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Srinivasan B, Zhou H, Kubanek J, Skolnick J. Experimental validation of FINDSITE(comb) virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders. J Cheminform 2014; 6:16. [PMID: 24936211 PMCID: PMC4038399 DOI: 10.1186/1758-2946-6-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 04/15/2014] [Indexed: 01/09/2023] Open
Abstract
Background Identification of ligand-protein binding interactions is a critical step in drug discovery. Experimental screening of large chemical libraries, in spite of their specific role and importance in drug discovery, suffer from the disadvantages of being random, time-consuming and expensive. To accelerate the process, traditional structure- or ligand-based VLS approaches are combined with experimental high-throughput screening, HTS. Often a single protein or, at most, a protein family is considered. Large scale VLS benchmarking across diverse protein families is rarely done, and the reported success rate is very low. Here, we demonstrate the experimental HTS validation of a novel VLS approach, FINDSITEcomb, across a diverse set of medically-relevant proteins. Results For eight different proteins belonging to different fold-classes and from diverse organisms, the top 1% of FINDSITEcomb’s VLS predictions were tested, and depending on the protein target, 4%-47% of the predicted ligands were shown to bind with μM or better affinities. In total, 47 small molecule binders were identified. Low nanomolar (nM) binders for dihydrofolate reductase and protein tyrosine phosphatases (PTPs) and micromolar binders for the other proteins were identified. Six novel molecules had cytotoxic activity (<10 μg/ml) against the HCT-116 colon carcinoma cell line and one novel molecule had potent antibacterial activity. Conclusions We show that FINDSITEcomb is a promising new VLS approach that can assist drug discovery.
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Affiliation(s)
- Bharath Srinivasan
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250, 14th Street, N.W., Atlanta, GA 30318, USA
| | - Hongyi Zhou
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250, 14th Street, N.W., Atlanta, GA 30318, USA
| | - Julia Kubanek
- School of Biology, Atlanta, GA 30332, USA ; School of Chemistry and Biochemistry, Aquatic Chemical Ecology Center, Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250, 14th Street, N.W., Atlanta, GA 30318, USA
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Zhou H, Skolnick J. FINDSITE(comb): a threading/structure-based, proteomic-scale virtual ligand screening approach. J Chem Inf Model 2012; 53:230-40. [PMID: 23240691 DOI: 10.1021/ci300510n] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Virtual ligand screening is an integral part of the modern drug discovery process. Traditional ligand-based, virtual screening approaches are fast but require a set of structurally diverse ligands known to bind to the target. Traditional structure-based approaches require high-resolution target protein structures and are computationally demanding. In contrast, the recently developed threading/structure-based FINDSITE-based approaches have the advantage that they are as fast as traditional ligand-based approaches and yet overcome the limitations of traditional ligand- or structure-based approaches. These new methods can use predicted low-resolution structures and infer the likelihood of a ligand binding to a target by utilizing ligand information excised from the target's remote or close homologous proteins and/or libraries of ligand binding databases. Here, we develop an improved version of FINDSITE, FINDSITE(filt), that filters out false positive ligands in threading identified templates by a better binding site detection procedure that includes information about the binding site amino acid similarity. We then combine FINDSITE(filt) with FINDSITE(X) that uses publicly available binding databases ChEMBL and DrugBank for virtual ligand screening. The combined approach, FINDSITE(comb), is compared to two traditional docking methods, AUTODOCK Vina and DOCK 6, on the DUD benchmark set. It is shown to be significantly better in terms of enrichment factor, dependence on target structure quality, and speed. FINDSITE(comb) is then tested for virtual ligand screening on a large set of 3576 generic targets from the DrugBank database as well as a set of 168 Human GPCRs. Excluding close homologues, FINDSITE(comb) gives an average enrichment factor of 52.1 for generic targets and 22.3 for GPCRs within the top 1% of the screened compound library. Around 65% of the targets have better than random enrichment factors. The performance is insensitive to target structure quality, as long as it has a TM-score ≥ 0.4 to native. Thus, FINDSITE(comb) makes the screening of millions of compounds across entire proteomes feasible. The FINDSITE(comb) web service is freely available for academic users at http://cssb.biology.gatech.edu/skolnick/webservice/FINDSITE-COMB/index.html.
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Affiliation(s)
- Hongyi Zhou
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street, N.W., Atlanta, Georgia 30318, USA
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Abstract
Results of a previous docking study are reanalyzed and extended to include results from the docking program FRED and a detailed statistical analysis of both structure reproduction and virtual screening results. FRED is run both in a traditional docking mode and in a hybrid mode that makes use of the structure of a bound ligand in addition to the protein structure to screen molecules. This analysis shows that most docking programs are effective overall but highly inconsistent, tending to do well on one system and poorly on the next. Comparing methods, the difference in mean performance on DUD is found to be statistically significant (95% confidence) 61% of the time when using a global enrichment metric (AUC). Early enrichment metrics are found to have relatively poor statistical power, with 0.5% early enrichment only able to distinguish methods to 95% confidence 14% of the time.
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Affiliation(s)
- Mark McGann
- OpenEye Scientific Software, Santa Fe, New Mexico 87508, United States.
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Cole DC, Olland AM, Jacob J, Brooks J, Bursavich MG, Czerwinski R, DeClercq C, Johnson M, Joseph-McCarthy D, Ellingboe JW, Lin L, Nowak P, Presman E, Strand J, Tam A, Williams CMM, Yao S, Tsao DHH, Fitz LJ. Identification and characterization of acidic mammalian chitinase inhibitors. J Med Chem 2010; 53:6122-8. [PMID: 20666458 DOI: 10.1021/jm100533p] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acidic mammalian chitinase (AMCase) is a member of the glycosyl hydrolase 18 family (EC 3.2.1.14) that has been implicated in the pathophysiology of allergic airway disease such as asthma. Small molecule inhibitors of AMCase were identified using a combination of high-throughput screening, fragment screening, and virtual screening techniques and characterized by enzyme inhibition and NMR and Biacore binding experiments. X-ray structures of the inhibitors in complex with AMCase revealed that the larger more potent HTS hits, e.g. 5-(4-(2-(4-bromophenoxy)ethyl)piperazine-1-yl)-1H-1,2,4-triazol-3-amine 1, spanned from the active site pocket to a hydrophobic pocket. Smaller fragments identified by FBS occupy both these pockets independently and suggest potential strategies for linking fragments. Compound 1 is a 200 nM AMCase inhibitor which reduced AMCase enzymatic activity in the bronchoalveolar lavage fluid in allergen-challenged mice after oral dosing.
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Affiliation(s)
- Derek C Cole
- WorldWide Medicinal Chemistry: Inflammation & Immunology, Pfizer Global Research & Development, Cambridge, MA 01240, USA.
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Cross JB, Thompson DC, Rai BK, Baber JC, Fan KY, Hu Y, Humblet C. Comparison of several molecular docking programs: pose prediction and virtual screening accuracy. J Chem Inf Model 2009; 49:1455-74. [PMID: 19476350 DOI: 10.1021/ci900056c] [Citation(s) in RCA: 329] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular docking programs are widely used modeling tools for predicting ligand binding modes and structure based virtual screening. In this study, six molecular docking programs (DOCK, FlexX, GLIDE, ICM, PhDOCK, and Surflex) were evaluated using metrics intended to assess docking pose and virtual screening accuracy. Cognate ligand docking to 68 diverse, high-resolution X-ray complexes revealed that ICM, GLIDE, and Surflex generated ligand poses close to the X-ray conformation more often than the other docking programs. GLIDE and Surflex also outperformed the other docking programs when used for virtual screening, based on mean ROC AUC and ROC enrichment values obtained for the 40 protein targets in the Directory of Useful Decoys (DUD). Further analysis uncovered general trends in accuracy that are specific for particular protein families. Modifying basic parameters in the software was shown to have a significant effect on docking and virtual screening results, suggesting that expert knowledge is critical for optimizing the accuracy of these methods.
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Affiliation(s)
- Jason B Cross
- Wyeth Research, Chemical Sciences, Collegeville, Pennsylvania 19426, USA.
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Baber JC, Thompson DC, Cross JB, Humblet C. GARD: A Generally Applicable Replacement for RMSD. J Chem Inf Model 2009; 49:1889-900. [DOI: 10.1021/ci9001074] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. Christian Baber
- Chemical Sciences, Wyeth Research, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140 and 865 Ridge Road, Princeton, New Jersey 08543, and Chemical Sciences, Wyeth Pharmaceuticals and Research Headquarters, 500 Arcola Road, Collegeville, Pennsylvania 19426
| | - David C. Thompson
- Chemical Sciences, Wyeth Research, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140 and 865 Ridge Road, Princeton, New Jersey 08543, and Chemical Sciences, Wyeth Pharmaceuticals and Research Headquarters, 500 Arcola Road, Collegeville, Pennsylvania 19426
| | - Jason B. Cross
- Chemical Sciences, Wyeth Research, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140 and 865 Ridge Road, Princeton, New Jersey 08543, and Chemical Sciences, Wyeth Pharmaceuticals and Research Headquarters, 500 Arcola Road, Collegeville, Pennsylvania 19426
| | - Christine Humblet
- Chemical Sciences, Wyeth Research, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140 and 865 Ridge Road, Princeton, New Jersey 08543, and Chemical Sciences, Wyeth Pharmaceuticals and Research Headquarters, 500 Arcola Road, Collegeville, Pennsylvania 19426
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Thompson DC, Humblet C, Joseph-McCarthy D. Investigation of MM-PBSA Rescoring of Docking Poses. J Chem Inf Model 2008; 48:1081-91. [DOI: 10.1021/ci700470c] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David C. Thompson
- Wyeth Research Chemical and Screening Sciences 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, and Wyeth Research Chemical and Screening Sciences 865 Ridge Road Princeton, New Jersey 08543
| | - Christine Humblet
- Wyeth Research Chemical and Screening Sciences 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, and Wyeth Research Chemical and Screening Sciences 865 Ridge Road Princeton, New Jersey 08543
| | - Diane Joseph-McCarthy
- Wyeth Research Chemical and Screening Sciences 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, and Wyeth Research Chemical and Screening Sciences 865 Ridge Road Princeton, New Jersey 08543
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