Granted Patent
B2
US 12,729,458 · App. 17/859,509 · Granted Sep 8, 2026
Discovery and evolution of biologically active metabolites
View Patent ↗
Loading inventors, assignments & file history…
Abstract
The disclosure provides systems, methods, reagents, apparatuses, vectors, and host cells for the discovery and evolution of metabolic pathways that produce small molecules that modulate enzyme function.
Claims (26)
1 . A method for the discovery and evolution of metabolic pathways that produce molecules that modulate protein activity, comprising:
contacting a plurality of host cells that comprise a protein of interest with a plurality of expression vectors that each comprise a different metabolic pathway of a plurality of metabolic pathways under conditions sufficient to express components of the plurality of metabolic pathways in the plurality of host cells, wherein each metabolic pathway of the plurality of metabolic pathways produces one or more metabolites, wherein the protein of interest comprises an enzyme, wherein the enzyme comprises a protein tyrosine phosphatase;
expressing the plurality of metabolic pathways in the plurality of host cells, wherein a host cell of the plurality of host cells or a subset of the plurality of host cells produces a detectable output when a metabolic pathway of the plurality of metabolic pathways produces one or more products comprising a metabolite of the one or more metabolites that modulates an activity of the enzyme, wherein the activity of the enzyme controls an assembly of a protein complex, and wherein assembly of the protein complex enhances transcription of a gene of interest to produce the detectable output;
screening the host cell or the subset of the plurality of host cells under conditions that enable measurement of the detectable output in the host cell or the subset of the plurality of host cells;
isolating the host cell or the subset of the plurality of host cells that produce the detectable output;
analyzing an expression vector of the plurality of expression vectors that yields a detectable output that is higher than an output of a reference vector comprising a reference pathway that causes a threshold level of transcription of the gene of interest; and
characterizing the one or more products of metabolic pathways of the plurality of metabolic pathways comprised by the expression vector that yielded the detectable output that is higher than the output of the reference vector.
2 . The method of claim 1 , wherein the plurality of host cells further comprises a genetically encoded system in which the activity of the enzyme controls the assembly of the protein complex with an activity that is not possessed by components of the protein complex when the components are dissociated, such that the detectable output is proportionate to an amount of the protein complex formed.
3 . The method of claim 2 , wherein the enzyme adds a post-translational modification to a component of the protein complex that causes the component to form the protein complex with another component of the protein complex, wherein the component and the another component are two proteins that are initially dissociated.
4 . The method of claim 2 , wherein the components of the protein complex comprise two proteins with a dissociation constant (K d ) less than or equal to the K d of binding between SH2 domains and their phosphorylated substrates.
5 . The method of claim 1 , wherein the one or more products comprises phenylpropanoids or nonribosomal peptides.
6 . The method of claim 1 , wherein each of the plurality of metabolic pathways comprises a mutation in one or more genes within a starting metabolic pathway relative to an otherwise identical starting metabolic pathway that does not comprise the mutation.
7 . The method of claim 1 , wherein one or more of the plurality of metabolic pathways comprises a set of genes of unknown biosynthetic capability.
8 . The method of claim 1 , wherein the expression vector that is analyzed comprises one or more metabolic pathways of the plurality of metabolic pathways that produces a product of the one or more products that differs from a reference product of another metabolic pathway of the plurality of metabolic pathways.
9 . The method of claim 1 , wherein the expression vector that is analyzed comprises one or more metabolic pathways of the plurality of metabolic pathways that produce a larger quantity of a product of the one or more products than a quantity of a reference product generated by another metabolic pathway of the plurality of metabolic pathways.
10 . The method of claim 1 , wherein the expression vector that is analyzed comprises one or more metabolic pathways of the plurality of metabolic pathways that exhibit a lower cellular toxicity than a reference cellular toxicity exhibited by another metabolic pathway of the plurality of metabolic pathways.
11 . The method of claim 1 , wherein the characterizing the one or more products of the metabolic pathways is performed by analytical methods comprising one or more of gas chromatography-mass spectrometry (GC/MS), liquid chromatography-mass spectrometry (LC/MS), and/or nuclear magnetic resonance (NMR) spectroscopy.
12 . The method of claim 1 , further comprising isolating the one or more products of the metabolic pathways encoded by the expression vector that yielded the detectable output that is higher than the output of the reference vector.
13 . The method of claim 12 , further comprising:
concentrating the one or more products of the metabolic pathways encoded by the expression vector that yielded the detectable output that is higher than the output of the reference vector.
14 . The method of claim 1 , further comprising testing an effect of the one or more products on the protein of interest.
15 . The method of claim 12 , further comprising:
testing the effects of the one or more products of the metabolic pathways encoded by the expression vectors that yield the detectable outputs that are higher than the output of the reference vector in the host cell or the subset of the plurality of host cells on the protein of interest.
16 . The method of claim 13 , wherein the concentrating the one or more products is performed using a rotary evaporator.
17 . The method of claim 3 , wherein the components of the protein complex are covalently coupled to each other to form the protein complex.
18 . The method of claim 1 , wherein the reference pathway does not produce molecules with concentrations, potencies, or a combination thereof that are sufficient to modulate the activity of the enzyme in the host cell or the subset of the population of host cells.
Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Aug 12, 2022
From: FOX, JEROME; SARKAR, ANKUR
To: THE REGENTS OF THE UNIVERSITY OF COLORADO, A BODY CORPORATE
Reel/Frame 061163/0296 →
Continuity (3)
Continuation
PCTUS2021012621
· Jan 8, 2021
Provisional Application
62958368
· Jan 8, 2020
References Cited (400)
US 6057103A
· Short
· 2000
[cited by examiner]
US 6200759B1
· Dove et al.
· 2001
[cited by applicant]
US 6303319B1
· Rickles
· 2001
[cited by applicant]
US 6428951B1
· Michnick et al.
· 2002
[cited by applicant]
US 7927794B2
· Keasling et al.
· 2011
[cited by applicant]
US 8586725B2
· Cummins et al.
· 2013
[cited by applicant]
US 8716460B2
· Alfano et al.
· 2014
[cited by applicant]
US 8859232B2
· Hahn et al.
· 2014
[cited by applicant]
US 20020120947A1
· Roch et al.
· 2002
[cited by applicant]
US 20020164587A1
· Camonis et al.
· 2002
[cited by applicant]
US 20050040550A1
· Short et al.
· 2005
[cited by applicant]
US 20050227357A1
· Bohlmann et al.
· 2005
[cited by applicant]
US 20060292155A1
· Golz et al.
· 2006
[cited by applicant]
US 20110046018A1
· Chen et al.
· 2011
[cited by applicant]
US 20180057545A9
· Liu et al.
· 2018
[cited by applicant]
US 20180111929A1
· Ibrahim et al.
· 2018
[cited by applicant]
CN 103160570A
· 2013
[cited by applicant]
EP 2116263A1
· 2009
[cited by applicant]
WO WO2004003550A2
· 2004
[cited by applicant]
WO WO2004048549A2
· 2004
[cited by applicant]
WO WO2008115420A2
· 2008
[cited by applicant]
WO WO2011002977A2
· 2011
[cited by applicant]
WO WO2011133493A2
· 2011
[cited by applicant]
WO WO2012111772A1
· 2012
[cited by applicant]
WO WO2013016693A2
· 2013
[cited by applicant]
WO WO2014022434A1
· 2014
[cited by applicant]
WO WO2015040197A1
· 2015
[cited by applicant]
WO WO2015189428A1
· 2015
[cited by applicant]
WO WO2018096150A1
· 2018
[cited by applicant]
WO WO2019032628A1
· 2019
[cited by applicant]
WO WO2019232025A2
· 2019
[cited by applicant]
WO WO2020010364A1
· 2020
[cited by applicant]
WO WO2021142207A1
· 2021
[cited by applicant]
Badran et al. (2016) Nature vol. 533 pp. 58 to 63 and supplementary information (Year: 2016).
[cited by examiner]
Abraham et al., GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 1-2: 19-25 (2015).
[cited by applicant]
Abu Bakar et al., Nonstructural proteins of alphavirus-potential targets for drug development. Viruses. 10(2):71 (2018).
[cited by applicant]
Adams et al., Potent and selective inhibitors of the proteasome: dipeptidyl boronic acids. Bioorg Med Chem Lett. 8(4):333-338 (1998).
[cited by applicant]
Aerts et al., Are public-private partnerships the solution to tackle neglected tropical diseases? A systematic review of the literature. Health Policy. 121(7):745-754 (2017).
[cited by applicant]
Afonine et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr. 68(Pt 4):352-367 (2012).
[cited by applicant]
Ajikumar et al. Isoprenoid pathway optimization for Taxol precursor overproduction in
[cited by applicant]
Akutsu et al., Molecular basis for ubiquitin and ISG15 cross-reactivity in viral ovarian tumor domains. Proc Natl Acad Sci USA. 108(6):2228-2233 (2011).
[cited by applicant]
Aleshin et al., Activity, specificity, and probe design for the smallpox virus protease K7L. J Biol Chem. 287(47):39470-39479 (2012).
[cited by applicant]
Aleshin et al., Structural evidence for regulation and specificity of flaviviral proteases and evolution of the Flaviviridae fold. Protein Sci. 16(5):795-806 (2007).
[cited by applicant]
Alonso et al., Protein tyrosine phosphatases in the human genome. Cell. 117(6):699-711 (2004 ).
[cited by applicant]
Amamuddy et al. Integrated computational approaches and tools for allosteric drug discovery. Int J Mol Sci. 21(3):847 (2020).
[cited by applicant]
Anderie et al., Characterization of the C-terminal ER membrane anchor of PTP1B. Exp Cell Res. 313(15):3189-3197 (2007).
[cited by applicant]
Antosch et al., Heterologous Reconstitution of Ikarugamycin Biosynthesis in
[cited by applicant]
Aramini et al., The RAS-binding domain of human BRAF protein serine/threonine kinase exhibits allosteric conformational changes upon binding HRAS. Structure. 23(8):1382-1393 (2015).
[cited by applicant]
Arregui et al., Protein tyrosine phosphatase PTP1B in cell adhesion and migration. Cell Adh Migr. 7(5): 418-423 (2013).
[cited by applicant]
Atanasov et al., Discovery and resupply of pharmacologically active plant-derived natural products: A review. Biotechnol Adv. 33(8):1582-1614 (2015).
[cited by applicant]
Atanasov et al., Natural products in drug discovery: Advances and opportunities. Nat Rev Drug Discov. 20(3):200-216 (2021).
[cited by applicant]
Attia et al., Molecular cloning and characterization of (+)-epi-α-bisabolol synthase, catalyzing the first step in the biosynthesis of the natural sweetener, hernandulcin, in Lippia dulcis. Arch Biochem Biophys. 527(1):…
[cited by applicant]
Auffinger et al., Halogen bonds in biological molecules. Proc Natl Acad Sci. USA. 101(48):16789-16794 (2004).
[cited by applicant]
Auldridge et al., Bacterial phytochromes: more than meets the light. Crit Rev Biochem Mol Biol. 46(1):67-88 (2011).
[cited by applicant]
Badran et al., Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance. Nature. 533(7601):58-63 (2016).
[cited by applicant]
Banno et al., PTP1B and SHP2 in POMC neurons reciprocally regulate energy balance in mice. J Clin Invest. 120(3):120, 720-734 (2010).
[cited by applicant]
Barr et al., Large-scale structural analysis of the classical human protein tyrosine phosphatome. Cell. 136(2):352-363 (2009).
[cited by applicant]
Bence et al., Neuronal PTP1B regulates body weight, adiposity and leptin action. Nat Med. 12(8):917-924 (2006).
[cited by applicant]
Benkert et al., Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics. 27(3):343-350 (2011).
[cited by applicant]
Bentires-Alj et al., Protein-tyrosine phosphatase 1B is required for HER2/Neu-induced breast cancer. Cancer Res. 67(6):2420-2424 (2007).
[cited by applicant]
Bergmann et al., The refined crystal structure of the 3C gene product from hepatitis A virus: specific proteinase activity and RNA recognition. J Virol. 71(3): 2436-2448 (1997).
[cited by applicant]
Bernhardt, Cytochromes P450 as versatile biocatalysts. J Biotechnol. 124(1):128-145 (2006).
[cited by applicant]
Bohlmann et al., Terpenoid-based defenses in conifers: cDNA cloning, characterization, and functional expression of wound-inducible (E)-alpha-bisabolene synthase from grand fir (Abies grandis). 95(12): 6756-6761 (1998).
[cited by applicant]
Boras et al., Preclinical characterization of an intravenous coronavirus 3CL protease inhibitor for the potential treatment of COVID19. Nat Commun. 12(1): 6055, 17pages (2021).
[cited by applicant]
Boulware et al., Protease specificity determination by using cellular libraries of peptide substrates (CLIPS). Proc Natl Acad Sci USA. 103(20):7583-7588 (2006).
[cited by applicant]
Bozhüyük et al., Modification and de novo design of non-ribosomal peptide synthetases using specific assembly points within condensation domains. Nat Chem. 11(7), 653-661 (2019).
[cited by applicant]
Braun et al., MuteinDB: the mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes. Database (Oxford). 2012: bas028, 1-9 (2012).
[cited by applicant]
Brown et al., Halogenase engineering for the generation of new natural product analogues. Chembiochem. 16(15): 2129-2135 (2015).
[cited by applicant]
Bullock et al., Assessing helical protein interfaces for inhibitor design J Am Chem Soc. 133(36):14220-14223 (2011).
[cited by applicant]
Burnham, K. P. & Anderson, D. R. Model Selection and Multimodel Inference: a Practical Information-theoretic Approach, 2nd edn. Springer-Verlag, New York. (2002).
[cited by applicant]
Bussi et al., Canonical sampling through velocity rescaling. J Chem Phys. 126(1):014101 (2007).
[cited by applicant]
Butler et al., Key mutations alter the cytochrome P450 BM3 conformational landscape and remove inherent substrate bias. J Biol Chem. 288(35):25387-25399 (2013).
[cited by applicant]
Calla et al., Cytochrome P450 diversification and hostplant utilization patterns in specialist and generalist moths: Birth, death and adaptation. Mol Ecol. 26(21):6021-6035 (2017).
[cited by applicant]
Camuesco et al., The intestinal anti-inflammatory effect of quercitrin is associated with an inhibition in iNOS expression. Br J Pharmacol. 143(7):908-918 (2004).
[cited by applicant]
Carlson et al., Negative selection and stringency modulation in phage-assisted continuous evolution. Nat Chem Biol. 10(3):216-222 (2014).
[cited by applicant]
Carter et al., Enthalpy-entropy compensation in biomolecular halogen bonds measured in DNA junctions. Biochemistry. 52(29):4891-4903 (2013).
[cited by applicant]
Carter-Franklin et al., Vanadium haloperoxidase-catalyzed bromination and cyclization of terpenes. J Am Chem Soc. 125(13):3688-3689 (2003).
[cited by applicant]
Chandramouli et al., Serotype-specific structural differences in the protease-cofactor complexes of the dengue virus family. J Virol. 84(6):3059-3067 (2010).
[cited by applicant]
Chang et al., Production of isoprenoid pharmaceuticals by engineered microbes. Nat Chem Biol. 2(12):674-681 (2006).
[cited by applicant]
Chang et al., Engineering
[cited by applicant]
Chatzivasileiou et al., Two-step pathway for isoprenoid synthesis. Proc Natl Acad Sci USA. 116(2):506-511 (2019).
[cited by applicant]
Chaudhury et al., Identification of structural mechanisms of HIV-1 protease specificity using computational peptide docking: implications for drug resistance. Structure. 17(12):1636-1648 (2009).
[cited by applicant]
Cheesman et al., Soluble and membrane-bound Drosophila melanogaster CYP6G1 expressed in
[cited by applicant]
Chen et al., Allosteric inhibition of SHP2 phosphatase inhibits cancers driven by receptor tyrosine kinases. Nature. 535(7610):148-152 (2016).
[cited by applicant]
Chen et al., Mechanisms of activation and inhibition of Zika virus NS2B-NS3 protease. Cell Res. 26(11):1260-1263 (2016).
[cited by applicant]
Chen et al., Genomics and evolution of protein phosphatases. Sci Signal. 10(474):eaag1796. (2017).
[cited by applicant]
Chen et al., A predictably selective aliphatic C-H oxidation reaction for complex molecule synthesis. Science. 318(5851):783-787 (2007).
[cited by applicant]
Chen, X. et al., Statistical experimental design guided optimization of a one-pot biphasic multienzyme total synthesis of amorpha-4,11-diene. PLoS One. 8(11):e79650. (2013).
[cited by applicant]
Chen, Y. et al., Emerging coronaviruses: Genome structure, replication, and pathogenesis. J Med Virol. 92(10):2249 (2020).
[cited by applicant]
Cheng, Y. et al., Kidney disease is associated with in-hospital death of patients with COVID-19. Kidney Int. 97(5):829-838 (2020).
[cited by applicant]
Cho, I. et al., Site-selective enzymatic C-H amidation for synthesis of diverse lactams. Science. 364(6440):575-578 (2019). Retraction (2020).
[cited by applicant]
Choi, E. et al., Mitotic regulators and the SHP2-MAPK pathway promote IR endocytosis and feedback regulation of insulin signaling. Nat Commun. 10(1):1473 (2019).
[cited by applicant]
Choi et al., Improvements to the ABSINTH force field for proteins based on experimentally derived amino acid specific backbone conformational statistics. J Chem Theory Comput. 15(2):1367-1382 (2019).
[cited by applicant]
Choi, O. et al. Biosynthesis of plant-specific phenylpropanoids by construction of an artificial biosynthetic pathway in Escherichia coli. J Ind Microbiol Biotechnol. 38(10):1657-1665 (2011).
[cited by applicant]
Choy et al., Conformational rigidity and protein dynamics at distinct timescales regulate PTP1B activity and allostery. Mol Cell 65(4):644-658 (2017).
[cited by applicant]
Christianson, Structural biology and chemistry of the terpenoid cyclases. Chem Rev. 106(8):3412-3442 (2006).
[cited by applicant]
Cortesio et al., Calpain 2 and PTP1B function in a novel pathway with Src to regulate invadopodia dynamics and breast cancer cell invasion. J Cell Biol. 180(5):957-971 (2008).
[cited by applicant]
Cosentino et al., Engineering of a light-gated potassium channel. Science. 348(6235):707-710 (2015).
[cited by applicant]
Cragg et al., Natural products: A continuing source of novel drug leads. Biochim Biophys Acta—Gen Subj. 1830(6):3670-3695 (2013).
[cited by applicant]
Criswell et al., A single residue change leads to a hydroxylated product from the class II diterpene cyclization catalyzed by abietadiene synthase. Org Lett. 14(23):5828-5831 (2012).
[cited by applicant]
Cui et al., A map of human cancer signaling. Mol Syst Biol. 3:152 (2007).
[cited by applicant]
Culp et al., Evolution-guided discovery of antibiotics that inhibit peptidoglycan remodelling. Nature. 578(7796):582-587 (2020).
[cited by applicant]
Cutler et al., The COVID-19 pandemic and the $16 trillion virus. Jama 324(15):1495-1496 (2020).
[cited by applicant]
Dagliyan et al., Engineering extrinsic disorder to control protein activity in living cells. Science. 354(6318):1441-1444 (2016).
[cited by applicant]
Danial et al., Cell death: critical control points. Cell. 116(2):205-219 (2004).
[cited by applicant]
D'Arcy et al., Purification and crystallization of dengue and West Nile virus NS2B-NS3 complexes. Acta Crystallogr Sect F Struct Biol Cryst Commun. 62(Pt 2):157-162 (2006).
[cited by applicant]
Darden et al., Particle mesh Ewald: An N.log(N) method for Ewald sums in large systems. J Chem Phys. 98:10089 (1993).
[cited by applicant]
Davis et al., Directing evolution: The next revolution in drug discovery? Nat Rev Drug Discov. 16(10):681-698 (2017).
[cited by applicant]
Davis, et al. Design, construction and characterization of a set of insulated bacterial promoters. Nucleic Acids Res. 39(3):1131-1141(2011).
[cited by applicant]
De Sousa et al., Flavonoids as noncompetitive inhibitors of Dengue virus NS2B-NS3 protease: inhibition kinetics and docking studies. Bioorg Med Chem. 23(3):466-470 (2015).
[cited by applicant]
Dempke et al., Targeting SHP-1, 2 and SHIP Pathways: A Novel Strategy for Cancer Treatment? Oncology. 95(5):257-269 (2018).
[cited by applicant]
Dias et al., A Historical overview of natural products in drug discovery. Metabolites. 2(2):303-36 (2012).
[cited by applicant]
Dietrich et al., A novel semi-biosynthetic route for artemisinin production using engineered substrate-promiscuous P450(BM3). ACS Chem Biol. 4(4):261-267 (2009).
[cited by applicant]
Dietrich et al., High-throughput metabolic engineering: advances in small-molecule screening and selection. Annu Rev Biochem. 79:563-590 (2010).
[cited by applicant]
Dong et al.; An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect Dis. 20(5):533-534 (2020).
[cited by applicant]
Douangamath et al., Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease. Nat Commun. 11(1):5047 (2020).
[cited by applicant]
Douzery et al., The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils? Proc Natl Acad Sci. USA. 101(43):15386-15391 (2004).
[cited by applicant]
Dove et al., Conversion of the ω subunit of
[cited by applicant]
Dove et al., Activation of prokaryotic transcription through arbitrary protein-protein contacts. Nature. 386(6625):627-630 (1997).
[cited by applicant]
Dube et al., Genetic ablation of protein tyrosine phosphatase 1B accelerates lymphomagenesis of p53-null mice through the regulation of B-cell development. Cancer Res. 65(21):10088-10095 (2005).
[cited by applicant]
Dubois et al., The SHP-1 protein tyrosine phosphatase negatively modulates glucose homeostasis. Nat Med. 12(5):549-556 (2006).
[cited by applicant]
Dye, Flow cytometric analysis of Cfp-Yfp Fret as a marker for in vivo protein-protein interaction. Clin. Appl. Immunol. Rev. 5: 307-324 (2005).
[cited by applicant]
Eche et al., Recombinant expression of HIV-1 protease using soluble fusion tags in
[cited by applicant]
Eden et al., Membrane contacts between endosomes and ER provide sites for PTP1B-epidermal growth factor receptor interaction. Nat Cell Biol. 12(3):267-72 (2010).
[cited by applicant]
Edgar et al., Mechanistic insights into taxadiene epoxidation by taxadiene-5α-hydroxylase. ACS Chem. Biol. 11(2):460-469 (2016).
[cited by applicant]
Emanuel et al., Fair allocation of scarce medical resources in the time of Covid-19. N Engl J Med. 382(21):2049-2055 (2020).
[cited by applicant]
Emsley et al. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr. 60(Pt 12 Pt 1):2126-2132 (2004).
[cited by applicant]
Erbel et al., Structural basis for the activation of flaviviral NS3 proteases from dengue and West Nile virus. Nat Struct Mol Biol. 13(4):372-373 (2006).
[cited by applicant]
Esvelt et al., A system for the continuous directed evolution of biomolecules. Nature. 472(7344):499-503 (2011).
[cited by applicant]
Faeder et al., Rule-based modeling of biochemical systems with BioNetGen. Methods Mol Biol. 500:113-167 (2009).
[cited by applicant]
Fan et al., Optical control of biological processes by light-switchable proteins. Wiley Interdiscip Rev Dev Biol 4(5):545-554 (2015).
[cited by applicant]
Fan et al., Protein-tyrosine phosphatase 1B antagonized signaling by insulin-like growth factor-1 receptor and kinase BRK/PTK6 in ovarian cancer cells. J Biol Chem. 288(34):24923-34 (2013).
[cited by applicant]
Fasan, Tuning P450 enzymes as oxidation catalysts. ACS Catal. 2(4):647-666 (2012).
[cited by applicant]
FDA Food and Drug Administration. Coronavirus (COVID-19) Drugs. at https://www.fda.gov/drugs/emergency-preparedness-drugs/coronavirus-covid-19-drugs (2022).
[cited by applicant]
FDA Food and Drug Administration. Emergency Use Authorization. https://www.fda.gov/emergency-preparedness-and-response/mcm-legal-regulatory-and-policy-framework/emergency-use-authorization#coviddrugs (2022).
[cited by applicant]
Fehr et al., In vivo imaging of the dynamics of glucose uptake in the cytosol of COS-7 cells by fluorescent nanosensors. J. Biol. Chem. 278: 19127-19133 (2003).
[cited by applicant]
Felgner et al., Lipofection: a highly efficient, lipid-mediated DNA-transfection procedure. Proc Natl Acad Sci USA. 84(21):7413-7417 (1987).
[cited by applicant]
Feiler et al., Directed evolution of mycobacterium tuberculosis ß-lactamase reveals gatekeeper residue that regulates antibiotic resistance and catalytic efficiency. PLoS One. 8(9):e73123 (2013).
[cited by applicant]
Ferguson et al., Kinase inhibitors: The road ahead. Nat Rev Drug Discov. 17(5):353-377 (2018).
[cited by applicant]
Ferreira et al., Molecular docking and structure-based drug design strategies. Molecules. 20(7): 13384-13421 (2015).
[cited by applicant]
Fox et al., Interactions between Hofmeister anions and the binding pocket of a protein. J Am Chem Soc. 137(11):3859-3866 (2015).
[cited by applicant]
Fox et al., Water-restructuring mutations can reverse the thermodynamic signature of ligand binding to human carbonic anhydrase. Angew Chem Int Ed Engl. 56(14):3833-3837 (2017).
[cited by applicant]
Fox et al., The molecular origin of enthalpy/entropy compensation in biomolecular recognition. Annu Rev Biophys. 47:223-250 (2018).
[cited by applicant]
Fürstenberg-Hägg et al., Plant defense against insect herbivores. Int J Mol Sci. 14(5):10242-10297 (2013).
[cited by applicant]
Fujimori et al., What's new in enzymatic halogenations. Curr Opin Chem Biol. 11(5):553-560 (2007).
[cited by applicant]
Fujisawa et al., Cloning and characterization of a novel gene that encodes (S)-ß-bisabolene synthase from ginger, Zingiber officinale. Planta 232(1):121-130 (2010).
[cited by applicant]
Galanie et al., Complete biosynthesis of opioids in yeast. Science. 349(6252):1095-1100 (2015).
[cited by applicant]
Gallagher, COVID19 therapeutics: Expanding the antiviral arsenal. EBioMedicine. 66:103289 (2021).
[cited by applicant]
Gao et al., Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science. 368(6492):779-782 (2020).
[cited by applicant]
Gautier et al., How to control proteins with light in living systems. Nat. Chem. Biol. 10: 533-41 (2014).
[cited by applicant]
Gavory et al., Discovery and characterization of highly potent and selective allosteric USP7 inhibitors. Nat Chem Biol.14(2):118-125 (2018).
[cited by applicant]
George et al., Isoprenoid drugs, biofuels, and chemicals—artemisinin, farnesene, and beyond. Adv Biochem Eng Biotechnol. 148: 355-389 (2015).
[cited by applicant]
Gershenzon et al., The function of terpene natural products in the natural world. Nat Chem Biol. 3(7):408-414 (2007).
[cited by applicant]
Gibbs et al., Inhibitor bound dengue NS2B-NS3pro reveals multiple dynamic binding modes. Biochemistry 57(10):1591-1602 (2018).
[cited by applicant]
Gil-Parrado et al., lonomycin-activated calpain triggers apoptosis. A probable role for Bcl-2 family members. J Biol Chem. 277(30): 27217-27226 (2002).
[cited by applicant]
Goldstein et al., Tyrosine dephosphorylation and deactivation of insulin receptor substrate-1 by protein-tyrosine phosphatase 1B. Possible facilitation by the formation of a ternary complex with the GRB2 adaptor protein…
[cited by applicant]
Gorbalenya et al., The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nature Microbiology 5(4):536-544 (2020).
[cited by applicant]
Gordon et al., A SARS-CoV-2-Human protein-protein interaction map reveals drug targets and potential drug-repurposing. Nature. 583(7816):459-468 (2020).
[cited by applicant]
Govindarajan et al., Estimating the total number of protein folds. Proteins 35(4): 408-414 (1999).
[cited by applicant]
Grangeasse et al., Bacterial tyrosine kinases: Evolution, biological function and structural insights. Philos Trans R Soc B Biol Sci. 367(1602):2640-2655 (2012).
[cited by applicant]
Gruet et al., One-step generation of error-prone PCR libraries using Gateway® technology. Microb Cell Fact. 11:14 (2012).
[cited by applicant]
Gu et al., COVID-19: gastrointestinal manifestations and potential fecal-oral transmission. Gastroenterology. 158(6):1518-1519 (2020).
[cited by applicant]
Guex et al., Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective. Electrophoresis. 30(Suppl 1):S162-S173 (2009).
[cited by applicant]
Gunst et al., Efficacy of the TMPRSS2 inhibitor camostat mesilate in patients hospitalized with Covid-19-a double-blind randomized controlled trial. EClinicalMedicine. 35:100849 (2021).
[cited by applicant]
Guo et al., Bisphosphonates target multiple sites in both cis- and trans-prenyltransferases. Proc Natl Acad Sci USA. 104(24):10022-10027(2007).
[cited by applicant]
Guo et al., Discovery of reactive microbiota-derived metabolites that inhibit host proteases. Cell. 168(3):517-526.e18 (2017).
[cited by applicant]
Haj et al., Imaging sites of receptor dephosphorylation by PTP1B on the surface of the endoplasmic reticulum. Science. 295(5560):1708-1711 (2002).
[cited by applicant]
Haj et al., Regulation of signaling at regions of cell-cell contact by endoplasmic reticulum-bound protein-tyrosine phosphatase 1B. PLoS One. 7(5): e36633 (2012).
[cited by applicant]
Halavaty et al., N- and C-terminal flanking regions modulate light-induced signal transduction in the LOV2 domain of the blue light sensor phototropin 1 from Avena sativa. Biochemistry. 46(49):14001-14009 (2007).
[cited by applicant]
Hamberger et al., Evolution of diterpene metabolism: Sitka spruce CYP720B4 catalyzes multiple oxidations in resin acid biosynthesis of conifer defense against insects. Plant Physiol. 157(4): 1677-1695 (2011).
[cited by applicant]
Hammamy et al., Development and Characterization of new peptidomimetic inhibitors of the West Nile Virus NS2B-NS3 Protease. ChemMedChem 8(2):231-241 (2013).
[cited by applicant]
Hartenfeller et al., De novo drug design. Chemoinformatics and Computational Chemical Biology (ed. Bajorath, J.). 672: 299-323 (2010).
[cited by applicant]
Harvey et al., The re-emergence of natural products for drug discovery in the genomics era. Nature reviews drug discovery 14(2):111-129 (2015).
[cited by applicant]
Harvey, Natural products in drug discovery. Drug Discov. 13(19-20):894-901 (2008).
[cited by applicant]
He et al., Protein tyrosine phosphatases as potential therapeutic targets. Acta Pharmacol Sin. 35(10):1227-1246 (2014).
[cited by applicant]
Henrich et al., Matching the power of high throughput screening to the chemical diversity of natural products. Nat Prod Rep. 30(10):1284-1298 (2013).
[cited by applicant]
Hert et al., Quantifying biogenic bias in screening libraries. Nat Chem Biol. 5(7): 479-483 (2009).
[cited by applicant]
Hess et al., LINCS: A linear constraint solver for molecular simulations. J Comput Chem. 18:1463-1472 (1997).
[cited by applicant]
Hjortness et al., Abietane-type diterpenoids inhibit protein tyrosine phosphatases by stabilizing an inactive enzyme conformation. Biochemistry 57(40):5886-5896 (2018).
[cited by applicant]
Hjortness et al., Evolutionarily Conserved Allosteric Communication in Protein Tyrosine Phosphatases. Biochemistry. 57(45):6443-6451 (2018).
[cited by applicant]
Ho et al., Critical assessment of the important residues involved in the dimerization and catalysis of MERS coronavirus main protease. PLOS One 10(12):e0144865 (2015).
[cited by applicant]
Hoffman et al., SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell. 181(2):271-280 (2020).
[cited by applicant]
Hu et al., Kinetic, mutational, and structural studies of the Venezuelan equine encephalitis virus nonstructural protein 2 cysteine protease. Biochemistry 55(21):3007-3019 (2016).
[cited by applicant]
Huang et al., Sesquiterpenes produced by truncated taxadiene synthase. Tetrahedron Lett. 41(50): 9701-9704 (2000).
[cited by applicant]
Huang et al., CHARMM36m: An improved force field for folded and intrinsically disordered proteins. Nat Methods. 14(1): 71-73 (2017).
[cited by applicant]
Huang et al., Understanding HIV-1 protease autoprocessing for novel therapeutic development. Future Med Chem. 5(11):1215-1229 (2013).
[cited by applicant]
Hubbard et al., Protein tyrosine kinase structure and function. Annu Rev Biochem. 69:373-398 (2000).
[cited by applicant]
Hubert et al., Dereplication strategies in natural product research: How many tools and methodologies behind the same concept? Phytochem Rev.16(1):55-95 (2017).
[cited by applicant]
Hughes et al., Principles of early drug discovery. Br J Pharmacol. 162(6):1239-1249 (2011).
[cited by applicant]
Ito et al., PTK6 inhibition suppresses metastases of triple-negative breast cancer via SNAIL-dependent E-cadherin regulation. Cancer Res. 76(15):4406-4417 (2016).
[cited by applicant]
Jantan et al., Plant-derived immunomodulators: an insight on their preclinical evaluation and clinical trials. Front Plant Sci. 6:655 (2015).
[cited by applicant]
Jendresen et al., Highly active and specific tyrosine ammonia-lyases from diverse origins enable enhanced production of aromatic compounds in bacteria and
[cited by applicant]
Jensen et al., Challenges and triumphs to genomics-based natural product discovery. J Ind Microbiol Biotechnol. 41(2):203-209 (2014).
[cited by applicant]
Jensen, Natural products and the gene cluster revolution. Trends Microbiol. 24(12): 968-977 (2016).
[cited by applicant]
Jewell et al., Hepatitis A virus 3C proteinase substrate specificity. Biochemistry 31(34): 7862-7869 (1992).
[cited by applicant]
Jia et al., Extreme promiscuity of a bacterial and a plant diterpene synthase enables combinatorial biosynthesis. Metab Eng. 37: 24-34 (2016).
[cited by applicant]
Jia et al., Combinatorial biosynthesis and the basis for substrate promiscuity in class I diterpene synthases. Metabolic Eng. 55:44-58 (2019).
[cited by applicant]
Jiang et al., Natural products possessing protein tyrosine phosphatase 1B (PTP1B) inhibitory activity found in the last decades. Acta Pharmacol Sin. 33(10):1217-1245 (2012). doi:10.1038/aps.2012.90.
[cited by applicant]
Jin et al., Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature. 582(7811):289-293 (2020).
[cited by applicant]
Johnson et al., Protein tyrosine phosphatase IB inhibitors for diabetes. Nat Rev Drug Discov. 1(9):696-709 (2002).
[cited by applicant]
Johnston et al., Continuous bioactivity-dependent evolution of an antibiotic biosynthetic pathway. Nat. Commun. 11(1):4202 (2020).
[cited by applicant]
Joosten et al., The PDB_REDO server for macromolecular structure model optimization. IUCrJ 1(Pt 4):213-220 (2014).
[cited by applicant]
Jung et al., Cytochrome P450: taming a wild type enzyme. Curr Opin Biotechnol. 22(6):809-817 (2011).
[cited by applicant]
Kaberniuk et al., A bacterial phytochrome-based optogenetic system controllable with near-infrared light. Nat Methods. 13(7):591-7 (2016).
[cited by applicant]
Kachroo et al., Systematic humanization of yeast genes reveals conserved functions and genetic modularity. Science. 348(6237):921-925 (2015).
[cited by applicant]
Kampranis et al., Rational conversion of substrate and product specificity in a Salvia monoterpene synthase: structural insights into the evolution of terpene synthase function. Plant Cell. 19(6):1994-2005 (2007).
[cited by applicant]
Kaneko et al. Superbinder SH2 domains act as antagonists of cell signaling. Sci Signal. 5(243):ra68 (2012).
[cited by applicant]
Karunarathne et al., Subcellular optogenetics—controlling signaling and single-cell behavior. J Cell Sci. 128(1):15-25 (2015).
[cited by applicant]
Keedy et al., An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering. Elife. 7:e36307 (2018).
[cited by applicant]
Kennedy, Signal-Processing Machines at the Postsynaptic Density. Science. 290(5492):750-754 (2000).
[cited by applicant]
Kennedy, Managing the drug discovery/development interface. Drug Discov Today. 2(10):436-444 (1997).
[cited by applicant]
Khaerunnisa et al., Potential Inhibitor of COVID-19 Main Protease (Mpro) from Several Medicinal Plant Compounds by Molecular Docking Study. Preprints. 14 pages (2020). doi:10.20944/preprints202003.0226.v1.
[cited by applicant]
Khrimian et al., Absolute configurations of stink bug- and plant-produced sesquipiperitols via synthesis of all stereoisomers. J Nat Prod. 83(7)2281-2286 (2020).
[cited by applicant]
Kitaoka et al., Optimization of recombinant expression enables discovery of novel cytochrome P450 activity in rice diterpenoid biosynthesis. Appl Microbiol Biotechnol. 99(18):7549-7558 (2015).
[cited by applicant]
Klebe, Applying thermodynamic profiling in lead finding and optimization. Nat Rev Drug Discov. 14(2):95-110 (2015).
[cited by applicant]
Koehn et al., The evolving role of natural products in drug discovery. Nat Rev Drug Discov. 4(3):206-220 (2005).
[cited by applicant]
Koh et al., Current trends in modem pharmaceutical analysis for drug discovery. Drug Discov Today. 8(19): 889-897 (2003).
[cited by applicant]
Konc et al., ProBiS-CHARMMing: web interface for prediction and optimization of ligands in protein binding sites. J Chem Inf Model. 55(11):2308-2314 (2015).
[cited by applicant]
Kondo et al., Yellow fever virus NS2B/NS3 protease: hydrolytic properties and substrate specificity. Biochem Biophys Res Commun. 407(4):640-644 (2011).
[cited by applicant]
Koren et al., Inhibition of the protein tyrosine phosphatase PTP1B: potential therapy for obesity, insulin resistance and type-2 diabetes mellitus. Best Pract Res Clin Endocrinol Metab. Metab. 21(4):621-640 (2007).
[cited by applicant]
Krauss et al., LOVely enzymes—towards engineering light-controllable biocatalysts. Microb Biotechnol. 3(1):15-23 (2010).
[cited by applicant]
Krimmer et al., Methyl, ethyl, propyl, butyl: futile but not for water, as the correlation of structure and thermodynamic signature shows in a congeneric series of thermolysin inhibitors. ChemMedChem 9(4):833-846 (2014).
[cited by applicant]
Krishnan et al., Anxious moments for the protein tyrosine phosphatase PTP1B. Trends Neurosci. 38(8):462-465 (2015).
[cited by applicant]
Krishnan et al., Targeting the disordered C terminus of PTP1B with an allosteric inhibitor. Nat Chem Biol. 10(7): 558-566 (2014).
[cited by applicant]
Krishnan et al. PTP1B inhibition suggests a therapeutic strategy for Rett syndrome. J Clin Invest. 125(8):3163-3177 (2015).
[cited by applicant]
Lancaster, J. et al., An IDS-type sesquiterpene synthase produces the pheromone precursor (Z)-α-bisabolene in Nezara viridula. J Chem Ecol. 45(2):187-197 (2019).
[cited by applicant]
Lange et al., Enzymology of monoterpene functionalization in glandular trichomes. J Exp Bot. 70(4):1095-1108 (2019).
[cited by applicant]
Lauchli et al., High-throughput screening for terpene-synthase-cyclization activity and directed evolution of a terpene synthase. Angew Chem Int Ed Engl. 52(21):5571-5574 (2013).
[cited by applicant]
Lee et al., Identification of novel small molecule inhibitors against NS2B/NS3 serine protease from Zika virus. Antiviral Res. 139, 49-58 (2017).
[cited by applicant]
Lee et al., Phosphorylation of the AMPA receptor GluR1 subunit is required for synaptic plasticity and retention of spatial memory. Cell. 112(5):631-643 (2003).
[cited by applicant]
Lee et al. Proteasome inhibitors: valuable new tools for cell biologists. Trends Cell Biol. 8(10):397-403 (1998).
[cited by applicant]
Lee et al., Surface sites for engineering allosteric control in proteins. Science. 322(5900):438-442 (2008).
[cited by applicant]
Lehmann et al., Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies. J Clin Invest. 121(7):2750-2767 (2011).
[cited by applicant]
Lei et al., Crystal structure of the papain-like protease of MERS coronavirus reveals unusual, potentially druggable active-site features. Antiviral Res. 109:72-82 (2014).
[cited by applicant]
Lei et al., Crystal structure of Zika virus NS2B-NS3 protease in complex with a boronate inhibitor. Science. 353(6298):503-505 (2016).
[cited by applicant]
Leonard et al., Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control. Proc Natl Acad Sci USA. 107(31):13654-13659 (2010).
[cited by applicant]
Lessard et al., PTP1B is an androgen receptor-regulated phosphatase that promotes the progression of prostate cancer. Cancer Res. 72(6):1529-1537 (2012).
[cited by applicant]
Lessard et al., The two faces of PTP1B in cancer. Biochim Biophys Acta. 1804(3):613-619 (2010).
[cited by applicant]
Lewis et al., Combinatorial alanine substitution enables rapid optimization of cytochrome P450BM3 for selective hydroxylation of large substrates. Chembiochem 11(18):2502-2505 (2010).
[cited by applicant]
Li et al., Reprogramming the chemodiversity of terpenoid cyclization by remolding the active site contour of epi-isozizaene synthase. Biochemistry. 53(7):1155-1168 (2014).
[cited by applicant]
Li et al., Therapeutic options for the 2019 novel coronavirus (2019-nCOV). Nat Rev Drug Discov. 19(3):149-150 (2020).
[cited by applicant]
Li et al., Crystal Structure and Substrate Specificity of PTPN12. Cell Rep. 15(6):1345-1358 (2016).
[cited by applicant]
Li et al., Production of plant-specific flavones baicalein and scutellarein in an engineered
[cited by applicant]
Li et al., Drug discovery and natural products: end of an era or an endless frontier? Science. 10;325(5937):161-165 (2009).
[cited by applicant]
Li et al., Complete biosynthesis of noscapine and halogenated alkaloids in yeast. Proc Natl Acad Sci USA. 115(17):E3922-E3931 (2018).
[cited by applicant]
Lim et al., (-)-α-Bisabolol production in engineered
[cited by applicant]
Lim et al., Human coronaviruses: A review of virus-host interactions. Diseases. 4(3):26 (2016).
[cited by applicant]
Lindner et al., The papain-like protease from the severe acute respiratory syndrome coronavirus is a deubiquitinating enzyme. J Virol. 79(24):15199-15208 (2005).
[cited by applicant]
Ling et al., Cytostatic and cytotoxic natural products against cancer cell models. Molecules. 24(10):2012 (2019).
[cited by applicant]
Liu et al., PTP1B promotes cell proliferation and metastasis through activating src and ERK1/2 in non-small cell lung cancer. Cancer Lett. 359(2):218-225 (2015).
[cited by applicant]
Loehr et al., Yellow fever virus NS3 protease: peptide-inhibition studies. J Gen Virol. 88(Pt 8):2223-2227 (2007).
[cited by applicant]
Lu et al., Co-expression of P450 BM3 and glucose dehydrogenase by recombinant
[cited by applicant]
Lukyanov et al., Innovation: Photoactivatable fluorescent proteins. Nat Rev Mol Cell Biol. 6(11):885-891 (2005).
[cited by applicant]
Luo et al., Crystal structure of the NS3 protease-helicase from dengue virus. J Virol 82(1): 173-183 (2008).
[cited by applicant]
Luo et al., Flexibility between the protease and helicase domains of the dengue virus NS3 protein conferred by the linker region and its functional implications. J Biol Chem. 285(24):18817-18827 (2010).
[cited by applicant]
Luo et al., Complete biosynthesis of cannabinoids and their unnatural analogues in yeast. Nature. 567(7746):123-126 (2019).
[cited by applicant]
Lv et al., HIV protease inhibitors: a review of molecular selectivity and toxicity. Hiv Aids (Auckl). 7:95-104. (2015).
[cited by applicant]
Mackerell et al., All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B. 102(18):3586-3616 (1998).
[cited by applicant]
Mafu et al., Probing the promiscuity of ent -kaurene oxidases via combinatorial biosynthesis. Proc Natl Acad Sci USA. 113(9):2526-2531 (2016).
[cited by applicant]
Maier, Design and synthesis of analogues of natural products. Org Biomol Chem. 13(19):5302-5343 (2015).
[cited by applicant]
Malcolm et al., Expression and characterization of recombinant hepatitis A virus 3C proteinase. Biochemistry. 31(13):3358-3363 (1992).
[cited by applicant]
Manguso et al. In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target. Nature. 547(7664):413-418 (2017).
[cited by applicant]
Mao et al., Neurologic manifestations of hospitalized patients with coronavirus disease 2019 in Wuhan, China. JAMA Neurol. 77(6):683-690 (2020).
[cited by applicant]
Martin et al., Engineering a mevalonate pathway in
[cited by applicant]
Martins et al., Marketed marine natural products in the pharmaceutical and cosmeceutical industries: tips for success. Mar drugs. 12(2):1066 -1101 (2014).
[cited by applicant]
Matulka et al., PTP1B is an effector of activin signaling and regulates neural specification of embryonic stem cells. Cell Stem Cell. 13(6):706-719 (2013).
[cited by applicant]
McAndrew et al., Structure of a three-domain sesquiterpene synthase: A prospective target for advanced biofuels production. Structure. 19(12):1876-1884 (2011).
[cited by applicant]
McKibbin et al., The Global Macroeconomic Impacts of COVID-19: Seven Scenarios. SSRN Electronic Journal. CAMA Working Paper No. 19/2020: 45 pages (2020).
[cited by applicant]
Medema et al., antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res. 39(Web Server issue): W339-46 (2011…
[cited by applicant]
Mehla et al., A comparison of two-hybrid approaches for detecting protein-protein interactions. Methods Enzymol. 586:333-358 (2017).
[cited by applicant]
Mellott et al., A clinical-stage cysteine protease inhibitor blocks SARS-CoV-2 infection of human and monkey cells. ACS Chem Biol. 16(4):642-650 (2021).
[cited by applicant]
Mendoza et al., Two detailed plaque assay protocols for the quantification of infectious SARS-CoV-2. Curr Protoc Microbiol. 57(1):ecpmc105 (2020).
[cited by applicant]
Menon et al., RadH: A versatile halogenase for integration into synthetic pathways. Angew Chem Int Ed Engl. 56(39):11841-11845 (2017).
[cited by applicant]
Merck. Merck and Ridgeback Biotherapeutics Provide Update on Results from MOVe-OUT Study of Molnupiravir, an Investigational Oral Antiviral Medicine, in At Risk Adults With Mild-to- Moderate COVID-19. at https://www.mer…
[cited by applicant]
Merck. Merck and Ridgeback's Investigational Oral Antiviral Molnupiravir Reduced the Risk of Hospitalization or Death by Approximately 50 Percent Compared to Placebo for Patients with Mild or Moderate COVID-19 in Positi…
[cited by applicant]
Mobley et al., Predicting binding free energies: frontiers and benchmarks. Annu. Rev. Biophys. 46:531-558 (2017).
[cited by applicant]
Montalibet et al., Using yeast to screen for inhibitors of protein tyrosine phosphatase 1B. Biochem Pharmacol. 68(9):1807-1814 (2004).
[cited by applicant]
Montalibet et al. Residues distant from the active site influence protein-tyrosine phosphatase 1B inhibitor binding. J Biol Chem. 281(8):5258-5266 (2006).
[cited by applicant]
Morrone et al., Increasing diterpene yield with a modular metabolic engineering system in
[cited by applicant]
Muangphrom et al., Identification and characterization of a novel sesquiterpene synthase, 4-amorphen-11-ol synthase, from artemisia maritima. Plant Biotechnol. 35(2):113-121 (2018).
[cited by applicant]
Muangphrom et al. Functional analysis of amorpha-4,11-diene synthase (ADS) homologs from non-artemisinin-producing artemisia species: The discovery of novel koidzumiol and (+)-α-Bisabolol synthases. Plant Cell Physiol. …
[cited by applicant]
Murphy et al., WScore: A flexible and accurate treatment of explicit water molecules in ligand-receptor docking. J Med Chem. 59(9):4364-4384 (2016).
[cited by applicant]
Muzzarelli et al., Structural and antiviral studies of the human norovirus GII.4 protease. Biochemistry. 58(7):900-907 (2019).
[cited by applicant]
Nakagawa et al., A bacterial platform for fermentative production of plant alkaloids. Nat Commun. 2:326 (2011).
[cited by applicant]
Nakamura et al., A norovirus protease structure provides insights into active and substrate binding site integrity. J Virol. 79(21):13685-13693 (2005).
[cited by applicant]
Nalam et al., Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance. J Virol. 84(10):5368-5378 (2010).
[cited by applicant]
Namchuk, Early returns on small molecule therapeutics for SARS-CoV-2. ACS Infect Dis. 7(6):1298-1302 (2021).
[cited by applicant]
Narwal et al., Crystal structure of chikungunya virus nsP2 cysteine protease reveals a putative flexible loop blocking its active site. Int J Biol Macromol. 116:451-462 (2018).
[cited by applicant]
Needle et al., Structures of the middle east respiratory syndrome coronavirus 3C-like protease reveal insights into substrate specificity. Acta Crystallogr D Biol Crystallogr. 71(Pt 5):1102-1111 (2015).
[cited by applicant]
Newman et al., Natural products as sources of new drugs from 1981 to 2014. Journal of Natural Products. 79(3):629-661 (2016).
[cited by applicant]
Next Generation Sequencing: Amplicon-EZ. at https://www.genewiz.com/en/Public/Services/Next-Generation-Sequencing/Amplicon-Sequencing-Services/Amplicon-EZ (2022).
[cited by applicant]
NIAID National Institute of Allergy and Infectious Diseases. Emerging Infectious Diseases/Pathogens. at https://www.niaid.nih.gov/research/emerging-infectious-diseases-pathogens (2018).
[cited by applicant]
Nitsche et al., Peptide-boronic acid inhibitors of flaviviral proteases: medicinal chemistry and structural biology. J Med Chem. 60(1):511-516 (2017).
[cited by applicant]
Nitsche, Proteases from dengue, West Nile and Zika viruses as drug targets. Biophys Rev. 11(2):157-165 (2019).
[cited by applicant]
Noble et al., Ligand-bound structures of the dengue virus protease reveal the active conformation. J Virol. 86(1):438-446 (2012).
[cited by applicant]
Noske et al., Structural characterization and polymorphism analysis of the NS2B-NS3 protease from the 2017 Brazilian circulating strain of Yellow Fever virus. Biochimica et Biophysica Acta (BBA)-General Subjects 1864(4)…
[cited by applicant]
O'Brien et al., Inparanoid: A comprehensive database of eukaryotic orthologs. Nucleic Acids Res. 33(Database issue):D476-D480 (2005).
[cited by applicant]
Oleinikovas et al., Understanding cryptic pocket formation in protein targets by enhanced sampling simulations. J Am Chem Soc. 138(43):14257-14263 (2016).
[cited by applicant]
Olsson et al., The thermodynamics of protein-ligand interaction and solvation: insights for ligand design. J Mol Biol. 384(4):1002-1017 (2008).
[cited by applicant]
O'Maille et al., Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases. Nat Chem Biol. 4(10):617-623 (2008).
[cited by applicant]
Otto et al., Cysteine proteases and their inhibitors. Chem Rev. 97(1):133-172 (1997).
[cited by applicant]
Ouyang et al., Determination of hierarchical relationship of Src and Rac at subcellular locations with FRET biosensors. Proc Natl Acad Sci USA. 105(38):14353-14358 (2008).
[cited by applicant]
Packer et al., Methods for the directed evolution of proteins. Nat Rev Genet. 16(7):379-394 (2015).
[cited by applicant]
Paddon et al., Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development. Nat Rev Microbiol. 12(5):355-367 (2014).
[cited by applicant]
Palazón-Riquelme et al., USP7 and USP47 deubiquitinases regulate NLRP3 inflammasome activation. EMBO Rep. 19(10):e44766 (2018).
[cited by applicant]
Paling et al., Role of the protein tyrosine phosphatase SHP-1 (Src homology phosphatase-1) in the regulation of interleukin-3-induced survival, proliferation and signalling. Biochem. J. 368(Pt 3):885-894 (2002).
[cited by applicant]
Pallesen et al., Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen. Proc Natl Acad Sci USA. 114(35):E7348-E7357 (2017).
[cited by applicant]
Park et al., Whole-cell biocatalysis using cytochrome P450 monooxygenases for biotransformation of sustainable bioresources (fatty acids, fatty alkanes, and aromatic amino acids). Biotechnol Adv. 40:107504 (2020).
[cited by applicant]
Parrinello, Polymorphic transitions in single crystals: A new molecular dynamics method. J Appl Phys. 52(12):7182 (1981).
[cited by applicant]
Pastorino et al., Expression and biochemical characterization of nsP2 cysteine protease of Chikungunya virus. Virus Res.131(2):293-298 (2008).
[cited by applicant]
Pastorino et al., Improvement of the purification of Saint Louis encephalitis virus NS2B-NS3 recombinant protease expressed in
[cited by applicant]
Pathan et al., Basic opioid pharmacology: an update. Br J Pain. 6(1):11-16 (2012).
[cited by applicant]
Paul et al., Tyrosine kinase—role and significance in Cancer. Int J Med Sci. 1(2):101-115 (2004).
[cited by applicant]
Paul et al., How to improve R&D productivity: The pharmaceutical industry's grand challenge. Nat Rev Drug Discov. 9(3):203-214 (2010).
[cited by applicant]
PCT/US2019/040896 International Preliminary Report on Patentability dated Jan. 12, 2021.
[cited by applicant]
PCT/US2019/040896 International Search Report and Written Opinion dated Nov. 8, 2019.
[cited by applicant]
PCT/US2021/012621 International Search Report and Written Opinion dated Apr. 6, 2021.
[cited by applicant]
Pelander et al., In silica methods for predicting metabolism and mass fragmentation applied to quetiapine in liquid chromatography/time-of-flight mass spectrometry urine drug screening. Rapid Commun Mass Spectrom. 23(4)…
[cited by applicant]
Peralta-Yahya et al. Identification and microbial production of a terpene-based advanced biofuel. Nat Commun. 2:483 (2011).
[cited by applicant]
Peter et al., Mechanism of signal transduction of the LOV2-Jα photosensor from Avena sativa. Nat Commun. 1:122 (2010).
[cited by applicant]
Peters et al., Abietadiene synthase catalysis: mutational analysis of a prenyl diphosphate ionization-initiated cyclization and rearrangement. Proc Natl Acad Sci USA. 99(2):580-584 (2002).
[cited by applicant]
Peters et al., Abietadiene synthase from grand fir (Abies grandis): Characterization and mechanism of action of the “pseudomature” recombinant enzyme. Biochemistry 39(50): 15592-15602 (2000).
[cited by applicant]
Pfeifer et al., Biosynthesis of Yersiniabactin, a complex polyketide-nonribosomal peptide, using
[cited by applicant]
Pfizer. Pfizer Seeks Emergency Use Authorization For Novel COVID-19 Oral Antiviral Candidate. at https://www.pfizer.com/news/press-release/press-release-detail/pfizer-seeks-emergency-use-authorization-novel-covid-19 (20…
[cited by applicant]
PHE Public Health Emergency. Pause in the Distribution of Bamlanivimab/Etesevimab. at https://www.phe.gov/emergency/events/COVID19/investigation-MCM/Bamlanivimab- etesevimab/Pages/bamlanivimab-etesevimab-distribution-pa…
[cited by applicant]
Phoo et al., Structures of Zika virus NS2B-NS3 protease in complex with peptidomimetic inhibitors. Antiviral Res. 160:17-24 (2018).
[cited by applicant]
Pike et al., Protein tyrosine phosphatase 1B is a regulator of the interleukin-10-induced transcriptional program in macrophages. Sci Signal. 7(324):ra43 (2014).
[cited by applicant]
Piserchio et al., Expression and purification of Src-family kinases for solution NMR studies. Methods Mol Biol. 831:111-131 (2012).
[cited by applicant]
Porter et al., Cooperative changes in solvent exposure identify cryptic pockets, switches, and allosteric coupling. Biophys J. 116(5):818-830 (2019).
[cited by applicant]
Price et al., FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS One 5(3):e9490 (2010).
[cited by applicant]
Qin et al., Chronic stress induces anxiety via an amygdalar intracellular cascade that impairs endocannabinoid signaling. Neuron. 85(6):1319-1331 (2015).
[cited by applicant]
Rani et al., Drug development post COVID-19 pandemic: toward a better system to meet current and future global health challenges. Expert Opin Drug Discov. 16(4):365-371 (2021).
[cited by applicant]
Ratia et al., Severe acute respiratory syndrome coronavirus papain-like protease: structure of a viral deubiquitinating enzyme. Proc Natl Acad Sci USA.103(15):5717-5722 (2006).
[cited by applicant]
Repina et al., At light speed: Advances in optogenetic systems for regulating cell signaling and behavior. Annu Rev Chem Biomol Eng. 8:13-39 (2017).
[cited by applicant]
Rhee et al., Protein tyrosine phosphatases in lymphocyte activation and autoimmunity. Nat Immunol. 13(5): 439-447 (2012).
[cited by applicant]
Rinkel et al., Stereochemical investigations on the biosynthesis of achiral (Z)-γ-bisabolene in Cryptosporangium arvum. Beilstein J Org Chem. 15:789-794 (2019).
[cited by applicant]
Rizzuti et al., Sub-micromolar inhibition of SARS-CoV-2 3CLpro by natural compounds. Pharmaceuticals (Basel) 14(9):892 (2021).
[cited by applicant]
Ro et al., Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature. 440(7086):940-943 (2006).
[cited by applicant]
Robin et al., Structure of West Nile virus NS3 protease: ligand stabilization of the catalytic conformation. J Mol Biol. 385(5):1568-1577 (2009).
[cited by applicant]
Robinson et al., Differential water thermodynamics determine PI3K-Beta/Delta selectivity for solvent-exposed ligand modifications. J Chem Inf Model. 56(5):886-894 (2016).
[cited by applicant]
Rodrigues et al., Counting on natural products for drug design. Nature chemistry 8(6):531-541 (2016).
[cited by applicant]
Rodriguez et al., The growing and glowing toolbox of fluorescent and photoactive proteins. Trends Biochem. Sci. 42(2):111-129 (2017).
[cited by applicant]
Romsicki et al., Protein tyrosine phosphatase-1B dephosphorylation of the insulin receptor occurs in a perinuclear endosome compartment in human embryonic kidney 293 cells. J Biol Chem. 279(13): 12868-12875 (2004).
[cited by applicant]
Rougéet al., Molecular understanding of USP7 substrate recognition and C-terminal activation. Structure. 24(8):1335-1345 (2016).
[cited by applicant]
Rowland et al., ER contact sites define the position and timing of endosome fission. Cell 159(5):1027-1041 (2014).
[cited by applicant]
Russo et al., The crystal structure of the Venezuelan equine encephalitis alphavirus nsP2 protease. Structure 14(9):1449-1458 (2006).
[cited by applicant]
Rut et al., Profiling of flaviviral NS2B-NS3 protease specificity provides a structural basis for the development of selective chemical tools that differentiate Dengue from Zika and West Nile viruses. Antiviral Research…
[cited by applicant]
Rutledge et al. Discovery of microbial natural products by activation of silent biosynthetic gene clusters. Nat Rev Microbiol. 13(8):509-523 (2015).
[cited by applicant]
Ruttkies et al., MetFrag relaunched: Incorporating strategies beyond in silica fragmentation. J Cheminform. 8:3 (2016).
[cited by applicant]
Salis, The ribosome binding site calculator. Methods Enzymol. 498:19-42 (2011).
[cited by applicant]
Sangster et al., New trends and future opportunities in the enzymatic formation of C-C, C-N, and C-O bonds. Chembiochem 23(6):e202100464. (2021).
[cited by applicant]
Sarkar et al., Microbially guided discovery and biosynthesis of biologically active natural products. ACS Synth Biol 10(6):1505-1519 (2021).
[cited by applicant]
Sarkar et al., Evolution-guided biosynthesis of terpenoid Inhibitors. ACS Synth Biol. 11(9):3015-3027 (2022).
[cited by applicant]
Sarrade-Loucheur et al., Synthetic derivatives of (+)-epi-α-bisabolol are formed by mammalian cytochromes P450 expressed in a yeast reconstituted pathway. ACS Synth Biol. 9(2):368-380 (2020).
[cited by applicant]
Sato et al., Fluorescent indicators for imaging protein phosphorylation in single living cells. Nat Biotechnol. 20(3):287-294 (2002).
[cited by applicant]
Scott et al., Targeting protein tyrosine phosphatases for anticancer drug discovery. Curr Pharm Des. 16(16):1843-1862 (2010).
[cited by applicant]
Seifert et al., Rational design of a minimal and highly enriched CYP102Al mutant library with improved regio-, stereo- and chemoselectivity. Chembiochem 10(5):853-861 (2009).
[cited by applicant]
Shang et al., Biochemical characterization of recombinant enterovirus 71 3C protease with fluorogenic model peptide substrates and development of a biochemical assay. Antimicrob Agents Chemother. 59(4):1827-1836 (2015).
[cited by applicant]
Shchelkunov et al., Analysis of the monkeypox virus genome. Virology. 297(2):172-194 (2002).
[cited by applicant]
Shepherd et al., A structure-guided switch in the regioselectivity of a tryptophan halogenase. Chembiochem 17(9):821-824 (2016).
[cited by applicant]
Shi et al., Discovery and biosynthesis of guanipiperazine from a NRPS-like pathway. Chem Sci. 12(8):2925-2930 (2021).
[cited by applicant]
Shimada et al., Selectivity of polycyclic inhibitors for human cytochrome P450s 1A1, 1A2, and 1B1. Chem. Res. Toxicol. 11(9):1048-1056 (1998).
[cited by applicant]
Shin et al., Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature. 587(7835):657-662 (2020).
[cited by applicant]
Smanski et al., Synthetic biology to access and expand nature's chemical diversity. Nat Rev Microbiol. 14(3):135-149 (2016).
[cited by applicant]
Snyder et al., Is it the shape of the cavity, or the shape of the water in the cavity? Eur Phys J. Special Topics. 223: 853-891 (2014).
[cited by applicant]
Soysal et al., PTP1B expression is an independent positive prognostic factor in human breast cancer. Breast Cancer Res Treat. 137(2):637-644 (2013).
[cited by applicant]
Stanford et al., Targeting tyrosine phosphatases: Time to end the stigma. Trends Pharmacol Sci. 38(6):524-540 (2017).
[cited by applicant]
Steele et al., Sesquiterpene synthases from grand fir (Abies grandis). Comparison of constitutive and wound-induced activities, and cDNA isolation, characterization, and bacterial expression of delta-selinene synthase a…
[cited by applicant]
Strickland et al., Rationally improving LOV domain-based photoswitches. Nat. Methods. 7(8):623-6 (2010).
[cited by applicant]
Su et al., Anti-SARS-CoV-2 activities in vitro of Shuanghuanglian preparations and bioactive ingredients. Acta Pharmacol Sinica 41(9):1167-1177 (2020).
[cited by applicant]
Su et al., Identification of pyrogallol as a warhead in design of covalent inhibitors for the SARS-CoV-2 3CL protease. Nat Commun. 12(1):3623 (2021).
[cited by applicant]
Sun et al., Crystal structure of PTP1B complexed with a potent and selective bidentate inhibitor. J Biol Chem. 278(14):12406-12414 (2003).
[cited by applicant]
Sun et al., Activity based fingerprinting of proteases using FRET peptides. 88(2):141-149 (2007).
[cited by applicant]
Sycz et al., LOV Histidine kinase modulates the general stress response system and affects the virB operon expression in Brucella abortus. PLoS One. 10(5): e0124058 (2015).
[cited by applicant]
Tachibana et al., Novel prenyltransferase gene encoding farnesylgeranyl diphosphate synthase from a hyperthermophilic archaeon, Aeropyrum pernix. Molecular evolution with alteration in product specificity. Eur J Biochem…
[cited by applicant]
Tan et al., 3C protease of enterovirus 68: structure-based design of Michael acceptor inhibitors and their broad-spectrum antiviral effects against picornaviruses. J Virol. 87(8):4339-4351 (2013).
[cited by applicant]
Tautz et al., Targeting the PTPome in human disease. Expert Opin Ther Targets 10(1):157-177 (2006).
[cited by applicant]
Teng et al., Structures, mechanisms and inhibitors of undecaprenyl diphosphate synthase: a cis-prenyltransferase for bacterial peptidoglycan biosynthesis. Bioorg Chem. 43:51-57 (2012).
[cited by applicant]
Tholl, Biosynthesis and biological functions of terpenoids in plants. Adv Biochem Eng Biotechnol. 148:63-106 (2015).
[cited by applicant]
Tian et al., Circular polymerase extension cloning of complex gene libraries and pathways. PLoS One. 4(7): e6441 (2009).
[cited by applicant]
Tiganis et al., Epidermal growth factor receptor and the adaptor protein p52Shc are specific substrates of T-cell protein tyrosine phosphatase. Mol Cell Biol. 18(3):1622-1634 (1998).
[cited by applicant]
Ting et al., Genetically encoded fluorescent reporters of protein tyrosine kinase activities in living cells. Proc Natl Acad Sci USA. 98(26):15003-15008 (2001).
[cited by applicant]
Tonks et al., A brake becomes an accelerator: PTP1B—a new therapeutic target for breast cancer. Cancer Cell 11(3):214-216 (2007).
[cited by applicant]
Tonks, Protein tyrosine phosphatases—from housekeeping enzymes to master regulators of signal transduction. FEBS J. 280(2):346-378 (2013).
[cited by applicant]
Tonks, Protein tyrosine phosphatases: from genes, to function, to disease. Nat Rev Mol Cell Biol. 7(11):833-846 (2006).
[cited by applicant]
Traves et al., Pivotal role of protein tyrosine phosphatase 1B (PTP1B) in the macrophage response to proinflammatory and anti-inflammatory challenge. Cell Death Dis. 5(3): e1125 (2014).
[cited by applicant]
Traylor et al., Recombinant expression and characterization of Lucilia cuprina CYP6G3: Activity and binding properties toward multiple pesticides. Insect Biochem Mol Biol. 90:14-22 (2017).
[cited by applicant]
Trouiller et al., Drug development for neglected diseases: a deficient market and a public-health policy failure. Lancet. 359(9324):2188-2194 (2002).
[cited by applicant]
Tzeng et al., Protein activity regulation by conformational entropy. Nature. 488(7410):236-240 (2012).
[cited by applicant]
Urlacher et.al.; Cytochrome P450 monooxygenases in biotechnology and synthetic biology. Trends Biotechnol. 37(8): 882-897 (2019).
[cited by applicant]
Ursu et al., Understanding drug-likeness. Wiley Interdisciplinary Reviews: Computational Molecular Science 1, 760-781 (2011).
[cited by applicant]