Prakash Masurekar’s research while affiliated with Merck & Co. and other places

Boxazomycins A-C are potent broad-spectrum antibiotics isolated from Actinomycetes strain G495-1 in 1987. We now report that boxazomycin A inhibits bacterial growth by selectively inhibiting protein synthesis, its effect is bacteriostatic, and it is equally active against drug resistant bacterial strains. No cross-resistance to protein synthesis inhibitors was observed suggesting that its inhibition is distinct from clinical protein synthesis inhibitors. We also report in vivo efficacy in a Staphylococcus aureus murine infection model supported by corresponding pharmacokinetic studies.

The Candida albicans fitness test is a whole cell screening platform that utilizes a mixed-pool of C. albicans mutants, each of which carries a heterozygous deletion of a particular gene. In the presence of an antifungal inhibitor, a subset of these mutants exhibits a growth phenotype of hypersensitivity or hyposensitivity. Collectively these mutants reflect aspects of the mechanism of action of the compound in question. In the course of screening natural products a culture of Streptomyces sp. MS-1-4 was discovered to produce a compound, dretamycin, which yielded a fitness profile exhibiting significant hypersensitivity of the DRE2 heterozygote and hyposensitivity of the DIP5 heterozygote. Herein we report the production, isolation, and structure elucidation of dretamycin.

This part introduction presents an overview of the key concepts discussed in the subsequent chapters of this book. It covers advances in cultivating microbial, plant, mammalian, and insect cells and their use for production of therapeutic compounds. The part includes miniaturization of methods used to grow microorganisms, technologies used for cultivating them in solid phase, and culturing plant, insect, and mammalian cells. It describes the use of bacterial cultures for the production of proteins and other biological products. Medium development for mammalian cell culture is also explored. The part provides a comprehensive report on heterologous protein expression in yeast and filamentous fungi. It also describes various medium components and their function in supporting the growth of plant cells. Solid‐phase fermentations used to prepare biocontrol agents are illustrated as well. A new development, mixed‐phase (solid and liquid) fermentation, is described.

This part introduction presents an overview of the key concepts discussed in the subsequent chapters of this book. It describes a number of molecular tools for enzyme discovery. The part provides insightful discussions on various directed evolution methods used in enzyme engineering. It discusses enzyme promiscuity and its role in creation of new protein functions, which is not only scientifically interesting but also practically important since novel biocatalysts are highly desirable in biocatalysis. There are a wide variety of biocatalysts capable of catalyzing numerous biological reactions. However, naturally occurring biocatalysts are often not optimal for many specific industrial applications, due to characteristics such as low stability and low activity. The part also discusses various aspects involved in the high‐level production of enzymes in the bacterium Escherichia coli, such as gene regulation, vector design, host selection, inducible gene expression, and high‐cell‐density fermentation.

This part introduction presents an overview of the key concepts discussed in the subsequent chapters of this book. It describes contemporary methods and strategies for engineering and improving some of the most widely used industrial microorganisms. Each is focused on a particular taxonomic grouping that shares similar methods of genetic manipulation and culturing. The part provides a historical context for the extensive work on the gram‐positive genus Corynebacterium, which is most famous for its use in large‐scale production of amino acids. It describes strategies for overcoming many of the obstacles encountered at the different stages of a bioprocess (e.g., expression vector construction, strain engineering, cell cultivation, and downstream processing), thereby improving recovery or activity of the recombinant protein. The part discusses the developed genetic tools for strain improvement and optimization of protein production in filamentous fungi.

One of the most significant recent developments affecting industrial microbiology has been the marked increase in activity and anticipation related to microbially produced chemicals and, especially, fuels. This introduction presents an overview of the key concepts discussed in the subsequent chapters of this book. The part addresses physiological and methodological aspects of cellulolytic microbial cultures. It also addresses the use of systems biology tools to further understand the industrial robustness of microorganisms. The conversion of lignocellulose to fuels and chemicals continues to be a prominent focus of industrial microbiologists and biotechnologists, appears close to commercial fruition after many decades of effort, and involves many important microbiological topics that still have much to contribute through yet‐to‐be‐realized advances. The part then considers the surface microbiology of cellulolytic bacteria.

This part introduction presents an overview of the key concepts discussed in the subsequent chapters of this book. It describes the initial stages of establishing an industrial microbiological process: culture isolation and preservation, screening, small‐scale fermentation, and process optimization. The part focuses broadly on two themes, namely, some central issues pertaining globally to industrial microbiology (isolation and characterization of organisms), and the routes to biodiscovery. It presents methods for selectively isolating members of one particular group of bacteria—the actinobacteria. The part describes cell‐based assays in screening for anti‐infective compounds and argues the case for these screens vis‐a‐vis cell‐free systems. It demonstrates the steps in metabolome analysis with reference to microfungi. The part also presents strategies for accessing microbial secondary metabolites from silent biosynthetic pathways.

This part introduction presents an overview of the key concepts discussed in the subsequent chapters of this book. It describes the biosynthesis of various glycosides of aromatic polyketides in various Streptomyces hosts, and how the understanding of the genetic bases of biosynthesis has enabled the production of novel, hybrid molecules. The importance of secondary metabolites has driven significant efforts in the understanding of the genetics of their biosynthesis. The part also describes the genetic basis for the production of the lipopetide daptomycin, a recently marketed antibiotic effective against methicillin‐resistant Staphylococcus aureus infections, and the methodology developed to enable manipulation of the corresponding peptide synthetase to result in the production of novel derivatives in the producing host, Streptomyces roseosporus. It describes the assembly of genes in Escherichia coli from bacteria and yeast to produce artemisinic acid, the sesquiterpene precursor to artemisinin.

This part introduction presents an overview of the key concepts discussed in the subsequent chapters of this book. It focuses on the major elements of biological engineering and scale‐up that are considered key for industrial process success. The part begins where most bioprocess development efforts start. The selection of raw materials and subsequent medium development for industrial fermentation processes has been, and continues to be, the foundation of sound bioprocess performance. The part describes advances in sensor and sampling technologies. It also describes the wide variety of sensor and automation philosophies available for implementation to match bioprocessing monitoring demands. The biopharmaceutical industry and academics working in this field consistently have been effective partners with equipment and instrument manufacturers.

This chapter describes the 15-year journey of discovery and development of caspofungin acetate (CANCIDAS) a parenteral antifungal agent. The precursor of caspofungin is a natural product lipophilic cyclic peptide, pneumocandin B0. The chapter is divided into five sections describing in chronological order: (i) discovery of the natural product pneumocandin B0 from fungal fermentations; (ii) fermentation development to improve the titer of B0 to make it commercially viable; (iii) semisynthetic modification by medicinal chemistry to successfully improve the properties of pneumocandin B0 leading to synthesis of caspofungin; (iv) development of commercial semisynthesis and purification, formulation development to improve stability; and (v) clinical development and approval of CANCIDAS as a drug that subsequently saved thousands of lives. This edition first published 2014