Faculty Appointments
Director of the Vanderbilt Institute of Chemical Biology Professor of Biochemistry
Professor of ChemistryWilliam Kelly Warren Sr. Chair in Biochemistry
Education
Ph.D., Chemistry, University of California, Berkeley, California
Research Description
biochemistry, cancer, cancer drug design, chemical biology, diabetes, imaging, synthetic biology, enzyme chemistry, enzymology, drug discovery, directed evolution, peptide engineering, enzyme engineering
Research Keywords
biochemistry, cancer, cancer drug design, chemical biology, diabetes, imaging, synthetic biology, enzyme chemistry, enzymology, drug discovery, directed evolution, peptide engineering, enzyme engineering
Publications
Cole CG, Zhang ZJ, Dommaraju SR, Dong Q, Pope RL, Son SS, McSpadden EJ, Woodson CK, Lin H, Dylla NP, Sidebottom AM, Sundararajan A, Mitchell DA, Pamer EG. Lantibiotic-producing bacteria impact microbiome resilience and colonization resistance. Cell Host Microbe [print-electronic]. 2025 Dec 12/1/2025; PMID: 41330369, PII: S1931-3128(25)00467-6, DOI: 10.1016/j.chom.2025.11.007, ISSN: 1934-6069.
Dommaraju SR, Kandy SK, Ren H, Luciano DP, Fujiki S, Sarlah D, Zhao H, Chekan JR, Mitchell DA. A Versatile Enzymatic Pathway for Modification of Peptide C-Termini. ACS Cent Sci. 2025 Nov 11/26/2025; 11(11): 2143-53. PMID: 41341041, PMCID: PMC12670281, DOI: 10.1021/acscentsci.5c01243, ISSN: 2374-7943.
Bregman MH, Cogan DP, Shelton KE, Rice AJ, Dommaraju SR, Nair SK, Mitchell DA. Structure-based discovery and definition of RiPP recognition elements. MSystems [print-electronic]. 2025 Nov 11/18/2025; e0125225. PMID: 41251348, DOI: 10.1128/msystems.01252-25, ISSN: 2379-5077.
Nguyen DT, Ramos-Figueroa JS, Vinogradov AA, Goto Y, Gadgil MG, Splain RA, Suga H, van der Donk WA, Mitchell DA. Aminoacyl-tRNA Specificity of a Ligase Catalyzing Non-ribosomal Peptide Extension. J Am Chem Soc [print-electronic]. 2025 Oct 10/22/2025; 147(42): 37893-8. PMID: 41066767, PMCID: PMC12550832, DOI: 10.1021/jacs.5c12610, ISSN: 1520-5126.
Rice AJ, Gadgil MG, Bisignano P, Stein RA, Mchaourab HS, Mitchell DA. Peptidic Tryptophan Halogenation by a Promiscuous Flavin-Dependent Enzyme. Angew Chem Int Ed Engl [print-electronic]. 2025 Oct 10/13/2025; 64(42): e202509729. PMID: 40883995, PMCID: PMC12518702, DOI: 10.1002/anie.202509729, ISSN: 1521-3773.
Mi X, Barrett SE, Mitchell DA, Shukla D. LassoESM a tailored language model for enhanced lasso peptide property prediction. Nat Commun. 2025 Sep 9/29/2025; 16(1): 8545. PMID: 41022741, PMCID: PMC12480086, PII: 10.1038/s41467-025-63412-3, DOI: 10.1038/s41467-025-63412-3, ISSN: 2041-1723.
Dommaraju SR, Kandy SK, Ren H, Luciano DP, Fujiki S, Sarlah D, Zhao H, Chekan JR, Mitchell DA. A versatile enzymatic pathway for modification of peptide C-termini. BioRxiv. 2025 Jul 7/16/2025; PMID: 40791510, PMCID: PMC12338566, PII: 2025.07.11.664356, DOI: 10.1101/2025.07.11.664356, ISSN: 2692-8205.
Rice AJ, Sword TT, Chengan K, Mitchell DA, Mouncey NJ, Moore SJ, Bailey CB. Cell-free synthetic biology for natural product biosynthesis and discovery. Chem Soc Rev. 2025 May 5/6/2025; 54(9): 4314-52. PMID: 40104998, PMCID: PMC11920963, DOI: 10.1039/d4cs01198h, ISSN: 1460-4744.
Clark JD, Mi X, Mitchell DA, Shukla D. Substrate prediction for RiPP biosynthetic enzymes via masked language modeling and transfer learning. Digit Discov. 2025 Feb 2/12/2025; 4(2): 343-54. PMID: 39649639, PMCID: PMC11622008, PII: d4dd00170b, DOI: 10.1039/d4dd00170b, ISSN: 2635-098X.
Zdouc MM, Blin K, Louwen NLL, Navarro J, Loureiro C, Bader CD, Bailey CB, Barra L, Booth TJ, Bozhüyük KAJ, Cediel-Becerra JDD, Charlop-Powers Z, Chevrette MG, Chooi YH, D'Agostino PM, de Rond T, Del Pup E, Duncan KR, Gu W, Hanif N, Helfrich EJN, Jenner M, Katsuyama Y, Korenskaia A, Krug D, Libis V, Lund GA, Mantri S, Morgan KD, Owen C, Phan CS, Philmus B, Reitz ZL, Robinson SL, Singh KS, Teufel R, Tong Y, Tugizimana F, Ulanova D, Winter JM, Aguilar C, Akiyama DY, Al-Salihi SAA, Alanjary M, Alberti F, Aleti G, Alharthi SA, Rojo MYA, Arishi AA, Augustijn HE, Avalon NE, Avelar-Rivas JA, Axt KK, Barbieri HB, Barbosa JCJ, Barboza Segato LG, Barrett SE, Baunach M, Beemelmanns C, Beqaj D, Berger T, Bernaldo-Agüero J, Bettenbühl SM, Bielinski VA, Biermann F, Borges RM, Borriss R, Breitenbach M, Bretscher KM, Brigham MW, Buedenbender L, Bulcock BW, Cano-Prieto C, Capela J, Carrion VJ, Carter RS, Castelo-Branco R, Castro-Falcón G, Chagas FO, Charria-Girón E, Chaudhri AA, Chaudhry V, Choi H, Choi Y, Choupannejad R, Chromy J, Donahey MSC, Collemare J, Connolly JA, Creamer KE, Crüsemann M, Cruz AA, Cumsille A, Dallery JF, Damas-Ramos LC, Damiani T, de Kruijff M, Martín BD, Sala GD, Dillen J, Doering DT, Dommaraju SR, Durusu S, Egbert S, Ellerhorst M, Faussurier B, Fetter A, Feuermann M, Fewer DP, Foldi J, Frediansyah A, Garza EA, Gavriilidou A, Gentile A, Gerke J, Gerstmans H, Gomez-Escribano JP, González-Salazar LA, Grayson NE, Greco C, Gomez JEG, Guerra S, Flores SG, Gurevich A, Gutiérrez-García K, Hart L, Haslinger K, He B, Hebra T, Hemmann JL, Hindra H, Höing L, Holland DC, Holme JE, Horch T, Hrab P, Hu J, Huynh TH, Hwang JY, Iacovelli R, Iftime D, Iorio M, Jayachandran S, Jeong E, Jing J, Jung JJ, Kakumu Y, Kalkreuter E, Kang KB, Kang S, Kim W, Kim GJ, Kim H, Kim HU, Klapper M, Koetsier RA, Kollten C, Kovács ÁT, Kriukova Y, Kubach N, Kunjapur AM, Kushnareva AK, Kust A, Lamber J, Larralde M, Larsen NJ, Launay AP, Le NT, Lebeer S, Lee BT, Lee K, Lev KL, Li SM, Li YX, Licona-Cassani C, Lien A, Liu J, Lopez JAV, Machushynets NV, Macias MI, Mahmud T, Maleckis M, Martinez-Martinez AM, Mast Y, Maximo MF, McBride CM, McLellan RM, Bhatt KM, Melkonian C, Merrild A, Metsä-Ketelä M, Mitchell DA, Müller AV, Nguyen GS, Nguyen HT, Niedermeyer THJ, O'Hare JH, Ossowicki A, Ostash BO, Otani H, Padva L, Paliyal S, Pan X, Panghal M, Parade DS, Park J, Parra J, Rubio MP, Pham HT, Pidot SJ, Piel J, Pourmohsenin B, Rakhmanov M, Ramesh S, Rasmussen MH, Rego A, Reher R, Rice AJ, Rigolet A, Romero-Otero A, Rosas-Becerra LR, Rosiles PY, Rutz A, Ryu B, Sahadeo LA, Saldanha M, Salvi L, Sánchez-Carvajal E, Santos-Medellin C, Sbaraini N, Schoellhorn SM, Schumm C, Sehnal L, Selem N, Shah AD, Shishido TK, Sieber S, Silviani V, Singh G, Singh H, Sokolova N, Sonnenschein EC, Sosio M, Sowa ST, Steffen K, Stegmann E, Streiff AB, Strüder A, Surup F, Svenningsen T, Sweeney D, Szenei J, Tagirdzhanov A, Tan B, Tarnowski MJ, Terlouw BR, Rey T, Thome NU, Torres Ortega LR, Tørring T, Trindade M, Truman AW, Tvilum M, Udwary DW, Ulbricht C, Vader L, van Wezel GP, Walmsley M, Warnasinghe R, Weddeling HG, Weir ANM, Williams K, Williams SE, Witte TE, Rocca SMW, Yamada K, Yang D, Yang D, Yu J, Zhou Z, Ziemert N, Zimmer L, Zimmermann A, Zimmermann C, van der Hooft JJJ, Linington RG, Weber T, Medema MH. MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration. Nucleic Acids Res. 2025 Jan 1/6/2025; 53(D1): D678-D690-D690. PMID: 39657789, PMCID: PMC11701617, PII: 7919508, DOI: 10.1093/nar/gkae1115, ISSN: 1362-4962.
Dommaraju SR, Kandy SK, Ren H, Luciano DP, Fujiki S, Sarlah D, Zhao H, Chekan JR, Mitchell DA. A Versatile Enzymatic Pathway for Modification of Peptide C-Termini. ACS Cent Sci. 2025 Nov 11/26/2025; 11(11): 2143-53. PMID: 41341041, PMCID: PMC12670281, DOI: 10.1021/acscentsci.5c01243, ISSN: 2374-7943.
Bregman MH, Cogan DP, Shelton KE, Rice AJ, Dommaraju SR, Nair SK, Mitchell DA. Structure-based discovery and definition of RiPP recognition elements. MSystems [print-electronic]. 2025 Nov 11/18/2025; e0125225. PMID: 41251348, DOI: 10.1128/msystems.01252-25, ISSN: 2379-5077.
Nguyen DT, Ramos-Figueroa JS, Vinogradov AA, Goto Y, Gadgil MG, Splain RA, Suga H, van der Donk WA, Mitchell DA. Aminoacyl-tRNA Specificity of a Ligase Catalyzing Non-ribosomal Peptide Extension. J Am Chem Soc [print-electronic]. 2025 Oct 10/22/2025; 147(42): 37893-8. PMID: 41066767, PMCID: PMC12550832, DOI: 10.1021/jacs.5c12610, ISSN: 1520-5126.
Rice AJ, Gadgil MG, Bisignano P, Stein RA, Mchaourab HS, Mitchell DA. Peptidic Tryptophan Halogenation by a Promiscuous Flavin-Dependent Enzyme. Angew Chem Int Ed Engl [print-electronic]. 2025 Oct 10/13/2025; 64(42): e202509729. PMID: 40883995, PMCID: PMC12518702, DOI: 10.1002/anie.202509729, ISSN: 1521-3773.
Mi X, Barrett SE, Mitchell DA, Shukla D. LassoESM a tailored language model for enhanced lasso peptide property prediction. Nat Commun. 2025 Sep 9/29/2025; 16(1): 8545. PMID: 41022741, PMCID: PMC12480086, PII: 10.1038/s41467-025-63412-3, DOI: 10.1038/s41467-025-63412-3, ISSN: 2041-1723.
Dommaraju SR, Kandy SK, Ren H, Luciano DP, Fujiki S, Sarlah D, Zhao H, Chekan JR, Mitchell DA. A versatile enzymatic pathway for modification of peptide C-termini. BioRxiv. 2025 Jul 7/16/2025; PMID: 40791510, PMCID: PMC12338566, PII: 2025.07.11.664356, DOI: 10.1101/2025.07.11.664356, ISSN: 2692-8205.
Rice AJ, Sword TT, Chengan K, Mitchell DA, Mouncey NJ, Moore SJ, Bailey CB. Cell-free synthetic biology for natural product biosynthesis and discovery. Chem Soc Rev. 2025 May 5/6/2025; 54(9): 4314-52. PMID: 40104998, PMCID: PMC11920963, DOI: 10.1039/d4cs01198h, ISSN: 1460-4744.
Clark JD, Mi X, Mitchell DA, Shukla D. Substrate prediction for RiPP biosynthetic enzymes via masked language modeling and transfer learning. Digit Discov. 2025 Feb 2/12/2025; 4(2): 343-54. PMID: 39649639, PMCID: PMC11622008, PII: d4dd00170b, DOI: 10.1039/d4dd00170b, ISSN: 2635-098X.
Zdouc MM, Blin K, Louwen NLL, Navarro J, Loureiro C, Bader CD, Bailey CB, Barra L, Booth TJ, Bozhüyük KAJ, Cediel-Becerra JDD, Charlop-Powers Z, Chevrette MG, Chooi YH, D'Agostino PM, de Rond T, Del Pup E, Duncan KR, Gu W, Hanif N, Helfrich EJN, Jenner M, Katsuyama Y, Korenskaia A, Krug D, Libis V, Lund GA, Mantri S, Morgan KD, Owen C, Phan CS, Philmus B, Reitz ZL, Robinson SL, Singh KS, Teufel R, Tong Y, Tugizimana F, Ulanova D, Winter JM, Aguilar C, Akiyama DY, Al-Salihi SAA, Alanjary M, Alberti F, Aleti G, Alharthi SA, Rojo MYA, Arishi AA, Augustijn HE, Avalon NE, Avelar-Rivas JA, Axt KK, Barbieri HB, Barbosa JCJ, Barboza Segato LG, Barrett SE, Baunach M, Beemelmanns C, Beqaj D, Berger T, Bernaldo-Agüero J, Bettenbühl SM, Bielinski VA, Biermann F, Borges RM, Borriss R, Breitenbach M, Bretscher KM, Brigham MW, Buedenbender L, Bulcock BW, Cano-Prieto C, Capela J, Carrion VJ, Carter RS, Castelo-Branco R, Castro-Falcón G, Chagas FO, Charria-Girón E, Chaudhri AA, Chaudhry V, Choi H, Choi Y, Choupannejad R, Chromy J, Donahey MSC, Collemare J, Connolly JA, Creamer KE, Crüsemann M, Cruz AA, Cumsille A, Dallery JF, Damas-Ramos LC, Damiani T, de Kruijff M, Martín BD, Sala GD, Dillen J, Doering DT, Dommaraju SR, Durusu S, Egbert S, Ellerhorst M, Faussurier B, Fetter A, Feuermann M, Fewer DP, Foldi J, Frediansyah A, Garza EA, Gavriilidou A, Gentile A, Gerke J, Gerstmans H, Gomez-Escribano JP, González-Salazar LA, Grayson NE, Greco C, Gomez JEG, Guerra S, Flores SG, Gurevich A, Gutiérrez-García K, Hart L, Haslinger K, He B, Hebra T, Hemmann JL, Hindra H, Höing L, Holland DC, Holme JE, Horch T, Hrab P, Hu J, Huynh TH, Hwang JY, Iacovelli R, Iftime D, Iorio M, Jayachandran S, Jeong E, Jing J, Jung JJ, Kakumu Y, Kalkreuter E, Kang KB, Kang S, Kim W, Kim GJ, Kim H, Kim HU, Klapper M, Koetsier RA, Kollten C, Kovács ÁT, Kriukova Y, Kubach N, Kunjapur AM, Kushnareva AK, Kust A, Lamber J, Larralde M, Larsen NJ, Launay AP, Le NT, Lebeer S, Lee BT, Lee K, Lev KL, Li SM, Li YX, Licona-Cassani C, Lien A, Liu J, Lopez JAV, Machushynets NV, Macias MI, Mahmud T, Maleckis M, Martinez-Martinez AM, Mast Y, Maximo MF, McBride CM, McLellan RM, Bhatt KM, Melkonian C, Merrild A, Metsä-Ketelä M, Mitchell DA, Müller AV, Nguyen GS, Nguyen HT, Niedermeyer THJ, O'Hare JH, Ossowicki A, Ostash BO, Otani H, Padva L, Paliyal S, Pan X, Panghal M, Parade DS, Park J, Parra J, Rubio MP, Pham HT, Pidot SJ, Piel J, Pourmohsenin B, Rakhmanov M, Ramesh S, Rasmussen MH, Rego A, Reher R, Rice AJ, Rigolet A, Romero-Otero A, Rosas-Becerra LR, Rosiles PY, Rutz A, Ryu B, Sahadeo LA, Saldanha M, Salvi L, Sánchez-Carvajal E, Santos-Medellin C, Sbaraini N, Schoellhorn SM, Schumm C, Sehnal L, Selem N, Shah AD, Shishido TK, Sieber S, Silviani V, Singh G, Singh H, Sokolova N, Sonnenschein EC, Sosio M, Sowa ST, Steffen K, Stegmann E, Streiff AB, Strüder A, Surup F, Svenningsen T, Sweeney D, Szenei J, Tagirdzhanov A, Tan B, Tarnowski MJ, Terlouw BR, Rey T, Thome NU, Torres Ortega LR, Tørring T, Trindade M, Truman AW, Tvilum M, Udwary DW, Ulbricht C, Vader L, van Wezel GP, Walmsley M, Warnasinghe R, Weddeling HG, Weir ANM, Williams K, Williams SE, Witte TE, Rocca SMW, Yamada K, Yang D, Yang D, Yu J, Zhou Z, Ziemert N, Zimmer L, Zimmermann A, Zimmermann C, van der Hooft JJJ, Linington RG, Weber T, Medema MH. MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration. Nucleic Acids Res. 2025 Jan 1/6/2025; 53(D1): D678-D690-D690. PMID: 39657789, PMCID: PMC11701617, PII: 7919508, DOI: 10.1093/nar/gkae1115, ISSN: 1362-4962.