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The interface of evolution and structure-based drug design.

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We strive to provide a constructive, respectful, and collegial environment, empowering scholars to work together to fulfill their potential as scientists having an outstanding impact both in fundamental research and translating to medicine. 

What we do

We aim to understand the molecular basis of drug resistance and to use our new paradigm of drug design to minimize the evolution of that resistance. Resistance occurs when a heterogeneous population of a drug target is challenged by the selective pressure of a drug. In cancer and viruses this heterogeneity is partially caused APOBEC3’s.  In our studies of viral proteases which include among others HIV, HCV and SARS-CoV-2.  We discovered resistance mutations occur either where drugs physically contact regions of the drug target that are not essential for substrate recognition or alter the ensemble dynamics of the drug target favoring substrate. We leverage these insights into new strategies in structure-based drug design to minimize the likelihood of resistance by designing inhibitors to stay within what we define as the substrate envelope. Our new paradigm of drug design minimizes chances of resistance. Realizing that disrupting the drug target’s activity is necessary but not sufficient for developing a robust drug that avoids resistance.

How we do it

We strive to apply a synergistic combination of various experimental and computational methods. We combine the experimental techniques of protein crystallography, cryoEM/ET, organic chemistry, enzymology, deep sequencing, and other biophysical techniques, with the computational strategies of parallel molecular dynamics simulations, homology modeling and docking, to elucidate the molecular mechanisms of drug resistance and develop new inhibition strategies.

Why we do it

Drug resistance is a major obstacle in modern medicine, negatively impacting the lives of millions of patients and costing our society billions of dollars each year. This often happens under the selective pressure of therapy in heterogenous bacterial, viral and fungal infections and cancer due to their rapid evolution. In many cases, resistance to drugs develops so rapidly that our most valuable drugs become obsolete shortly after their introduction to clinic. Instead of considering resistance only after a drug fails, we need a paradigm shift to incorporate preemptive strategies into drug design to avoid resistance.

Recent Publications

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  • Contributions of Hyperactive Mutations in Mpro from SARS-CoV-2 to Drug Resistance

    Tuesday, March 12, 2024
    Author(s): Julia M Flynn,Sarah N Zvornicanin,Tenzin Tsepal,Ala M Shaqra,Nese Kurt Yilmaz,Weiping Jia,Stephanie Moquin,Dustin Dovala,Celia A Schiffer,Daniel N A Bolon
    Source: ACS infectious diseases
    The appearance and spread of mutations that cause drug resistance in rapidly evolving diseases, including infections by the SARS-CoV-2 virus, are major concerns for human health. Many drugs target enzymes, and resistance-conferring mutations impact inhibitor binding or enzyme activity. Nirmatrelvir, the most widely used inhibitor currently used to treat SARS-CoV-2 infections, targets the main protease (M^(pro)) preventing it from processing the viral polyprotein into active subunits. Our...
  • Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors

    Thursday, November 09, 2023
    Author(s): Melissa L Boby,Daren Fearon,Matteo Ferla,Mihajlo Filep,Lizbé Koekemoer,Matthew C Robinson,COVID Moonshot Consortium‡,John D Chodera,Alpha A Lee,Nir London,Annette von Delft,Frank von Delft,Hagit Achdout,Anthony Aimon,Dominic S Alonzi,Robert Arbon,Jasmin C Aschenbrenner,Blake H Balcomb,Elad Bar-David,Haim Barr,Amir Ben-Shmuel,James Bennett,Vitaliy A Bilenko,Bruce Borden,Pascale Boulet,Gregory R Bowman,Lennart Brewitz,Juliane Brun,Sarma Bvnbs,Mark Calmiano,Anna Carbery,Daniel W Carney,Emma Cattermole,Edcon Chang,Eugene Chernyshenko,Austin Clyde,Joseph E Coffland,Galit Cohen,Jason C Cole,Alessandro Contini,Lisa Cox,Tristan Ian Croll,Milan Cvitkovic,Steven De Jonghe,Alex Dias,Kim Donckers,David L Dotson,Alice Douangamath,Shirly Duberstein,Tim Dudgeon,Louise E Dunnett,Peter Eastman,Noam Erez,Charles J Eyermann,Michael Fairhead,Gwen Fate,Oleg Fedorov,Rafaela S Fernandes,Lori Ferrins,Richard Foster,Holly Foster,Laurent Fraisse,Ronen Gabizon,Adolfo García-Sastre,Victor O Gawriljuk,Paul Gehrtz,Carina Gileadi,Charline Giroud,William G Glass,Robert C Glen,Itai Glinert,Andre S Godoy,Marian Gorichko,Tyler Gorrie-Stone,Ed J Griffen,Amna Haneef,Storm Hassell Hart,Jag Heer,Michael Henry,Michelle Hill,Sam Horrell,Qiu Yu Judy Huang,Victor D Huliak,Matthew F D Hurley,Tomer Israely,Andrew Jajack,Jitske Jansen,Eric Jnoff,Dirk Jochmans,Tobias John,Benjamin Kaminow,Lulu Kang,Anastassia L Kantsadi,Peter W Kenny,J L Kiappes,Serhii O Kinakh,Boris Kovar,Tobias Krojer,Van Ngoc Thuy La,Sophie Laghnimi-Hahn,Bruce A Lefker,Haim Levy,Ryan M Lithgo,Ivan G Logvinenko,Petra Lukacik,Hannah Bruce Macdonald,Elizabeth M MacLean,Laetitia L Makower,Tika R Malla,Peter G Marples,Tatiana Matviiuk,Willam McCorkindale,Briana L McGovern,Sharon Melamed,Kostiantyn P Melnykov,Oleg Michurin,Pascal Miesen,Halina Mikolajek,Bruce F Milne,David Minh,Aaron Morris,Garrett M Morris,Melody Jane Morwitzer,Demetri Moustakas,Charles E Mowbray,Aline M Nakamura,Jose Brandao Neto,Johan Neyts,Luong Nguyen,Gabriela D Noske,Vladas Oleinikovas,Glaucius Oliva,Gijs J Overheul,C David Owen,Ruby Pai,Jin Pan,Nir Paran,Alexander Matthew Payne,Benjamin Perry,Maneesh Pingle,Jakir Pinjari,Boaz Politi,Ailsa Powell,Vladimír Pšenák,Iván Pulido,Reut Puni,Victor L Rangel,Rambabu N Reddi,Paul Rees,St Patrick Reid,Lauren Reid,Efrat Resnick,Emily Grace Ripka,Ralph P Robinson,Jaime Rodriguez-Guerra,Romel Rosales,Dominic A Rufa,Kadi Saar,Kumar Singh Saikatendu,Eidarus Salah,David Schaller,Jenke Scheen,Celia A Schiffer,Christopher J Schofield,Mikhail Shafeev,Aarif Shaikh,Ala M Shaqra,Jiye Shi,Khriesto Shurrush,Sukrit Singh,Assa Sittner,Peter Sjö,Rachael Skyner,Adam Smalley,Bart Smeets,Mihaela D Smilova,Leonardo J Solmesky,John Spencer,Claire Strain-Damerell,Vishwanath Swamy,Hadas Tamir,Jenny C Taylor,Rachael E Tennant,Warren Thompson,Andrew Thompson,Susana Tomásio,Charles W E Tomlinson,Igor S Tsurupa,Anthony Tumber,Ioannis Vakonakis,Ronald P van Rij,Laura Vangeel,Finny S Varghese,Mariana Vaschetto,Einat B Vitner,Vincent Voelz,Andrea Volkamer,Martin A Walsh,Walter Ward,Charlie Weatherall,Shay Weiss,Kris M White,Conor Francis Wild,Karolina D Witt,Matthew Wittmann,Nathan Wright,Yfat Yahalom-Ronen,Nese Kurt Yilmaz,Daniel Zaidmann,Ivy Zhang,Hadeer Zidane,Nicole Zitzmann,Sarah N Zvornicanin
    Source: Science (New York, N.Y.)
    We report the results of the COVID Moonshot, a fully open-science, crowdsourced, and structure-enabled drug discovery campaign targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease. We discovered a noncovalent, nonpeptidic inhibitor scaffold with lead-like properties that is differentiated from current main protease inhibitors. Our approach leveraged crowdsourcing, machine learning, exascale molecular simulations, and high-throughput structural biology and...
  • FruitFire: a luciferase based on a fruit fly metabolic enzyme

    Monday, July 10, 2023
    Author(s): Spencer T Adams,Jacqueto Zephyr,Markus F Bohn,Celia A Schiffer,Stephen C Miller
    Source: bioRxiv : the preprint server for biology
    Firefly luciferase is homologous to fatty acyl-CoA synthetases from insects that are not bioluminescent. Here, we determined the crystal structure of the fruit fly fatty acyl-CoA synthetase CG6178 to 2.5 Å. Based on this structure, we mutated a steric protrusion in the active site to create the artificial luciferase FruitFire, which prefers the synthetic luciferin CycLuc2 to d-luciferin by >1000-fold. FruitFire enabled in vivo bioluminescence imaging in the brains of mice using the pro-luciferin...