scispace - formally typeset
Search or ask a question
Journal ArticleDOI

Molecular obesity, potency and other addictions in drug discovery

01 May 2011-MedChemComm (The Royal Society of Chemistry)-Vol. 2, Iss: 5, pp 349-355
TL;DR: The term Molecular Obesity is introduced to describe the authors' tendency to build potency into molecules by the inappropriate use of lipophilicity which leads to the premature demise of drug candidates.
Abstract: Despite the increase in global biology and chemistry knowledge the discovery of effective and safe new drugs seems to become harder rather than easier. Some of this challenge is due to increasing demands for safety and novelty, but some of the risk involved in this should be controllable if we had more effectively learnt from our failures. This perspective reflects on some of the learnings of recent years in relation to the causes of attrition. The term Molecular Obesity is introduced to describe our tendency to build potency into molecules by the inappropriate use of lipophilicity which leads to the premature demise of drug candidates.
Citations
More filters
Journal ArticleDOI
TL;DR: The utility of QED is extended by applying it to the problem of molecular target druggability assessment by prioritizing a large set of published bioactive compounds and may also capture the abstract notion of aesthetics in medicinal chemistry.
Abstract: Drug-likeness is a key consideration when selecting compounds during the early stages of drug discovery. However, evaluation of drug-likeness in absolute terms does not reflect adequately the whole spectrum of compound quality. More worryingly, widely used rules may inadvertently foster undesirable molecular property inflation as they permit the encroachment of rule-compliant compounds towards their boundaries. We propose a measure of drug-likeness based on the concept of desirability called the quantitative estimate of drug-likeness (QED). The empirical rationale of QED reflects the underlying distribution of molecular properties. QED is intuitive, transparent, straightforward to implement in many practical settings and allows compounds to be ranked by their relative merit. We extended the utility of QED by applying it to the problem of molecular target druggability assessment by prioritizing a large set of published bioactive compounds. The measure may also capture the abstract notion of aesthetics in medicinal chemistry.

1,161 citations

Journal ArticleDOI
TL;DR: To better define the unknown chemical space, 166.4 billion molecules of up to 17 atoms of C, N, O, S, and halogens forming the chemical universe database GDB-17 are enumerated, covering a size range containing many drugs and typical for lead compounds.
Abstract: Drug molecules consist of a few tens of atoms connected by covalent bonds. How many such molecules are possible in total and what is their structure? This question is of pressing interest in medicinal chemistry to help solve the problems of drug potency, selectivity, and toxicity and reduce attrition rates by pointing to new molecular series. To better define the unknown chemical space, we have enumerated 166.4 billion molecules of up to 17 atoms of C, N, O, S, and halogens forming the chemical universe database GDB-17, covering a size range containing many drugs and typical for lead compounds. GDB-17 contains millions of isomers of known drugs, including analogs with high shape similarity to the parent drug. Compared to known molecules in PubChem, GDB-17 molecules are much richer in nonaromatic heterocycles, quaternary centers, and stereoisomers, densely populate the third dimension in shape space, and represent many more scaffold types.

974 citations

Journal ArticleDOI
TL;DR: The theoretical background defining its strength and directionality, a systematic analysis of its occurrence and interaction geometries in protein-ligand complexes, and recent examples where halogen bonding has been successfully harnessed for lead identification and optimization are provided.
Abstract: Halogen bonding has been known in material science for decades, but until recently, halogen bonds in protein–ligand interactions were largely the result of serendipitous discovery rather than rational design. In this Perspective, we provide insights into the phenomenon of halogen bonding, with special focus on its role in drug discovery. We summarize the theoretical background defining its strength and directionality, provide a systematic analysis of its occurrence and interaction geometries in protein–ligand complexes, and give recent examples where halogen bonding has been successfully harnessed for lead identification and optimization. In light of these data, we discuss the potential and limitations of exploiting halogen bonds for molecular recognition and rational drug design.

934 citations

Journal ArticleDOI
TL;DR: Optimize ligand efficiency metrics based on both molecular mass and lipophilicity, when set in the context of the specific target, has the potential to ameliorate the inflation of these properties that has been observed in current medicinal chemistry practice, and to increase the quality of drug candidates.
Abstract: The judicious application of ligand or binding efficiency metrics, which quantify the molecular properties required to obtain binding affinity for a drug target, is gaining traction in the selection and optimization of fragments, hits and leads. Retrospective analysis of recently marketed oral drugs shows that they frequently have highly optimized ligand efficiency values for their targets. Optimizing ligand efficiency metrics based on both molecular mass and lipophilicity, when set in the context of the specific target, has the potential to ameliorate the inflation of these properties that has been observed in current medicinal chemistry practice, and to increase the quality of drug candidates.

797 citations

Journal ArticleDOI
TL;DR: How to design fragment libraries, how to select screening techniques and how to make the most of information gleaned from them are discussed, and how concepts from FBDD have permeated and enhanced drug discovery efforts are shown.
Abstract: Fragment-based methods have made substantial contributions to drug discovery in the past 20 years, particularly for challenging targets. Erlanson and colleagues discuss progress in the field, key aspects such as the design of fragment libraries and the choice of screening technique, and how current challenges in fragment-based drug discovery might be overcome.

639 citations

References
More filters
Journal ArticleDOI
TL;DR: Experimental and computational approaches to estimate solubility and permeability in discovery and development settings are described in this article, where the rule of 5 is used to predict poor absorption or permeability when there are more than 5 H-bond donors, 10 Hbond acceptors, and the calculated Log P (CLogP) is greater than 5 (or MlogP > 415).

14,026 citations

Journal ArticleDOI
TL;DR: The pharmaceutical industry faces considerable challenges, both politically and fiscally, and the fiscal pressures that face the industry from the perspective of R&D are dealt with.
Abstract: The pharmaceutical industry faces considerable challenges, both politically and fiscally. Politically, governments around the world are trying to contain costs and, as health care budgets constitute a very significant part of governmental spending, these costs are the subject of intense scrutiny. In the United States, drug costs are also the subject of intense political discourse. This article deals with the fiscal pressures that face the industry from the perspective of R&D. What impinges on productivity? How can we improve current reduced R&D productivity?

3,746 citations


"Molecular obesity, potency and othe..." refers background in this paper

  • ..., attrition) in 1991 to those in 2000 showed a shift to an increase in failure attributed to toxicological reasons [2]....

    [...]

Journal ArticleDOI
TL;DR: A consensus number of current drug targets for all classes of approved therapeutic drugs is proposed, and an emerging realization of the importance of polypharmacology and also the power of a gene-family-led approach in generating novel and important therapies is highlighted.
Abstract: For the past decade, the number of molecular targets for approved drugs has been debated. Here, we reconcile apparently contradictory previous reports into a comprehensive survey, and propose a consensus number of current drug targets for all classes of approved therapeutic drugs. One striking feature is the relatively constant historical rate of target innovation (the rate at which drugs against new targets are launched); however, the rate of developing drugs against new families is significantly lower. The recent approval of drugs that target protein kinases highlights two additional trends: an emerging realization of the importance of polypharmacology, and also the power of a gene-family-led approach in generating novel and important therapies.

3,284 citations

Journal ArticleDOI
TL;DR: A detailed analysis based on comprehensive, recent, industry-wide data is presented to identify the relative contributions of each of the steps in the drug discovery and development process to overall R&D productivity and propose specific strategies that could have the most substantial impact in improving R &D productivity.
Abstract: The pharmaceutical industry is under growing pressure from a range of environmental issues, including major losses of revenue owing to patent expirations, increasingly cost-constrained healthcare systems and more demanding regulatory requirements. In our view, the key to tackling the challenges such issues pose to both the future viability of the pharmaceutical industry and advances in healthcare is to substantially increase the number and quality of innovative, cost-effective new medicines, without incurring unsustainable R&D costs. However, it is widely acknowledged that trends in industry R&D productivity have been moving in the opposite direction for a number of years. Here, we present a detailed analysis based on comprehensive, recent, industry-wide data to identify the relative contributions of each of the steps in the drug discovery and development process to overall R&D productivity. We then propose specific strategies that could have the most substantial impact in improving R&D productivity.

2,901 citations

Journal ArticleDOI
TL;DR: It is demonstrated that saturation correlates with solubility, an experimental physical property important to success in the drug discovery setting, and both complexity and the presence of chiral centers correlate with success as compounds transition from discovery, through clinical testing, to drugs.
Abstract: The medicinal chemistry community has become increasingly aware of the value of tracking calculated physical properties such as molecular weight, topological polar surface area, rotatable bonds, and hydrogen bond donors and acceptors. We hypothesized that the shift to high-throughput synthetic practices over the past decade may be another factor that may predispose molecules to fail by steering discovery efforts toward achiral, aromatic compounds. We have proposed two simple and interpretable measures of the complexity of molecules prepared as potential drug candidates. The first is carbon bond saturation as defined by fraction sp3 (Fsp3) where Fsp3 = (number of sp3 hybridized carbons/total carbon count). The second is simply whether a chiral carbon exists in the molecule. We demonstrate that both complexity (as measured by Fsp3) and the presence of chiral centers correlate with success as compounds transition from discovery, through clinical testing, to drugs. In an attempt to explain these observations,...

2,396 citations


"Molecular obesity, potency and othe..." refers background in this paper

  • ...drug discovery process is enhanced by an increase in the fraction of sp3 hybridized carbon atoms and the number of chiral centers present [9]....

    [...]