backbone of Asn^117 and Tyr^143 and projecting
toward the bulk solvent. These bound water
molecules can be exploited for the develop-
ment of improved compounds.
Within the substrate envelope, differences
in geometry of the catalytic pockets, their over-
all volume, and the locations of bound water
molecules, among other features, all matter
for understanding INSTI interactions. The
current work highlights how small changes
in the active site modulate drug binding and
have implications for drug design. Structures
of wild-type and mutant HIV intasomes bound
to INSTIs should improve our understanding
of resistance mechanisms and lead to the de-
velopment of better drugs to be used in com-
bination antiretroviral therapy for targeting
viral escape mutants.
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ACKNOWLEDGMENTS
The authors acknowledge B. Anderson at The Scripps Research
Institute for help with EM data collection, P. Baldwin at Salk
for assistance with the local computational infrastructure,
T. Grant at Janelia Research Campus for providing the beam-tilt
refinement program, and V. Dandey at the National Resource
for Automated Molecular Microscopy (NRAMM) for early work
identifying conditions for sample vitrification.Funding:NRAMM
is supported by a grant from the National Institute of General
Medical Sciences (9 P41 GM103310) from the NIH. Molecular
graphics and analyses were performed with the UCSF Chimera
package (supported by NIH P41 GM103331). This work was
supported by NIH grants R01 AI136680 and R01 AI146017 (to D.L.),
R01 GM069832 (to S.F.), and U54 AI150472 (to D.L. and S.F.)
and by the Intramural Programs of the National Institute
of Diabetes and Digestive Diseases (R.C.), the National Cancer
Institute (X.Z.Z., T.R.B., S.J.S., and S.H.H.), and the Intramural
AIDS Targeted Antiviral Program (IATAP) of the NIH.Author
contributions:D.O.P. collected and processed cryo-EM data.
M.L. assembled and purified intasomes and performed biochemical
assays. I.K.J., D.O.P., and D.L. built and refined atomic models.
X.Z.Z. prepared the INSTIs. R.Y. purified IN. Y.J. assisted
with sample vitrification and data collection. S.J.S. determined
the effects of mutations in IN on the potency of INSTIs. S.F. and
D.S.-M. performed computational calculations and helped with
the chemical and structural analysis of the models. S.H.H., T.R.B.,
R.C., and D.L. supervised experiments. D.L., D.O.P., and M.L.
conceived the study. D.L., D.O.P., and I.K.J. wrote the manuscript
with help from all authors.Competing interests:X.Z.Z., S.J.S.,
S.H.H., and T.R.B. are inventors on provisional patent applications
U.S. 9,676,771 and U.S. 10,208,035 held by the National Cancer
Institute.Data and materials availability:The cryo-EM
maps and atomic models have been deposited into the Electron
Microscopy Data Bank and Protein Data Bank under the
following accession codes: CSCAPO(EMD-20481 and 6PUT);
CSCBIC(EMD-20483 and 6PUW); CSC4d(EMD-20484 and
6PUY); CSC4f(EMD-20485 and 6PUZ); and CSC4c(EMD-21038
and 6V3K). The inhibitors4c,4d,and4fare available from
T.R.B. or S.H.H. under a material transfer agreement with
the National Cancer Institute.SUPPLEMENTARY MATERIALS
science.sciencemag.org/content/367/6479/810/suppl/DC1
Materials and Methods
Supplementary Text
Figs. S1 to S16
Tables S1 and S2
References ( 32 – 48 )
View/request a protocol for this paper fromBio-protocol.
18 July 2019; accepted 17 January 2020
Published online 30 January 2020
10.1126/science.aay8015Passoset al.,Science 367 , 810–814 (2020) 14 February 2020 4of4
Fig. 4. Interactions of naphthyridine-based INSTIs and HIV intasomes.Schematic representation that
recapitulates the receptor molecular environment and the water (W) networks with which the naphthyridine
scaffold ligands interact when coordinating the Mg2+ions. The scheme summarizes interactions by their
locations with respect to the metal coordination plane of the naphthyridine scaffold (above, in-plane, or
below). For clarity, the two water molecules coordinating the Mg2+ions from above are not shown.
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