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Macalino SJY, Basith S, Clavio NAB, Chang H, Kang S, Choi S. Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. Molecules 2018; 23:E1963. [PMID: 30082644 PMCID: PMC6222862 DOI: 10.3390/molecules23081963] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/03/2018] [Accepted: 08/04/2018] [Indexed: 12/14/2022] Open
Abstract
The advent of advanced molecular modeling software, big data analytics, and high-speed processing units has led to the exponential evolution of modern drug discovery and better insights into complex biological processes and disease networks. This has progressively steered current research interests to understanding protein-protein interaction (PPI) systems that are related to a number of relevant diseases, such as cancer, neurological illnesses, metabolic disorders, etc. However, targeting PPIs are challenging due to their "undruggable" binding interfaces. In this review, we focus on the current obstacles that impede PPI drug discovery, and how recent discoveries and advances in in silico approaches can alleviate these barriers to expedite the search for potential leads, as shown in several exemplary studies. We will also discuss about currently available information on PPI compounds and systems, along with their usefulness in molecular modeling. Finally, we conclude by presenting the limits of in silico application in drug discovery and offer a perspective in the field of computer-aided PPI drug discovery.
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Affiliation(s)
- Stephani Joy Y Macalino
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
| | - Shaherin Basith
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
| | - Nina Abigail B Clavio
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
| | - Hyerim Chang
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
| | - Soosung Kang
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
| | - Sun Choi
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
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Matter H, Sotriffer C. Applications and Success Stories in Virtual Screening. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2011. [DOI: 10.1002/9783527633326.ch12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Bohn L, Meyer AS, Rasmussen SK. Phytate: impact on environment and human nutrition. A challenge for molecular breeding. J Zhejiang Univ Sci B 2008; 9:165-91. [PMID: 18357620 DOI: 10.1631/jzus.b0710640] [Citation(s) in RCA: 271] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Phytic acid (PA) is the primary storage compound of phosphorus in seeds accounting for up to 80% of the total seed phosphorus and contributing as much as 1.5% to the seed dry weight. The negatively charged phosphate in PA strongly binds to metallic cations of Ca, Fe, K, Mg, Mn and Zn making them insoluble and thus unavailable as nutritional factors. Phytate mainly accumulates in protein storage vacuoles as globoids, predominantly located in the aleurone layer (wheat, barley and rice) or in the embryo (maize). During germination, phytate is hydrolysed by endogenous phytase(s) and other phosphatases to release phosphate, inositol and micronutrients to support the emerging seedling. PA and its derivatives are also implicated in RNA export, DNA repair, signalling, endocytosis and cell vesicular trafficking. Our recent studies on purification of phytate globoids, their mineral composition and dephytinization by wheat phytase will be discussed. Biochemical data for purified and characterized phytases isolated from more than 23 plant species are presented, the dephosphorylation pathways of phytic acid by different classes of phytases are compared, and the application of phytase in food and feed is discussed.
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Affiliation(s)
- Lisbeth Bohn
- Department of Agricultural Sciences, Faculty of Life Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
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Prykhod'ko AO, Yakovenko OY, Golub AG, Bdzhola VG, Yarmoluk SM. Evaluation of 4H-4-chromenone derivatives as inhibitors of protein kinase CK2. ACTA ACUST UNITED AC 2005. [DOI: 10.7124/bc.0006f4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- A. O. Prykhod'ko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - O. Ya. Yakovenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - A. G. Golub
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - V. G. Bdzhola
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - S. M. Yarmoluk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
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Park H, Lee S. Determination of the Active Site Protonation State of β-Secretase from Molecular Dynamics Simulation and Docking Experiment: Implications for Structure-Based Inhibitor Design. J Am Chem Soc 2003; 125:16416-22. [PMID: 14692784 DOI: 10.1021/ja0304493] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Memapsin 2 (BACE) is an aspartyl protease known as beta-secretase that acts on the production of the beta-amyloid peptide in the human brain, a key event in the pathogenesis of Alzheimer's disease. Although it is expected that the net charge of the catalytic Asp diad would be -1 as in other kinds of aspartyl proteases, the exact protonation states of Asp32 and Asp228 have not been known without ambiguity. Two independent molecular dynamics (MD) simulations of BACE in complex with the potent inhibitor OM99-2 are carried out to determine the preferred protonation state of the Asp diad in the context that is consistent with the previous X-ray crystal structure. The results show that a strong hydrogen bond between the inhibitor hydroxyl group and Asp228 can be maintained only when Asp32 is neutral and Asp228 is ionized. The preference of this protonation state is further supported from the energetic and structural features found in the docking experiment of a novel potent inhibitor with the BACE active site. Thus, both MD and docking studies suggest that the role of hydrogen bond acceptor for the hydroxyl and piperazine groups of the inhibitors should be played by Asp228 instead of Asp32. This may be a key piece of information for the structure-based design/discovery of new inhibitor drugs.
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Affiliation(s)
- Hwangseo Park
- School of Chemistry and Molecular Engineering, and Center for Molecular Catalysis, Seoul National University, Seoul 151-747, South Korea.
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Vangrevelinghe E, Zimmermann K, Schoepfer J, Portmann R, Fabbro D, Furet P. Discovery of a potent and selective protein kinase CK2 inhibitor by high-throughput docking. J Med Chem 2003; 46:2656-62. [PMID: 12801229 DOI: 10.1021/jm030827e] [Citation(s) in RCA: 161] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To assess the potential of protein kinase CK2 as a target for developing new antitumor agents, we have undertaken a search for inhibitors of this enzyme. As part of this effort, we report here the discovery of the potent and selective CK2 inhibitor (5-oxo-5,6-dihydroindolo[1,2-a]quinazolin-7-yl)acetic acid. We identified this inhibitor of a novel structural type by high-throughput docking of our corporate compound collection in the ATP binding site of a homology model of human CK2, using an appropriate protocol. The synthesis of the inhibitor as well as that of related analogues whose CK2 inhibitory activities give support to the binding mode proposed by the docking program is described. The results obtained suggest that virtual screening of a 3D database by molecular docking is a useful approach for lead finding provided that adapted postdocking filtering and reranking procedures are applied to the primary hit list.
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Filikov AV, Hayes RJ, Luo P, Stark DM, Chan C, Kundu A, Dahiyat BI. Computational stabilization of human growth hormone. Protein Sci 2002; 11:1452-61. [PMID: 12021444 PMCID: PMC2373623 DOI: 10.1110/ps.3500102] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Recombinant human growth hormone (hGH) is used worldwide for the treatment of pediatric hypopituitary dwarfism and in children suffering from low levels of hGH. It has limited stability in solution, and because of poor oral absorption, is administered by injection, typically several times a week. Development has therefore focused on more stable or sustained-release formulations and alternatives to injectable delivery that would increase bioavailability and make it easier for patients to use. We redesigned hGH computationally to improve its thermostability. A more stable variant of hGH could have improved pharmacokinetics or enhanced shelf-life, or be more amenable to use in alternate delivery systems and formulations. The computational design was performed using a previously developed combinatorial optimization algorithm based on the dead-end elimination theorem. The algorithm uses an empirical free energy function for scoring designed sequences. This function was augmented with a term that accounts for the loss of backbone and side-chain conformational entropy. The weighting factors for this term, the electrostatic interaction term, and the polar hydrogen burial term were optimized by minimizing the number of mutations designed by the algorithm relative to wild-type. Forty-five residues in the core of the protein were selected for optimization with the modified potential function. The proteins designed using the developed scoring function contained six to 10 mutations, showed enhancement in the melting temperature of up to 16 degrees C, and were biologically active in cell proliferation studies. These results show the utility of our free energy function in automated protein design.
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Lind KE, Du Z, Fujinaga K, Peterlin BM, James TL. Structure-based computational database screening, in vitro assay, and NMR assessment of compounds that target TAR RNA. CHEMISTRY & BIOLOGY 2002; 9:185-93. [PMID: 11880033 DOI: 10.1016/s1074-5521(02)00106-0] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
There has been little prior effort to discover new drugs on the basis of a unique RNA structure. Binding of the viral transactivator Tat to the 5' bulge of the transactivation response (TAR) element is necessary for HIV-1 replication, so TAR RNA is a superb target. A computational approach was developed to screen a large chemical library for binding to a three-dimensional RNA structure. Scoring function development, flexible ligand docking, and limited target flexibility were essential. From the ranked list of compounds predicted to bind TAR, 43 were assayed for inhibition of the Tat-TAR interaction via electrophoretic mobility shift assays. Eleven compounds (between 0.1 and 1 microM) inhibited the Tat-TAR interaction, and some inhibited Tat transactivation in cells. NMR spectra verified specific binding to the 5' bulge and no interaction with other regions of TAR.
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Affiliation(s)
- Kenneth E Lind
- Department of Pharmaceutical Chemistry, Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA
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Bissantz C, Folkers G, Rognan D. Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J Med Chem 2000; 43:4759-67. [PMID: 11123984 DOI: 10.1021/jm001044l] [Citation(s) in RCA: 525] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three different database docking programs (Dock, FlexX, Gold) have been used in combination with seven scoring functions (Chemscore, Dock, FlexX, Fresno, Gold, Pmf, Score) to assess the accuracy of virtual screening methods against two protein targets (thymidine kinase, estrogen receptor) of known three-dimensional structure. For both targets, it was generally possible to discriminate about 7 out of 10 true hits from a random database of 990 ligands. The use of consensus lists common to two or three scoring functions clearly enhances hit rates among the top 5% scorers from 10% (single scoring) to 25-40% (double scoring) and up to 65-70% (triple scoring). However, in all tested cases, no clear relationships could be found between docking and ranking accuracies. Moreover, predicting the absolute binding free energy of true hits was not possible whatever docking accuracy was achieved and scoring function used. As the best docking/consensus scoring combination varies with the selected target and the physicochemistry of target-ligand interactions, we propose a two-step protocol for screening large databases: (i) screening of a reduced dataset containing a few known ligands for deriving the optimal docking/consensus scoring scheme, (ii) applying the latter parameters to the screening of the entire database.
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Affiliation(s)
- C Bissantz
- Department of Applied Biosciences, ETH Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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Filikov AV, Mohan V, Vickers TA, Griffey RH, Cook PD, Abagyan RA, James TL. Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR. J Comput Aided Mol Des 2000; 14:593-610. [PMID: 10921774 DOI: 10.1023/a:1008121029716] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Binding of the Tat protein to TAR RNA is necessary for viral replication of HIV-1. We screened the Available Chemicals Directory (ACD) to identify ligands to bind to a TAR RNA structure using a four-step docking procedure: rigid docking first, followed by three steps of flexible docking using a pseudobrownian Monte Carlo minimization in torsion angle space with progressively more detailed conformational sampling on a progressively smaller list of top-ranking compounds. To validate the procedure, we successfully docked ligands for five RNA complexes of known structure. For ranking ligands according to binding avidity, an empirical binding free energy function was developed which accounts, in particular, for solvation, isomerization free energy, and changes in conformational entropy. System-specific parameters for the function were derived on a training set of RNA/ligand complexes with known structure and affinity. To validate the free energy function, we screened the entire ACD for ligands for an RNA aptamer which binds L-arginine tightly. The native ligand ranked 17 out of ca. 153,000 compounds screened, i.e., the procedure is able to filter out >99.98% of the database and still retain the native ligand. Screening of the ACD for TAR ligands yielded a high rank for all known TAR ligands contained in the ACD and suggested several other potential TAR ligands. Eight of the highest ranking compounds not previously known to be ligands were assayed for inhibition of the Tat-TAR interaction, and two exhibited a CD50 of ca. 1 microM.
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Affiliation(s)
- A V Filikov
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446, USA
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