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Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses.

Badger J, Minor I, Oliveira MA, Smith TJ, Rossmann MG
Proteins 6 1-19 (1989)
Related entries: 1r08, 1rmu, 2r06, 2r07, 2rm2, 2rmu, 2rr1, 2rs1, 2rs3, 2rs5

Cited: 30 times
EuropePMC logo PMID: 2558377

Abstract

X-Ray diffraction data have been obtained for nine related antiviral agents ("WIN compounds") while bound to human rhinovirus 14 (HRV14). These compounds can inhibit both viral attachment to host cells and uncoating. To calculate interpretable electron density maps it was necessary to account for (1) the low (approximately 60%) occupancies of these compounds in the crystal, (2) the large (up to 7.9 A) conformational changes induced at the attachment site, and (3) the incomplete diffraction data. Application of a density difference map technique, which exploits the 20-fold noncrystallographic redundancy in HRV14, resulted in clear images of the HRV14:WIN complexes. A real-space refinement procedure was used to fit atomic models to these maps. The binding site of WIN compounds in HRV14 is a hydrophobic pocket composed mainly from residues that form the beta-barrel of VP1. Among rhinoviruses, the residues associated with the binding pocket are far more conserved than external residues and are mostly contained within regular secondary structural elements. Molecular dynamics simulations of three HRV14:WIN complexes suggest that portions of the WIN compounds and viral protein near the entrance of the binding pocket are more flexible than portions deeper within the beta-barrel.

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  2. The human rhinovirus: human-pathological impact, mechanisms of antirhinoviral agents, and strategies for their discovery. Rollinger JM, Schmidtke M. Med Res Rev 31 42-92 (2011)
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  4. The Dynamic Life of Virus Capsids. Sherman MB, Smith HQ, Smith TJ. Viruses 12 E618 (2020)

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Related citations provided by authors (12)

  1. The Use of Molecular Replacement Phases for the Refinement of the Human Rhinovirus 14 Structure. Arnold E, Rossmann MG To be Published -
  2. Analysis of the Structure of a Common Cold Virus, Human Rhinovirus 14, Refined at a Resolution of 3.0 Angstroms. Arnold E, Rossmann MG To be Published -
  3. Three-dimensional structures of drug-resistant mutants of human rhinovirus 14.. Badger J, Krishnaswamy S, Kremer MJ, Oliveira MA, Rossmann MG, Heinz BA, Rueckert RR, Dutko FJ, McKinlay MA J Mol Biol 207 163-74 (1989)
  4. Structural Analysis of a Series of Antiviral Agents Complexed with Human Rhinovirus 14. Badger J, Minor I, Kremer MJ, Oliveira MA, Smith TJ, Griffith JP, Guerin DMA, Krishnaswamy S, Luo M, Rossmann MG, Mckinlay MA, Diana GD, Dutko FJ, Fancher M, Rueckert RR, Heinz BA Proc. Natl. Acad. Sci. U.S.A. 85 3304- (1988)
  5. The Structure Determination of a Common Cold Virus, Human Rhinovirus 14. Arnold E, Vriend G, Luo M, Griffith JP, Kamer G, Erickson JW, Johnson JE, Rossmann MG Acta Crystallogr., A, Found. Crystallogr. 43 346- (1987)
  6. Implications of the Picornavirus Capsid Structure for Polyprotein Structure. Arnold E, Luo M, Vriend G, Rossmann MG, Palmenberg AC, Parks GD, Nicklin MJH, Wimmer E Proc. Natl. Acad. Sci. U.S.A. 84 21- (1987)
  7. The site of attachment in human rhinovirus 14 for antiviral agents that inhibit uncoating.. Smith TJ, Kremer MJ, Luo M, Vriend G, Arnold E, Kamer G, Rossmann MG, McKinlay MA, Diana GD, Otto MJ Science 233 1286-93 (1986)
  8. The Structure of a Human Common Cold Virus (Rhinovirus 14) and its Evolutionary Relations to Other Viruses. Rossmann MG, Arnold E, Erickson JW, Frankenberger EA, Griffith JP, Hecht H-J, Johnson JE, Kamer G, Luo M, Vriend G Chem Scr 26 313- (1987)
  9. Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses. Rossmann MG, Arnold E, Erickson JW, Frankenberger EA, Griffith JP, Hecht H-J, Johnson JE, Kamer G, Luo M, Mosser AG, Rueckert RR, Sherry B, Vriend G Nature 317 145- (1985)
  10. Virion orientation in cubic crystals of the human common cold virus HRV14.. Arnold E, Erickson JW, Fout GS, Frankenberger EA, Hecht HJ, Luo M, Rossman MG, Rueckert RR J Mol Biol 177 417-30 (1984)
  11. Picornaviruses of two different genera have similar structures.. Luo M, Arnold E, Erickson JW, Rossmann MG, Boege U, Scraba DG J Mol Biol 180 703-14 (1984)
  12. Crystallization of a Common Cold Virus, Human Rhinovirus 14. (Quote)Isomorphism(Quote) with Poliovirus Crystals. Erickson JW, Frankenberger EA, Rossmann MG, Fout GS, Medappa KC, Rueckert RR Proc. Natl. Acad. Sci. U.S.A. 80 931- (1983)

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