Multi-parameter optimization: identifying high quality compounds with a balance of properties.

A successful, efficacious and safe drug must have a balance of properties, including potency against its intended target, appropriate absorption, distribution, metabolism, and elimination (ADME) properties and an acceptable safety profile. Achieving this balance of, often conflicting, requirements is a major challenge in drug discovery. Approaches to simultaneously optimizing many factors in a design are broadly described under the term 'multi-parameter optimization' (MPO). In this review, we will describe how MPO can be applied to efficiently design and select high quality compounds and describe the range of methods that have been employed in drug discovery, including; simple 'rules of thumb' such as Lipinski's rule; desirability functions; Pareto optimization; and probabilistic approaches that take into consideration the uncertainty in all drug discovery data due to predictive error and experimental variability. We will explore how these methods have been applied to predicted and experimental data to reduce attrition and improve the productivity of the drug discovery process.

[1]  Matthew Segall,et al.  Beyond Profiling: Using ADMET Models to Guide Decisions , 2009, Chemistry & biodiversity.

[2]  Yvonne C. Martin,et al.  Application of Belief Theory to Similarity Data Fusion for Use in Analog Searching and Lead Hopping , 2008, J. Chem. Inf. Model..

[3]  Christopher W Murray,et al.  Fragment-based lead discovery: leads by design. , 2005, Drug discovery today.

[4]  Constantinos S. Pattichis,et al.  De Novo Drug Design Using Multiobjective Evolutionary Graphs , 2009, J. Chem. Inf. Model..

[5]  Thomas J. Raub,et al.  Characterization of the human colon carcinoma cell line (Caco-2) as a model system for intestinal epithelial permeability. , 1989, Gastroenterology.

[6]  C. Humblet,et al.  Escape from flatland: increasing saturation as an approach to improving clinical success. , 2009, Journal of medicinal chemistry.

[7]  Li Xing,et al.  Influence of molecular flexibility and polar surface area metrics on oral bioavailability in the rat. , 2004, Journal of medicinal chemistry.

[8]  Ross McGuire,et al.  A molecular informatics view on best practice in multi-parameter compound optimization. , 2011, Drug discovery today.

[9]  David E. Clark,et al.  Evolutionary algorithms in computer-aided molecular design , 1996, J. Comput. Aided Mol. Des..

[10]  Peter J. Fleming,et al.  Genetic Algorithms for Multiobjective Optimization: FormulationDiscussion and Generalization , 1993, ICGA.

[11]  Jeffrey R. Huth,et al.  Enhancement of chemical rules for predicting compound reactivity towards protein thiol groups , 2007, J. Comput. Aided Mol. Des..

[12]  A. Hopkins,et al.  Ligand efficiency: a useful metric for lead selection. , 2004, Drug discovery today.

[13]  Gareth Jones,et al.  Genetic and Evolutionary Algorithms , 2002 .

[14]  R. W. Hansen,et al.  The price of innovation: new estimates of drug development costs. , 2003, Journal of health economics.

[15]  David A. Price,et al.  Role of Physicochemical Properties and Ligand Lipophilicity Efficiency in Addressing Drug Safety Risks , 2010 .

[16]  György G Ferenczy,et al.  Thermodynamics guided lead discovery and optimization. , 2010, Drug discovery today.

[17]  Nigel Greene,et al.  Physicochemical drug properties associated with in vivo toxicological outcomes: a review , 2009, Expert opinion on drug metabolism & toxicology.

[18]  Nathan Brown,et al.  Molecular optimization using computational multi-objective methods. , 2007, Current opinion in drug discovery & development.

[19]  Dimitris K. Agrafiotis,et al.  The Diversity of Chemical Libraries , 2002 .

[20]  Johann Gasteiger,et al.  Structure and reaction based evaluation of synthetic accessibility , 2007, J. Comput. Aided Mol. Des..

[21]  William T. Scherer,et al.  "The desirability function: underlying assumptions and application implications" , 1998, SMC'98 Conference Proceedings. 1998 IEEE International Conference on Systems, Man, and Cybernetics (Cat. No.98CH36218).

[22]  P. Leeson,et al.  The influence of drug-like concepts on decision-making in medicinal chemistry , 2007, Nature Reviews Drug Discovery.

[23]  Stephen R. Johnson,et al.  Molecular properties that influence the oral bioavailability of drug candidates. , 2002, Journal of medicinal chemistry.

[24]  Young Bin Choy,et al.  The Rule of Five for Non-Oral Routes of Drug Delivery: Ophthalmic, Inhalation and Transdermal , 2011, Pharmaceutical Research.

[25]  K. Stewart,et al.  Drug Guru: a computer software program for drug design using medicinal chemistry rules. , 2006, Bioorganic & medicinal chemistry.

[26]  W. Guida,et al.  The art and practice of structure‐based drug design: A molecular modeling perspective , 1996, Medicinal research reviews.

[27]  Johann Gasteiger,et al.  A Graph-Based Genetic Algorithm and Its Application to the Multiobjective Evolution of Median Molecules. , 2004 .

[28]  Johann Gasteiger,et al.  A novel workflow for the inverse QSPR problem using multiobjective optimization , 2006, J. Comput. Aided Mol. Des..

[29]  Sean Ekins,et al.  Evolving molecules using multi-objective optimization: applying to ADME/Tox. , 2010, Drug discovery today.

[30]  Joelle M. R. Gola,et al.  Focus on success: using a probabilistic approach to achieve an optimal balance of compound properties in drug discovery , 2006, Expert opinion on drug metabolism & toxicology.

[31]  Brett A Tounge,et al.  The role of molecular size in ligand efficiency. , 2007, Bioorganic & medicinal chemistry letters.

[32]  Ryan H. Lilien,et al.  Applying Medicinal Chemistry Transformations and Multiparameter Optimization to Guide the Search for High-Quality Leads and Candidates , 2011, J. Chem. Inf. Model..

[33]  C. Abad-Zapatero,et al.  Ligand efficiency indices for effective drug discovery , 2007, Expert opinion on drug discovery.

[34]  Gerhard Klebe,et al.  Adding calorimetric data to decision making in lead discovery: a hot tip , 2010, Nature Reviews Drug Discovery.

[35]  Thomas Bäck,et al.  Combining Aggregation with Pareto Optimization: A Case Study in Evolutionary Molecular Design , 2009, EMO.

[36]  György M. Keserü,et al.  The influence of lead discovery strategies on the properties of drug candidates , 2009, Nature Reviews Drug Discovery.

[37]  T. Ritchie,et al.  The impact of aromatic ring count on compound developability--are too many aromatic rings a liability in drug design? , 2009, Drug discovery today.

[38]  F. Lombardo,et al.  Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. , 2001, Advanced drug delivery reviews.

[39]  A. Chadwick,et al.  Overcoming psychological barriers to good discovery decisions. , 2010, Drug discovery today.

[40]  D J Rogers,et al.  A Computer Program for Classifying Plants. , 1960, Science.

[41]  B. E. Evans,et al.  Methods for drug discovery: development of potent, selective, orally effective cholecystokinin antagonists. , 1988, Journal of medicinal chemistry.

[42]  Peter J. Fleming,et al.  Combinatorial Library Design Using a Multiobjective Genetic Algorithm , 2002, J. Chem. Inf. Comput. Sci..

[43]  E. Débiton,et al.  Cytotoxic effects of 110 reference compounds on HepG2 cells and for 60 compounds on HeLa, ECC-1 and CHO cells. II mechanistic assays on NAD(P)H, ATP and DNA contents. , 2005, Toxicology in vitro : an international journal published in association with BIBRA.

[44]  G. Derringer,et al.  Simultaneous Optimization of Several Response Variables , 1980 .

[45]  Charles C. Persinger,et al.  How to improve R&D productivity: the pharmaceutical industry's grand challenge , 2010, Nature Reviews Drug Discovery.

[46]  D. Rogers,et al.  Using Extended-Connectivity Fingerprints with Laplacian-Modified Bayesian Analysis in High-Throughput Screening Follow-Up , 2005, Journal of biomolecular screening.

[47]  M. Edwards,et al.  Using the Golden Triangle to optimize clearance and oral absorption. , 2009, Bioorganic & medicinal chemistry letters.

[48]  I. Kola,et al.  Can the pharmaceutical industry reduce attrition rates? , 2004, Nature Reviews Drug Discovery.

[49]  W. Jaffe Pareto Translated: A Review Article , 1972 .

[50]  Phillip Jeffrey,et al.  The Practice of Medicinal Chemistry , 2004 .

[51]  P. Verhoest,et al.  Moving beyond rules: the development of a central nervous system multiparameter optimization (CNS MPO) approach to enable alignment of druglike properties. , 2010, ACS chemical neuroscience.