201
|
Recht MI, Sridhar V, Badger J, Bounaud PY, Logan C, Chie-Leon B, Nienaber V, Torres FE. Identification and optimization of PDE10A inhibitors using fragment-based screening by nanocalorimetry and X-ray crystallography. ACTA ACUST UNITED AC 2013; 19:497-507. [PMID: 24375910 DOI: 10.1177/1087057113516493] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Fragment-based lead discovery (FBLD) is a technique in which small, low-complexity chemical fragments of 6 to 15 heavy atoms are screened for binding to or inhibiting activity of the target. Hits are then linked and/or elaborated into tightly binding ligands, ideally yielding early lead compounds for drug discovery. Calorimetry provides a label-free method to assay binding and enzymatic activity that is unaffected by the spectroscopic properties of the sample. Conventional microcalorimetry is hampered by requiring large quantities of reagents and long measurement times. Nanocalorimeters can overcome these limitations of conventional isothermal titration calorimetry. Here we use enthalpy arrays, which are arrays of nanocalorimeters, to perform an enzyme activity-based fragment screen for competitive inhibitors of phosphodiesterase 10A (PDE10A). Two dozen fragments with KI <2 mM were identified and moved to crystal soaking trials. All soak experiments yielded high-resolution diffraction, with two-thirds of the fragments yielding high-resolution co-crystal structures with PDE10A. The structural information was used to elaborate fragment hits, yielding leads with KI <1 µM. This study shows how array calorimetry can be used as a prescreening method for fragment-based lead discovery with enzyme targets and paired successfully with an X-ray crystallography secondary screen.
Collapse
|
202
|
Morley AD, Pugliese A, Birchall K, Bower J, Brennan P, Brown N, Chapman T, Drysdale M, Gilbert IH, Hoelder S, Jordan A, Ley SV, Merritt A, Miller D, Swarbrick ME, Wyatt PG. Fragment-based hit identification: thinking in 3D. Drug Discov Today 2013; 18:1221-7. [DOI: 10.1016/j.drudis.2013.07.011] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 06/17/2013] [Accepted: 07/16/2013] [Indexed: 12/11/2022]
|
203
|
Yuan H, Tai W, Hu S, Liu H, Zhang Y, Yao S, Ran T, Lu S, Ke Z, Xiong X, Xu J, Chen Y, Lu T. Fragment-based strategy for structural optimization in combination with 3D-QSAR. J Comput Aided Mol Des 2013; 27:897-915. [DOI: 10.1007/s10822-013-9687-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/24/2013] [Indexed: 12/14/2022]
|
204
|
Ligand efficiency as a guide in fragment hit selection and optimization. DRUG DISCOVERY TODAY. TECHNOLOGIES 2013; 7:e147-202. [PMID: 24103767 DOI: 10.1016/j.ddtec.2010.11.003] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
205
|
Alder CM, Ambler M, Campbell AJ, Champigny AC, Deakin AM, Harling JD, Harris CA, Longstaff T, Lynn S, Maxwell AC, Mooney CJ, Scullion C, Singh OMP, Smith IED, Somers DO, Tame CJ, Wayne G, Wilson C, Woolven JM. Identification of a Novel and Selective Series of Itk Inhibitors via a Template-Hopping Strategy. ACS Med Chem Lett 2013; 4:948-52. [PMID: 24900590 DOI: 10.1021/ml400206q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 08/12/2013] [Indexed: 12/23/2022] Open
Abstract
Inhibition of Itk potentially constitutes a novel, nonsteroidal treatment for asthma and other T-cell mediated diseases. In-house kinase cross-screening resulted in the identification of an aminopyrazole-based series of Itk inhibitors. Initial work on this series highlighted selectivity issues with several other kinases, particularly AurA and AurB. A template-hopping strategy was used to identify a series of aminobenzothiazole Itk inhibitors, which utilized an inherently more selective hinge binding motif. Crystallography and modeling were used to rationalize the observed selectivity. Initial exploration of the SAR around this series identified potent Itk inhibitors in both enzyme and cellular assays.
Collapse
Affiliation(s)
- Catherine M. Alder
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Martin Ambler
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Amanda J. Campbell
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Aurelie C. Champigny
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Angela M. Deakin
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - John D. Harling
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Carol A. Harris
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Tim Longstaff
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Sean Lynn
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Aoife C. Maxwell
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Chris J. Mooney
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Callum Scullion
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Onkar M. P. Singh
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Ian E. D. Smith
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Donald O. Somers
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Christopher J. Tame
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Gareth Wayne
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - Caroline Wilson
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| | - James M. Woolven
- Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals, Medicines Research Centre, Gunnels
Wood Road, Stevenage, SG1 2NY, U.K
| |
Collapse
|
206
|
Reduced dimensionality (4,3)D-hnCOCANH experiment: an efficient backbone assignment tool for NMR studies of proteins. ACTA ACUST UNITED AC 2013; 14:109-18. [PMID: 23982149 DOI: 10.1007/s10969-013-9161-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 08/19/2013] [Indexed: 10/26/2022]
Abstract
Sequence specific resonance assignment of proteins forms the basis for variety of structural and functional proteomics studies by NMR. In this context, an efficient standalone method for rapid assignment of backbone ((1)H, (15)N, (13)C(α) and (13)C') resonances of proteins has been presented here. Compared to currently available strategies used for the purpose, the method employs only a single reduced dimensionality experiment--(4,3)D-hnCOCANH and exploits the linear combinations of backbone ((13)C(α) and (13)C') chemical shifts to achieve a dispersion relatively better compared to those of individual chemical shifts (see the text). The resulted increased dispersion of peaks--which is different in sum (CA + CO) and difference (CA - CO) frequency regions--greatly facilitates the analysis of the spectrum by resolving the problems (associated with routine assignment strategies) arising because of degenerate amide (15)N and backbone (13)C chemical shifts. Further, the spectrum provides direct distinction between intra- and inter-residue correlations because of their opposite peak signs. The other beneficial feature of the spectrum is that it provides: (a) multiple unidirectional sequential (i→i + 1) (15)N and (13)C correlations and (b) facile identification of certain specific triplet sequences which serve as check points for mapping the stretches of sequentially connected HSQC cross peaks on to the primary sequence for assigning the resonances sequence specifically. On top of all this, the F₂-F₃ planes of the spectrum corresponding to sum (CA + CO) and difference (CA - CO) chemical shifts enable rapid and unambiguous identification of sequential HSQC peaks through matching their coordinates in these two planes (see the text). Overall, the experiment presented here will serve as an important backbone assignment tool for variety of structural and functional proteomics and drug discovery research programs by NMR involving well behaved small folded proteins (MW < 15 kDa) or a range of intrinsically disordered proteins.
Collapse
|
207
|
Lamberth C, Jeanmart S, Luksch T, Plant A. Current Challenges and Trends in the Discovery of Agrochemicals. Science 2013; 341:742-6. [DOI: 10.1126/science.1237227] [Citation(s) in RCA: 274] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Crop protection chemistry has come a long way from its “alchemic” beginnings in the late 19th century to a high-tech science that supports the sustainable production of food, feed, and fiber for a rapidly growing population. Cutting-edge developments in the design and synthesis of agrochemicals help to tackle today’s challenges of weed and pest resistance, higher regulatory safety margins, and higher cost of goods with the invention of selective, environmentally benign, low use rate, and cost-effective active ingredients.
Collapse
Affiliation(s)
- Clemens Lamberth
- Syngenta Crop Protection AG, Research Chemistry, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Stephane Jeanmart
- Syngenta Crop Protection AG, Research Chemistry, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Torsten Luksch
- Syngenta Crop Protection AG, Research Chemistry, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Andrew Plant
- Syngenta Crop Protection AG, Research Chemistry, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| |
Collapse
|
208
|
Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery. Proc Natl Acad Sci U S A 2013; 110:12984-9. [PMID: 23872845 DOI: 10.1073/pnas.1304045110] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In fragment-based drug discovery, the weak affinities exhibited by fragments pose significant challenges for screening. Biophysical techniques are used to address this challenge, but there is no clear consensus on which cascade of methods is best suited to identify fragment hits that ultimately translate into bound X-ray structures and provide bona fide starting points for synthesis. We have benchmarked an integrated biophysical approach for fragment screening and validation against Mycobacterium tuberculosis pantothenate synthetase. A primary screen of 1,250 fragments library was performed by thermal shift, followed by secondary screen using one-dimensional NMR spectroscopy (water ligand observed gradient spectroscopy and saturation transfer difference binding experiments) and ultimate hit validation by isothermal titration calorimetry and X-ray crystallography. Our multibiophysical approach identified three distinct binding sites for fragments and laid a solid foundation for successful structure-based elaboration into potent inhibitors.
Collapse
|
209
|
Regnström K, Yan J, Nguyen L, Callaway K, Yang Y, Diep L, Xing W, Adhikari A, Beroza P, Hom RK, Riley B, Rudolph D, Jobling MF, Baker J, Johnston J, Konradi A, Bova MP, Artis DR. Label free fragment screening using surface plasmon resonance as a tool for fragment finding - analyzing parkin, a difficult CNS target. PLoS One 2013; 8:e66879. [PMID: 23861750 PMCID: PMC3702509 DOI: 10.1371/journal.pone.0066879] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 05/12/2013] [Indexed: 11/18/2022] Open
Abstract
Surface Plasmon Resonance (SPR) is rarely used as a primary High-throughput Screening (HTS) tool in fragment-based approaches. With SPR instruments becoming increasingly high-throughput it is now possible to use SPR as a primary tool for fragment finding. SPR becomes, therefore, a valuable tool in the screening of difficult targets such as the ubiquitin E3 ligase Parkin. As a prerequisite for the screen, a large number of SPR tests were performed to characterize and validate the active form of Parkin. A set of compounds was designed and used to define optimal SPR assay conditions for this fragment screen. Using these conditions, more than 5000 pre-selected fragments from our in-house library were screened for binding to Parkin. Additionally, all fragments were simultaneously screened for binding to two off target proteins to exclude promiscuous binding compounds. A low hit rate was observed that is in line with hit rates usually obtained by other HTS screening assays. All hits were further tested in dose responses on the target protein by SPR for confirmation before channeling the hits into Nuclear Magnetic Resonance (NMR) and other hit-confirmation assays.
Collapse
|
210
|
Hudson SA, Surade S, Coyne AG, McLean KJ, Leys D, Munro AW, Abell C. Overcoming the limitations of fragment merging: rescuing a strained merged fragment series targeting Mycobacterium tuberculosis CYP121. ChemMedChem 2013; 8:1451-6. [PMID: 23788280 PMCID: PMC4281926 DOI: 10.1002/cmdc.201300219] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Sean A Hudson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | | | | | | | | | | | | |
Collapse
|
211
|
Ebadi A, Razzaghi-Asl N, Khoshneviszadeh M, Miri R. Comparative amino acid decomposition analysis of potent type I p38α inhibitors. ACTA ACUST UNITED AC 2013; 21:41. [PMID: 23714278 PMCID: PMC3680208 DOI: 10.1186/2008-2231-21-41] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Accepted: 05/25/2013] [Indexed: 12/21/2022]
Abstract
Background and purpose of the study p38α is a member of mitogen-activated protein kinases (MAPK) considered as a prominent target in development of anti-inflammatory agents. Any abnormality in the phosphorylation process leads to the different human diseases such as cancer, diabetes and inflammatory diseases. Several small molecule p38α inhibitors have been developed up to now. In this regard, structural elucidation of p38 inhibitors needs to be done enabling us in rational lead development strategies. Methods Various interactions of three potent inhibitors with p38α active site have been evaluated in terms of binding energies and bond lengths via density function theory and MD simulations. Results Our comparative study showed that both ab initio and MD simulation led to the relatively similar results in pharmacophore discrimination of p38α inhibitors. Conclusion The results of the present study may find their usefulness in pharmacophore based modification of p38α inhibitors.
Collapse
Affiliation(s)
- Ahmad Ebadi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, PO Box 3288-71345, Shiraz, Iran.
| | | | | | | |
Collapse
|
212
|
Stevens BD. Structure-Based Fragment Screening Is Demonstrated To Be a Practical Lead Discovery Method for a Representative G-Protein-Coupled Receptor. J Med Chem 2013; 56:3444-5. [DOI: 10.1021/jm400561w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Benjamin D. Stevens
- Cambridge Laboratories, Pfizer Worldwide Research and Development, 620 Memorial Drive, Cambridge,
Massachusetts 02139, United States
| |
Collapse
|
213
|
Miller RM, Paavilainen VO, Krishnan S, Serafimova IM, Taunton J. Electrophilic fragment-based design of reversible covalent kinase inhibitors. J Am Chem Soc 2013; 135:5298-301. [PMID: 23540679 PMCID: PMC3665406 DOI: 10.1021/ja401221b] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Fragment-based ligand design and covalent targeting of noncatalytic cysteines have been employed to develop potent and selective kinase inhibitors. Here, we combine these approaches, starting with a panel of low-molecular-weight, heteroaryl-susbstituted cyanoacrylamides, which we have previously shown to form reversible covalent bonds with cysteine thiols. Using this strategy, we identify electrophilic fragments with sufficient ligand efficiency and selectivity to serve as starting points for the first reported inhibitors of the MSK1 C-terminal kinase domain. Guided by X-ray co-crystal structures, indazole fragment 1 was elaborated to afford 12 (RMM-46), a reversible covalent inhibitor that exhibits high ligand efficiency and selectivity for MSK/RSK-family kinases. At nanomolar concentrations, 12 blocked activation of cellular MSK and RSK, as well as downstream phosphorylation of the critical transcription factor, CREB.
Collapse
Affiliation(s)
- Rand M. Miller
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, CA 94158
| | | | | | - Iana M. Serafimova
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, CA 94158
| | - Jack Taunton
- Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
| |
Collapse
|
214
|
Van Molle I, Thomann A, Buckley DL, So EC, Lang S, Crews CM, Ciulli A. Dissecting fragment-based lead discovery at the von Hippel-Lindau protein:hypoxia inducible factor 1α protein-protein interface. ACTA ACUST UNITED AC 2013; 19:1300-12. [PMID: 23102223 DOI: 10.1016/j.chembiol.2012.08.015] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 08/10/2012] [Accepted: 08/16/2012] [Indexed: 01/06/2023]
Abstract
Fragment screening is widely used to identify attractive starting points for drug design. However, its potential and limitations to assess the tractability of often challenging protein:protein interfaces have been underexplored. Here, we address this question by means of a systematic deconstruction of lead-like inhibitors of the pVHL:HIF-1α interaction into their component fragments. Using biophysical techniques commonly employed for screening, we could only detect binding of fragments that violate the Rule of Three, are more complex than those typically screened against classical druggable targets, and occupy two adjacent binding subsites at the interface rather than just one. Analyses based on ligand and group lipophilicity efficiency of anchored fragments were applied to dissect the individual subsites and probe for binding hot spots. The implications of our findings for targeting protein interfaces by fragment-based approaches are discussed.
Collapse
Affiliation(s)
- Inge Van Molle
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | | | | | | | | | | | | |
Collapse
|
215
|
Sharpless KB, Manetsch R. In situ click chemistry: a powerful means for lead discovery. Expert Opin Drug Discov 2013; 1:525-38. [PMID: 23506064 DOI: 10.1517/17460441.1.6.525] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Combinatorial chemistry and parallel synthesis are important and regularly applied tools for lead identification and optimisation, although they are often accompanied by challenges related to the efficiency of library synthesis and the purity of the compound library. In the last decade, novel means of lead discovery approaches have been investigated where the biological target is actively involved in the synthesis of its own inhibitory compound. These fragment-based approaches, also termed target-guided synthesis (TGS), show great promise in lead discovery applications by combining the synthesis and screening of libraries of low molecular weight compounds in a single step. Of all the TGS methods, the kinetically controlled variant is the least well known, but it has the potential to emerge as a reliable lead discovery method. The kinetically controlled TGS approach, termed in situ click chemistry, is discussed in this article.
Collapse
Affiliation(s)
- K Barry Sharpless
- WM Keck Professor, Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, BCC-315 La Jolla, CA 92037, USA.
| | | |
Collapse
|
216
|
Barker J, Courtney S, Hesterkamp T, Ullmann D, Whittaker M. Fragment screening by biochemical assay. Expert Opin Drug Discov 2013; 1:225-36. [PMID: 23495844 DOI: 10.1517/17460441.1.3.225] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The use of high concentration biochemical assays to identify weak binding fragment molecules can be an effective method to identify novel starting points for medicinal chemistry programmes. The combination of a high-quality fragment library with sensitive biochemical screening methods is a viable alternative to the more commonly used fragment screening methods such as nuclear magnetic resonance screening or high-throughput X-ray crystallography. Notably, there are a number of literature reports where fragment molecules have been identified by a high concentration biochemical assay. The use of high concentration screening of fragments using a portfolio of single-molecule fluorescence correlation spectroscopy detection techniques to ensure the highest reproducibility and sensitivity have been demonstrated, as well as the use of and X-ray crystallography to determine the binding mode of active fragments.
Collapse
Affiliation(s)
- John Barker
- Evotec, 111 Milton Park, Abingdon, Oxon, OX14 4RZ, UK.
| | | | | | | | | |
Collapse
|
217
|
Alizadeh A, Ghanbaripour R. A Novel and Efficient Synthesis of 3-[(4,5-Dihydro-1H-pyrrol-3-yl)carbonyl]-2H-chromen-2-ones (=3-[(4,5-Dihydro-1H-pyrrol-3-yl)carbonyl]-2H-1-benzopyran-2-ones). Helv Chim Acta 2013. [DOI: 10.1002/hlca.201200216] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
218
|
Chiappori F, Merelli I, Milanesi L, Marabotti A. Static and dynamic interactions between GALK enzyme and known inhibitors: guidelines to design new drugs for galactosemic patients. Eur J Med Chem 2013; 63:423-34. [PMID: 23517731 DOI: 10.1016/j.ejmech.2013.02.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 02/08/2013] [Accepted: 02/18/2013] [Indexed: 10/27/2022]
Abstract
The search for inhibitors of galactokinase (GALK) enzyme is interesting for their possible therapeutic application capable to alleviate symptoms in people with classic galactosemia. Several high-throughput screenings in the past have found candidate ligands showing a moderate affinity for GALK. Computational analysis of the binding mode of these compounds in comparison to their target protein has been performed only on crystallographic static structures, therefore missing the evolution of the complex during time. In this work, we applied static and dynamics simulations to analyze the interactions between GALK and its potential inhibitors, while taking into account the temporal evolution of the complexes. The collected data allowed us to identify the most important and persistent anchoring points of the known active site and of the newly identified secondary cavity. These data will be of use to increase the specificity and the affinity of a new generation of GALK inhibitors.
Collapse
Affiliation(s)
- Federica Chiappori
- Institute of Biomedical Technologies, Italian National Research Council, Via F.lli Cervi 93, 20090 Segrate, MI, Italy
| | | | | | | |
Collapse
|
219
|
Kobe A, Caaveiro JMM, Tashiro S, Kajihara D, Kikkawa M, Mitani T, Tsumoto K. Incorporation of Rapid Thermodynamic Data in Fragment-Based Drug Discovery. J Med Chem 2013; 56:2155-9. [DOI: 10.1021/jm301603n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Akihiro Kobe
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Department of Medical Genome
Science, School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Jose M. M. Caaveiro
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Department of Medical Genome
Science, School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Shinya Tashiro
- Department of Medical Genome
Science, School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Daisuke Kajihara
- Life Science Division, GE Healthcare Japan, 3-25-1 Hyakuninicho, Shinjuku,
Tokyo 169-0073, Japan
| | - Masato Kikkawa
- Life Science Division, GE Healthcare Japan, 3-25-1 Hyakuninicho, Shinjuku,
Tokyo 169-0073, Japan
| | - Tomoya Mitani
- Life Science Division, GE Healthcare Japan, 3-25-1 Hyakuninicho, Shinjuku,
Tokyo 169-0073, Japan
| | - Kouhei Tsumoto
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Department of Medical Genome
Science, School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
- Department
of Chemistry and
Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| |
Collapse
|
220
|
Practical purification of hydrophilic fragments and lead/drug-like molecules by reverse phase flash chromatography: tips, tricks and contemporary developments. Drug Discov Today 2013; 18:148-54. [DOI: 10.1016/j.drudis.2012.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 08/03/2012] [Accepted: 09/05/2012] [Indexed: 11/23/2022]
|
221
|
Chen H, Yang Z, Ding C, Chu L, Zhang Y, Terry K, Liu H, Shen Q, Zhou J. Fragment-based drug design and identification of HJC0123, a novel orally bioavailable STAT3 inhibitor for cancer therapy. Eur J Med Chem 2013; 62:498-507. [PMID: 23416191 DOI: 10.1016/j.ejmech.2013.01.023] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 01/14/2013] [Accepted: 01/17/2013] [Indexed: 01/05/2023]
Abstract
Fragment-based drug design (FBDD) is a promising approach for the generation of lead molecules with enhanced activity and especially drug-like properties against therapeutic targets. Herein, we report the fragment-based drug design, systematic chemical synthesis and pharmacological evaluation of novel scaffolds as potent anticancer agents by utilizing six privileged fragments from known STAT3 inhibitors. Several new molecules such as compounds 5, 12, and 19 that may act as advanced chemical leads have been identified. The most potent compound 5 (HJC0123) has demonstrated to inhibit STAT3 promoter activity, downregulate phosphorylation of STAT3, increase the expression of cleaved caspase-3, inhibit cell cycle progression and promote apoptosis in breast and pancreatic cancer cells with low micromolar to nanomolar IC50 values. Furthermore, compound 5 significantly suppressed estrogen receptor (ER)-negative breast cancer MDA-MB-231 xenograft tumor growth in vivo (p.o.), indicating its great potential as an efficacious and orally bioavailable drug candidate for human cancer therapy.
Collapse
Affiliation(s)
- Haijun Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, United States
| | | | | | | | | | | | | | | | | |
Collapse
|
222
|
Heinrich T, Seenisamy J, Emmanuvel L, Kulkarni SS, Bomke J, Rohdich F, Greiner H, Esdar C, Krier M, Grädler U, Musil D. Fragment-based discovery of new highly substituted 1H-pyrrolo[2,3-b]- and 3H-imidazolo[4,5-b]-pyridines as focal adhesion kinase inhibitors. J Med Chem 2013; 56:1160-70. [PMID: 23294348 DOI: 10.1021/jm3016014] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Focal adhesion kinase (FAK) is considered as an attractive target for oncology, and small-molecule inhibitors are reported to be in clinical testing. In a surface plasmon resonance (SPR)-mediated fragment screening campaign, we discovered bicyclic scaffolds like 1H-pyrazolo[3,4-d]pyrimidines binding to the hinge region of FAK. By an accelerated knowledge-based fragment growing approach, essential pharmacophores were added. The establishment of highly substituted unprecedented 1H-pyrrolo[2,3-b]pyridine derivatizations provided compounds with submicromolar cellular FAK inhibition potential. The combination of substituents on the bicyclic templates and the nature of the core structure itself have a significant impact on the compounds FAK selectivity. Structural analysis revealed that the appropriately substituted pyrrolo[2,3-b]pyridine induced a rare helical DFG-loop conformation. The discovered synthetic route to introduce three different substituents independently paves the way for versatile applications of the 7-azaindole core.
Collapse
Affiliation(s)
- Timo Heinrich
- Merck Serono Research, Merck KGaA , 64271 Darmstadt, Germany.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
223
|
Matschinsky FM. GKAs for diabetes therapy: why no clinically useful drug after two decades of trying? Trends Pharmacol Sci 2013; 34:90-9. [PMID: 23305809 DOI: 10.1016/j.tips.2012.11.007] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 11/29/2012] [Accepted: 11/30/2012] [Indexed: 12/17/2022]
Abstract
Results of basic biochemical and physiological research, strongly endorsed by findings in human pathophysiology and genetics, had characterized the glucose phosphorylating enzyme glucokinase as a critical player in normal glucose homeostasis, diabetes mellitus, and hyperinsulinemic hypoglycemia, and identified the enzyme as a promising new drug target. R&D initiated in the early 1990s and directed at this target discovered glucokinase activators (GKAs) as a new class of potentially antidiabetic drugs. GKAs were characterized as nonessential allosteric activators that increase glucose affinity and V(max) of the enzyme, thus stimulating glucose metabolism in glucokinase expressing tissue, of foremost functional significance in the insulin producing pancreatic beta cells and the liver. The results of preclinical testing of GKAs by many pharmaceutical companies demonstrated uniformly high hypoglycemic efficacy in normal and diabetic animals. GKAs were also highly effective in Phase I trials in patients with type 2 diabetes mellitus (T2DM). However, results of a recent Phase II trial were less encouraging because patients developed hyperlipidemia and vascular hypertension, and the drug lost efficacy within several months. This outcome is prompting a reappraisal of the GKA strategy. In this opinion article, the 'pros and cons' of the strategy to use these compounds in diabetes management are critically reexamined and suggestions are made that might facilitate progress of GKA R&D that could still result in a novel antidiabetic medicine.
Collapse
Affiliation(s)
- Franz M Matschinsky
- Department of Biochemistry and Biophysics, Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-5160, USA.
| |
Collapse
|
224
|
Balewski Ł, Sączewski F, Gdaniec M, Bednarski PJ, Jara I. Synthesis of N-(2-pyridyl)imidazolidin-2-ones and 1-(2-pyridyl)-2,3,7,8-tetrahydro-1H-imidazo[2,1-b][1,3,5]triazepin-5(6H)-ones with potential biological activities. HETEROCYCL COMMUN 2013. [DOI: 10.1515/hc-2013-0125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
|
225
|
Lim SS, Debono CO, MacRaild CA, Chandrashekaran IR, Dolezal O, Anders RF, Simpson JS, Scanlon MJ, Devine SM, Scammells PJ, Norton RS. Development of Inhibitors of Plasmodium falciparum Apical Membrane Antigen 1 Based on Fragment Screening. Aust J Chem 2013. [DOI: 10.1071/ch13266] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Apical membrane antigen 1 (AMA1) is an essential component of the moving junction complex used by Plasmodium falciparum to invade human red blood cells. AMA1 has a conserved hydrophobic cleft that is the site of key interactions with the rhoptry neck protein complex. Our goal is to develop small molecule inhibitors of AMA1 with broad strain specificity, which we are pursuing using a fragment-based approach. In our screening campaign, we identified fragments that bind to the hydrophobic cleft with a hit rate of 5 %. The high hit rate observed strongly suggests that a druggable pocket is present within the cleft.
Collapse
|
226
|
Zhang Z, Liu C, Li X, Song T, Wu Z, Liang X, Zhao Y, Shen X, Chen H. Fragment-based design, synthesis, and biological evaluation of N-substituted-5-(4-isopropylthiophenol)-2-hydroxynicotinamide derivatives as novel Mcl-1 inhibitors. Eur J Med Chem 2012; 60:410-20. [PMID: 23314054 DOI: 10.1016/j.ejmech.2012.12.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 10/29/2012] [Accepted: 12/09/2012] [Indexed: 10/27/2022]
Abstract
We have previously reported a nanomolar inhibitor of antiapoptotic Mcl-1 protein, 3-thiomorpholin-8-oxo-8H-acenaphtho [1,2-b] pyrrole-9-carbonitrile (S1). S1 plays its function by binding to the BH3 groove of Mcl-1. Basing on this spacial structural characteristic, we developed a novel class of Mcl-1 inhibitor using fragment-based drug discovery approach. By dissecting S1, we identified the compound 4 with a 2-hydroxypyridine core as the starting fragment. In the following molecular growth, we used the ligand efficiency evaluation and fit quality score to assess the fragments. A novel potent compound, N-benzyl-5-(4-isopropylthiophenol)-2-hydroxyl nicotinamide (12c), which binds Mcl-1 with an IC(50) value of 54 nM was obtained. Compound 12c demonstrated a better aqueous solubility than S1.
Collapse
Affiliation(s)
- Zhichao Zhang
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology, No.2 Linggong Road, Dalian 116012, PR China.
| | | | | | | | | | | | | | | | | |
Collapse
|
227
|
Ramesh K, Karnakar K, Satish G, Anil Kumar B, Nageswar Y. A concise aqueous phase supramolecular synthesis of 2-phenyl-2,3-dihydroquinazolin-4(1H)-one derivatives. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.10.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
228
|
Zhu F, Logan G, Reynisson J. Wine Compounds as a Source for HTS Screening Collections. A Feasibility Study. Mol Inform 2012; 31:847-55. [PMID: 27476738 DOI: 10.1002/minf.201200103] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Accepted: 10/10/2012] [Indexed: 12/25/2022]
Abstract
High throughput screening (HTS) is extensively used to identify hit and lead compounds in drug discovery programmes. Designing quality screening libraries is a challenge in terms of water solubility, stability and potential oral bioavailability of the compounds. Wines are widely consumed and wine compounds are inherently water soluble, stable and relatively non-toxic. Furthermore, many wine compounds have been proved health-beneficial. To evaluate the feasibility to use wine compounds 3317 were collected from the literature. Their physiochemical properties were evaluated with main stream molecular descriptors. According to the results ∼25 % of the compounds are lead-like; nearly 80 % lie within drug-like chemical space and finally 90 % conform to known drug space (KDS). The rotatable bonds descriptor was the most effective defining lead-like space. The results suggest that many of the wine compounds are interesting and suitable candidates for screening libraries after suitable filtering.
Collapse
Affiliation(s)
- Feng Zhu
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand tel: 64-9-373-7599 ext. 83746; fax: 64-9-373-7422
| | - Gerard Logan
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand tel: 64-9-373-7599 ext. 83746; fax: 64-9-373-7422
| | - Jóhannes Reynisson
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand tel: 64-9-373-7599 ext. 83746; fax: 64-9-373-7422.
| |
Collapse
|
229
|
Lam B, Zhang Z, Stafford JA, Skene RJ, Shi L, Gwaltney SL. Structure-based design of pyridopyrimidinediones as dipeptidyl peptidase IV inhibitors. Bioorg Med Chem Lett 2012; 22:6628-31. [DOI: 10.1016/j.bmcl.2012.08.110] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 08/21/2012] [Accepted: 08/28/2012] [Indexed: 11/24/2022]
|
230
|
Ramesh K, Karnakar K, Satish G, Harsha Vardhan Reddy K, Nageswar Y. Tandem supramolecular synthesis of substituted 2-aryl-2,3-dihydroquinazolin-4(1H)-ones in the presence of β-cyclodextrin in water. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.08.141] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
231
|
Nonoo RH, Armstrong A, Mann DJ. Kinetic Template-Guided Tethering of Fragments. ChemMedChem 2012; 7:2082-6. [DOI: 10.1002/cmdc.201200404] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Indexed: 11/11/2022]
|
232
|
Dandapani S, Rosse G, Southall N, Salvino JM, Thomas CJ. Selecting, Acquiring, and Using Small Molecule Libraries for High-Throughput Screening. ACTA ACUST UNITED AC 2012; 4:177-191. [PMID: 26705509 DOI: 10.1002/9780470559277.ch110252] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The selection, acquisition and use of high quality small molecule libraries for screening is an essential aspect of drug discovery and chemical biology programs. Screening libraries continue to evolve as researchers gain a greater appreciation of the suitability of small molecules for specific biological targets, processes and environments. The decisions surrounding the make-up of any given small molecule library is informed by a multitude of variables and opinions vary on best-practices. The fitness of any collection relies upon upfront filtering to avoiding problematic compounds, assess appropriate physicochemical properties, install the ideal level of structural uniqueness and determine the desired extent of molecular complexity. These criteria are under constant evaluation and revision as academic and industrial organizations seek out collections that yield ever improving results from their screening portfolios. Practical questions including cost, compound management, screening sophistication and assay objective also play a significant role in the choice of library composition. This overview attempts to offer advice to all organizations engaged in small molecule screening based upon current best practices and theoretical considerations in library selection and acquisition.
Collapse
Affiliation(s)
- Sivaraman Dandapani
- Chemical Biology Platform, The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge Massachusetts 02142 USA
| | - Gerard Rosse
- Dart NeuroScience LLC, 7473 Lusk Boulevard, San Diego, CA 92121 USA
| | - Noel Southall
- NIH Chemical Genomics Center, National Human Genome Research Institute, 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - Joseph M Salvino
- Alliance Discovery, Inc, Biotechnology Center 3805 Old Easton Road, Doylestown, PA 18902 USA
| | - Craig J Thomas
- NIH Chemical Genomics Center, National Human Genome Research Institute, 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| |
Collapse
|
233
|
Hudson SA, McLean KJ, Surade S, Yang YQ, Leys D, Ciulli A, Munro AW, Abell C. Application of Fragment Screening and Merging to the Discovery of Inhibitors of theMycobacterium tuberculosisCytochrome P450 CYP121. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202544] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
234
|
Hudson SA, McLean KJ, Surade S, Yang YQ, Leys D, Ciulli A, Munro AW, Abell C. Application of Fragment Screening and Merging to the Discovery of Inhibitors of theMycobacterium tuberculosisCytochrome P450 CYP121. Angew Chem Int Ed Engl 2012; 51:9311-6. [DOI: 10.1002/anie.201202544] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Revised: 06/10/2012] [Indexed: 02/03/2023]
|
235
|
Zhang F, Arnatt CK, Haney KM, Fang HC, Bajacan JE, Richardson AC, Ware JL, Zhang Y. Structure activity relationship studies of natural product chemokine receptor CCR5 antagonist anibamine toward the development of novel anti prostate cancer agents. Eur J Med Chem 2012; 55:395-408. [PMID: 22901310 DOI: 10.1016/j.ejmech.2012.07.049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 07/25/2012] [Accepted: 07/31/2012] [Indexed: 10/28/2022]
Abstract
Recent studies have indicated that the CCR5 chemokine receptor may be a potential target for treating prostate cancer. Thus, development of CCR5 antagonists may provide novel prostate cancer therapy. Anibamine, a novel pyridine quaternary alkaloid isolated from Aniba sp., was found to effectively compete with (125)I-gp120 in binding to the chemokine receptor CCR5, with an IC(50) = 1 μM. Anibamine is the first natural product reported as a CCR5 antagonist, and thus provides a novel structural skeleton unique from other lead compounds that have generally been identified from high-throughput screening efforts. In order to refine the lead compound's structure and improve the therapeutic index of anibamine derivatives as potential anti prostate cancer agents, the approach of "deconstruction-reconstruction-elaboration" was applied in the structure-activity relationship studies of this work. Here, we report the design, syntheses and anti prostate cancer activities of anibamine and 17 analogues. The results from the in vitro and in vivo studies described here show that this class of compounds has potential to provide novel leads as anti prostate cancer agents.
Collapse
Affiliation(s)
- Feng Zhang
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 E Leigh Street, Richmond, VA 23298-0540, USA
| | | | | | | | | | | | | | | |
Collapse
|
236
|
Abstract
Structure-based drug design has become an essential tool for rapid lead discovery and optimization. As available structural information has increased, researchers have become increasingly aware of the importance of protein flexibility for accurate description of the native state. Typical protein-ligand docking efforts still rely on a single rigid receptor, which is an incomplete representation of potential binding conformations of the protein. These rigid docking efforts typically show the best performance rates between 50 and 75%, while fully flexible docking methods can enhance pose prediction up to 80-95%. This review examines the current toolbox for flexible protein-ligand docking and receptor surface mapping. Present limitations and possibilities for future development are discussed.
Collapse
Affiliation(s)
- Katrina W. Lexa
- Department of Medicinal Chemistry, University of Michigan, 428 Church Street, Ann Arbor, MI 48109-1065, USA
| | - Heather A. Carlson
- Department of Medicinal Chemistry, University of Michigan, 428 Church Street, Ann Arbor, MI 48109-1065, USA
| |
Collapse
|
237
|
Zerbe BS, Hall DR, Vajda S, Whitty A, Kozakov D. Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces. J Chem Inf Model 2012; 52:2236-44. [PMID: 22770357 DOI: 10.1021/ci300175u] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In the context of protein-protein interactions, the term "hot spot" refers to a residue or cluster of residues that makes a major contribution to the binding free energy, as determined by alanine scanning mutagenesis. In contrast, in pharmaceutical research, a hot spot is a site on a target protein that has high propensity for ligand binding and hence is potentially important for drug discovery. Here we examine the relationship between these two hot spot concepts by comparing alanine scanning data for a set of 15 proteins with results from mapping the protein surfaces for sites that can bind fragment-sized small molecules. We find the two types of hot spots are largely complementary; the residues protruding into hot spot regions identified by computational mapping or experimental fragment screening are almost always themselves hot spot residues as defined by alanine scanning experiments. Conversely, a residue that is found by alanine scanning to contribute little to binding rarely interacts with hot spot regions on the partner protein identified by fragment mapping. In spite of the strong correlation between the two hot spot concepts, they fundamentally differ, however. In particular, while identification of a hot spot by alanine scanning establishes the potential to generate substantial interaction energy with a binding partner, there are additional topological requirements to be a hot spot for small molecule binding. Hence, only a minority of hot spots identified by alanine scanning represent sites that are potentially useful for small inhibitor binding, and it is this subset that is identified by experimental or computational fragment screening.
Collapse
Affiliation(s)
- Brandon S Zerbe
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
| | | | | | | | | |
Collapse
|
238
|
Hao GF, Wang F, Li H, Zhu XL, Yang WC, Huang LS, Wu JW, Berry EA, Yang GF. Computational discovery of picomolar Q(o) site inhibitors of cytochrome bc1 complex. J Am Chem Soc 2012; 134:11168-76. [PMID: 22690928 DOI: 10.1021/ja3001908] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A critical challenge to the fragment-based drug discovery (FBDD) is its low-throughput nature due to the necessity of biophysical method-based fragment screening. Herein, a method of pharmacophore-linked fragment virtual screening (PFVS) was successfully developed. Its application yielded the first picomolar-range Q(o) site inhibitors of the cytochrome bc(1) complex, an important membrane protein for drug and fungicide discovery. Compared with the original hit compound 4 (K(i) = 881.80 nM, porcine bc(1)), the most potent compound 4f displayed 20 507-fold improved binding affinity (K(i) = 43.00 pM). Compound 4f was proved to be a noncompetitive inhibitor with respect to the substrate cytochrome c, but a competitive inhibitor with respect to the substrate ubiquinol. Additionally, we determined the crystal structure of compound 4e (K(i) = 83.00 pM) bound to the chicken bc(1) at 2.70 Å resolution, providing a molecular basis for understanding its ultrapotency. To our knowledge, this study is the first application of the FBDD method in the discovery of picomolar inhibitors of a membrane protein. This work demonstrates that the novel PFVS approach is a high-throughput drug discovery method, independent of biophysical screening techniques.
Collapse
Affiliation(s)
- Ge-Fei Hao
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | | | | | | | | | | | | | | | | |
Collapse
|
239
|
Zhang Y, Arnatt CK, Zhang F, Wang J, Haney KM, Fang X. The potential role of anibamine, a natural product CCR5 antagonist, and its analogues as leads toward development of anti-ovarian cancer agents. Bioorg Med Chem Lett 2012; 22:5093-7. [PMID: 22770928 DOI: 10.1016/j.bmcl.2012.05.127] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 05/22/2012] [Accepted: 05/29/2012] [Indexed: 01/17/2023]
Abstract
Chemokines and their receptors play important roles in the development of primary tumors and their metastases. Particularly CC chemokine receptor 5 (CCR5) and its ligand CC chemokine ligand 5 (CCL5/RANTES) seem to be critical in proliferation and invasion of ovarian cancer, the leading cause of death from gynecological malignancies in the United States. Anibamine, the first natural product CCR5 antagonist, and its analogues were examined for their effects on proliferation of the OVCAR-3 ovarian cancer cells in order to validate their candidacy as leads to develop novel anti-ovarian cancer agents. Acting as CCR5 antagonists, anibamine and its analogues significantly suppressed CCL5-induced intracellular Ca(2+) flux. The compounds also inhibited the proliferation of OVCAR-3 at micromolar to submicromolar range. Moreover, anibamine and several analogues did not show significant cytotoxicity in NIH 3T3 cells at concentrations up to 20μM. Based on these results, anibamine and one of its synthetic analogues were defined as potential leads to develop novel agents against ovarian cancer.
Collapse
Affiliation(s)
- Yan Zhang
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA.
| | | | | | | | | | | |
Collapse
|
240
|
Grimme D, González-ruiz D, Gohlke* H. Computational Strategies and Challenges for Targeting Protein–Protein Interactions with Small Molecules. PHYSICO-CHEMICAL AND COMPUTATIONAL APPROACHES TO DRUG DISCOVERY 2012. [DOI: 10.1039/9781849735377-00319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
241
|
Scott DE, Coyne AG, Hudson SA, Abell C. Fragment-Based Approaches in Drug Discovery and Chemical Biology. Biochemistry 2012; 51:4990-5003. [DOI: 10.1021/bi3005126] [Citation(s) in RCA: 324] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Duncan E. Scott
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Anthony G. Coyne
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Sean A. Hudson
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Chris Abell
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| |
Collapse
|
242
|
Raman EP, Vanommeslaeghe K, Mackerell AD. Site-Specific Fragment Identification Guided by Single-Step Free Energy Perturbation Calculations. J Chem Theory Comput 2012; 8:3513-3525. [PMID: 23144598 DOI: 10.1021/ct300088r] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The in-silico Site Identification by Ligand Competitive Saturation (SILCS) approach identifies the binding sites of representative chemical entities on the entire protein surface, information that can be applied for computational fragment-based drug design. In this study, we report an efficient computational protocol that uses sampling of the protein-fragment conformational space obtained from the SILCS simulations and performs single step free energy perturbation (SSFEP) calculations to identify site-specific favorable chemical modifications of benzene involving substitutions of ring hydrogens with individual non-hydrogen atoms. The SSFEP method is able to capture the experimental trends in relative hydration free energies of benzene analogues and for two datasets of experimental relative binding free energies of congeneric series of ligands of the proteins α-thrombin and P38 MAP kinase. The approach includes a protocol in which data obtained from SILCS simulations of the proteins is first analyzed to identify favorable benzene binding sites following which an ensemble of benzene-protein conformations for that site is obtained. The SSFEP protocol applied to that ensemble results in good reproduction of experimental free energies of the α-thrombin ligands, but not for P38 MAP kinase ligands. Comparison with results from a P38 full-ligand simulation and analysis of conformations reveals the reason for the poor agreement being the connectivity with the remainder of the ligand, a limitation inherent in fragment-based methods. Since the SSFEP approach can identify favorable benzene modifications as well as identify the most favorable fragment conformations, the obtained information can be of value for fragment linking or structure-based optimization.
Collapse
Affiliation(s)
- E Prabhu Raman
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street HSF II, Baltimore MD 21201
| | | | | |
Collapse
|
243
|
Novel indoleamine 2,3-dioxygenase-1 inhibitors from a multistep in silico screen. Bioorg Med Chem 2012; 20:1354-63. [DOI: 10.1016/j.bmc.2011.10.068] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 10/15/2011] [Accepted: 10/22/2011] [Indexed: 11/17/2022]
|
244
|
Recht MI, Sridhar V, Badger J, Hernandez L, Chie-Leon B, Nienaber V, Torres FE. Fragment-based screening for inhibitors of PDE4A using enthalpy arrays and X-ray crystallography. ACTA ACUST UNITED AC 2012; 17:469-80. [PMID: 22223051 DOI: 10.1177/1087057111430987] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fragment-based screening has typically relied on X-ray or nuclear magnetic resonance methods to identify low-affinity ligands that bind to therapeutic targets. These techniques are expensive in terms of material and time, so it useful to have a higher throughput method to reliably prescreen a fragment library to identify a subset of compounds for structural analysis. Calorimetry provides a label-free method to assay binding and enzymatic activity that is unaffected by the spectroscopic properties of the sample. Conventional microcalorimetry is hampered by requiring large quantities of reagents and long measurement times. Nanocalorimeters can overcome these limitations of conventional isothermal titration calorimetry. Here we have used enthalpy arrays, which are arrays of nanocalorimeters, to perform an enzyme activity-based fragment screen for competitive inhibitors of phosphodiesterase 4A (PDE4A). Several inhibitors with K ( I ) <2 mM were identified and moved to X-ray crystallization trials. Although the co-crystals did not yield high-resolution data, evidence of binding was observed, and the chemical structures of the hits were consistent with motifs of known PDE4 inhibitors. This study shows how array calorimetry can be used as a prescreening method for fragment-based lead discovery with enzyme targets and provides a list of candidate fragments for inhibition of PDE4A.
Collapse
|
245
|
Yadav MR, Murumkar PR, Zambre VP. Advances in studies on collagenase inhibitors. EXPERIENTIA SUPPLEMENTUM (2012) 2012; 103:83-135. [PMID: 22642191 DOI: 10.1007/978-3-0348-0364-9_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Matrix metalloproteinases (MMPs) play an important role in many physiological and pathological processes. Development of MMP inhibitors, in particular collagenase inhibitors, for the treatment of arthritis has been more challenging, undoubtedly. Small-molecular-weight collagenase inhibitors may be classified into several different arbitrary structural classes, depending on the catalytic zinc-binding function as well as other structural elements of the inhibitors. This chapter tries to make an attempt in providing the reader with an overall flavor of the type of scaffolds reported in the past few years along with the molecular modeling studies.
Collapse
Affiliation(s)
- Mange Ram Yadav
- Pharmacy Department, The M.S. University of Baroda, Vadodara 390 001, Gujarat, India.
| | | | | |
Collapse
|
246
|
Cerulli V, Banfi L, Basso A, Rocca V, Riva R. Diversity oriented and chemoenzymatic synthesis of densely functionalized pyrrolidines through a highly diastereoselective Ugi multicomponent reaction. Org Biomol Chem 2012; 10:1255-74. [DOI: 10.1039/c1ob06632c] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
247
|
Chen D, Ma L, Kanalas JJ, Gao J, Pawlik J, Jimenez ME, Walter MA, Peterson JW, Gilbertson SR, Schein CH. Structure-based redesign of an edema toxin inhibitor. Bioorg Med Chem 2012; 20:368-76. [PMID: 22154558 PMCID: PMC3251925 DOI: 10.1016/j.bmc.2011.10.091] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 10/17/2011] [Accepted: 10/25/2011] [Indexed: 11/17/2022]
Abstract
Edema factor (EF) toxin of Bacillus anthracis (NIAID category A), and several other toxins from NIAID category B Biodefense target bacteria are adenylyl cyclases or adenylyl cyclase agonists that catalyze the conversion of ATP to 3',5'-cyclic adenosine monophosphate (cAMP). We previously identified compound 1 (3-[(9-oxo-9H-fluorene-1-carbonyl)-amino]-benzoic acid), that inhibits EF activity in cultured mammalian cells, and reduces diarrhea caused by enterotoxigenic Escherichia coli (ETEC) at an oral dosage of 15μg/mouse. Here, molecular docking was used to predict improvements in potency and solubility of new derivatives of compound 1 in inhibiting edema toxin (ET)-catalyzed stimulation of cyclic AMP production in murine monocyte-macrophage cells (RAW 264.7). Structure-activity relationship (SAR) analysis of the bioassay results for 22 compounds indicated positions important for activity. Several derivatives demonstrated superior pharmacological properties compared to our initial lead compound, and are promising candidates to treat anthrax infections and diarrheal diseases induced by toxin-producing bacteria.
Collapse
Affiliation(s)
- Deliang Chen
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX 77555-0857, USA
| | - Lili Ma
- Department of Chemistry, University of Houston. Houston, TX 77004, USA
| | | | - Jian Gao
- Mission Pharmacal Company, San Antonio, TX USA
| | - Jennifer Pawlik
- Sealy Center for Vaccine Development, Center for Biodefense and Emerging Infections, UTMB, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, UTMB, Galveston, TX 77555-1070, USA
| | | | | | - Johnny W. Peterson
- Sealy Center for Vaccine Development, Center for Biodefense and Emerging Infections, UTMB, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, UTMB, Galveston, TX 77555-1070, USA
| | | | - Catherine H. Schein
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX 77555-0857, USA
- Sealy Center for Vaccine Development, Center for Biodefense and Emerging Infections, UTMB, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, UTMB, Galveston, TX 77555-1070, USA
- Member, Institute for Translational Studies, UTMB
| |
Collapse
|
248
|
Gobbi A, Lee ML. Handling of Tautomerism and Stereochemistry in Compound Registration. J Chem Inf Model 2011; 52:285-92. [DOI: 10.1021/ci200330x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alberto Gobbi
- Discovery Chemistry, Genentech Incorporated, 1 DNA Way, South San Francisco, California 94080, United States
| | - Man-Ling Lee
- Discovery Chemistry, Genentech Incorporated, 1 DNA Way, South San Francisco, California 94080, United States
| |
Collapse
|
249
|
Behnen J, Köster H, Neudert G, Craan T, Heine A, Klebe G. Experimental and computational active site mapping as a starting point to fragment-based lead discovery. ChemMedChem 2011; 7:248-61. [PMID: 22213702 DOI: 10.1002/cmdc.201100490] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 11/23/2011] [Indexed: 11/06/2022]
Abstract
Small highly soluble probe molecules such as aniline, urea, N-methylurea, 2-bromoacetate, 1,2-propanediol, nitrous oxide, benzamidine, and phenol were soaked into crystals of various proteins to map their binding pockets and to detect hot spots of binding with respect to hydrophobic and hydrophilic properties. The selected probe molecules were first tested at the zinc protease thermolysin. They were then applied to a wider range of proteins such as protein kinase A, D-xylose isomerase, 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, endothiapepsin, and secreted aspartic protease 2. The crystal structures obtained clearly show that the probe molecules populate the protein binding pockets in an ordered fashion. The thus characterized, experimentally observed hot spots of binding were subjected to computational active site mapping using HotspotsX. This approach uses knowledge-based pair potentials to detect favorable binding positions for various atom types. Good agreement between the in silico hot spot predictions and the experimentally observed positions of the polar hydrogen bond forming functional groups and hydrophobic portions was obtained. Finally, we compared the observed poses of the small-molecule probes with those of much larger structurally related ligands. They coincide remarkably well with the larger ligands, considering their spatial orientation and the experienced interaction patterns. This observation confirms the fundamental hypothesis of fragment-based lead discovery: that binding poses, even of very small molecular probes, do not significantly deviate or move once a ligand is grown further into the binding site. This underscores the fact that these probes populate given hot spots and can be regarded as relevant seeds for further design.
Collapse
Affiliation(s)
- Jürgen Behnen
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | | | | | | | | | | |
Collapse
|
250
|
Hall DR, Ngan CH, Zerbe BS, Kozakov D, Vajda S. Hot spot analysis for driving the development of hits into leads in fragment-based drug discovery. J Chem Inf Model 2011; 52:199-209. [PMID: 22145575 DOI: 10.1021/ci200468p] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Fragment-based drug design (FBDD) starts with finding fragment-sized compounds that are highly ligand efficient and can serve as a core moiety for developing high-affinity leads. Although the core-bound structure of a protein facilitates the construction of leads, effective design is far from straightforward. We show that protein mapping, a computational method developed to find binding hot spots and implemented as the FTMap server, provides information that complements the fragment screening results and can drive the evolution of core fragments into larger leads with a minimal loss or, in some cases, even a gain in ligand efficiency. The method places small molecular probes, the size of organic solvents, on a dense grid around the protein and identifies the hot spots as consensus clusters formed by clusters of several probes. The hot spots are ranked based on the number of probe clusters, which predicts the binding propensity of the subsites and hence their importance for drug design. Accordingly, with a single exception the main hot spot identified by FTMap binds the core compound found by fragment screening. The most useful information is provided by the neighboring secondary hot spots, indicating the regions where the core can be extended to increase its affinity. To quantify this information, we calculate the density of probes from mapping, which describes the binding propensity at each point, and show that the change in the correlation between a ligand position and the probe density upon extending or repositioning the core moiety predicts the expected change in ligand efficiency.
Collapse
Affiliation(s)
- David R Hall
- Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, Massachusetts 02215, USA
| | | | | | | | | |
Collapse
|