1
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Eyush E, Kumar S, Sen K, Sakarwal A, Ram H, Yadav D, Kumar A, Panwar A. Protective efficacy of nafronyl in diabetic retinopathy through targeted inhibition of key enzymes. Biotechnol Appl Biochem 2024. [PMID: 38898746 DOI: 10.1002/bab.2625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 05/27/2024] [Indexed: 06/21/2024]
Abstract
Diabetic retinopathy is governed by abnormal apoptosis, increased capillary pressure, and other linked pathology that needs an efficient treatment by multitargeted approaches. Thus, the current study aimed to explore the potential of inhibition of targeted enzymes (DPP4, ACE-2, and aldose reductase) and free radical scavenging capabilities of selected compounds (nafronyl or naftidrofuryl) through in silico and in vivo investigations. Significant binding energies were observed in complexes of aldolase reductase, angiotensin type 1 receptor, and DPP4 against the nafronyl and sitagliptin more than -7.5 kcal/mol. Further validation of free energy was confirmed by calculations of molecular mechanics Poisson-Boltzmann surface area (MMPBSA), and configurational stabilities examined by PCA (principal component analysis). Additionally, drug-likeness was examined by the Swiss ADME web tool, which showed significant findings. Consequently, in vivo experimentations showed significant inflammation and alterations in retinal layers of inner plexiform (inner limiting membrane, nerve fibers, and ganglionic cells), inner nuclear layer (bipolar cells and horizontal cells), and photoreceptors cells. Whereas the treatments (nafronyl and sitagliptin) caused significant improvements in the histoarchitecture of the retina. Additionally, the HOMA indices (IR-insulin resistance, sensitivity, and β cells functioning) and levels of free radicals were significantly altered in the diabetic control group in comparison to intact control. Nafronyl administration showed significant ameliorations in HOMA indices as well as antioxidant levels. Based on the results, it can be concluded that nafronyl efficiently interacts with target enzymes, which may result in potent inhibition and ameliorations in retinal histology as well as glucose homeostasis and antioxidants.
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Affiliation(s)
- Eyush Eyush
- Department of Biochemistry, Central University of Haryana, Mahendragrah, India
| | - Shivani Kumar
- School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Karishma Sen
- Department of Zoology, Jai Narain Vyas University, Jodhpur, India
| | - Anita Sakarwal
- Department of Zoology, Jai Narain Vyas University, Jodhpur, India
| | - Heera Ram
- Department of Zoology, Jai Narain Vyas University, Jodhpur, India
| | - Dharamveer Yadav
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, India
| | - Antresh Kumar
- Department of Biochemistry, Central University of Haryana, Mahendragrah, India
| | - Anil Panwar
- Department of Bioinformatics and Computational Biology, CCS Haryana Agricultural University, Hisar, India
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2
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Mi T, Gao Z, Mituta Z, Burgess K. Dual-Capped Helical Interface Mimics. J Am Chem Soc 2024; 146:10331-10341. [PMID: 38573124 PMCID: PMC11027154 DOI: 10.1021/jacs.3c11717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/25/2024] [Accepted: 03/01/2024] [Indexed: 04/05/2024]
Abstract
Disruption of protein-protein interactions is medicinally important. Interface helices may be mimicked in helical probes featuring enhanced rigidities, binding to protein targets, stabilities in serum, and cell uptake. This form of mimicry is dominated by stapling between side chains of helical residues: there has been less progress on helical N-caps, and there were no generalizable C-caps. Conversely, in natural proteins, helicities are stabilized and terminated by C- and N-caps but not staples. Bicyclic caps previously introduced by us enable interface helical mimicry featuring rigid synthetic caps at both termini in this work. An unambiguously helical dual-capped system proved to be conformationally stable, binding cyclins A and E, and showed impressive cellular uptake. In addition, the dual-capped mimic was completely resistant to proteolysis in serum over an extended period when compared with "gold standard" hydrocarbon-stapled controls. Dual-capped peptidomimetics are a new, generalizable paradigm for helical interface probe design.
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Affiliation(s)
- Tianxiong Mi
- Department
of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| | - Zhe Gao
- Department
of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| | - Zeynep Mituta
- ZentriForce
Pharma Research GmbH, Carl-Friedrich-Gauss-Ring 5, 69124 Heidelberg, Germany
| | - Kevin Burgess
- Department
of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
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3
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Mi T, Siriwibool S, Burgess K. Streamlined Protein-Protein Interface Loop Mimicry. Angew Chem Int Ed Engl 2023; 62:e202307092. [PMID: 37849440 DOI: 10.1002/anie.202307092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]
Abstract
Cyclic peptides comprising endocyclic organic fragments, "cyclo-organopeptides", can be probes for perturbing protein-protein interactions (PPIs). Finding loop mimics is difficult because of high conformational variability amongst targets. Backbone Matching (BM), introduced here, helps solve this problem in the illustrative cases by facilitating efficient evaluation of virtual cyclo-organopeptide core-structure libraries. Thus, 86 rigid organic fragments were selected to build a library of 602 cyclo-organopeptides comprising Ala and organic parts: "cyclo-{-(Ala)n -organo-}". The central hypothesis is "hit" library members have accessible low energy conformers corresponding to backbone structures of target protein loops, while library members which cannot attain this conformation are probably unworthy of further evaluation. BM thereby prioritizes candidate loop mimics, so that less than 10 cyclo-organopeptides are needed to be prepared to find leads for two illustrative PPIs: iNOS ⋅ SPSB2, and uPA ⋅ uPAR.
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Affiliation(s)
- Tianxiong Mi
- Department of Chemistry, Texas A & M University, 77842, College Station, TX, USA
| | - Siriwalee Siriwibool
- School of Chemistry, Institute of Science, Suranaree University of Technology, 30000, Nakhon Ratchasima, Thailand
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, 77842, College Station, TX, USA
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4
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Caniceiro AB, Bueschbell B, Barreto CA, Preto AJ, Moreira IS. MUG: A mutation overview of GPCR subfamily A17 receptors. Comput Struct Biotechnol J 2022; 21:586-600. [PMID: 36659920 PMCID: PMC9822836 DOI: 10.1016/j.csbj.2022.12.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
G protein-coupled receptors (GPCRs) mediate several signaling pathways through a general mechanism that involves their activation, upholding a chain of events that lead to the release of molecules responsible for cytoplasmic action and further regulation. These physiological functions can be severely altered by mutations in GPCR genes. GPCRs subfamily A17 (dopamine, serotonin, adrenergic and trace amine receptors) are directly related with neurodegenerative diseases, and as such it is crucial to explore known mutations on these systems and their impact in structure and function. A comprehensive and detailed computational framework - MUG (Mutations Understanding GPCRs) - was constructed, illustrating key reported mutations and their effect on receptors of the subfamily A17 of GPCRs. We explored the type of mutations occurring overall and in the different families of subfamily A17, as well their localization within the receptor and potential effects on receptor functionality. The mutated residues were further analyzed considering their pathogenicity. The results reveal a high diversity of mutations in the GPCR subfamily A17 structures, drawing attention to the considerable number of mutations in conserved residues and domains. Mutated residues were typically hydrophobic residues enriched at the ligand binding pocket and known activating microdomains, which may lead to disruption of receptor function. MUG as an interactive web application is available for the management and visualization of this dataset. We expect that this interactive database helps the exploration of GPCR mutations, their influence, and their familywise and receptor-specific effects, constituting the first step in elucidating their structures and molecules at the atomic level.
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Affiliation(s)
- Ana B. Caniceiro
- CNC - Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- PhD in Biosciences, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Beatriz Bueschbell
- CNC - Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- PhD Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Casa Costa Alemão, 3030-789 Coimbra, Portugal
| | - Carlos A.V. Barreto
- CNC - Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- PhD Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Casa Costa Alemão, 3030-789 Coimbra, Portugal
| | - António J. Preto
- CNC - Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- PhD Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Casa Costa Alemão, 3030-789 Coimbra, Portugal
| | - Irina S. Moreira
- CNC - Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- Corresponding author at: Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal.
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Jaipal N, Ram H, Charan J, Dixit A, Singh G, Singh BP, Kumar A, Panwar A. HMG‐CoA reductase inhibition medicated hypocholesterolemic and antiatherosclerotic potential of phytoconstituents of an aqueous pod extract of
Prosopis cineraria
(L.) Druce: In silico, in vitro, and in vivo studies. EFOOD 2022. [DOI: 10.1002/efd2.42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Noopur Jaipal
- Department of Zoology Jai Narain Vyas University Jodhpur Rajasthan India
| | - Heera Ram
- Department of Zoology Jai Narain Vyas University Jodhpur Rajasthan India
| | - Jaykaran Charan
- Department of Pharmacology All India Institute of Medical Sciences Jodhpur Rajasthan India
| | | | - Garima Singh
- Department of Botany Pachhunga University College Aizawl Mizoram India
| | - Bhim P. Singh
- Department of Agriculture & Environmental Sciences (AES) National Institute of Food Technology Entrepreneurship & Management (NIFTEM) Sonepat Haryana India
| | - Ashok Kumar
- Centre for Systems Biology and Bioinformatics Panjab University Chandigarh Punjab India
| | - Anil Panwar
- Centre for Systems Biology and Bioinformatics Panjab University Chandigarh Punjab India
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6
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Boumezber S, Yelekçi K. Screening of novel and selective inhibitors for neuronal nitric oxide synthase (nNOS) via structure-based drug design techniques. J Biomol Struct Dyn 2022; 41:3607-3629. [PMID: 35322764 DOI: 10.1080/07391102.2022.2054471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
NO, or nitric oxide, is produced by a family of enzymes called nitric oxide synthase (NOS) from L-arginine. NO regulates many physiological functions such as smooth muscle relaxation, immune defense, and memory function. The overproduction of NO by the neuronal isoform of nitric oxide synthase (nNOS) is implicated in neurodegeneration and neuropathic pain, making nNOS inhibition a promising therapeutic approach. Many developed nNOS inhibitors, generally L-arginine mimetics, have some issues in selectivity and bioavailability. According to earlier studies, targeting nNOS has the advantage of decreasing excess NO in the brain while avoiding the negative consequences of inhibiting the two isozymes: endothelial NOS (eNOS) and inducible NOS (iNOS). This study applied structure-based virtual screening, molecular docking, and molecular dynamics simulations to design potent and selective inhibitors against nNOS over related isoforms (eNOS and iNOS) using human X-ray crystal structures of the NOS isoforms. It was discovered that some compounds displayed a very good inhibitory potency for hnNOS and moderate selectivity for the other isozymes, eNOS and iNOS, in addition to good solubility and desirable physiochemical properties. The compounds which showed good stability and selectivity with nNOS, such as ZINC000013485422, can be interesting and informative guidance for designing more potent human nNOS inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sarah Boumezber
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
| | - Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
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7
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Marques-Pereira C, Pires MN, Gouveia RP, Pereira NN, Caniceiro AB, Rosário-Ferreira N, Moreira IS. SARS-CoV-2 Membrane Protein: From Genomic Data to Structural New Insights. Int J Mol Sci 2022; 23:2986. [PMID: 35328409 PMCID: PMC8948900 DOI: 10.3390/ijms23062986] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 01/27/2023] Open
Abstract
Severe Acute Respiratory Syndrome CoronaVirus-2 (SARS-CoV-2) is composed of four structural proteins and several accessory non-structural proteins. SARS-CoV-2's most abundant structural protein, Membrane (M) protein, has a pivotal role both during viral infection cycle and host interferon antagonism. This is a highly conserved viral protein, thus an interesting and suitable target for drug discovery. In this paper, we explain the structural nature of M protein homodimer. To do so, we developed and applied a detailed and robust in silico workflow to predict M protein dimeric structure, membrane orientation, and interface characterization. Single Nucleotide Polymorphisms (SNPs) in M protein were retrieved from over 1.2 M SARS-CoV-2 genomes and proteins from the Global Initiative on Sharing All Influenza Data (GISAID) database, 91 of which were located at the predicted dimer interface. Among those, we identified SNPs in Variants of Concern (VOC) and Variants of Interest (VOI). Binding free energy differences were evaluated for dimer interfacial SNPs to infer mutant protein stabilities. A few high-prevalent mutated residues were found to be especially relevant in VOC and VOI. This realization may be a game-changer to structure-driven formulation of new therapeutics for SARS-CoV-2.
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Affiliation(s)
- Catarina Marques-Pereira
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
- IIIs—Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Manuel N. Pires
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
- Department of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Raquel P. Gouveia
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
| | - Nádia N. Pereira
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
| | - Ana B. Caniceiro
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
| | - Nícia Rosário-Ferreira
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
- CQC—Coimbra Chemistry Center, Chemistry Department, Faculty of Science and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Irina S. Moreira
- Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-535 Coimbra, Portugal
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8
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Chouhan H, Purohit A, Ram H, Chowdhury S, Kashyap P, Panwar A, Kumar A. The interaction capabilities of phytoconstituents of ethanolic seed extract of cumin (
Cuminum cyminum
L.) with HMG‐CoA reductase to subside the hypercholesterolemia: A mechanistic approach. FOOD FRONTIERS 2021. [DOI: 10.1002/fft2.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
| | - Ashok Purohit
- Department of Zoology Jai Narain Vyas University Jodhpur India
| | - Heera Ram
- Department of Zoology Jai Narain Vyas University Jodhpur India
| | - Suman Chowdhury
- University School of Biotechnology Guru Gobind Singh Indraprastha University New Delhi India
| | - Priya Kashyap
- University School of Biotechnology Guru Gobind Singh Indraprastha University New Delhi India
| | - Anil Panwar
- Department of Molecular Biology Biotechnology and Bioinformatics CCS Haryana Agricultural University Hisar India
- Centre for System Biology and Bioinformatics Panjab University Chandigarh India
| | - Ashok Kumar
- Centre for System Biology and Bioinformatics Panjab University Chandigarh India
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9
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Matos-Filipe P, Preto AJ, Koukos PI, Mourão J, Bonvin AMJJ, Moreira IS. MENSAdb: a thorough structural analysis of membrane protein dimers. Database (Oxford) 2021; 2021:baab013. [PMID: 33822911 PMCID: PMC8023553 DOI: 10.1093/database/baab013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 01/19/2021] [Accepted: 03/01/2021] [Indexed: 11/14/2022]
Abstract
Membrane proteins (MPs) are key players in a variety of different cellular processes and constitute the target of around 60% of all Food and Drug Administration-approved drugs. Despite their importance, there is still a massive lack of relevant structural, biochemical and mechanistic information mainly due to their localization within the lipid bilayer. To help fulfil this gap, we developed the MEmbrane protein dimer Novel Structure Analyser database (MENSAdb). This interactive web application summarizes the evolutionary and physicochemical properties of dimeric MPs to expand the available knowledge on the fundamental principles underlying their formation. Currently, MENSAdb contains features of 167 unique MPs (63% homo- and 37% heterodimers) and brings insights into the conservation of residues, accessible solvent area descriptors, average B-factors, intermolecular contacts at 2.5 Å and 4.0 Å distance cut-offs, hydrophobic contacts, hydrogen bonds, salt bridges, π-π stacking, T-stacking and cation-π interactions. The regular update and organization of all these data into a unique platform will allow a broad community of researchers to collect and analyse a large number of features efficiently, thus facilitating their use in the development of prediction models associated with MPs. Database URL: http://www.moreiralab.com/resources/mensadb.
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Affiliation(s)
- Pedro Matos-Filipe
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra 3005-504, Portugal
| | - António J Preto
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra 3005-504, Portugal
- PhD Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research, University of Coimbra, Coimbra, 3030-789, Portugal
| | - Panagiotis I Koukos
- Bijvoet Centre for Biomolecular Research, Faculty of Science—Chemistry, Utrecht University, Utrecht, 3584, CH, Netherlands
| | - Joana Mourão
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra 3005-504, Portugal
| | - Alexandre M J J Bonvin
- Bijvoet Centre for Biomolecular Research, Faculty of Science—Chemistry, Utrecht University, Utrecht, 3584, CH, Netherlands
| | - Irina S Moreira
- Department of Life Sciences, University of Coimbra, Coimbra, 3000-456, Portugal
- Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
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10
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Nandakumar R, Dinu V. Developing a machine learning model to identify protein–protein interaction hotspots to facilitate drug discovery. PeerJ 2020; 8:e10381. [PMID: 33354416 PMCID: PMC7727375 DOI: 10.7717/peerj.10381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/27/2020] [Indexed: 02/01/2023] Open
Abstract
Throughout the history of drug discovery, an enzymatic-based approach for identifying new drug molecules has been primarily utilized. Recently, protein–protein interfaces that can be disrupted to identify small molecules that could be viable targets for certain diseases, such as cancer and the human immunodeficiency virus, have been identified. Existing studies computationally identify hotspots on these interfaces, with most models attaining accuracies of ~70%. Many studies do not effectively integrate information relating to amino acid chains and other structural information relating to the complex. Herein, (1) a machine learning model has been created and (2) its ability to integrate multiple features, such as those associated with amino-acid chains, has been evaluated to enhance the ability to predict protein–protein interface hotspots. Virtual drug screening analysis of a set of hotspots determined on the EphB2-ephrinB2 complex has also been performed. The predictive capabilities of this model offer an AUROC of 0.842, sensitivity/recall of 0.833, and specificity of 0.850. Virtual screening of a set of hotspots identified by the machine learning model developed in this study has identified potential medications to treat diseases caused by the overexpression of the EphB2-ephrinB2 complex, including prostate, gastric, colorectal and melanoma cancers which are linked to EphB2 mutations. The efficacy of this model has been demonstrated through its successful ability to predict drug-disease associations previously identified in literature, including cimetidine, idarubicin, pralatrexate for these conditions. In addition, nadolol, a beta blocker, has also been identified in this study to bind to the EphB2-ephrinB2 complex, and the possibility of this drug treating multiple cancers is still relatively unexplored.
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11
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Preto AJ, Moreira IS. SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features. Int J Mol Sci 2020; 21:ijms21197281. [PMID: 33019775 PMCID: PMC7582262 DOI: 10.3390/ijms21197281] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/26/2020] [Accepted: 09/30/2020] [Indexed: 01/02/2023] Open
Abstract
Protein Hot-Spots (HS) are experimentally determined amino acids, key to small ligand binding and tend to be structural landmarks on protein–protein interactions. As such, they were extensively approached by structure-based Machine Learning (ML) prediction methods. However, the availability of a much larger array of protein sequences in comparison to determined tree-dimensional structures indicates that a sequence-based HS predictor has the potential to be more useful for the scientific community. Herein, we present SPOTONE, a new ML predictor able to accurately classify protein HS via sequence-only features. This algorithm shows accuracy, AUROC, precision, recall and F1-score of 0.82, 0.83, 0.91, 0.82 and 0.85, respectively, on an independent testing set. The algorithm is deployed within a free-to-use webserver, only requiring the user to submit a FASTA file with one or more protein sequences.
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Affiliation(s)
- A. J. Preto
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal;
| | - Irina S. Moreira
- Department of Life Sciences, Center for Neuroscience and Cell Biology, Coimbra University, 3000-456 Coimbra, Portugal
- Correspondence:
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12
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Yan W, Hu G, Liang Z, Zhou J, Yang Y, Chen J, Shen B. Node-Weighted Amino Acid Network Strategy for Characterization and Identification of Protein Functional Residues. J Chem Inf Model 2018; 58:2024-2032. [PMID: 30107728 DOI: 10.1021/acs.jcim.8b00146] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The study of functional residues (FRs) is essential for understanding protein functions and biological processes. The amino acid network (AAN) has become an emerging paradigm for studying FRs during the past decade. Current AAN models ignore the heterogeneity of nodes and treat amino acids in the AAN as the same. However, the properties of each amino acid node are of fundamental importance. We here proposed a node-weighted AAN strategy termed the node-weighted amino acid contact energy network (NACEN) to characterize and predict three types of FRs, namely, hot spots, catalytic residues, and allosteric residues. We first constructed NACENs with their nodes weighted based on structural, sequence, physicochemical, and dynamical properties of the amino acids and then characterized the FRs with the NACEN parameters. We finally built machine learning predictors to identify each type of FR. The results revealed that residues characterized with NACEN parameters are more distinguishable between FRs and non-FRs than those with unweighted network ones. With few features for classification, NACEN yields comparable performance for FR identification and provides residue level prediction for allosteric regulation. The proposed strategy can be easily implemented to other functional residue identification. An R package is also provided for NACEN construction and analysis at http://sysbio.suda.edu.cn/NACEN/index.html .
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Affiliation(s)
- Wenying Yan
- Center for systems biology , Soochow University , Suzhou 215006 , China
| | - Guang Hu
- Center for systems biology , Soochow University , Suzhou 215006 , China
| | - Zhongjie Liang
- Center for systems biology , Soochow University , Suzhou 215006 , China
| | - Jianhong Zhou
- Center for systems biology , Soochow University , Suzhou 215006 , China
| | - Yang Yang
- School of computer science and technology , Soochow University , Suzhou 215006 , China
| | - Jiajia Chen
- School of Chemistry, Biology and Material Engineering , Suzhou University of Science and Technology , Suzhou 215011 , China
| | - Bairong Shen
- Center for systems biology , Soochow University , Suzhou 215006 , China
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13
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Moreira IS, Koukos PI, Melo R, Almeida JG, Preto AJ, Schaarschmidt J, Trellet M, Gümüş ZH, Costa J, Bonvin AMJJ. SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots. Sci Rep 2017; 7:8007. [PMID: 28808256 PMCID: PMC5556074 DOI: 10.1038/s41598-017-08321-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/07/2017] [Indexed: 12/21/2022] Open
Abstract
We present SpotOn, a web server to identify and classify interfacial residues as Hot-Spots (HS) and Null-Spots (NS). SpotON implements a robust algorithm with a demonstrated accuracy of 0.95 and sensitivity of 0.98 on an independent test set. The predictor was developed using an ensemble machine learning approach with up-sampling of the minor class. It was trained on 53 complexes using various features, based on both protein 3D structure and sequence. The SpotOn web interface is freely available at: http://milou.science.uu.nl/services/SPOTON/.
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Affiliation(s)
- Irina S Moreira
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1°andar, Universidade de Coimbra, 3004-517, Coimbra, Portugal. .,Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, 3584CH, The Netherlands.
| | - Panagiotis I Koukos
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, 3584CH, The Netherlands
| | - Rita Melo
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1°andar, Universidade de Coimbra, 3004-517, Coimbra, Portugal.,Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (ao km 139,7), 2695-066, Bobadela LRS, Portugal
| | - Jose G Almeida
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1°andar, Universidade de Coimbra, 3004-517, Coimbra, Portugal
| | - Antonio J Preto
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1°andar, Universidade de Coimbra, 3004-517, Coimbra, Portugal
| | - Joerg Schaarschmidt
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, 3584CH, The Netherlands
| | - Mikael Trellet
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, 3584CH, The Netherlands
| | - Zeynep H Gümüş
- Department of Genetics and Genomics and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joaquim Costa
- CMUP/FCUP, Centro de Matemática da Universidade do Porto, Faculdade de Ciências, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Alexandre M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, 3584CH, The Netherlands.
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14
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Protein binding hot spots prediction from sequence only by a new ensemble learning method. Amino Acids 2017; 49:1773-1785. [DOI: 10.1007/s00726-017-2474-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 07/24/2017] [Indexed: 01/31/2023]
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15
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Melo R, Fieldhouse R, Melo A, Correia JDG, Cordeiro MNDS, Gümüş ZH, Costa J, Bonvin AMJJ, Moreira IS. A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces. Int J Mol Sci 2016; 17:E1215. [PMID: 27472327 PMCID: PMC5000613 DOI: 10.3390/ijms17081215] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/11/2016] [Accepted: 07/18/2016] [Indexed: 12/17/2022] Open
Abstract
Understanding protein-protein interactions is a key challenge in biochemistry. In this work, we describe a more accurate methodology to predict Hot-Spots (HS) in protein-protein interfaces from their native complex structure compared to previous published Machine Learning (ML) techniques. Our model is trained on a large number of complexes and on a significantly larger number of different structural- and evolutionary sequence-based features. In particular, we added interface size, type of interaction between residues at the interface of the complex, number of different types of residues at the interface and the Position-Specific Scoring Matrix (PSSM), for a total of 79 features. We used twenty-seven algorithms from a simple linear-based function to support-vector machine models with different cost functions. The best model was achieved by the use of the conditional inference random forest (c-forest) algorithm with a dataset pre-processed by the normalization of features and with up-sampling of the minor class. The method has an overall accuracy of 0.80, an F1-score of 0.73, a sensitivity of 0.76 and a specificity of 0.82 for the independent test set.
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Affiliation(s)
- Rita Melo
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (ao km 139,7), 2695-066 Bobadela LRS, Portugal.
- CNC-Center for Neuroscience and Cell Biology; Rua Larga, Faculdade de Medicina, Polo I, 1ºandar, Universidade de Coimbra, 3004-504 Coimbra, Portugal.
| | - Robert Fieldhouse
- Department of Genetics and Genomics and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - André Melo
- REQUIMTE (Rede de Química e Tecnologia), Faculdade de Ciências da Universidade do Porto, Departamento de Química e Bioquímica, Rua do Campo Alegre, 4169-007 Porto, Portugal.
| | - João D G Correia
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (ao km 139,7), 2695-066 Bobadela LRS, Portugal.
| | - Maria Natália D S Cordeiro
- REQUIMTE (Rede de Química e Tecnologia), Faculdade de Ciências da Universidade do Porto, Departamento de Química e Bioquímica, Rua do Campo Alegre, 4169-007 Porto, Portugal.
| | - Zeynep H Gümüş
- Department of Genetics and Genomics and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Joaquim Costa
- CMUP/FCUP, Centro de Matemática da Universidade do Porto, Faculdade de Ciências, Rua do Campo Alegre, 4169-007 Porto, Portugal.
| | - Alexandre M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Utrecht 3584CH, The Netherlands.
| | - Irina S Moreira
- CNC-Center for Neuroscience and Cell Biology; Rua Larga, Faculdade de Medicina, Polo I, 1ºandar, Universidade de Coimbra, 3004-504 Coimbra, Portugal.
- Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Utrecht 3584CH, The Netherlands.
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16
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Ochoa R, Rodriguez CA, Zuluaga AF. Perspectives for the structure-based design of acetylcholinesterase reactivators. J Mol Graph Model 2016; 68:176-183. [PMID: 27450771 DOI: 10.1016/j.jmgm.2016.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/31/2016] [Accepted: 07/17/2016] [Indexed: 02/03/2023]
Abstract
Rational design of active molecules through structure-based methods has been gaining adepts during the last decades due to the wider availability of protein structures, most of them conjugated with relevant ligands. Acetylcholinesterase (AChE) is a molecular target with a considerable amount of data related to its sequence and 3-dimensional structure. In addition, there are structural insights about the mechanism of action of the natural substrate and drugs used in Alzheimer's disease, organophosphorus compounds, among others. We looked for AChE structural data useful for in silico design of potential interacting molecules. In particular, we focused on information regarding the design of ligands aimed to reactivate AChE catalytic activity. The structures of 178 AChE were annotated and categorized on different subsets according to the nature of the ligand, source organisms and experimental details. We compared sequence homology among the active site from Torpedo californica, Mus musculus and Homo sapiens with the latter two species having the closest relationship (88.9% identity). In addition, the mechanism of organophosphorus binding and the design of effective reactivators are reviewed. A curated data collection obtained with information from several sources was included for researchers working on the field. Finally, a molecular dynamics simulation with human AChE indicated that the catalytic pocket volume stabilizes around 600 Å(3), providing additional clues for drug design.
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Affiliation(s)
- Rodrigo Ochoa
- CIEMTO: Centro de Información y Estudio de Medicamentos y Tóxicos, Departamento de Farmacología y Toxicología, Facultad de Medicina, Universidad de Antioquia, Carrera 51D No. 62-42 Medellín, Colombia.
| | - Carlos A Rodriguez
- CIEMTO: Centro de Información y Estudio de Medicamentos y Tóxicos, Departamento de Farmacología y Toxicología, Facultad de Medicina, Universidad de Antioquia, Carrera 51D No. 62-42 Medellín, Colombia; GRIPE: Grupo Investigador de Problemas en Enfermedades Infecciosas, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
| | - Andres F Zuluaga
- CIEMTO: Centro de Información y Estudio de Medicamentos y Tóxicos, Departamento de Farmacología y Toxicología, Facultad de Medicina, Universidad de Antioquia, Carrera 51D No. 62-42 Medellín, Colombia; GRIPE: Grupo Investigador de Problemas en Enfermedades Infecciosas, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
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17
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Li B, Mendenhall J, Nguyen ED, Weiner BE, Fischer AW, Meiler J. Accurate Prediction of Contact Numbers for Multi-Spanning Helical Membrane Proteins. J Chem Inf Model 2016; 56:423-34. [PMID: 26804342 PMCID: PMC5537626 DOI: 10.1021/acs.jcim.5b00517] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Prediction of the three-dimensional (3D) structures of proteins by computational methods is acknowledged as an unsolved problem. Accurate prediction of important structural characteristics such as contact number is expected to accelerate the otherwise slow progress being made in the prediction of 3D structure of proteins. Here, we present a dropout neural network-based method, TMH-Expo, for predicting the contact number of transmembrane helix (TMH) residues from sequence. Neuronal dropout is a strategy where certain neurons of the network are excluded from back-propagation to prevent co-adaptation of hidden-layer neurons. By using neuronal dropout, overfitting was significantly reduced and performance was noticeably improved. For multi-spanning helical membrane proteins, TMH-Expo achieved a remarkable Pearson correlation coefficient of 0.69 between predicted and experimental values and a mean absolute error of only 1.68. In addition, among those membrane protein-membrane protein interface residues, 76.8% were correctly predicted. Mapping of predicted contact numbers onto structures indicates that contact numbers predicted by TMH-Expo reflect the exposure patterns of TMHs and reveal membrane protein-membrane protein interfaces, reinforcing the potential of predicted contact numbers to be used as restraints for 3D structure prediction and protein-protein docking. TMH-Expo can be accessed via a Web server at www.meilerlab.org .
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Affiliation(s)
- Bian Li
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jeffrey Mendenhall
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Elizabeth Dong Nguyen
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Brian E. Weiner
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Axel W. Fischer
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
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18
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Munteanu CR, Pimenta AC, Fernandez-Lozano C, Melo A, Cordeiro MNDS, Moreira IS. Solvent accessible surface area-based hot-spot detection methods for protein-protein and protein-nucleic acid interfaces. J Chem Inf Model 2015; 55:1077-86. [PMID: 25845030 DOI: 10.1021/ci500760m] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Due to the importance of hot-spots (HS) detection and the efficiency of computational methodologies, several HS detecting approaches have been developed. The current paper presents new models to predict HS for protein-protein and protein-nucleic acid interactions with better statistics compared with the ones currently reported in literature. These models are based on solvent accessible surface area (SASA) and genetic conservation features subjected to simple Bayes networks (protein-protein systems) and a more complex multi-objective genetic algorithm-support vector machine algorithms (protein-nucleic acid systems). The best models for these interactions have been implemented in two free Web tools.
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Affiliation(s)
- Cristian R Munteanu
- †Information and Communication Technologies Department, Computer Science Faculty, University of A Coruna, Campus de Elviña s/n, 15071 A Coruña, Spain
| | - António C Pimenta
- ‡REQUIMTE/Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Carlos Fernandez-Lozano
- †Information and Communication Technologies Department, Computer Science Faculty, University of A Coruna, Campus de Elviña s/n, 15071 A Coruña, Spain
| | - André Melo
- ‡REQUIMTE/Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria N D S Cordeiro
- ‡REQUIMTE/Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Irina S Moreira
- ‡REQUIMTE/Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal.,§CNC-Center for Neuroscience and Cell Biology, Universidade de Coimbra, Rua Larga, FMUC, Polo I, 1°andar, 3004-517 Coimbra, Portugal
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19
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Moreira IS, Martins JM, Coimbra JTS, Ramos MJ, Fernandes PA. A new scoring function for protein-protein docking that identifies native structures with unprecedented accuracy. Phys Chem Chem Phys 2014; 17:2378-87. [PMID: 25490550 DOI: 10.1039/c4cp04688a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein-protein (P-P) 3D structures are fundamental to structural biology and drug discovery. However, most of them have never been determined. Many docking algorithms were developed for that purpose, but they have a very limited accuracy in generating native-like structures and identifying the most correct one, in particular when a single answer is asked for. With such a low success rate it is difficult to point out one docked structure as being native-like. Here we present a new, high accuracy, scoring method to identify the 3D structure of P-P complexes among a set of trial poses. It incorporates alanine scanning mutagenesis experimental data that need to be obtained a priori. The scoring scheme works by matching the computational and the experimental alanine scanning mutagenesis results. The size of the trial P-P interface area is also taken into account. We show that the method ranks the trial structures and identifies the native-like structures with unprecedented accuracy (∼94%), providing the correct P-P 3D structures that biochemists and molecular biologists need to pursue their studies. With such a success rate, the bottleneck of protein-protein docking moves from the scoring to searching algorithms.
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Affiliation(s)
- Irina S Moreira
- REQUIMTE/Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal.
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20
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Pimenta AC, Dourado DFAR, Martins JM, Melo A, Dias Soeiro Cordeiro MN, Almeida RD, Morra G, Moreira IS. Dynamic Structure of NGF and proNGF Complexed with p75NTR: Pro-Peptide Effect. J Chem Inf Model 2014; 54:2051-67. [DOI: 10.1021/ci500101n] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- A. C. Pimenta
- REQUIMTE
Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - D. F. A. R. Dourado
- Department
of Cell and Molecular Biology, Computational and Systems Biology, Uppsala Biomedicinska Centrum BMC, Box 596 751 24, Uppsala, Sweden
| | - J. M. Martins
- REQUIMTE
Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - A. Melo
- REQUIMTE
Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - M. N. Dias Soeiro Cordeiro
- REQUIMTE
Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - R. D. Almeida
- CNC-Center
for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - G. Morra
- Istituto di Chimica
del Riconoscimento Molecolare, CNR, 20131 Milano, Milano, Italy
| | - I. S. Moreira
- REQUIMTE
Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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21
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Liu Q, Hoi SCH, Kwoh CK, Wong L, Li J. Integrating water exclusion theory into β contacts to predict binding free energy changes and binding hot spots. BMC Bioinformatics 2014; 15:57. [PMID: 24568581 PMCID: PMC3941611 DOI: 10.1186/1471-2105-15-57] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 02/19/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Binding free energy and binding hot spots at protein-protein interfaces are two important research areas for understanding protein interactions. Computational methods have been developed previously for accurate prediction of binding free energy change upon mutation for interfacial residues. However, a large number of interrupted and unimportant atomic contacts are used in the training phase which caused accuracy loss. RESULTS This work proposes a new method, βACVASA, to predict the change of binding free energy after alanine mutations. βACVASA integrates accessible surface area (ASA) and our newly defined β contacts together into an atomic contact vector (ACV). A β contact between two atoms is a direct contact without being interrupted by any other atom between them. A β contact's potential contribution to protein binding is also supposed to be inversely proportional to its ASA to follow the water exclusion hypothesis of binding hot spots. Tested on a dataset of 396 alanine mutations, our method is found to be superior in classification performance to many other methods, including Robetta, FoldX, HotPOINT, an ACV method of β contacts without ASA integration, and ACVASA methods (similar to βACVASA but based on distance-cutoff contacts). Based on our data analysis and results, we can draw conclusions that: (i) our method is powerful in the prediction of binding free energy change after alanine mutation; (ii) β contacts are better than distance-cutoff contacts for modeling the well-organized protein-binding interfaces; (iii) β contacts usually are only a small fraction number of the distance-based contacts; and (iv) water exclusion is a necessary condition for a residue to become a binding hot spot. CONCLUSIONS βACVASA is designed using the advantages of both β contacts and water exclusion. It is an excellent tool to predict binding free energy changes and binding hot spots after alanine mutation.
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Affiliation(s)
- Qian Liu
- Advanced Analytics Institute and Center for Health Technologies, Faculty of Engineering and IT, University of Technology, Sydney, Australia
- School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Steven CH Hoi
- School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Chee Keong Kwoh
- School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Limsoon Wong
- School of Computing, National University of Singapore, Singapore 117417, Singapore
| | - Jinyan Li
- Advanced Analytics Institute and Center for Health Technologies, Faculty of Engineering and IT, University of Technology, Sydney, Australia
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