LarissaPodust

Associate Professor, UCSD

Skaggs School of Pharmacy & Pharmaceutical Sciences

Structural Biology & X-ray Crystallography Core Director, CDIPD

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Follow me: https://pharmacy.ucsd.edu/faculty/bios/podust.shtml

I received my PhD in Chemistry from Novosibirsk State University and subsequently completed postdoctoral training, first in the enzymology of DNA replication at the University Zurich-Irchel, and then in protein x-ray crystallography at Vanderbilt University.

My research is focused on the structure-aided drug discovery for diseases representing global health problems and on the mechanisms of oxidative enzimatic reactions in bacterial biosynthetic systems producing antibiotics. Chagas Disease, caused by the protozoan parasite, Trypanosoma cruzi is the leading cause of heart disease in Latin America and an emerging infection in the United States, Europe and Asia. Chagas disease is primarily a disease of economically disadvantaged individuals and there is little interest in drug development in the pharmaceutical industry. I am principal investigator of an NIH R01 grant which has as its aim to discover and develop new therapy for Chagas Disease based on inhibition of parasite sterol biosynthesis. In collaboration with William Roush, Director of Medicinal Chemistry at Scripps Florida, and members of the Center for Discovery and Innovation in Parasitic Diseases, we have identified several promising chemical scaffolds including compounds that not only inhibit CYP51, a central enzyme in sterol biosynthesis, but which also inhibit parasite replication in a mouse model of infection. These the compounds are currently being "rationally" optimized through a productive collaboration using our structural biology advances, the medicinal chemistry expertise of Drs. Roush and Choi, and computational resources and structure-based drug-discovery expertise provided by Ruben Abagyan laboratory, UC San Diego Skaggs School of Pharmacy. Some of the leads for this project came from a screen supported by the CEND Target of the Year Award (UC Berkeley) funded my collaboration with Michelle Arkin of the UCSF Small Molecule Discovery Center (SMDC).

We collaborate with David Sherman, University of Michigan, to study enzymatic oxidative modifications of natural products, an untapped source of novel chemical space that could be explored for discovery of new drugs for neglected diseases. I am providing tools of structural biology to detail the catalytic mechanism of microbial enzymes responsible for natural product biosynthesis. 

PUBLICATIONS

Rapid Chagas Disease Drug Target Discovery Using Directed Evolution in Drug-Sensitive Yeast. ACS Chem Biol. 2017 Feb 17;12(2):422-434. doi: 10.1021/acschembio.6b01037. Ottilie S, Goldgof GM, Calvet CM, Jennings GK, LaMonte G, Schenken J, Vigil E, Kumar P, McCall LI, Lopes ES, Gunawan F, Yang J, Suzuki Y, Siqueira-Neto JL, McKerrow JH, Amaro RE, Podust LM, Durrant JD, Winzeler EA.

Biochemical and Structural Characterization of MycCI, a Versatile P450 Biocatalyst from the Mycinamicin Biosynthetic Pathway. ACS Chem Biol. 2016 Aug 5. [Epub ahead of print] DeMars MD 2nd, Sheng F, Park SR, Lowell AN, Podust LM, Sherman DH.

X-ray structures of thioredoxin and thioredoxin reductase from Entamoeba histolytica and prevailing hypothesis of the mechanism of Auranofin action. J Struct Biol. 2016 May;194(2):180-90. doi: 10.1016/j.jsb.2016.02.015. Epub 2016 Feb 12. Parsonage D, Sheng F, Hirata K, Debnath A, McKerrow JH, Reed SL, Abagyan R, Poole LB, Podust LM.

The Schistosoma mansoni Cytochrome P450 (CYP3050A1) Is Essential for Worm Survival and Egg Development. PLoS Negl Trop Dis. 2015 Dec;9(12):e0004279. doi: 10.1371/journal.pntd.0004279. Erratum in: PLoS Negl Trop Dis. 2016 Feb;10(2):e0004439. Ziniel PD, Karumudi B, Barnard AH, Fisher EM, Thatcher GR, Podust LM, Williams DL.

Enzymatic hydroxylation of an unactivated methylene C-H bond guided by molecular dynamics simulations. Nat Chem. 2015 Aug;7(8):653-60. doi: 10.1038/nchem.2285. Epub 2015 Jun 29. Narayan AR, Jiménez-Osés G, Liu P, Negretti S, Zhao W, Gilbert MM, Ramabhadran RO, Yang YF, Furan LR, Li Z, Podust LM, Montgomery J, Houk KN, Sherman DH.

Targeting Ergosterol biosynthesis in Leishmania donovani: essentiality of sterol 14 alpha-demethylase. PLoS Negl Trop Dis. 2015 Mar;9(3):e0003588. doi: 10.1371/journal.pntd.0003588. McCall LI, El Aroussi A, Choi JY, Vieira DF, De Muylder G, Johnston JB, Chen S, Kellar D, Siqueira-Neto JL, Roush WR, Podust LM, McKerrow JH.

Binding mode and potency of N-indolyloxopyridinyl-4-aminopropanyl-based inhibitors targeting Trypanosoma cruzi CYP51. J Med Chem. 2014 Dec 11;57(23):10162-75. doi: 10.1021/jm501568b. Epub 2014 Nov 25. Vieira DF, Choi JY, Calvet CM, Siqueira-Neto JL, Johnston JB, Kellar D, Gut J, Cameron MD, McKerrow JH, Roush WR, Podust LM.

Drug strategies targeting CYP51 in neglected tropical diseases. Chem Rev. 2014 Oct 22. [Epub ahead of print] No abstract available. Choi JY, Podust LM, Roush WR.

4-Aminopyridyl-based CYP51 inhibitors as anti-Trypanosoma cruzi drug leads with improved pharmacokinetic profile and in vivo potency. J Med Chem. 2014 Aug 28;57(16):6989-7005. doi: 10.1021/jm500448u. Epub 2014 Aug 19. Calvet CM, Vieira DF, Choi JY, Kellar D, Cameron MD, Siqueira-Neto JL, Gut J, Johnston JB, Lin L, Khan S, McKerrow JH, Roush WR, Podust LM.

R-Configuration of 4-aminopyridyl-based inhibitors of CYP51 confers superior efficacy against Trypanosoma cruzi. ACS Med Chem Lett. 2014 Apr 10;5(4):434-9. doi: 10.1021/ml500010m. Choi JY, Calvet CM, Vieira DF, Gunatilleke SS, Cameron MD, McKerrow JH, Podust LM, Roush WR.

Expanding the binding envelope of CYP51 inhibitors targeting Trypanosoma cruzi with 4-aminopyridyl-based sulfonamide derivatives. Chembiochem. 2014 May 26;15(8):1111-20. doi: 10.1002/cbic.201402027. Epub 2014 Apr 25. Vieira DF, Choi JY, Roush WR, Podust LM.

Directing group-controlled regioselectivity in an enzymatic C-H bond oxygenation. J Am Chem Soc. 2014 Apr 2;136(13):4901-4. doi: 10.1021/ja5016052. Epub 2014 Mar 21. Negretti S, Narayan AR, Chiou KC, Kells PM, Stachowski JL, Hansen DA, Podust LM, Montgomery J, Sherman DH.

New reactions and products resulting from alternative interactions between the P450 enzyme and redox partners. J Am Chem Soc. 2014 Mar 5;136(9):3640-6. doi: 10.1021/ja4130302. Epub 2014 Feb 25. Zhang W, Liu Y, Yan J, Cao S, Bai F, Yang Y, Huang S, Yao L, Anzai Y, Kato F, Podust LM, Sherman DH, Li S.

Rational development of 4-aminopyridyl-based inhibitors targeting Trypanosoma cruzi CYP51 as anti-chagas agents. J Med Chem. 2013 Oct 10;56(19):7651-68. doi: 10.1021/jm401067s. Epub 2013 Sep 30. Choi JY, Calvet CM, Gunatilleke SS, Ruiz C, Cameron MD, McKerrow JH, Podust LM, Roush WR.

A highly conserved mycobacterial cholesterol catabolic pathway. Environ Microbiol. 2013 Aug;15(8):2342-59. doi: 10.1111/1462-2920.12108. Epub 2013 Mar 14. García-Fernández E, Frank DJ, Galán B, Kells PM, Podust LM, García JL, Ortiz de Montellano PR.

Chemical-biological characterization of a cruzain inhibitor reveals a second target and a mammalian off-target. Beilstein J Org Chem. 2013;9:15-25. doi: 10.3762/bjoc.9.3. Epub 2013 Jan 4. Choy JW, Bryant C, Calvet CM, Doyle PS, Gunatilleke SS, Leung SS, Ang KK, Chen S, Gut J, Oses-Prieto JA, Johnston JB, Arkin MR, Burlingame AL, Taunton J, Jacobson MP, McKerrow JM, Podust LM, Renslo AR.

Substrate recognition by the multifunctional cytochrome P450 MycG in mycinamicin hydroxylation and epoxidation reactions. J Biol Chem. 2012 Nov 2;287(45):37880-90. doi: 10.1074/jbc.M112.410340. Epub 2012 Sep 5. Li S, Tietz DR, Rutaganira FU, Kells PM, Anzai Y, Kato F, Pochapsky TC, Sherman DH, Podust LM.

Diverse inhibitor chemotypes targeting Trypanosoma cruzi CYP51. PLoS Negl Trop Dis. 2012;6(7):e1736. doi: 10.1371/journal.pntd.0001736. Epub 2012 Jul 31. Gunatilleke SS, Calvet CM, Johnston JB, Chen CK, Erenburg G, Gut J, Engel JC, Ang KK, Mulvaney J, Chen S, Arkin MR, McKerrow JH, Podust LM.

Diversity of P450 enzymes in the biosynthesis of natural products. Nat Prod Rep. 2012 Oct;29(10):1251-66. doi: 10.1039/c2np20020a. Epub 2012 Jul 23. Review. Podust LM, Sherman DH.

Tirandamycin biosynthesis is mediated by co-dependent oxidative enzymes. Nat Chem. 2011 Jul 17;3(8):628-33. doi: 10.1038/nchem.1087. Carlson JC, Li S, Gunatilleke SS, Anzai Y, Burr DA, Podust LM, Sherman DH.

Reverse type I inhibitor of Mycobacterium tuberculosis CYP125A1. Bioorg Med Chem Lett. 2011 Jan 1;21(1):332-7. doi: 10.1016/j.bmcl.2010.11.007. Epub 2010 Nov 5. Ouellet H, Kells PM, Ortiz de Montellano PR, Podust LM.

Structure of cytochrome P450 PimD suggests epoxidation of the polyene macrolide pimaricin occurs via a hydroperoxoferric intermediate. Chem Biol. 2010 Aug 27;17(8):841-51. doi: 10.1016/j.chembiol.2010.05.026. Kells PM, Ouellet H, Santos-Aberturas J, Aparicio JF, Podust LM.

Structural control of cytochrome P450-catalyzed ω-hydroxylation. Arch Biochem Biophys. 2011 Mar 1;507(1):86-94. doi: 10.1016/j.abb.2010.08.011. Epub 2010 Aug 19. Review. Johnston JB, Ouellet H, Podust LM, Ortiz de Montellano PR.

FMN binding site of yeast NADPH-cytochrome P450 reductase exposed at the surface is highly specific. ACS Chem Biol. 2010 Aug 20;5(8):767-76. doi: 10.1021/cb100055v. Ivanov AS, Gnedenko OV, Molnar AA, Archakov AI, Podust LM.

Mycobacterium tuberculosis CYP125A1, a steroid C27 monooxygenase that detoxifies intracellularly generated cholest-4-en-3-one. Mol Microbiol. 2010 Aug;77(3):730-42. doi: 10.1111/j.1365-2958.2010.07243.x. Epub 2010 Jun 10. Ouellet H, Guan S, Johnston JB, Chow ED, Kells PM, Burlingame AL, Cox JS, Podust LM, de Montellano PR.

A nonazole CYP51 inhibitor cures Chagas' disease in a mouse model of acute infection. Antimicrob Agents Chemother. 2010 Jun;54(6):2480-8. doi: 10.1128/AAC.00281-10. Epub 2010 Apr 12. Doyle PS, Chen CK, Johnston JB, Hopkins SD, Leung SS, Jacobson MP, Engel JC, McKerrow JH, Podust LM.

Structural characterization of CYP51 from Trypanosoma cruzi and Trypanosoma brucei bound to the antifungal drugs posaconazole and fluconazole. PLoS Negl Trop Dis. 2010 Apr 6;4(4):e651. doi: 10.1371/journal.pntd.0000651. Chen CK, Leung SS, Guilbert C, Jacobson MP, McKerrow JH, Podust LM.

Identification of small-molecule scaffolds for p450 inhibitors. Curr Protoc Microbiol. 2010 Feb;Chapter 17:Unit17.4. doi: 10.1002/9780471729259.mc1704s16. von Kries JP, Warrier T, Podust LM.

Biochemical and structural characterization of CYP124: a methyl-branched lipid omega-hydroxylase from Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2009 Dec 8;106(49):20687-92. doi: 10.1073/pnas.0907398106. Epub 2009 Nov 20. Johnston JB, Kells PM, Podust LM, Ortiz de Montellano PR.

Selective oxidation of carbolide C-H bonds by an engineered macrolide P450 mono-oxygenase. Proc Natl Acad Sci U S A. 2009 Nov 3;106(44):18463-8. doi: 10.1073/pnas.0907203106. Epub 2009 Oct 15. Li S, Chaulagain MR, Knauff AR, Podust LM, Montgomery J, Sherman DH.

Two approaches to discovering and developing new drugs for Chagas disease. Mem Inst Oswaldo Cruz. 2009 Jul;104 Suppl 1:263-9. McKerrow JH, Doyle PS, Engel JC, Podust LM, Robertson SA, Ferreira R, Saxton T, Arkin M, Kerr ID, Brinen LS, Craik CS.

Interaction of Mycobacterium tuberculosis CYP130 with heterocyclic arylamines. J Biol Chem. 2009 Sep 11;284(37):25211-9. doi: 10.1074/jbc.M109.017632. Epub 2009 Jul 15. Podust LM, Ouellet H, von Kries JP, de Montellano PR.

Trypanosoma cruzi CYP51 inhibitor derived from a Mycobacterium tuberculosis screen hit. PLoS Negl Trop Dis. 2009;3(2):e372. doi: 10.1371/journal.pntd.0000372. Epub 2009 Feb 3. Chen CK, Doyle PS, Yermalitskaya LV, Mackey ZB, Ang KK, McKerrow JH, Podust LM.

Analysis of transient and catalytic desosamine-binding pockets in cytochrome P-450 PikC from Streptomyces venezuelae. J Biol Chem. 2009 Feb 27;284(9):5723-30. doi: 10.1074/jbc.M807592200. Epub 2009 Jan 4. Li S, Ouellet H, Sherman DH, Podust LM.

2.3 A X-ray structure of the heme-bound GAF domain of sensory histidine kinase DosT of Mycobacterium tuberculosis. Biochemistry. 2008 Nov 25;47(47):12523-31. doi: 10.1021/bi8012356. Podust LM, Ioanoviciu A, Ortiz de Montellano PR.

X-ray structure of 4,4'-dihydroxybenzophenone mimicking sterol substrate in the active site of sterol 14alpha-demethylase (CYP51). J Biol Chem. 2008 May 30;283(22):15152-9. doi: 10.1074/jbc.M801145200. Epub 2008 Mar 26. Eddine AN, von Kries JP, Podust MV, Warrier T, Kaufmann SH, Podust LM.

Mycobacterium tuberculosis CYP130: crystal structure, biophysical characterization, and interactions with antifungal azole drugs. J Biol Chem. 2008 Feb 22;283(8):5069-80. Epub 2007 Dec 18. Ouellet H, Podust LM, de Montellano PR.

Engineering and analysis of a self-sufficient biosynthetic cytochrome P450 PikC fused to the RhFRED reductase domain. J Am Chem Soc. 2007 Oct 31;129(43):12940-1. Epub 2007 Oct 4. No abstract available. Li S, Podust LM, Sherman DH.

Small-molecule scaffolds for CYP51 inhibitors identified by high-throughput screening and defined by X-ray crystallography. Antimicrob Agents Chemother. 2007 Nov;51(11):3915-23. Epub 2007 Sep 10. Podust LM, von Kries JP, Eddine AN, Kim Y, Yermalitskaya LV, Kuehne R, Ouellet H, Warrier T, Alteköster M, Lee JS, Rademann J, Oschkinat H, Kaufmann SH, Waterman MR.

The structural basis for substrate anchoring, active site selectivity, and product formation by P450 PikC from Streptomyces venezuelae. J Biol Chem. 2006 Sep 8;281(36):26289-97. Epub 2006 Jul 6. Sherman DH, Li S, Yermalitskaya LV, Kim Y, Smith JA, Waterman MR, Podust LM.

Ligand-assisted inhibition in cytochrome P450 158A2 from Streptomyces coelicolor A3(2). Biochemistry. 2006 Jun 20;45(24):7493-500. Zhao B, Waterman MR, Isin EM, Sundaramoorthy M, Podust LM.

A second FMN binding site in yeast NADPH-cytochrome P450 reductase suggests a mechanism of electron transfer by diflavin reductases. Structure. 2006 Jan;14(1):51-61. Lamb DC, Kim Y, Yermalitskaya LV, Yermalitsky VN, Lepesheva GI, Kelly SL, Waterman MR, Podust LM.

Expansion of substrate specificity of cytochrome P450 2A6 by random and site-directed mutagenesis. J Biol Chem. 2005 Dec 9;280(49):41090-100. Epub 2005 Oct 7. Wu ZL, Podust LM, Guengerich FP.

Binding of two flaviolin substrate molecules, oxidative coupling, and crystal structure of Streptomyces coelicolor A3(2) cytochrome P450 158A2. J Biol Chem. 2005 Mar 25;280(12):11599-607. Epub 2005 Jan 19. Zhao B, Guengerich FP, Bellamine A, Lamb DC, Izumikawa M, Lei L, Podust LM, Sundaramoorthy M, Kalaitzis JA, Reddy LM, Kelly SL, Moore BS, Stec D, Voehler M, Falck JR, Shimada T, Waterman MR.

Estriol bound and ligand-free structures of sterol 14alpha-demethylase. Structure. 2004 Nov;12(11):1937-45. Podust LM, Yermalitskaya LV, Lepesheva GI, Podust VN, Dalmasso EA, Waterman MR.

Identification of amino acids in rat pregnane X receptor that determine species-specific activation. Mol Pharmacol. 2004 Jan;65(1):36-44. Tirona RG, Leake BF, Podust LM, Kim RB.

Comparison of the 1.85 A structure of CYP154A1 from Streptomyces coelicolor A3(2) with the closely related CYP154C1 and CYPs from antibiotic biosynthetic pathways. Protein Sci. 2004 Jan;13(1):255-68. Podust LM, Bach H, Kim Y, Lamb DC, Arase M, Sherman DH, Kelly SL, Waterman MR.

The 1.92-A structure of Streptomyces coelicolor A3(2) CYP154C1. A new monooxygenase that functionalizes macrolide ring systems. J Biol Chem. 2003 Apr 4;278(14):12214-21. Epub 2003 Jan 7. Podust LM, Kim Y, Arase M, Neely BA, Beck BJ, Bach H, Sherman DH, Lamb DC, Kelly SL, Waterman MR.

Sterol 14alpha-demethylase activity in Streptomyces coelicolor A3(2) is associated with an unusual member of the CYP51 gene family. Biochem J. 2002 Jun 1;364(Pt 2):555-62. Lamb DC, Fowler K, Kieser T, Manning N, Podust LM, Waterman MR, Kelly DE, Kelly SL.

The cytochrome P450 complement (CYPome) of Streptomyces coelicolor A3(2). J Biol Chem. 2002 Jul 5;277(27):24000-5. Epub 2002 Apr 9. Lamb DC, Skaug T, Song HL, Jackson CJ, Podust LM, Waterman MR, Kell DB, Kelly DE, Kelly SL.

Substrate recognition sites in 14alpha-sterol demethylase from comparative analysis of amino acid sequences and X-ray structure of Mycobacterium tuberculosis CYP51. J Inorg Biochem. 2001 Dec 15;87(4):227-35. Podust LM, Stojan J, Poulos TL, Waterman MR.

Folding requirements are different between sterol 14alpha-demethylase (CYP51) from Mycobacterium tuberculosis and human or fungal orthologs. J Biol Chem. 2001 Jul 27;276(30):28413-20. Epub 2001 May 23. Lepesheva GI, Podust LM, Bellamine A, Waterman MR.

Crystal structure of cytochrome P450 14alpha -sterol demethylase (CYP51) from Mycobacterium tuberculosis in complex with azole inhibitors. Proc Natl Acad Sci U S A. 2001 Mar 13;98(6):3068-73. Podust LM, Poulos TL, Waterman MR.

Crystal structure of the CCAAT box/enhancer-binding protein beta activating transcription factor-4 basic leucine zipper heterodimer in the absence of DNA. J Biol Chem. 2001 Jan 5;276(1):505-13. Podust LM, Krezel AM, Kim Y.

Tyrosine 114 is essential for the trimeric structure and the functional activities of human proliferating cell nuclear antigen. EMBO J. 1995 Nov 15;14(22):5745-51. Jónsson ZO, Podust VN, Podust LM, Hübscher U.

Mechanism of inhibition of proliferating cell nuclear antigen-dependent DNA synthesis by the cyclin-dependent kinase inhibitor p21. Biochemistry. 1995 Jul 11;34(27):8869-75. Podust VN, Podust LM, Goubin F, Ducommun B, Hübscher U.

Mammalian DNA polymerase auxiliary proteins: analysis of replication factor C-catalyzed proliferating cell nuclear antigen loading onto circular double-stranded DNA. Mol Cell Biol. 1995 Jun;15(6):3072-81. Podust LM, Podust VN, Sogo JM, Hübscher U.

DNA polymerase delta holoenzyme: action on single-stranded DNA and on double-stranded DNA in the presence of replicative DNA helicases. Biochemistry. 1995 Apr 18;34(15):5003-10. Podust VN, Podust LM, Müller F, Hübscher U.

Assembly of DNA polymerase delta and epsilon holoenzymes depends on the geometry of the DNA template. Nucleic Acids Res. 1994 Aug 11;22(15):2970-5. Podust LM, Podust VN, Floth C, Hübscher U.

The influence of the target structure on the efficiency of alkylation of single-stranded DNA with the reactive derivatives of antisense oligonucleotides. FEBS Lett. 1992 May 4;302(1):47-50. Fedorova OS, Podust LM, Maksakova GA, Gorn VV, Knorre DG.

Sequence-specific chemical modification of double-stranded DNA with alkylating oligodeoxyribonucleotide derivatives. Gene. 1988 Dec 10;72(1-2):313-22. Vlassov VV, Gaidamakov SA, Zarytova VF, Knorre DG, Levina AS, Nikonova AA, Podust LM, Fedorova OS.

Application of tris(2,2'-bipyridyl)ruthenium(III) for the investigation of DNA spatial structure by a chemical modification method. J Inorg Biochem. 1988 Nov;34(3):149-55. Fedorova OS, Podust LM.

Complementary addressed modification of double-stranded DNA within a ternary complex. FEBS Lett. 1988 Feb 15;228(2):273-6. Fedorova OS, Knorre DG, Podust LM, Zarytova VF.