Directed Evolution of Enzymes Driving Innovation in API Manufacturing at GSK

[1]  P. Bork,et al.  ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data , 2016, Molecular biology and evolution.

[2]  Yuguo Zheng,et al.  Engineering the epoxide hydrolase from Agromyces mediolanus for enhanced enantioselectivity and activity in the kinetic resolution of racemic epichlorohydrin , 2015 .

[3]  Sudhir Kumar,et al.  MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. , 2018, Molecular biology and evolution.

[4]  William F. DeGrado,et al.  Amino Acid Propensities are Position-dependent Throughout the Length of α-Helices , 2004 .

[5]  D. G. Gibson,et al.  Vibrio natriegens as a fast-growing host for molecular biology , 2016, Nature Methods.

[6]  Michael C Jewett,et al.  Cell-Free Synthetic Biology: Engineering Beyond the Cell. , 2016, Cold Spring Harbor perspectives in biology.

[7]  Johannes Söding,et al.  Protein homology detection by HMM?CHMM comparison , 2005, Bioinform..

[8]  Hiroki Shirai,et al.  Use of Amino Acid Composition to Predict Ligand-Binding Sites , 2007, J. Chem. Inf. Model..

[9]  Andrei N. Lupas,et al.  CLANS: a Java application for visualizing protein families based on pairwise similarity , 2004, Bioinform..

[10]  Alessandro Barbato,et al.  Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12 , 2018, Proteins.

[11]  David A. Lee,et al.  CATH: an expanded resource to predict protein function through structure and sequence , 2016, Nucleic Acids Res..

[12]  R. Pazdur,et al.  FDA drug approval summary: nelarabine (Arranon) for the treatment of T-cell lymphoblastic leukemia/lymphoma. , 2008, The oncologist.

[13]  Frank DiMaio,et al.  Automatic structure prediction of oligomeric assemblies using Robetta in CASP12 , 2018, Proteins.

[14]  Muhammed Tilahun Muhammed,et al.  Homology modeling in drug discovery: Overview, current applications, and future perspectives , 2018, Chemical biology & drug design.

[15]  Sean R. Eddy,et al.  Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..

[16]  P. Labute proteins STRUCTURE O FUNCTION O BIOINFORMATICS Protonate3D: Assignment of ionization , 2013 .

[17]  Tom Halgren,et al.  New Method for Fast and Accurate Binding‐site Identification and Analysis , 2007, Chemical biology & drug design.

[18]  R. Goldstein Efficient rotamer elimination applied to protein side-chains and related spin glasses. , 1994, Biophysical journal.

[19]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[20]  M. Reetz,et al.  Directed Evolution of an Enantioselective Enoate-Reductase: Testing the Utility of Iterative Saturation Mutagenesis , 2009 .

[21]  Anne A. Ollis,et al.  Chiral synthesis of LSD1 inhibitor GSK2879552 enabled by directed evolution of an imine reductase , 2019, Nature Catalysis.

[22]  Manfred T Reetz,et al.  Directed Evolution of Proteins Based on Mutational Scanning. , 2018, Methods in molecular biology.

[23]  Joseph P. Adams,et al.  New Technologies in Process Development , 2018, Early Drug Development.

[24]  D. Baker,et al.  Role of conformational sampling in computing mutation‐induced changes in protein structure and stability , 2011, Proteins.

[25]  Philippe Bogaerts,et al.  Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0 , 2009, Bioinform..

[26]  Matthias Rarey,et al.  Analyzing the Topology of Active Sites: On the Prediction of Pockets and Subpockets , 2010, J. Chem. Inf. Model..

[27]  Huimin Zhao,et al.  Engineering biological systems using automated biofoundries. , 2017, Metabolic engineering.

[28]  Yang Zhang,et al.  I-TASSER server for protein 3D structure prediction , 2008, BMC Bioinformatics.

[29]  Douglas C. Friedman,et al.  Building a global alliance of biofoundries , 2019, Nature Communications.

[30]  Jian Peng,et al.  Template-based protein structure modeling using the RaptorX web server , 2012, Nature Protocols.

[31]  Stephen H. White,et al.  Experimentally determined hydrophobicity scale for proteins at membrane interfaces , 1996, Nature Structural Biology.

[32]  L. Serrano,et al.  Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. , 2002, Journal of molecular biology.

[33]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[34]  Christopher K Prier,et al.  Recent preparative applications of redox enzymes. , 2019, Current opinion in chemical biology.

[35]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[36]  Johannes Söding,et al.  Clustering huge protein sequence sets in linear time , 2017, Nature Communications.

[37]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[38]  Juergen Haas,et al.  The Protein Model Portal—a comprehensive resource for protein structure and model information , 2013, Database J. Biol. Databases Curation.

[39]  Yuguo Zheng,et al.  A novel enantioselective epoxide hydrolase from Agromyces mediolanus ZJB120203: Cloning, characterization and application , 2014 .

[40]  Hege S. Beard,et al.  Applying Physics-Based Scoring to Calculate Free Energies of Binding for Single Amino Acid Mutations in Protein-Protein Complexes , 2013, PloS one.

[41]  Silvio C. E. Tosatto,et al.  InterPro in 2017—beyond protein family and domain annotations , 2016, Nucleic Acids Res..

[42]  Peter W. Sutton,et al.  Development of an Enzymatic Process for the Production of (R)-2-Butyl-2-ethyloxirane , 2017 .

[43]  Paul N. Devine,et al.  Biocatalytic Asymmetric Synthesis of Chiral Amines from Ketones Applied to Sitagliptin Manufacture , 2010, Science.

[44]  Radka Snajdrova,et al.  A combination of in vivo selection and cell sorting for the identification of enantioselective biocatalysts. , 2011, Angewandte Chemie.

[45]  A. Bordner Force fields for homology modeling. , 2012, Methods in molecular biology.

[46]  Manfred T Reetz,et al.  Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes , 2007, Nature Protocols.

[47]  Ge Qu,et al.  The Crucial Role of Methodology Development in Directed Evolution of Selective Enzymes. , 2020, Angewandte Chemie.

[48]  N. Turner,et al.  Discovery, Engineering, and Synthetic Application of Transaminase Biocatalysts , 2017 .

[49]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[50]  Randy J. Read,et al.  Overview of the CCP4 suite and current developments , 2011, Acta crystallographica. Section D, Biological crystallography.

[51]  Peter W. Sutton,et al.  N-Alkyl-α-amino acids in Nature and their biocatalytic preparation. , 2019, Journal of biotechnology.

[52]  Y. Asano,et al.  Introduction – Principles and Historical Landmarks of Enzyme Catalysis in Organic Synthesis , 2012 .

[53]  Keehyoung Joo,et al.  Methods for accurate homology modeling by global optimization. , 2012, Methods in molecular biology.

[54]  Nicholas J Turner,et al.  Imine reductases (IREDs). , 2017, Current opinion in chemical biology.

[55]  A. Biegert,et al.  HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment , 2011, Nature Methods.

[56]  T. Graedel Green Chemistry and Sustainable Development , 2007 .

[57]  Johannes Söding,et al.  Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling , 2015, PLoS Comput. Biol..

[58]  L Regan,et al.  A thermodynamic scale for the beta-sheet forming tendencies of the amino acids. , 1994, Biochemistry.

[59]  Darrell Hurt,et al.  Comparison of common homology modeling algorithms: application of user-defined alignments. , 2012, Methods in molecular biology.

[60]  T. Creamer,et al.  Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides. , 1996, Biochemistry.

[61]  Feng Xu,et al.  Synthesis of Vibegron Enabled by a Ketoreductase Rationally Designed for High pH Dynamic Kinetic Reduction. , 2018, Angewandte Chemie.

[62]  Thomas A. Halgren,et al.  Identifying and Characterizing Binding Sites and Assessing Druggability , 2009, J. Chem. Inf. Model..

[63]  Kristin K. Brown,et al.  Efficient Biocatalytic Reductive Aminations by Extending the Imine Reductase Toolbox , 2017 .

[64]  Dmitri B. Kireev,et al.  Structural Protein–Ligand Interaction Fingerprints (SPLIF) for Structure-Based Virtual Screening: Method and Benchmark Study , 2014, J. Chem. Inf. Model..

[65]  Markus A. Lill,et al.  Protein Pharmacophore Selection Using Hydration-Site Analysis , 2012, J. Chem. Inf. Model..

[66]  N. Turner,et al.  A highly efficient synthesis of telaprevir by strategic use of biocatalysis and multicomponent reactions. , 2010, Chemical communications.

[67]  David E. Kim,et al.  Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules. , 2016, Journal of chemical theory and computation.

[68]  Jeffrey M. Kallemeyn,et al.  The Delivery of Flexibility from the Application of QbD to API Development , 2018, Journal of Pharmaceutical Innovation.

[69]  Kristin K. Brown,et al.  Biocatalytic Synthesis of Chiral N-Functionalized Amino Acids. , 2018, Angewandte Chemie.

[70]  M. Truppo,et al.  A highly efficient asymmetric synthesis of vernakalant. , 2014, Organic letters.