1
|
Xu M, Shen C, Yang J, Wang Q, Huang N. Systematic Investigation of Docking Failures in Large-Scale Structure-Based Virtual Screening. ACS Omega 2022; 7:39417-39428. [PMID: 36340123 PMCID: PMC9632257 DOI: 10.1021/acsomega.2c05826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
In recent years, large-scale structure-based virtual screening has attracted increasing levels of interest for identification of novel compounds corresponding to potential drug targets. It is critical to understand the strengths and weaknesses of docking algorithms to increase the success rate in practical applications. Here, we systematically investigated the docking successes and failures of two representative docking programs: UCSF DOCK 3.7 and AutoDock Vina. DOCK 3.7 performed better in early enrichment on the Directory of Useful Decoys: Enhanced (DUD-E) data set, although both docking methods were roughly comparable in overall enrichment performance. DOCK 3.7 also showed superior computational efficiency. Intriguingly, the Vina scoring function showed a bias toward compounds with higher molecular weights. Both the tested docking approaches yielded incorrectly predicted ligand binding poses caused by the limitations of torsion sampling. Based on a careful analysis of docking results from six representative cases, we propose the reasons underlying docking failures; furthermore, we provide a few solutions, representing practical guidance for large-scale virtual screening campaigns and future docking algorithm development.
Collapse
Affiliation(s)
- Min Xu
- College
of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
- National
Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science
Park, Beijing 102206, China
| | - Cheng Shen
- National
Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science
Park, Beijing 102206, China
- Graduate
School of Peking Union Medical College, Chinese Academy of Medical Sciences, No. 9, Dongdan Santiao, Dongcheng District, Beijing 100730, China
| | - Jincai Yang
- National
Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science
Park, Beijing 102206, China
| | - Qing Wang
- National
Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science
Park, Beijing 102206, China
- School
of Pharmaceutical Science and Technology, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Niu Huang
- National
Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science
Park, Beijing 102206, China
- Tsinghua
Institute of Multidisciplinary Biomedical Research, Tsinghua University, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| |
Collapse
|
2
|
Velcicky J, Schlapbach A, Heng R, Revesz L, Pflieger D, Blum E, Hawtin S, Huppertz C, Feifel R, Hersperger R. Modulating ADME Properties by Fluorination: MK2 Inhibitors with Improved Oral Exposure. ACS Med Chem Lett 2018; 9:392-396. [PMID: 29670707 DOI: 10.1021/acsmedchemlett.8b00098] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 03/16/2018] [Indexed: 02/07/2023] Open
Abstract
MAP-activated protein kinase 2 (MK2) plays an important role in the regulation of innate immune response as well as in cell survival upon DNA damage. Despite its potential for the treatment of inflammation and cancer, to date no MK2 low molecular weight inhibitors have reached the clinic, mainly due to inadequate absorption, distribution, metabolism, and excretion (ADME) properties. We describe here an approach based on specifically placed fluorine within a recently described pyrrole-based MK2 inhibitor scaffold for manipulation of its physicochemical and ADME properties. While preserving target potency, the novel fluoro-derivatives showed greatly improved permeability as well as enhanced solubility and reduced in vivo clearance leading to significantly increased oral exposure.
Collapse
Affiliation(s)
- Juraj Velcicky
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Achim Schlapbach
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Richard Heng
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Laszlo Revesz
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Daniel Pflieger
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Ernst Blum
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Stuart Hawtin
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | | | - Roland Feifel
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Rene Hersperger
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| |
Collapse
|
3
|
Fiore M, Forli S, Manetti F. Targeting Mitogen-Activated Protein Kinase-Activated Protein Kinase 2 (MAPKAPK2, MK2): Medicinal Chemistry Efforts To Lead Small Molecule Inhibitors to Clinical Trials. J Med Chem 2015; 59:3609-34. [PMID: 26502061 DOI: 10.1021/acs.jmedchem.5b01457] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The p38/MAPK-activated kinase 2 (MK2) pathway is involved in a series of pathological conditions (inflammation diseases and metastasis) and in the resistance mechanism to antitumor agents. None of the p38 inhibitors entered advanced clinical trials because of their unwanted systemic side effects. For this reason, MK2 was identified as an alternative target to block the pathway but avoiding the side effects of p38 inhibition. However, ATP-competitive MK2 inhibitors suffered from low solubility, poor cell permeability, and scarce kinase selectivity. Fortunately, non-ATP-competitive inhibitors of MK2 have been already discovered that allowed circumventing the selectivity issue. These compounds showed the additional advantage to be effective at lower concentrations in comparison to the ATP-competitive inhibitors. Therefore, although the significant difficulties encountered during the development of these inhibitors, MK2 is still considered as an attractive target to treat inflammation and related diseases to prevent tumor metastasis and to increase tumor sensitivity to chemotherapeutics.
Collapse
Affiliation(s)
- Mario Fiore
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena , via A. Moro 2, I-53100 Siena, Italy
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Fabrizio Manetti
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena , via A. Moro 2, I-53100 Siena, Italy
| |
Collapse
|
4
|
Lin S, Malkani S, Lombardo M, Yang L, Mills SG, Chapman K, Thompson JE, Zhang WX, Wang R, Cubbon RM, O’neill EA, Hale JJ. Design, synthesis, and biological evaluation of aminopyrazine derivatives as inhibitors of mitogen-activated protein kinase-activated protein kinase 2 (MK-2). Bioorg Med Chem Lett 2015; 25:5402-8. [DOI: 10.1016/j.bmcl.2015.09.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/02/2015] [Accepted: 09/07/2015] [Indexed: 11/22/2022]
|
5
|
Lindin I, Wuxiuer Y, Ravna AW, Moens U, Sylte I. Comparative molecular dynamics simulations of mitogen-activated protein kinase-activated protein kinase 5. Int J Mol Sci 2014; 15:4878-902. [PMID: 24651460 DOI: 10.3390/ijms15034878] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 02/21/2014] [Accepted: 02/28/2014] [Indexed: 12/28/2022] Open
Abstract
The mitogen-activated protein kinase-activated protein kinase MK5 is a substrate of the mitogen-activated protein kinases p38, ERK3 and ERK4. Cell culture and animal studies have demonstrated that MK5 is involved in tumour suppression and promotion, embryogenesis, anxiety, cell motility and cell cycle regulation. In the present study, homology models of MK5 were used for molecular dynamics (MD) simulations of: (1) MK5 alone; (2) MK5 in complex with an inhibitor; and (3) MK5 in complex with the interaction partner p38α. The calculations showed that the inhibitor occupied the active site and disrupted the intramolecular network of amino acids. However, intramolecular interactions consistent with an inactive protein kinase fold were not formed. MD with p38α showed that not only the p38 docking region, but also amino acids in the activation segment, αH helix, P-loop, regulatory phosphorylation region and the C-terminal of MK5 may be involved in forming a very stable MK5-p38α complex, and that p38α binding decreases the residual fluctuation of the MK5 model. Electrostatic Potential Surface (EPS) calculations of MK5 and p38α showed that electrostatic interactions are important for recognition and binding.
Collapse
|
6
|
Moens U, Kostenko S, Sveinbjørnsson B. The Role of Mitogen-Activated Protein Kinase-Activated Protein Kinases (MAPKAPKs) in Inflammation. Genes (Basel) 2013; 4:101-33. [PMID: 24705157 PMCID: PMC3899974 DOI: 10.3390/genes4020101] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/18/2013] [Accepted: 03/20/2013] [Indexed: 01/18/2023] Open
Abstract
Mitogen-activated protein kinase (MAPK) pathways are implicated in several cellular processes including proliferation, differentiation, apoptosis, cell survival, cell motility, metabolism, stress response and inflammation. MAPK pathways transmit and convert a plethora of extracellular signals by three consecutive phosphorylation events involving a MAPK kinase kinase, a MAPK kinase, and a MAPK. In turn MAPKs phosphorylate substrates, including other protein kinases referred to as MAPK-activated protein kinases (MAPKAPKs). Eleven mammalian MAPKAPKs have been identified: ribosomal-S6-kinases (RSK1-4), mitogen- and stress-activated kinases (MSK1-2), MAPK-interacting kinases (MNK1-2), MAPKAPK-2 (MK2), MAPKAPK-3 (MK3), and MAPKAPK-5 (MK5). The role of these MAPKAPKs in inflammation will be reviewed.
Collapse
Affiliation(s)
- Ugo Moens
- Molecular Inflammation Research Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, NO-9037 Tromsø, Norway.
| | - Sergiy Kostenko
- Molecular Inflammation Research Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, NO-9037 Tromsø, Norway.
| | - Baldur Sveinbjørnsson
- Molecular Inflammation Research Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, NO-9037 Tromsø, Norway.
| |
Collapse
|
7
|
Wang TJ, Zhou L, Fei J, Li ZC, He LF. Applications of 3D-QSAR and structure-based pharmacophore modeling, virtual screening, ADMET, and molecular docking of putative MAPKAP-K2 (MK2) inhibitors. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0492-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
8
|
Kosugi T, Mitchell DR, Fujino A, Imai M, Kambe M, Kobayashi S, Makino H, Matsueda Y, Oue Y, Komatsu K, Imaizumi K, Sakai Y, Sugiura S, Takenouchi O, Unoki G, Yamakoshi Y, Cunliffe V, Frearson J, Gordon R, Harris CJ, Kalloo-Hosein H, Le J, Patel G, Simpson DJ, Sherborne B, Thomas PS, Suzuki N, Takimoto-Kamimura M, Kataoka KI. Mitogen-activated protein kinase-activated protein kinase 2 (MAPKAP-K2) as an antiinflammatory target: discovery and in vivo activity of selective pyrazolo[1,5-a]pyrimidine inhibitors using a focused library and structure-based optimization approach. J Med Chem 2012; 55:6700-15. [PMID: 22746295 DOI: 10.1021/jm300411k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A novel class of mitogen-activated protein kinase-activated protein kinase 2 (MAPKAP-K2) inhibitors was discovered through screening a kinase-focused library. A homology model of MAPKAP-K2 was generated and used to guide the initial SAR studies and to rationalize the observed selectivity over CDK2. An X-ray crystal structure of a compound from the active series bound to crystalline MAPKAP-K2 confirmed the predicted binding mode. This has enabled the discovery of a series of pyrazolo[1,5-a]pyrimidine derivatives showing good in vitro cellular potency as anti-TNF-α agents and in vivo efficacy in a mouse model of endotoxin shock.
Collapse
Affiliation(s)
- Tomomi Kosugi
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd. , Hino, Tokyo 191-8512, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Abstract
Despite the success of anti-TNFα biologicals, there remains a significant unmet need for novel oral anti-inflammatory drugs for the treatment of rheumatoid arthritis and related diseases. Vigorous exploration of many potential targets for inhibition of, for example, pro-inflammatory cytokine production has led to efforts to find inhibitor leads targeting many enzymes including the p38α substrate kinase MK2. MK2 has a key role in the production of several pro-inflammatory cytokines, and studies with knockout animals and inhibitor leads support the promise of MK2 as an anti-inflammatory target. However, MK2 has additional biological roles such as in cell cycle checkpoint control, suggesting caution in the use of MK2 inhibitors for chronic non-life-threatening clinical indications such as inflammation. MK2 inhibitor lead identification and optimization efforts in several labs have resulted in a variety of potent and specific lead molecules, some of which display in-vivo activity. However, potency loss from enzyme to cell, and cell to in vivo, is commonly significant. Further, poor enzyme to cell potency correlations are also common for MK2 lead chemical series, suggesting uncontrolled confounding factors in lead inhibitor properties, or that the biological roles of MK2 and related enzymes may still be poorly understood. While further efforts in identification of MK2 inhibitors may yet yield viable drug leads, efforts to date suggest caution with this target.
Collapse
|
10
|
|
11
|
Ward BC, Kavalukas S, Brugnano J, Barbul A, Panitch A. Peptide inhibitors of MK2 show promise for inhibition of abdominal adhesions. J Surg Res 2011; 169:e27-36. [PMID: 21492875 DOI: 10.1016/j.jss.2011.01.043] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Revised: 11/24/2010] [Accepted: 01/21/2011] [Indexed: 12/12/2022]
Abstract
BACKGROUND Abdominal adhesions are a common side effect of surgical procedures with complications including infertility, chronic pain, and bowel obstruction, which may lead to the need for surgical lyses of the adhesions. Mitogen-activated protein kinase-activated protein kinase 2 (MK2) has been implicated in several diseases, involving inflammation and fibrosis. Thus, the development of a cell-penetrating peptide (CPP) that modulates MK2 activity may confer therapeutic benefit after abdominal surgery in general and more specifically after bowel anastomosis. METHODS This study evaluated the function of a CPP inhibitor of MK2 in human mesothelial cells and in a rat bowel anastomosis model. To determine IC50 and basic specificity, kinase inhibition was performed using a radiometric assay. Enzyme-linked immunoassay (ELISA) was used to evaluate interleukin-6 (IL-6) expression in response to IL-1β and tumor necrosis factor-α (TNF-α) stimulation in vitro to validate MK2 kinase inhibition. Following bowel anastomosis (10 rats for each control and treatment at 4 and 10 d), the rats were evaluated for weight loss, normal healing (colonic burst strength and hydroxyproline content at the anastomosis), and number and density of adhesions. RESULTS The IC50 of the MK2 inhibitor peptide (22 μM) was similar to that of the nonspecific small molecule rottlerin (IC50 = 5 μM). The MK2 inhibitor peptide was effective at suppressing IL-1β and TNF-α stimulated IL-6 expression in mesothelial cells. In vivo, the MK2 inhibitor peptide was effective at suppressing both the density and number of adhesions formed as a result of bowel an anastamosis. Importantly, the peptide had no negative effect on normal healing. CONCLUSIONS In conclusion, the peptide inhibitor of MK2, MMI-0100, has the potential to significantly reduce inflammation through suppression of inflammatory cytokine expression and showed promise as a therapeutic for abdominal adhesions.
Collapse
Affiliation(s)
- Brian C Ward
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907-2032, USA
| | | | | | | | | |
Collapse
|