Annual Report 2011 - Center for Advanced Biotechnology and ...

atomic detail and have yielded numerous novel insights into polymerase structure-function
relationships, detailed mechanisms of drug inhibition and resistance, and structure-based
design of RT inhibitors. The team has solved a variety of crystal structures representing
multiple functional states of HIV-1 RT. These structures include HIV-1 RT in complex with a
double-stranded DNA template-primer, HIV-1 RT complexes with RNA:DNA templateprimers,
structures of RT with AZTMP-terminated primer representing pre-translocation and
post-translocation complexes, and ternary complexes of wild-type and drug-resistant RT with
DNA, and AZT-triphosphate/tenofovir-diphosphate. We have also determined the structures
of numerous non-nucleoside inhibitors with wild-type and drug resistant HIV-1 RT, and the
structural information was used in the design of two recently approved non-nucleoside drugs.
Also, we have obtained structures of RT:RNase H inhibitor and RT:DNA:AZTppppA (an
ATP-mediated AZT excision product) complexes (Tu et al., 2010).
Drug development against and structural studies of a molecule as complex as HIV RT require
immense and highly coordinated resources. The Arnold group has been fortunate to have
successful long-term collaborations with the groups of Stephen Hughes (NIH NCI-Frederick),
Roger Jones (Rutgers), Michael Parniak (U. of Pittsburgh), and Ronald Levy (Rutgers). The
group also benefits from generous access to synchrotron X-radiation sources (CHESS, APS,
and BNLS). Hughes and his coworkers have contributed expertise in protein engineering,
production, and biochemistry at every stage of the RT project since its inception.
Through collaboration with the late Dr. Paul Janssen we participated in a structure-based drug
design effort that resulted in the discovery and development of non-nucleoside inhibitors
(diarylpyrimidine, or DAPY analogs) with high potency against all known drug-resistant
variants of HIV-1 RT. Crystallographic work from the Arnold and Hughes laboratories
allowed precise visualization of how potential anti-HIV drug candidates latch onto RT, their
molecular target. Janssen and colleagues at the Center for Molecular Design successfully
used this structural information to guide the design and synthesis of new molecules with
improved potency against wild-type and drug-resistant HIV-1 strains. Scientists at Tibotec, a
subsidiary of Johnson & Johnson, tested the compounds for antiviral activity against wild-type
and resistant HIV-1, and have led the clinical trials.
The DAPY compounds are simple, inexpensive to make and have near ideal pharmacological
properties. Etravirine (TMC125/Intelence) was approved for treatment of HIV infection by
the FDA in 2008, and rilpivirine (TMC278) was approved as Edurant in May 2011. In what
may be unprecedented for a new best-in-class drug, Johnson & Johnson is permitting
rilpivirine to be available in generic form immediately in developing nations; this will make
the drug available to millions of people. The prototypical DAPY compound,
TMC120/dapivirine, is now being developed as a microbicide for blocking sexual
transmission of HIV-1. A broader outcome of this study is a drug design concept for
overcoming drug resistance; the strategic flexibility that permits the DAPY compounds to
“wiggle” and “jiggle” in a binding pocket to accommodate mutations apparently accounts for
their potency against a wide range of drug-resistant variants. Through a systematic protein
engineering effort we obtained high-resolution crystals of HIV-1 RT and demonstrated that
strategic flexibility of rilpivirine was responsible for its resilience against drug-resistant RT
variants. Recent efforts include using the high-
Dr. Ramaswamy
S. Vijayan
Postdoctoral Associate
Dr. Angela
McKoy
Postdoctoral Fellow
Dabyaben Patel
Graduate Student
Joseph Thomas
Eck
Graduate Fellow
Arthur Clark
Laboratory Researcher
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