3.283 to 3.671 Å were observed. Such motif patterns are thought to be conducive for better charge transport in organic semiconductors and enhanced device performance. Intramolecular charge transfer is evident from the shortening of the observed experimental bond lengths in all three compounds. The nitrogen atoms (of the cyano groups) have been shown to be extensively involved in short contacts in all three structures, primarily through C-H···NC interactions with distances as short as 2.462 Å. The compounds reported here are (3,3-dicyano-2-(4-(diphenylamino)phenyl)-1λ3-allylidene)amide or tricyanovinyltriphenylamine, Ph3NTCV (1); 2-(4-(diphenylamino)benzylidene)-malononitrile or dicyanovinyltriphenylamine, Ph3NDCV (2); and (3,3-dicyano-2-(4-(di-p-tolylamino)phenyl)-1λ3-allylidene)amide or dimethyltricyanovinyltriphenylamine, Me2Ph3NTCV (3). Results of density functional theory calculations using DFT-B3LYP/6-31G(d,p) indicate the lowering of LUMO levels as a result of the introduction of these groups with band gaps of 3.13, 2.61, and 2.55 eV for compounds 1-3, respectively, compared with 4.65 eV calculated for triphenylamine. This is supported by the electronic and fluorescence spectra of these molecules with absorption λmax of 483, 515, and 545 nm for compounds 1, 2, and 3, respectively.

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Structural and computational studies of HIV-1 RNA.

Publications

Structural and computational studies of HIV-1 RNA.

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