UNIVERSITY OF PENNSYLVANIA - PERELMAN SCHOOL OF MEDICINE Curriculum Vitae Date: 05/24/2014 Rahul M. Kohli, M.D., Ph.D Address:

502B Johnson Pavilion Division of Infectious Disease, Department of Medicine 3610 Hamilton Walk Philadelphia, PA 19104-6073 USA

Education: 1998 2004

B.S. Ph.D.

2004

M.D.

University of Michigan (Biochemistry) Harvard Medical School (Biochem & Mol Pharm, Advisor: Christopher T. Walsh) Harvard Medical School

Postgraduate Training and Fellowship Appointments: 2004-2005 Internship in Medicine, Department of Medicine, Hospital of the University of Pennsylvania 2005-2006 Resident in Internal Medicine, Hospital of the University of Pennsylvania 2006-2010 Postdoctoral Fellow in Infectious Diseases, Johns Hopkins Hospital Faculty Appointments: 2010-present 2010-present

Assistant Professor of Medicine, University of Pennsylvania School of Medicine Assistant Professor of Biochemistry and Biophysics, University of Pennsylvania School of Medicine (Secondary)

Hospital and/or Administrative Appointments: 2010-Present Attending Physician, Infectious Diseases, Hospital of the University of Pennsylvania Other Appointments: 2010-Present 2010-Present 2010-Present 2010-Present 2010-Present Specialty Certification: 2008 2009

Member, Immunology Graduate Group Member, Pharmacological Sciences Graduate Group Member, Biochemistry and Molecular Biophysics Graduate Group Member, Cell and Molecular Biology Graduate Group Penn Scholar in Molecular Medicine, Department of Medicine Internal Medicine Infectious Diseases

Rahul M. Kohli, M.D., Ph.D

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Licensure: 2009-2010 2010-present

Medical License - State of Maryland Medical License - State of Pennsylvania

Awards, Honors and Membership in Honorary Societies: 1994-1998 Angel Scholar. University of Michigan 1994 Leveque Prize in Pure Mathematics. University of Michigan 1996-1998 Barry M. Goldwater Scholar 1998 American Institute of Chemists. Biochemistry Award. University of Michigan. 2006 Resident Teaching Award. Internal Medicine. Hospital of the University of Pennsylvania 2009-2010 BMS Virology Fellow Award 2010 Albert L. Lehninger Outstanding Postdoctoral Scientist Award. Johns Hopkins University 2010 Nature Chemical Biology: Grand Challenges in Chemical Biology. Award Winner. 2011-2017 Rita Allen Foundation Scholar 2011 Damon Runyon Rachleff Innovator Award Finalist. 2012-2015 Doris Duke Clinical Scientist Development Award 2012-2017 NIH Director's New Innovator Award 2012-2016 Edward J. Mallickrodt Jr. Foundation Scholar 2013 Discovery Fast Track Competition Award Winner, GlaxoSmithKline 2014-2016 Harrington Scholar-Innovator Award, Harrington Discovery Institute Memberships in Professional and Scientific Societies and Other Professional Activities: National: 2003-Present American Chemical Society (Member) 2009-Present Infectious Disease Society of America (Member) 2011-Present American Association for the Advancement of Science (Member) 2013 Macromolecular Structure and Function E Study Section [MSFE] (ad hoc study section committee member, 2013) Editorial Positions: 2011-Present 2011-Present 2011-Present 2011-Present 2012-Present 2012-Present 2012-Present 2013-Present 2013-Present

ad hoc reviewer, Biochemistry ad hoc reviewer, Science ad hoc reviewer, Infection, Genetics and Evolution ad hoc reviewer, Journal of Virology ad hoc reviewer, PLOS Pathogens ad hoc reviewer, Journal of the American Chemical Society ad hoc reviewer, Current Genomics ad hoc reviewer, Proceedings of the National Academy of Sciences ad hoc reviewer, Nature Chemical Biology

Rahul M. Kohli, M.D., Ph.D 2013-Present 2013-Present

Page 3 ad hoc reviewer, ACS Chemical Biology ad hoc reviewer, Analytical Biochemistry

Academic and Institutional Committees: 2010-Present Committee Member, MD/PhD Admissions Committee 2011-Present Member, BMB Graduate Group Lab Rotation Talk Committee 2011-Present Member, Biochemistry and Biophysics, MD/PhD Admissions Committee 2011-2013 Member, Search Committee, Biochemistry and Biophysics Faculty Search 2012-2013 Member, Search Committee, Associate Director of Healthcare Epidemiology, Infection Prevention and Control 2012-Present Member, Executive Committee, Biochemistry and Molecular Biophysics Graduate Group 2012-Present Member, Retreat Planning Committee, Biochemistry and Biophysics 2013-Present Member, Executive Committee, Infectious Diseases Division 2013-Present Director, Biochemistry and Biophysics, MD/PhD Admission Committee 2013-Present Co-Chair, Division of Infectious Diseases Fellowship Mentoring Committee 2014-Present Associate Director and Member of Steering Committee, MD/PhD Program Bibliography: Research Publications, peer reviewed (print or other media): 1. Kohli RM: Site-directed mutagenesis using PCR-mediated introduction of silent mutations. Biotechniques 25: 184-188, 1998. 2. Kohli RM, Massey V: The oxidative half-reaction of Old Yellow Enzyme: the role of tyrosine 196. J Biol Chem 273: 32763-32770, 1998. 3. Xu D, Kohli RM, Massey V: The role of threonine 37 in flavin reactivity of the old yellow enzyme. Proc Natl Acad Sci USA 96: 3556-3561, 1999. 4. Trauger JW, Kohli RM, Mootz HD, Marahiel MA, Walsh CT: Peptide cyclization catalysed by the thioesterase domain of tyrocidine synthetase. Nature 407: 215218, 2000. 5. Kohli RM, Trauger JW, Schwarzer D, Marahiel MA, Walsh CT: Generality of peptide cyclization catalyzed by isolated thioesterase domains of nonribosomal peptide synthetases. Biochemistry 40: 7099-7108, 2001. 6. Trauger JW, Kohli RM, Walsh CT: Cyclization of backbone-substituted peptides catalyzed by the thioesterase domain from the tyrocidine nonribosomal peptide synthetase. Biochemistry 40: 7092-7098, 2001.

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7. Bruner SD, Weber T, Kohli RM, Schwarzer D, Marahiel MA, Walsh CT, Stubbs MT: Structural basis for the cyclization of the lipopeptide antibiotic surfactin by the thioesterase domain SrfTE. Structure 10: 301-310, 2002. 8. Kohli RM, Takagi J, Walsh CT: The thioesterase domain from a nonribosomal peptide synthetase as a cyclization catalyst for integrin binding peptides. Proc Natl Acad Sci USA 99: 1247-1252, 2002. 9. Kohli RM, Walsh CT, Burkart MD: Biomimetic synthesis and optimization of cyclic peptide antibiotics. Nature 418: 658-661, 2002. 10. Luo L, Kohli RM, Onishi M, Linne U, Marahiel MA, Walsh CT: Timing of epimerization and condensation reactions in nonribosomal peptide assembly lines: kinetic analysis of phenylalanine activating elongation modules of tyrocidine synthetase B. Biochemistry 41: 9184-9196, 2002. 11. Tseng CC, Bruner SD, Kohli RM, Marahiel MA, Walsh CT, Sieber SA: Characterization of the surfactin synthetase C-terminal thioesterase domain as a cyclic depsipeptide synthase. Biochemistry 41: 13350-13359, 2002. 12. Kohli RM, Burke MD, Tao J, Walsh CT: Chemoenzymatic route to macrocyclic hybrid peptide/polyketide-like molecules. J Am Chem Soc 125: 7160-7161, 2003. 13. Yeh E, Kohli RM, Bruner SD, Walsh CT: TYPE II thioesterase restores activity of a NRPS module stalled with an aminoacyl-S-enzyme that cannot be elongated. Chembiochem 5: 1290-1293, 2004. 14. Yeh E, Lin H, Clugston SL, Kohli RM, Walsh CT: Enhanced macrocyclizing activity of the thioesterase from tyrocidine synthetase in presence of nonionic detergent. Chem Biol 11: 1573-1582, 2004. 15. McMahon MA, Siliciano JD, Lai L, Liu JO, Stivers JT, Siliciano RF, Kohli RM: The antiherpetic drug acyclovir inhibits HIV replication and selects the V75I reverse transcriptase multidrug resistance mutation. J Biol Chem 283: 31289-31293, 2008. 16. Ho RS, Kohli RM, Maragakis LL: When to think of zebras. Am J Med 122: 424-426, 2009. 17. Kohli RM, Abrams SR, Gajula KS, Maul RW, Gearhart PJ, Stivers JT: A portable hotspot recognition loop transfers sequence preferences from APOBEC family members to activation-induced cytidine deaminase. J Biol Chem 284: 2289822904, 2009.

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18. Kohli RM: The Chemistry of a Dynamic Genome. Nature Chem Biol 6(12): 866-868, 2010. 19. Kohli RM, Maul RW, Guminski AF, McClure RL, Gajula KS, Saribasak H, McMahon MA, Siliciano RF, Gearhart PJ, Stivers JT.: Local sequence targeting in the AID/APOBEC family differentially impacts retroviral restriction and antibody diversification. J Biol Chem 285(52): 40956-40964, 2010. 20. McMahon MA, Siliciano JD, Kohli RM, Siliciano RF: Sensitivity of V75I HIV-1 reverse transcriptase mutant selected in vitro by acyclovir to anti-HIV drugs. AIDS 24: 319-323, 2010. 21. Nabel CS, Jia H, Ye Y, Shen L, Goldschmidt HL, Stivers JT, Zhang Y, Kohli RM.: AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation. Nature Chem Biol 8(9): 751-758, 2012. 22. Macmillan AL, Kohli RM, Ross SR: APOBEC3 inhibition of MMTV infection: the role of cytidine deamination versus inhibition of reverse transcription. J Virol 87(9): 4808-17, 2013. 23. Nabel CS, Lee JW, Wang LC, Kohli RM: Nucleic acid determinants for selective deamination of DNA over RNA by activation-induced deaminase. Proc Natl Acad Sci USA 110(35): 14225-30, 2013. 24. Mo CY, Birdwell LD, Kohli RM.: Specificity Determinants for Autoproteolysis of LexA, a Key Regulator of Bacterial SOS Mutagenesis. Biochemistry 53: 3158-68, 2014. 25. Stavrou S, Crawford DJ, Blouch K, Browne EP, Kohli RM and Ross SR: Transgenic mice demonstrate different modes of retrovirus restriction by APOBEC3A and APOBEC3G in vivo. PLOS Pathogens 2014. Research Publications, peer-reviewed reviews: 1. Keating TA, Ehmann DE, Kohli RM, Marshall CG, Trauger JW, Walsh CT: Chain termination steps in nonribosomal peptide synthetase assembly lines: directed acyl-S-enzyme breakdown in antibiotic and siderophore biosynthesis. Chembiochem 2: 99-107, 2001. 2. Kohli RM, Walsh CT: Enzymology of acyl chain macrocyclization in natural product biosynthesis. Chem Commun 7: 297-307, 2003. 3. Nabel CS, Manning SA, Kohli RM: The Curious Chemical Biology of Cytosine: Deamination, Methylation and Oxidation as Modulators of Genomic Potential. ACS Chemical Biology 7(1): 20-30, 2012.

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4. Kohli RM, Zhang Y: TET enzymes, TDG and the Dynamics of DNA Demethylation. Nature 502: 472-9, 2013. 5. Nabel CS, Schutsky EK, Kohli RM.: Molecular targeting of mutagenic AID and APOBEC deaminases. Cell Cycle 13(2), 2014. Editorials, Reviews, Chapters, including participation in committee reports (print or other media): 1. Nabel CS, Kohli RM: Demystifying DNA Demethylation. Science 333: 1229-1230, 2011. Patents: Harvard College.: Methods for Preparation of Macrocylic Molecules, Macrocyclic Molecules Prepared Thereby and Substrates and Solid Supports for Use Therein. Inventors: Christopher T. Walsh, Rahul M. Kohli, Michael D. Burkart, Martin D. Burke. USA Patent Number Appl # 10/289,157, 2002. Harvard College: Methods for Preparation of Macrocyclic Molecules and Macrocyclic Molecules Prepared Thereby. Inventors: Christopher T. Walsh, John W. Trauger, Rahul M. Kohli, Michael D. Burkart, Mohammed A. Marshall, Henning Dieter Mootz, Dirk Schwarzer. USA Patent Number US 7,279,304 B2, 2007.

2014-06-CV.pdf

catalyzed by the thioesterase domain from the tyrocidine nonribosomal peptide. synthetase. Biochemistry 40: 7092-7098, 2001. Page 3 of 6. 2014-06-CV.pdf.

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