Board of Governors Professor
Distinguished Professor
Department of Chemistry and Chemical Biology
Rutgers–New Brunswick, School of Arts and Sciences

Cancer Institute of New Jersey

Ph.D., 1982, Cornell University

Telephone: (848) 445-9777
Fax: (732) 235-5788

HIV, AIDS, drugs, vaccines, crystallography, structural biology

Many of the underlying biological and chemical processes of life are being detailed at the molecular level, providing unprecedented opportunities for the development of novel approaches to the treatment, cure and prevention of human disease. A broad base of advances in chemistry, biology, and medicine has led to an exciting era in which knowledge of the intricate structure of life’s machinery can help to accelerate the development of new small molecule drugs and biomaterials such as engineered viral vaccines. Drs. Eddy Arnold and his colleagues are working to understand molecular mechanisms of drug resistance and apply structure-based drug design for the treatment of serious human diseases. In pursuit of these goals, the laboratory uses research tools from diverse fields, including X-ray crystallography, molecular biology, virology, protein biochemistry, and macromolecular engineering. Eddy’s team of very experienced and gifted coworkers is the driving force behind the continuing progress.

Since its establishment at CABM in 1987, our laboratory has studied the structure and function of reverse transcriptase (RT), an essential component of the AIDS virus and the target of most widely used anti-AIDS drugs. Using the powerful techniques of X-ray crystallography, we have solved the three-dimensional structures of HIV-1 RT in complex with a variety of antiviral drugs and model segments of the HIV genome. These studies have revealed the workings of an intricate and fascinating biological machine in 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 template-primers, 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 were 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., Nat. Struct. Mol. Biol. 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 collaborations with the groups of Stephen Hughes (NIH NCI-Frederick), Roger Jones (Rutgers), Michael Parniak (U. of Pittsburgh), Ronald Levy (Rutgers), and Joe Marcotrigiano (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 and inexpensive to make and have nearly 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 infected individuals. 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 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-resolution HIV-1 RT crystals for drug-like fragment screening. A number of novel allosteric sites for inhibition of both polymerase and RNase H activity have been identified from the fragment screening effort. Also, the group solved the first structure of HIV-1 RT in complex with nevirapine, confirming that nonnucleoside drugs displace the primer terminus near the polymerase active site (Das et al., Nat. Struct. Mol. Biol. 2012). This type of structure, which had been elusive for decades, was one of the key missing pieces in the HIV-1 RT structure/function puzzle.

In addition to working to study HIV-1 RT and to develop chemotherapeutic agents, the laboratory aims to gain greater insights into the basic molecular processes of living systems. Other projects currently being pursued in the lab include structural studies of: 1) bacterial RNA polymerase holoenzyme complexes with inhibitors and substrates in collaboration with Dr. Richard Ebright at Rutgers University and 2) influenza virus polymerase. A recent highlight was the high-resolution structure determination of a bacterial RNA polymerase transcription initiation complex (Zhang et al., Science 2012). This structure shows how RNA polymerase recognize and melts the promoter DNA, and how the interactions help to pre-organize the DNA so it is poised at the active site to initiate transcription.

Selected Publications

Patel D, Antwi J, Koneru PC, Serrao E, Forli S, Kessl JJ, Feng L, Deng N, Levy RM, Fusch JR, Olson AJ, Engelman AN, Bauman JD, Kvaratskhelia M, Arnold E. (2016) A new class of allosteric HIV-1 integrase inhibitors identified by crystallographic fragment screening of the catalytic core domain. J Biol Chem 291:23569-77

Das K, Balzarini J, Miller MT, Maguire AR, DeStefano JJ, Arnold E. (2016) Conformational states of HIV-1 reverse transcriptase for nucleotide incorporation vs pyrophosphorolysis-binding of foscarnet. ACS Chem Biol 11:2158-64

Bauman JD, Harrison JJ, Arnold E. (2016) Rapid experimental SAD phasing and hot-spot identification with halogenated fragments. IUCRj 3(PT1):51-60

Miller MT, Tuske S, Das K, Destefano JJ, Arnold E. (2016) Structure of HIV-1 reverse transcriptase bound to a novel 38-mer hairpin template-primer DNA aptamer. Protein Sci 25:46-55

Goswami D, Tuske S, Pascal BD, Bauman JD, Patel D, Arnold E, Griffin PR. (2015) Differential isotopic enrichment to facilitate characterization of asymmetric multimeric proteins using hydrogen/deuterium exchange mass spectrometry. Anal Chem 87:4015-22

Balzarini J, Das K, Bernatchez JA, Martinez SE, Ngure M, Keane S, Ford A, Maguire N, Mullins N, John J, Kim Y, Dehaen W, Vande Voorde J, Liekens S, Naesens L, Götte M, Maguire AR, Arnold E. (2015) Alpha-carboxy nucleoside phosphonates as universal nucleoside triphosphate mimics. Proc Natl Acad Sci USA 112:3475-80

Das K, Martinez SE, Bandwar RP, Arnold E. (2014) Structures of HIV-1 RT-RNA/DNA ternary complexes with dATP and nevirapine reveal conformational flexibility of RNA/DNA: insights into requirements for RNase H cleavage. Nucleic Acids Res 42:8125-37

Bauman JD, Patel D, Baker SF, Vijayan RS, Xiang A, Parhi AK, Martínez-Sobrido L, LaVoie EJ, Das K, Arnold E. (2013) Crystallographic fragment screening and structure-based optimization yields a new class of influenza endonuclease inhibitors. ACS Chem Biol 8:2501-8

Bauman JD, Patel D, Dharia C, Fromer MW, Ahmed S, Frenkel Y, Vijayan RS, Eck JT, Ho WC, Das K, Shatkin AJ, Arnold E. (2013) Detecting allosteric sites of HIV-1 reverse transcriptase by X-ray crystallographic fragment screening. J Med Chem 56:2738-46

Kuroda, DG, Bauman JD, Challa JR, Patel D, Troxler T, Das K, Arnold E, Hochstrasser RM. (2013) Snapshot of the equilibrium dynamics of a drug bound to HIV-1 reverse transcriptase. Nat Chem 5:174-81 (Journal cover displayed a figure based on our publication.)

Zhang Y, Feng Y, Chatterjee S, Tuske S, Ho MX, Arnold E, Ebright RH. (2012) Structural basis of transcription initiation. Science 338:1076-80

Das K, Martinez SE, Bauman JD, Arnold E. (2012) HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism. Nat Struct Mol Biol 19:253-9