[Frontiers in Bioscience, Landmark, 22, 21-47, January 1, 2017]

Binding kinetics in drug discovery – A current perspective

Victoria Georgi 1 , Dorothee Andres 1 , Amaury E. Fernandez-Montalvan 1 , Christian M. Stegmann 1 , Andreas Becker 1 , Anke Mueller-Fahrnow 1

1Bayer Pharma AG, Lead Discovery Berlin, Muellerstrasse 178, 13353 Berlin, Germany

TABLE OF CONTENTS

1. Abstract
2. Introduction
3. Structure-kinetic relationships
    3.1. Conformational changes and flexibility
        3.1.1. Nexavar (Sorafenib) induces a DFG out movement in Raf1
        3.1.2. Compound and target rigidity affects residence time on Pseudomonas aeruginosa LpxC
        3.1.3. Conformational adaptation upon inhibitor binding in DOT1L results in longer residence time
    3.2. Hydrogen bonds and hydrophobicity
        3.2.1. Long residence time of CDK8/CycC inhibitors depend on hydrophobic stacking
        3.2.2. Aromatic stacking could drive kinetics in ERK1/2
        3.2.3. Hydrophobic interactions between Melagatran and Thrombin increase residence time
    3.3. Water molecules
    3.4. Covalent and reversible-covalent binders
4. Methods for investigation of binding kinetics in drug discovery
    4.1. Binding assay formats
        4.1.1. Direct measurement of binding kinetics
        4.1.2. Indirect measurement of binding kinetics
    4.2. Functional assay formats
        4.2.1. Enzymatic activity assays
        4.2.2. Cellular activity assays
        4.2.3. Ex vivo and in vivo assays
    4.3. Considerations for the choice of assay formats
    4.4. Assay configurations and readout technologies
        4.4.1. Assays for investigation of target-compound interactions in solution
            4.4.1.1. Radioligand binding kinetic assays
            4.4.1.2. Fluorescent-labeled ligand binding kinetic assays
                4.4.1.2.1. Non-homogenous fluorescent assays
                4.4.1.2.2. Homogenous fluorescent assays
            4.4.1.3. Bioluminescent label binding kinetic assays
        4.4.2. Biosensor-based assays
            4.4.2.1. Electro-optical biosensors
            4.4.2.2. Electromechanical biosensors
    4.5. Structure-based analysis
    4.6. Current use and future trends for binding kinetics methods
5. Integration of binding kinetics in the lead discovery process
6. Acknowledgement
7. References

1. ABSTRACT

The impact of target binding kinetics (BK) on the clinical performance of therapeutic agents is presently a topic of intense debate in drug discovery. While retrospective studies suggest that BK is a differentiating parameter in marketed medicines, it is yet unclear how this information could be used to prioritize drug candidates during lead optimization. Motivated by the question whether BK can be understood and rationally optimized, we review the most relevant literature in the field, with special focus on selected examples from our organization. First we discuss structure-kinetic relationships (SKR), and how they can be influenced by factors such as conformational changes, molecular flexibility, hydrogen bonds, hydrophobicity, water molecules and (reversible-) covalent bonds. We then introduce the methodologies currently used for the investigation of BK parameters, briefly commenting on their strengths, weaknesses and future trends. Finally, we present our current perspective on the integration of BK in the drug discovery process, aiming to stimulate further thoughts on this important subject.

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Key Words: Binding Kinetics, Residence Time, Structure-Kinetic Relationships, On-Rate, Off-Rate, Review

Send correspondence to: Anke Mueller-Fahrnow, Bayer Pharma AG, Lead Discovery Berlin, Muellerstrasse 178, 13353 Berlin, Germany. Tel: 49 30 468 17699, Fax: 49 30 468 97699, E-mail: anke.mueller-fahrnow@bayer.com