Searching for Molecular Solutions: Empirical Discovery and Its Future

Acknowledgments.

Introduction.

1 If It Works, it Works: Pragmatic Molecular Discovery.

Overview.

Three Ways of Discovery.

The Three Wise (Serendipitous) Men and Other Stories.

An Empirical Fable.

Productively Applying Empiricism.

Screening versus Selection.

How to be a Librarian.

Demon-strating the Power of Empirical Screening and Selection.

Dreaming of Pandemonium: a Universal Molecular Space.

Mode of Molecular Discovery.

The Borderland of Rational Design.

2 Empirical Miracles: Nature’s Precedents for Empirical Solutions.

Overview.

Evolution Itself.

Evolution: Natural and Artificial.

To Opine on Design.

Natural Evolution at Work.

The Raw Materials: Diversity Enough and Time.

GOD from Mutation.

GOD from Recombination and Other Things.

A Sexual Interlude.

Doubling Up and Reassorting.

Lateral Thinking.

The Process: Old Ideas and Newer Wrinkles.

The Marks of Lamarck?

Evolution by Order?

Orderly Beginnings.

The Arrow of Complexity?

Drivers of Complexity.

Complexity and Molecular Discovery.

Molecules of Evolution and Design Boundaries.

Evolving Proteins.

Enzymatic Bounty.

Combinatorial Catalysis and Its Helpers.

Enzymes to the Limit.

Absent by Irreducibility, or Lack of an Access Route?

Food for Evolutionary Thought.

3 Evolution’s Gift: Natural Somatic Diversification and Molecular Design.

Overview.

Immune Systems: a Biological Fundamental.

The Selfish Scheme.

The Xenobiotic "Immune System" and Beyond.

Innately Selfish.

How to Shoot Moving Targets.

The Empirical Basis of the Adaptive Immune System.

The Evolved GOD of the Adaptive Immune System.

The T Cell Repertoire and Its Special GOD.

The Range and Utility of Adaptive Immunity.

Antibodies and Molecular Recognition in General.

Selfishness Revisited.

Antibody Libraries and Iterative Selection: Natural and Artificial.

Iteratively Speaking.

Such Selfish Systems Send Selfless Sermons: The Largesse of  Immune Systems.

GOD in the Brain and Its Extensions.

Molecular Sensing.

A Bittersweet Worldview.

Smelling a Rat, and Many Other Things.

Multirecognition.

Messages in Biological Molecular Recognition and Empirical Design.

4 Evolution While You Wait.

Overview.

Putting Evolution to Work.

Levels of Selectable Replicators.

The Score and Implementation of Evolution as a Workhorse.

GOD in the Laboratory.

Mutations at Will.

Sex for Biotechnologists.

Artificial Evolution Becomes HOT.

Evolution on the Laboratory Bench.

Screen (Properly) And Ye Shall Find.

A Highly Rational Empirical Process.

Mutations and Libraries.

Crossing the Valley of the Shadow of Low Fitness: Journeys across Molecular Spaces.

Colorful Neutral Springboards.

Punctuating Sequence Space, Naturally or Otherwise.

The Power of Display.

Show Me Your Coat: Phage on Display.

Display Without Cells: Doing it In Vitro.

Making Compartments.

Test it, Replicate It, Evolve It.

5 The Blind Protein Maker.

Overview.

Applying Natural Protein Evolution Principles.

Productively Playing with Enzymes.

Room for Improvement.

Tougher Enzymes.

Better Enzymes.

Altered and Novel Enzymes.

Enzymes from Scratch.

De Novo Protein Design the Empirical Way.

Return to the Fold.

Alphabets and Patterning.

Finding and Evolving Folds.

De Novo Enzymes.

Natural and Unnatural Acts.

Unnatural Insertions.

In Vitro opportunities.

New codes In Vivo.

Unnatural Rewards and Limits.

6 The Blind Shaper of Nucleic Acids.

Overview.

Functional Nucleic Acids and their Directed Evolution.

Early Days.

Protein-Free Enzymes.

Finding Functional RNAs.

Novel Ribozymes.

Ribozyme Replication and Other Things.

Comparisons with Proteins.

Aiming for Stability.

Recombination: Still Good for RNA?

Folding in Two Worlds.

Working with the Ribozyme Repertoire.

Calling for Cofactors.

Alphabetic Acrobatics.

Angling for Aptamers with Aptitude.

DNA Can Do It Too.

Natural Aptamers and Riboswitches.

An Aptamerican Adventure.

Allosteric Ribozymes and Aptamers.

Payoffs from Functional Nucleic Acids.

Aptamer Tools: Better than Antibodies?

Moving Aptamers Toward the Clinic.

Extending the Functional Range of Nucleic Acids.

Extended Alphabets.

The Virtual Molecular Museum.

Altered Backbones.

The Best of Both Worlds?

7 Evolving and Creating Recognition Molecules.

Overview.

The Immune System in a Bottle and on a Leash.

New Wrinkles on the Old Way to Antibodies.

Antibodies and Libraries.

The GOD of Small Things: Minimizing Antibodies.

Antibodies as Catalysts.

Alternatives to Antibodies.

Other Protein Scaffolds for Molecular Recognition.

Finding and Designing Proteins for Diversification.

Molecular Imprinting: Making its Mark.

Imprinting of Macromolecules.

Comparing Recognition Alternatives.

Generalizing to Foldamers.

8 Molecules Small and Large.

Overview.

As Small as Possible, but No Smaller.

Small and Natural, Small and Useful.

How to Find New Drugs.

Know Your NME.

Aiming in the Right Direction.

Druggable Struggles.

High-throughput Put Through High Loops.

Chemical Libraries and the GOD of Small Molecules.

Generalities, and the Natural Approach.

Make Your Own Library.

Frag-mental Inspiration.

Self-Assembling Molecular Combinatorics.

Codes for Small Molecules.

Tag Team Technology: Encoded Combinatorial Chemistry.

Marrying Chemistry and Biology with Tags.

An Evolutionary Analogy.

From Small to Large and Back Again.

9 An Empirical-Rational Loop Forwards.

Overview.

Approaching Rational Design.

Scope of Rational Design.

Pathways to Rational Design.

Quantum Chemistry and Rational Design.

Small Molecules the Rational Way.

Virtual Virtues.

The De Novo Ultimate?

Proteins by the Book.

Getting Folding Right.

Making Rational Predictions.

Making Rational Proteins.

Designer Nucleic Acids.

Systems, Pathways, and Networks.

10 Exploring the Limits.

Overview.

The Limits of Rational Design.

Rational Design and Determinism.

Bootstrapping and Interplay.

Reverse-engineering Biocomplexity for Design Insights.

Time, Knowledge, and Molecules.

Outer Boundaries.

Patterns for the Future.

Primordial Alphabet Soup.

On Molecular Translations.

Effectors and Replicators.

The Universal Power of Combinatorics.

A Kaleidoscopic View.

Glossary.

Bibliography.

References in Figure Legends.

Index.