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Qing X, Wang Q, Xu H, Liu P, Lai L. Designing Cyclic-Constrained Peptides to Inhibit Human Phosphoglycerate Dehydrogenase. Molecules 2023; 28:6430. [PMID: 37687259 PMCID: PMC10563079 DOI: 10.3390/molecules28176430] [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: 08/05/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Although loop epitopes at protein-protein binding interfaces often play key roles in mediating oligomer formation and interaction specificity, their binding sites are underexplored as drug targets owing to their high flexibility, relatively few hot spots, and solvent accessibility. Prior attempts to develop molecules that mimic loop epitopes to disrupt protein oligomers have had limited success. In this study, we used structure-based approaches to design and optimize cyclic-constrained peptides based on loop epitopes at the human phosphoglycerate dehydrogenase (PHGDH) dimer interface, which is an obligate homo-dimer with activity strongly dependent on the oligomeric state. The experimental validations showed that these cyclic peptides inhibit PHGDH activity by directly binding to the dimer interface and disrupting the obligate homo-oligomer formation. Our results demonstrate that loop epitope derived cyclic peptides with rationally designed affinity-enhancing substitutions can modulate obligate protein homo-oligomers, which can be used to design peptide inhibitors for other seemingly intractable oligomeric proteins.
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Affiliation(s)
- Xiaoyu Qing
- BNLMS, Peking-Tsinghua Center for Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; (X.Q.); (H.X.); (P.L.)
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China;
| | - Hanyu Xu
- BNLMS, Peking-Tsinghua Center for Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; (X.Q.); (H.X.); (P.L.)
| | - Pei Liu
- BNLMS, Peking-Tsinghua Center for Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; (X.Q.); (H.X.); (P.L.)
| | - Luhua Lai
- BNLMS, Peking-Tsinghua Center for Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; (X.Q.); (H.X.); (P.L.)
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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2
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Abrego J, Sanford-Crane H, Oon C, Xiao X, Betts CB, Sun D, Nagarajan S, Diaz L, Sandborg H, Bhattacharyya S, Xia Z, Coussens LM, Tontonoz P, Sherman MH. A Cancer Cell-Intrinsic GOT2-PPARδ Axis Suppresses Antitumor Immunity. Cancer Discov 2022; 12:2414-2433. [PMID: 35894778 PMCID: PMC9533011 DOI: 10.1158/2159-8290.cd-22-0661] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/10/2022] [Accepted: 07/22/2022] [Indexed: 01/16/2023]
Abstract
Despite significant recent advances in precision medicine, pancreatic ductal adenocarcinoma (PDAC) remains near uniformly lethal. Although immune-modulatory therapies hold promise to meaningfully improve outcomes for patients with PDAC, the development of such therapies requires an improved understanding of the immune evasion mechanisms that characterize the PDAC microenvironment. Here, we show that cancer cell-intrinsic glutamic-oxaloacetic transaminase 2 (GOT2) shapes the immune microenvironment to suppress antitumor immunity. Mechanistically, we find that GOT2 functions beyond its established role in the malate-aspartate shuttle and promotes the transcriptional activity of nuclear receptor peroxisome proliferator-activated receptor delta (PPARδ), facilitated by direct fatty acid binding. Although GOT2 is dispensable for cancer cell proliferation in vivo, the GOT2-PPARδ axis promotes spatial restriction of both CD4+ and CD8+ T cells from the tumor microenvironment. Our results demonstrate a noncanonical function for an established mitochondrial enzyme in transcriptional regulation of immune evasion, which may be exploitable to promote a productive antitumor immune response. SIGNIFICANCE Prior studies demonstrate the important moonlighting functions of metabolic enzymes in cancer. We find that the mitochondrial transaminase GOT2 binds directly to fatty acid ligands that regulate the nuclear receptor PPARδ, and this functional interaction critically regulates the immune microenvironment of pancreatic cancer to promote tumor progression. See related commentary by Nwosu and di Magliano, p. 2237.. This article is highlighted in the In This Issue feature, p. 2221.
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Affiliation(s)
- Jaime Abrego
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Hannah Sanford-Crane
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Chet Oon
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Xu Xiao
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Courtney B. Betts
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Duanchen Sun
- Computational Biology Program, Oregon Health & Science University, Portland, Oregon
| | - Shanthi Nagarajan
- Medicinal Chemistry Core, Oregon Health & Science University, Portland, Oregon
| | - Luis Diaz
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Holly Sandborg
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Sohinee Bhattacharyya
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Zheng Xia
- Computational Biology Program, Oregon Health & Science University, Portland, Oregon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Lisa M. Coussens
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Peter Tontonoz
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, California
| | - Mara H. Sherman
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
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3
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Skolnick J, Zhou H. Implications of the Essential Role of Small Molecule Ligand Binding Pockets in Protein-Protein Interactions. J Phys Chem B 2022; 126:6853-6867. [PMID: 36044742 PMCID: PMC9484464 DOI: 10.1021/acs.jpcb.2c04525] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/18/2022] [Indexed: 11/28/2022]
Abstract
Protein-protein interactions (PPIs) and protein-metabolite interactions play a key role in many biochemical processes, yet they are often viewed as being independent. However, the fact that small molecule drugs have been successful in inhibiting PPIs suggests a deeper relationship between protein pockets that bind small molecules and PPIs. We demonstrate that 2/3 of PPI interfaces, including antibody-epitope interfaces, contain at least one significant small molecule ligand binding pocket. In a representative library of 50 distinct protein-protein interactions involving hundreds of mutations, >75% of hot spot residues overlap with small molecule ligand binding pockets. Hence, ligand binding pockets play an essential role in PPIs. In representative cases, evolutionary unrelated monomers that are involved in different multimeric interactions yet share the same pocket are predicted to bind the same metabolites/drugs; these results are confirmed by examples in the PDB. Thus, the binding of a metabolite can shift the equilibrium between monomers and multimers. This implicit coupling of PPI equilibria, termed "metabolic entanglement", was successfully employed to suggest novel functional relationships among protein multimers that do not directly interact. Thus, the current work provides an approach to unify metabolomics and protein interactomics.
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Affiliation(s)
- Jeffrey Skolnick
- Center for the Study of Systems
Biology, School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, NW, Atlanta, Georgia 30332, United States
| | - Hongyi Zhou
- Center for the Study of Systems
Biology, School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, NW, Atlanta, Georgia 30332, United States
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4
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Ricci F, Gitto R, Pitasi G, De Luca L. In Silico Insights towards the Identification of SARS-CoV-2 NSP13 Helicase Druggable Pockets. Biomolecules 2022; 12:biom12040482. [PMID: 35454070 PMCID: PMC9029846 DOI: 10.3390/biom12040482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
The merging of distinct computational approaches has become a powerful strategy for discovering new biologically active compounds. By using molecular modeling, significant efforts have recently resulted in the development of new molecules, demonstrating high efficiency in reducing the replication of severe acute respiratory coronavirus 2 (SARS-CoV-2), the agent responsible for the COVID-19 pandemic. We have focused our interest on non-structural protein Nsp13 (NTPase/helicase), as a crucial protein, embedded in the replication–transcription complex (RTC), that controls the virus life cycle. To assist in the identification of the most druggable surfaces of Nsps13, we applied a combination of four computational tools: FTMap, SiteMap, Fpocket and LigandScout. These software packages explored the binding sites for different three-dimensional structures of RTC complexes (PDB codes: 6XEZ, 7CXM, 7CXN), thus, detecting several hot spots, that were clustered to obtain ensemble consensus sites, through a combination of four different approaches. The comparison of data provided new insights about putative druggable sites that might be employed for further docking simulations on druggable surfaces of Nsps13, in a scenario of repurposing drugs.
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Abstract
![]()
The coronavirus disease 2019 (COVID-19)
pandemic has a significant
impact on healthcare systems and our lives. Vaccines against severe
acute respiratory syndrome coronavirus 2 (SARS-CoV-2) provide protection
against SARS-CoV-2. However, mutations in the viral genome are common,
raising concerns about the effectiveness of existing vaccines for
SARS-CoV-2. The receptor-binding domain (RBD) of SARS-CoV-2 uses angiotensin-converting
enzyme-2 (ACE-2) as a gateway to enter host cells. Therefore, the
ACE-2-RBD interaction may be targeted by antiviral drugs. In this
context, allosteric modulation of ACE-2 may offer a promising approach.
It may lead to allosteric inhibition of the interaction between ACE-2
and SARS-CoV-2.
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Affiliation(s)
- Kunal Dutta
- Department of Human Physiology, Vidyasagar University, Midnapore, 721102 West Bengal, India
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6
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Abstract
We studied the molecular details of the recognition of antigens by the variable domain of their cognate antibodies in as well as those elicited by the constant domains, which do not directly interact with antigens. Such effects are difficult to study experimentally; however, molecular dynamics simulations and subsequent residue interaction network analysis provide insight into the allosteric communication between the antigen-binding CDR region and the constant domain. We performed MD simulations of the complex of Fab and prion-associated peptide in the apo and bound forms and follow the conformational changes in the antibody and cross-talk between its subunits and with antigens. These protocols could be generally applied for studies of other antigens-antibody recognition systems.
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Affiliation(s)
- Jun Zhao
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, USA
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, USA
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, USA.
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7
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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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8
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Abstract
Protein function can be allosterically regulated by changes in structure or dynamics. PDZ domains are classic examples for studies of allostery in single protein domains. However, PDZ domains are often found in multidomain proteins; in particular, PDZ3 is located in a supramodule containing three domains. The allosteric network in PDZ3 has never been studied in the presence of the adjacent domains. Here we map the allosteric network for a PDZ3:ligand complex, both in isolation and in the context of a supramodule. We demonstrate that the allosteric network is highly dependent on this supertertiary structure, with broad implications for studies of allostery in single domains. The notion that protein function is allosterically regulated by structural or dynamic changes in proteins has been extensively investigated in several protein domains in isolation. In particular, PDZ domains have represented a paradigm for these studies, despite providing conflicting results. Furthermore, it is still unknown how the association between protein domains in supramodules, consitituting so-called supertertiary structures, affects allosteric networks. Here, we experimentally mapped the allosteric network in a PDZ:ligand complex, both in isolation and in the context of a supramodular structure, and show that allosteric networks in a PDZ domain are highly dependent on the supertertiary structure in which they are present. This striking sensitivity of allosteric networks to the presence of adjacent protein domains is likely a common property of supertertiary structures in proteins. Our findings have general implications for prediction of allosteric networks from primary and tertiary structures and for quantitative descriptions of allostery.
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9
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Singh AK, Wadsworth PA, Tapia CM, Aceto G, Ali SR, Chen H, D'Ascenzo M, Zhou J, Laezza F. Mapping of the FGF14:Nav1.6 complex interface reveals FLPK as a functionally active peptide modulating excitability. Physiol Rep 2020; 8:e14505. [PMID: 32671946 PMCID: PMC7363588 DOI: 10.14814/phy2.14505] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 02/07/2023] Open
Abstract
The voltage-gated sodium (Nav) channel complex is comprised of pore-forming α subunits (Nav1.1-1.9) and accessory regulatory proteins such as the intracellular fibroblast growth factor 14 (FGF14). The cytosolic Nav1.6 C-terminal tail binds directly to FGF14 and this interaction modifies Nav1.6-mediated currents with effects on intrinsic excitability in the brain. Previous studies have identified the FGF14V160 residue within the FGF14 core domain as a hotspot for the FGF14:Nav1.6 complex formation. Here, we used three short amino acid peptides around FGF14V160 to probe for the FGF14 interaction with the Nav1.6 C-terminal tail and to evaluate the activity of the peptide on Nav1.6-mediated currents. In silico docking predicts FLPK to bind to FGF14V160 with the expectation of interfering with the FGF14:Nav1.6 complex formation, a phenotype that was confirmed by the split-luciferase assay (LCA) and surface plasmon resonance (SPR), respectively. Whole-cell patch-clamp electrophysiology studies demonstrate that FLPK is able to prevent previously reported FGF14-dependent phenotypes of Nav1.6 currents, but that its activity requires the FGF14 N-terminal tail, a domain that has been shown to contribute to Nav1.6 inactivation independently from the FGF14 core domain. In medium spiny neurons in the nucleus accumbens, where both FGF14 and Nav1.6 are abundantly expressed, FLPK significantly increased firing frequency by a mechanism consistent with the ability of the tetrapeptide to interfere with Nav1.6 inactivation and potentiate persistent Na+ currents. Taken together, these results indicate that FLPK might serve as a probe for characterizing molecular determinants of neuronal excitability and a peptide scaffold to develop allosteric modulators of Nav channels.
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Affiliation(s)
- Aditya K. Singh
- Department of Pharmacology & ToxicologyUniversità Cattolica del Sacro CuoreRomeItaly
| | - Paul A. Wadsworth
- Department of Pharmacology & ToxicologyUniversità Cattolica del Sacro CuoreRomeItaly
- M.D.‐Ph.D. Combined Degree ProgramUniversità Cattolica del Sacro CuoreRomeItaly
- Biochemistry and Molecular Biology Graduate ProgramUniversità Cattolica del Sacro CuoreRomeItaly
| | - Cynthia M. Tapia
- Department of Pharmacology & ToxicologyUniversità Cattolica del Sacro CuoreRomeItaly
- NIEHS Environmental Toxicology Training ProgramUniversità Cattolica del Sacro CuoreRomeItaly
| | - Giuseppe Aceto
- Institute of Human PhysiologyUniversità Cattolica del Sacro CuoreRomeItaly
- Department of NeuroscienceUniversità Cattolica del Sacro CuoreRomeItaly
- Fondazione Policlinico Universitario A. GemelliIRCCSRomeItaly
| | - Syed R. Ali
- Department of Pharmacology & ToxicologyUniversità Cattolica del Sacro CuoreRomeItaly
| | - Haiying Chen
- Department of Pharmacology & ToxicologyUniversità Cattolica del Sacro CuoreRomeItaly
| | - Marcello D'Ascenzo
- Institute of Human PhysiologyUniversità Cattolica del Sacro CuoreRomeItaly
- Department of NeuroscienceUniversità Cattolica del Sacro CuoreRomeItaly
- Fondazione Policlinico Universitario A. GemelliIRCCSRomeItaly
| | - Jia Zhou
- Department of Pharmacology & ToxicologyUniversità Cattolica del Sacro CuoreRomeItaly
- Center for Addiction ResearchUniversity of Texas Medical BranchGalvestonTXUSA
| | - Fernanda Laezza
- Department of Pharmacology & ToxicologyUniversità Cattolica del Sacro CuoreRomeItaly
- Center for Addiction ResearchUniversity of Texas Medical BranchGalvestonTXUSA
- Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTXUSA
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10
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Bera I, Payghan PV. Use of Molecular Dynamics Simulations in Structure-Based Drug Discovery. Curr Pharm Des 2020; 25:3339-3349. [PMID: 31480998 DOI: 10.2174/1381612825666190903153043] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/01/2019] [Indexed: 12/31/2022]
Abstract
BACKGROUND Traditional drug discovery is a lengthy process which involves a huge amount of resources. Modern-day drug discovers various multidisciplinary approaches amongst which, computational ligand and structure-based drug designing methods contribute significantly. Structure-based drug designing techniques require the knowledge of structural information of drug target and drug-target complexes. Proper understanding of drug-target binding requires the flexibility of both ligand and receptor to be incorporated. Molecular docking refers to the static picture of the drug-target complex(es). Molecular dynamics, on the other hand, introduces flexibility to understand the drug binding process. OBJECTIVE The aim of the present study is to provide a systematic review on the usage of molecular dynamics simulations to aid the process of structure-based drug design. METHOD This review discussed findings from various research articles and review papers on the use of molecular dynamics in drug discovery. All efforts highlight the practical grounds for which molecular dynamics simulations are used in drug designing program. In summary, various aspects of the use of molecular dynamics simulations that underline the basis of studying drug-target complexes were thoroughly explained. RESULTS This review is the result of reviewing more than a hundred papers. It summarizes various problems that use molecular dynamics simulations. CONCLUSION The findings of this review highlight how molecular dynamics simulations have been successfully implemented to study the structure-function details of specific drug-target complexes. It also identifies the key areas such as stability of drug-target complexes, ligand binding kinetics and identification of allosteric sites which have been elucidated using molecular dynamics simulations.
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Affiliation(s)
- Indrani Bera
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, United States
| | - Pavan V Payghan
- Structural Biology and Bioinformatics Department, CSIR-IICB, Kolkata, India.,Department of Pharmaceutical Sciences, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, WA, United States
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11
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Serapian SA, Colombo G. Designing Molecular Spanners to Throw in the Protein Networks. Chemistry 2020; 26:4656-4670. [DOI: 10.1002/chem.201904523] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/18/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Stefano A. Serapian
- Department of ChemistryUniversity of Pavia Via Taramelli 12 27100 Pavia Italy
| | - Giorgio Colombo
- Department of ChemistryUniversity of Pavia Via Taramelli 12, 27 100 Pavia Italy
- SCITEC-CNR Via Mario Bianco 9 20131 Milano Italy
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12
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Díaz L, Soler D, Tresadern G, Buyck C, Perez-Benito L, Saen-Oon S, Guallar V, Soliva R. Monte Carlo simulations using PELE to identify a protein-protein inhibitor binding site and pose. RSC Adv 2020; 10:7058-7064. [PMID: 35493910 PMCID: PMC9049779 DOI: 10.1039/d0ra01127d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/06/2020] [Indexed: 12/18/2022] Open
Abstract
In silico binding site location and pose prediction for a molecule targeted at a large protein surface is a challenging task. We report a blind test with two peptidomimetic molecules that bind the flu virus hemagglutinin (HA) surface antigen, JNJ7918 and JNJ4796 (recently disclosed in van Dongen et al., Science, 2019, 363). Tests with a series of conventional approaches such as rigid (receptor) docking against available X-ray crystal structures or against an ensemble of structures generated by quick methodologies (NMA, homology modeling) gave mixed results, due to the shallowness and flexibility of the binding site and the sheer size of the target. However, tests with our Monte Carlo platform PELE in two protocols involving either exploration of the whole protein surface (global exploration), or the latter followed by refinement of best solutions (local exploration) yielded remarkably good results by locating the actual binding site and generating binding modes that recovered all native contacts found in the X-ray structures. Thus, the Monte Carlo scheme of PELE seems promising as a quick methodology to overcome the challenge of identifying entirely unknown binding sites and modes for protein–protein disruptors. PELE prospectively unveils the binding site and mode of a protein–protein disruptor.![]()
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Affiliation(s)
- Lucía Díaz
- Nostrum Biodiscovery Jordi Girona 29, Nexus II D128 08034 Barcelona Spain
| | - Daniel Soler
- Nostrum Biodiscovery Jordi Girona 29, Nexus II D128 08034 Barcelona Spain
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V. Turnhoutseweg 30, B-2340 Beerse Belgium
| | - Christophe Buyck
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V. Turnhoutseweg 30, B-2340 Beerse Belgium
| | - Laura Perez-Benito
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V. Turnhoutseweg 30, B-2340 Beerse Belgium
| | - Suwipa Saen-Oon
- Nostrum Biodiscovery Jordi Girona 29, Nexus II D128 08034 Barcelona Spain
| | - Victor Guallar
- Barcelona Supercomputing Center, Join IRB-BSC Program in Computational Biology Spain.,ICREA Passeig Lluís Companys 23 E-08010 Barcelona Spain
| | - Robert Soliva
- Nostrum Biodiscovery Jordi Girona 29, Nexus II D128 08034 Barcelona Spain
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13
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Trinh HC, Kwon YK. RMut: R package for a Boolean sensitivity analysis against various types of mutations. PLoS One 2019; 14:e0213736. [PMID: 30889216 PMCID: PMC6424452 DOI: 10.1371/journal.pone.0213736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 02/27/2019] [Indexed: 12/13/2022] Open
Abstract
There have been many in silico studies based on a Boolean network model to investigate network sensitivity against gene or interaction mutations. However, there are no proper tools to examine the network sensitivity against many different types of mutations, including user-defined ones. To address this issue, we developed RMut, which is an R package to analyze the Boolean network-based sensitivity by efficiently employing not only many well-known node-based and edgetic mutations but also novel user-defined mutations. In addition, RMut can specify the mutation area and the duration time for more precise analysis. RMut can be used to analyze large-scale networks because it is implemented in a parallel algorithm using the OpenCL library. In the first case study, we observed that the real biological networks were most sensitive to overexpression/state-flip and edge-addition/-reverse mutations among node-based and edgetic mutations, respectively. In the second case study, we showed that edgetic mutations can predict drug-targets better than node-based mutations. Finally, we examined the network sensitivity to double edge-removal mutations and found an interesting synergistic effect. Taken together, these findings indicate that RMut is a flexible R package to efficiently analyze network sensitivity to various types of mutations. RMut is available at https://github.com/csclab/RMut.
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Affiliation(s)
- Hung-Cuong Trinh
- Faculty of Information Technology, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Yung-Keun Kwon
- Department of Electrical/Electronic and Computer Engineering, University of Ulsan, Nam-gu, Ulsan, Korea
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14
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Petit AP, Garcia-Petit C, Bueren-Calabuig JA, Vuillard LM, Ferry G, Boutin JA. A structural study of the complex between neuroepithelial cell transforming gene 1 (Net1) and RhoA reveals a potential anticancer drug hot spot. J Biol Chem 2018; 293:9064-9077. [PMID: 29695506 DOI: 10.1074/jbc.ra117.001123] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/18/2018] [Indexed: 12/20/2022] Open
Abstract
The GTPase RhoA is a major player in many different regulatory pathways. RhoA catalyzes GTP hydrolysis, and its catalysis is accelerated when RhoA forms heterodimers with proteins of the guanine nucleotide exchange factor (GEF) family. Neuroepithelial cell transforming gene 1 (Net1) is a RhoA-interacting GEF implicated in cancer, but the structural features supporting the RhoA/Net1 interaction are unknown. Taking advantage of a simple production and purification process, here we solved the structure of a RhoA/Net1 heterodimer with X-ray crystallography at 2-Å resolution. Using a panel of several techniques, including molecular dynamics simulations, we characterized the RhoA/Net1 interface. Moreover, deploying an extremely simple peptide-based scanning approach, we found that short peptides (penta- to nonapeptides) derived from the protein/protein interaction region of RhoA could disrupt the RhoA/Net1 interaction and thereby diminish the rate of nucleotide exchange. The most inhibitory peptide, EVKHF, spanning residues 102-106 in the RhoA sequence, displayed an IC50 of ∼100 μm without further modifications. The peptides identified here could be useful in further investigations of the RhoA/Net1 interaction region. We propose that our structural and functional insights might inform chemical approaches for transforming the pentapeptide into an optimized pseudopeptide that antagonizes Net1-mediated RhoA activation with therapeutic anticancer potential.
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Affiliation(s)
- Alain-Pierre Petit
- From the Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery and
| | - Christel Garcia-Petit
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom and
| | | | - Laurent M Vuillard
- Pôle d'Expertise Biotechnologie, Chimie, Biologie, Institut de Recherches SERVIER, 78290 Croissy-sur-Seine, France
| | - Gilles Ferry
- Pôle d'Expertise Biotechnologie, Chimie, Biologie, Institut de Recherches SERVIER, 78290 Croissy-sur-Seine, France
| | - Jean A Boutin
- Pôle d'Expertise Biotechnologie, Chimie, Biologie, Institut de Recherches SERVIER, 78290 Croissy-sur-Seine, France
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15
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Akbar R, Helms V. ALLO: A tool to discriminate and prioritize allosteric pockets. Chem Biol Drug Des 2018; 91:845-853. [DOI: 10.1111/cbdd.13161] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 11/05/2017] [Accepted: 12/01/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Rahmad Akbar
- Center for Bioinformatics; Saarland University; Saarbruecken Germany
| | - Volkhard Helms
- Center for Bioinformatics; Saarland University; Saarbruecken Germany
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16
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Sahlgren C, Meinander A, Zhang H, Cheng F, Preis M, Xu C, Salminen TA, Toivola D, Abankwa D, Rosling A, Karaman DŞ, Salo-Ahen OMH, Österbacka R, Eriksson JE, Willför S, Petre I, Peltonen J, Leino R, Johnson M, Rosenholm J, Sandler N. Tailored Approaches in Drug Development and Diagnostics: From Molecular Design to Biological Model Systems. Adv Healthc Mater 2017; 6. [PMID: 28892296 DOI: 10.1002/adhm.201700258] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 05/04/2017] [Indexed: 12/13/2022]
Abstract
Approaches to increase the efficiency in developing drugs and diagnostics tools, including new drug delivery and diagnostic technologies, are needed for improved diagnosis and treatment of major diseases and health problems such as cancer, inflammatory diseases, chronic wounds, and antibiotic resistance. Development within several areas of research ranging from computational sciences, material sciences, bioengineering to biomedical sciences and bioimaging is needed to realize innovative drug development and diagnostic (DDD) approaches. Here, an overview of recent progresses within key areas that can provide customizable solutions to improve processes and the approaches taken within DDD is provided. Due to the broadness of the area, unfortunately all relevant aspects such as pharmacokinetics of bioactive molecules and delivery systems cannot be covered. Tailored approaches within (i) bioinformatics and computer-aided drug design, (ii) nanotechnology, (iii) novel materials and technologies for drug delivery and diagnostic systems, and (iv) disease models to predict safety and efficacy of medicines under development are focused on. Current developments and challenges ahead are discussed. The broad scope reflects the multidisciplinary nature of the field of DDD and aims to highlight the convergence of biological, pharmaceutical, and medical disciplines needed to meet the societal challenges of the 21st century.
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Affiliation(s)
- Cecilia Sahlgren
- Faculty of Science and Engineering; Cell Biology; Åbo Akademi University; FI-20520 Turku Finland
- Turku Centre for Biotechnology; Åbo Akademi University and University of Turku; FI-20520 Turku Finland
- Department of Biomedical Engineering; Technical University of Eindhoven; 5613 DR Eindhoven Netherlands
| | - Annika Meinander
- Faculty of Science and Engineering; Cell Biology; Åbo Akademi University; FI-20520 Turku Finland
| | - Hongbo Zhang
- Faculty of Science and Engineering; Pharmaceutical Sciences Laboratory; Åbo Akademi University; FI-20520 Turku Finland
| | - Fang Cheng
- Faculty of Science and Engineering; Cell Biology; Åbo Akademi University; FI-20520 Turku Finland
| | - Maren Preis
- Faculty of Science and Engineering; Pharmaceutical Sciences Laboratory; Åbo Akademi University; FI-20520 Turku Finland
| | - Chunlin Xu
- Faculty of Science and Engineering; Natural Materials Technology; Åbo Akademi University; FI-20500 Turku Finland
| | - Tiina A. Salminen
- Faculty of Science and Engineering; Structural Bioinformatics Laboratory; Åbo Akademi University; FI-20520 Turku Finland
| | - Diana Toivola
- Faculty of Science and Engineering; Cell Biology; Åbo Akademi University; FI-20520 Turku Finland
- Turku Center for Disease Modeling; University of Turku; FI-20520 Turku Finland
| | - Daniel Abankwa
- Department of Biomedical Engineering; Technical University of Eindhoven; 5613 DR Eindhoven Netherlands
| | - Ari Rosling
- Faculty of Science and Engineering; Polymer Technologies; Åbo Akademi University; FI-20500 Turku Finland
| | - Didem Şen Karaman
- Faculty of Science and Engineering; Pharmaceutical Sciences Laboratory; Åbo Akademi University; FI-20520 Turku Finland
| | - Outi M. H. Salo-Ahen
- Faculty of Science and Engineering; Pharmaceutical Sciences Laboratory; Åbo Akademi University; FI-20520 Turku Finland
- Faculty of Science and Engineering; Structural Bioinformatics Laboratory; Åbo Akademi University; FI-20520 Turku Finland
| | - Ronald Österbacka
- Faculty of Science and Engineering; Physics; Åbo Akademi University; FI-20500 Turku Finland
| | - John E. Eriksson
- Faculty of Science and Engineering; Cell Biology; Åbo Akademi University; FI-20520 Turku Finland
- Turku Centre for Biotechnology; Åbo Akademi University and University of Turku; FI-20520 Turku Finland
| | - Stefan Willför
- Faculty of Science and Engineering; Natural Materials Technology; Åbo Akademi University; FI-20500 Turku Finland
| | - Ion Petre
- Faculty of Science and Engineering; Computer Science; Åbo Akademi University; FI-20500 Turku Finland
| | - Jouko Peltonen
- Faculty of Science and Engineering; Physical Chemistry; Åbo Akademi University; FI-20500 Turku Finland
| | - Reko Leino
- Faculty of Science and Engineering; Organic Chemistry; Johan Gadolin Process Chemistry Centre; Åbo Akademi University; FI-20500 Turku Finland
| | - Mark Johnson
- Faculty of Science and Engineering; Structural Bioinformatics Laboratory; Åbo Akademi University; FI-20520 Turku Finland
| | - Jessica Rosenholm
- Faculty of Science and Engineering; Pharmaceutical Sciences Laboratory; Åbo Akademi University; FI-20520 Turku Finland
| | - Niklas Sandler
- Faculty of Science and Engineering; Pharmaceutical Sciences Laboratory; Åbo Akademi University; FI-20520 Turku Finland
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17
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Sahlgren C, Meinander A, Zhang H, Cheng F, Preis M, Xu C, Salminen TA, Toivola D, Abankwa D, Rosling A, Karaman DŞ, Salo-Ahen OMH, Österbacka R, Eriksson JE, Willför S, Petre I, Peltonen J, Leino R, Johnson M, Rosenholm J, Sandler N. Tailored Approaches in Drug Development and Diagnostics: From Molecular Design to Biological Model Systems. Adv Healthc Mater 2017. [DOI: 10.1002/adhm.201700258 10.1002/adhm.201700258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Affiliation(s)
- Cecilia Sahlgren
- Faculty of Science and Engineering; Cell Biology; Åbo Akademi University; FI-20520 Turku Finland
- Turku Centre for Biotechnology; Åbo Akademi University and University of Turku; FI-20520 Turku Finland
- Department of Biomedical Engineering; Technical University of Eindhoven; 5613 DR Eindhoven Netherlands
| | - Annika Meinander
- Faculty of Science and Engineering; Cell Biology; Åbo Akademi University; FI-20520 Turku Finland
| | - Hongbo Zhang
- Faculty of Science and Engineering; Pharmaceutical Sciences Laboratory; Åbo Akademi University; FI-20520 Turku Finland
| | - Fang Cheng
- Faculty of Science and Engineering; Cell Biology; Åbo Akademi University; FI-20520 Turku Finland
| | - Maren Preis
- Faculty of Science and Engineering; Pharmaceutical Sciences Laboratory; Åbo Akademi University; FI-20520 Turku Finland
| | - Chunlin Xu
- Faculty of Science and Engineering; Natural Materials Technology; Åbo Akademi University; FI-20500 Turku Finland
| | - Tiina A. Salminen
- Faculty of Science and Engineering; Structural Bioinformatics Laboratory; Åbo Akademi University; FI-20520 Turku Finland
| | - Diana Toivola
- Faculty of Science and Engineering; Cell Biology; Åbo Akademi University; FI-20520 Turku Finland
- Turku Center for Disease Modeling; University of Turku; FI-20520 Turku Finland
| | - Daniel Abankwa
- Department of Biomedical Engineering; Technical University of Eindhoven; 5613 DR Eindhoven Netherlands
| | - Ari Rosling
- Faculty of Science and Engineering; Polymer Technologies; Åbo Akademi University; FI-20500 Turku Finland
| | - Didem Şen Karaman
- Faculty of Science and Engineering; Pharmaceutical Sciences Laboratory; Åbo Akademi University; FI-20520 Turku Finland
| | - Outi M. H. Salo-Ahen
- Faculty of Science and Engineering; Pharmaceutical Sciences Laboratory; Åbo Akademi University; FI-20520 Turku Finland
- Faculty of Science and Engineering; Structural Bioinformatics Laboratory; Åbo Akademi University; FI-20520 Turku Finland
| | - Ronald Österbacka
- Faculty of Science and Engineering; Physics; Åbo Akademi University; FI-20500 Turku Finland
| | - John E. Eriksson
- Faculty of Science and Engineering; Cell Biology; Åbo Akademi University; FI-20520 Turku Finland
- Turku Centre for Biotechnology; Åbo Akademi University and University of Turku; FI-20520 Turku Finland
| | - Stefan Willför
- Faculty of Science and Engineering; Natural Materials Technology; Åbo Akademi University; FI-20500 Turku Finland
| | - Ion Petre
- Faculty of Science and Engineering; Computer Science; Åbo Akademi University; FI-20500 Turku Finland
| | - Jouko Peltonen
- Faculty of Science and Engineering; Physical Chemistry; Åbo Akademi University; FI-20500 Turku Finland
| | - Reko Leino
- Faculty of Science and Engineering; Organic Chemistry; Johan Gadolin Process Chemistry Centre; Åbo Akademi University; FI-20500 Turku Finland
| | - Mark Johnson
- Faculty of Science and Engineering; Structural Bioinformatics Laboratory; Åbo Akademi University; FI-20520 Turku Finland
| | - Jessica Rosenholm
- Faculty of Science and Engineering; Pharmaceutical Sciences Laboratory; Åbo Akademi University; FI-20520 Turku Finland
| | - Niklas Sandler
- Faculty of Science and Engineering; Pharmaceutical Sciences Laboratory; Åbo Akademi University; FI-20520 Turku Finland
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18
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Molecular Dynamics Simulations and Dynamic Network Analysis Reveal the Allosteric Unbinding of Monobody to H-Ras Triggered by R135K Mutation. Int J Mol Sci 2017; 18:ijms18112249. [PMID: 29072601 PMCID: PMC5713219 DOI: 10.3390/ijms18112249] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/13/2017] [Accepted: 10/24/2017] [Indexed: 12/12/2022] Open
Abstract
Ras proteins, as small GTPases, mediate cell proliferation, survival and differentiation. Ras mutations have been associated with a broad spectrum of human cancers and thus targeting Ras represents a potential way forward for cancer therapy. A recently reported monobody NS1 allosterically disrupts the Ras-mediated signaling pathway, but its efficacy is reduced by R135K mutation in H-Ras. However, the detailed mechanism is unresolved. Here, using molecular dynamics (MD) simulations and dynamic network analysis, we explored the molecular mechanism for the unbinding of NS1 to H-Ras and shed light on the underlying allosteric network in H-Ras. MD simulations revealed that the overall structures of the two complexes did not change significantly, but the H-Ras–NS1 interface underwent significant conformational alteration in the mutant Binding free energy analysis showed that NS1 binding was unfavored after R135K mutation, which resulted in the unfavorable binding of NS1. Furthermore, the critical residues on H-Ras responsible for the loss of binding of NS1 were identified. Importantly, the allosteric networks for these important residues were revealed, which yielded a novel insight into the allosteric regulatory mechanism of H-Ras.
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19
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Comparing atom-based with residue-based descriptors in predicting binding site similarity: do backbone atoms matter? Future Med Chem 2016; 8:1871-1885. [PMID: 27629811 DOI: 10.4155/fmc-2016-0077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
AIM We question the level of detail required in protein 3D-representation to detect site similarity which is relevant for polypharmacology prediction. RESULTS We modified the in-house program SiteAlign to replace generic pharmacophoric descriptors of cavity-lining amino acids by descriptors accounting for solvent exposure. Benchmarking the novel, atom-based, method (SiteAlign2) revealed no global improvement of performance. However, in the rare cases of no sequence or global structure similarities between the compared proteins, SiteAlign2 was more successful if backbone atoms are key determinants of ligand binding. CONCLUSION SiteAlign suits the comparison of binding sites for close or distant homologs. SiteAlign2 provides a better insight into the physical model of site similarity between nonhomologs, but at the expense of an increased sensitivity to atomic coordinates.
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20
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Wei G, Xi W, Nussinov R, Ma B. Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell. Chem Rev 2016; 116:6516-51. [PMID: 26807783 PMCID: PMC6407618 DOI: 10.1021/acs.chemrev.5b00562] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
All soluble proteins populate conformational ensembles that together constitute the native state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the distributions of the states on the energy landscape are determined by statistical thermodynamics; however, they are optimized to perform their biological functions. In this review we briefly describe advances in free energy landscape studies of protein conformational ensembles. Experimental (nuclear magnetic resonance, small-angle X-ray scattering, single-molecule spectroscopy, and cryo-electron microscopy) and computational (replica-exchange molecular dynamics, metadynamics, and Markov state models) approaches have made great progress in recent years. These address the challenging characterization of the highly flexible and heterogeneous protein ensembles. We focus on structural aspects of protein conformational distributions, from collective motions of single- and multi-domain proteins, intrinsically disordered proteins, to multiprotein complexes. Importantly, we highlight recent studies that illustrate functional adjustment of protein conformational ensembles in the crowded cellular environment. We center on the role of the ensemble in recognition of small- and macro-molecules (protein and RNA/DNA) and emphasize emerging concepts of protein dynamics in enzyme catalysis. Overall, protein ensembles link fundamental physicochemical principles and protein behavior and the cellular network and its regulation.
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Affiliation(s)
- Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China
| | - Wenhui Xi
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
- Sackler Inst. of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
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21
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Wagner JR, Lee CT, Durrant JD, Malmstrom RD, Feher VA, Amaro RE. Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. Chem Rev 2016; 116:6370-90. [PMID: 27074285 PMCID: PMC4901368 DOI: 10.1021/acs.chemrev.5b00631] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Allosteric drug development holds
promise for delivering medicines
that are more selective and less toxic than those that target orthosteric
sites. To date, the discovery of allosteric binding sites and lead
compounds has been mostly serendipitous, achieved through high-throughput
screening. Over the past decade, structural data has become more readily
available for larger protein systems and more membrane protein classes
(e.g., GPCRs and ion channels), which are common allosteric drug targets.
In parallel, improved simulation methods now provide better atomistic
understanding of the protein dynamics and cooperative motions that
are critical to allosteric mechanisms. As a result of these advances,
the field of predictive allosteric drug development is now on the
cusp of a new era of rational structure-based computational methods.
Here, we review algorithms that predict allosteric sites based on
sequence data and molecular dynamics simulations, describe tools that
assess the druggability of these pockets, and discuss how Markov state
models and topology analyses provide insight into the relationship
between protein dynamics and allosteric drug binding. In each section,
we first provide an overview of the various method classes before
describing relevant algorithms and software packages.
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Affiliation(s)
- Jeffrey R Wagner
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
| | - Christopher T Lee
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
| | - Jacob D Durrant
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
| | - Robert D Malmstrom
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
| | - Victoria A Feher
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
| | - Rommie E Amaro
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
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22
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Hu G, Xiao F, Li Y, Li Y, Vongsangnak W. Protein-Protein Interface and Disease: Perspective from Biomolecular Networks. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 160:57-74. [PMID: 27928579 DOI: 10.1007/10_2016_40] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions are involved in many important biological processes and molecular mechanisms of disease association. Structural studies of interfacial residues in protein complexes provide information on protein-protein interactions. Characterizing protein-protein interfaces, including binding sites and allosteric changes, thus pose an imminent challenge. With special focus on protein complexes, approaches based on network theory are proposed to meet this challenge. In this review we pay attention to protein-protein interfaces from the perspective of biomolecular networks and their roles in disease. We first describe the different roles of protein complexes in disease through several structural aspects of interfaces. We then discuss some recent advances in predicting hot spots and communication pathway analysis in terms of amino acid networks. Finally, we highlight possible future aspects of this area with respect to both methodology development and applications for disease treatment.
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Affiliation(s)
- Guang Hu
- Center for Systems Biology, School of Electronic and Information Engineering, Soochow University, Suzhou, 215006, China.
| | - Fei Xiao
- School of Basic Medicine and Biological Sciences, Medical College of Soochow University, Suzhou, 215123, China
| | - Yuqian Li
- School of Electronic Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Yuan Li
- Center for Systems Biology, School of Electronic and Information Engineering, Soochow University, Suzhou, 215006, China
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
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23
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Maheshwari S, Brylinski M. Template-based identification of protein–protein interfaces using eFindSitePPI. Methods 2016; 93:64-71. [DOI: 10.1016/j.ymeth.2015.07.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/12/2015] [Accepted: 07/29/2015] [Indexed: 11/26/2022] Open
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24
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Xie L, Bourne PE. Developing multi-target therapeutics to fine-tune the evolutionary dynamics of the cancer ecosystem. Front Pharmacol 2015; 6:209. [PMID: 26441664 PMCID: PMC4585080 DOI: 10.3389/fphar.2015.00209] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/07/2015] [Indexed: 12/12/2022] Open
Affiliation(s)
- Lei Xie
- Department of Computer Science, Hunter College, The City University of New York New York, NY, USA ; The Graduate Center, The City University of New York New York, NY, USA
| | - Philip E Bourne
- Office of the Director, National Institutes of Health Bethesda, MD, USA
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25
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Haliloglu T, Bahar I. Adaptability of protein structures to enable functional interactions and evolutionary implications. Curr Opin Struct Biol 2015; 35:17-23. [PMID: 26254902 DOI: 10.1016/j.sbi.2015.07.007] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/15/2015] [Accepted: 07/20/2015] [Indexed: 12/21/2022]
Abstract
Several studies in recent years have drawn attention to the ability of proteins to adapt to intermolecular interactions by conformational changes along structure-encoded collective modes of motions. These so-called soft modes, primarily driven by entropic effects, facilitate, if not enable, functional interactions. They represent excursions on the conformational space along principal low-ascent directions/paths away from the original free energy minimum, and they are accessible to the protein even before protein-protein/ligand interactions. An emerging concept from these studies is the evolution of structures or modular domains to favor such modes of motion that will be recruited or integrated for enabling functional interactions. Structural dynamics, including the allosteric switches in conformation that are often stabilized upon formation of complexes and multimeric assemblies, emerge as key properties that are evolutionarily maintained to accomplish biological activities, consistent with the paradigm sequence→structure→dynamics→function where 'dynamics' bridges structure and function.
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Affiliation(s)
- Turkan Haliloglu
- Department of Chemical Engineering and Polymer Research Center, and Center for Life Sciences and Technologies, Bogazici University, 34342 Istanbul, Turkey; Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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26
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Kurkcuoglu Z, Findik D, Akten ED, Doruker P. How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics. Biophys J 2015; 109:1169-78. [PMID: 26190635 DOI: 10.1016/j.bpj.2015.06.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/18/2015] [Accepted: 06/08/2015] [Indexed: 10/23/2022] Open
Abstract
The tunnel region at triosephosphate isomerase (TIM)'s dimer interface, distant from its catalytic site, is a target site for certain benzothiazole derivatives that inhibit TIM's catalytic activity in Trypanosoma cruzi, the parasite that causes Chagas disease. We performed multiple 100-ns molecular-dynamics (MD) simulations and elastic network modeling (ENM) on both apo and complex structures to shed light on the still unclear inhibitory mechanism of one such inhibitor, named bt10. Within the time frame of our MD simulations, we observed stabilization of aromatic clusters at the dimer interface and enhancement of intersubunit hydrogen bonds in the presence of bt10, which point to an allosteric effect rather than destabilization of the dimeric structure. The collective dynamics dictated by the topology of TIM is known to facilitate the closure of its catalytic loop over the active site that is critical for substrate entrance and product release. We incorporated the ligand's effect on vibrational dynamics by applying mixed coarse-grained ENM to each one of 54,000 MD snapshots. Using this computationally efficient technique, we observed altered collective modes and positive shifts in eigenvalues due to the constraining effect of bt10 binding. Accordingly, we observed allosteric changes in the catalytic loop's dynamics, flexibility, and correlations, as well as the solvent exposure of catalytic residues. A newly (to our knowledge) introduced technique that performs residue-based ENM scanning of TIM revealed the tunnel region as a key binding site that can alter global dynamics of the enzyme.
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Affiliation(s)
- Zeynep Kurkcuoglu
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey
| | - Doga Findik
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey
| | - Ebru Demet Akten
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Cibali, Istanbul, Turkey
| | - Pemra Doruker
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey.
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27
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Hu J, Zhang X, Liu X, Tang J. Prediction of hot regions in protein-protein interaction by combining density-based incremental clustering with feature-based classification. Comput Biol Med 2015; 61:127-37. [PMID: 25899802 DOI: 10.1016/j.compbiomed.2015.03.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 03/19/2015] [Accepted: 03/20/2015] [Indexed: 11/25/2022]
Abstract
Discovering hot regions in protein-protein interaction is important for drug and protein design, while experimental identification of hot regions is a time-consuming and labor-intensive effort; thus, the development of predictive models can be very helpful. In hot region prediction research, some models are based on structure information, and others are based on a protein interaction network. However, the prediction accuracy of these methods can still be improved. In this paper, a new method is proposed for hot region prediction, which combines density-based incremental clustering with feature-based classification. The method uses density-based incremental clustering to obtain rough hot regions, and uses feature-based classification to remove the non-hot spot residues from the rough hot regions. Experimental results show that the proposed method significantly improves the prediction performance of hot regions.
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Affiliation(s)
- Jing Hu
- School of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan 430065, Hubei, China; Hubei Province Key Laboratory of Intelligent Information Processing and Real-time Industrial System, Wuhan 430065, Hubei, China
| | - Xiaolong Zhang
- School of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan 430065, Hubei, China; Hubei Province Key Laboratory of Intelligent Information Processing and Real-time Industrial System, Wuhan 430065, Hubei, China.
| | - Xiaoming Liu
- School of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan 430065, Hubei, China; Hubei Province Key Laboratory of Intelligent Information Processing and Real-time Industrial System, Wuhan 430065, Hubei, China
| | - Jinshan Tang
- School of Technology, Michigan Technological University, Houghton, MI 49931, USA.
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28
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Kuenemann MA, Sperandio O, Labbé CM, Lagorce D, Miteva MA, Villoutreix BO. In silico design of low molecular weight protein-protein interaction inhibitors: Overall concept and recent advances. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:20-32. [PMID: 25748546 DOI: 10.1016/j.pbiomolbio.2015.02.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 02/18/2015] [Accepted: 02/24/2015] [Indexed: 12/22/2022]
Abstract
Protein-protein interactions (PPIs) are carrying out diverse functions in living systems and are playing a major role in the health and disease states. Low molecular weight (LMW) "drug-like" inhibitors of PPIs would be very valuable not only to enhance our understanding over physiological processes but also for drug discovery endeavors. However, PPIs were deemed intractable by LMW chemicals during many years. But today, with the new experimental and in silico technologies that have been developed, about 50 PPIs have already been inhibited by LMW molecules. Here, we first focus on general concepts about protein-protein interactions, present a consensual view about ligandable pockets at the protein interfaces and the possibilities of using fast and cost effective structure-based virtual screening methods to identify PPI hits. We then discuss the design of compound collections dedicated to PPIs. Recent financial analyses of the field suggest that LMW PPI modulators could be gaining momentum over biologics in the coming years supporting further research in this area.
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Affiliation(s)
- Mélaine A Kuenemann
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 Inserm, Paris 75013, France; Inserm, U973, Paris 75013, France
| | - Olivier Sperandio
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 Inserm, Paris 75013, France; Inserm, U973, Paris 75013, France; CDithem, Faculté de Pharmacie, 1 rue du Prof Laguesse, 59000 Lille, France
| | - Céline M Labbé
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 Inserm, Paris 75013, France; Inserm, U973, Paris 75013, France; CDithem, Faculté de Pharmacie, 1 rue du Prof Laguesse, 59000 Lille, France
| | - David Lagorce
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 Inserm, Paris 75013, France; Inserm, U973, Paris 75013, France
| | - Maria A Miteva
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 Inserm, Paris 75013, France; Inserm, U973, Paris 75013, France
| | - Bruno O Villoutreix
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 Inserm, Paris 75013, France; Inserm, U973, Paris 75013, France; CDithem, Faculté de Pharmacie, 1 rue du Prof Laguesse, 59000 Lille, France.
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Ramakrishnan G, Chandra NR, Srinivasan N. From workstations to workbenches: Towards predicting physicochemically viable protein-protein interactions across a host and a pathogen. IUBMB Life 2014; 66:759-74. [DOI: 10.1002/iub.1331] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/06/2014] [Accepted: 11/16/2014] [Indexed: 01/03/2023]
Affiliation(s)
- Gayatri Ramakrishnan
- Indian Institute of Science Mathematics Initiative; Indian Institute of Science; Bangalore Karnataka India
- Molecular Biophysics Unit; Indian Institute of Science; Bangalore Karnataka India
| | - Nagasuma R. Chandra
- Department of Biochemistry; Indian Institute of Science; Bangalore Karnataka India
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Ma B, Kolb S, Diprima M, Karna M, Tosato G, Yang Q, Huang Q, Nussinov R. Investigation of the interactions between the EphB2 receptor and SNEW peptide variants. Growth Factors 2014; 32:236-46. [PMID: 25410963 PMCID: PMC4627370 DOI: 10.3109/08977194.2014.985786] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
EphB2 interacts with cell surface-bound ephrin ligands to relay bidirectional signals. Overexpression of the EphB2 receptor protein has been linked to different types of cancer. The SNEW (SNEWIQPRLPQH) peptide binds with high selectivity and moderate affinity to EphB2, inhibiting Eph-ephrin interactions by competing with ephrin ligands for the EphB2 high-affinity pocket. We used rigorous free energy perturbation (FEP) calculations to re-evaluate the binding interactions of SNEW peptide with the EphB2 receptor, followed by experimental testing of the computational results. Our results provide insight into dynamic interactions of EphB2 with SNEW peptide. While the first four residues of the SNEW peptide are already highly optimized, change of the C-terminal end of the peptide has the potential to improve SNEW-binding affinity. We identified a PXSPY motif that can be similarly aligned with several other EphB2-binding peptides.
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Affiliation(s)
- Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Stephanie Kolb
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Michael Diprima
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Molleshree Karna
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Giovanna Tosato
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Qiqi Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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Cukuroglu E, Engin HB, Gursoy A, Keskin O. Hot spots in protein–protein interfaces: Towards drug discovery. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 116:165-73. [DOI: 10.1016/j.pbiomolbio.2014.06.003] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/30/2014] [Accepted: 06/12/2014] [Indexed: 11/16/2022]
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Sudha G, Nussinov R, Srinivasan N. An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 116:141-50. [PMID: 25077409 DOI: 10.1016/j.pbiomolbio.2014.07.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 07/13/2014] [Indexed: 12/20/2022]
Abstract
Rich data bearing on the structural and evolutionary principles of protein-protein interactions are paving the way to a better understanding of the regulation of function in the cell. This is particularly the case when these interactions are considered in the framework of key pathways. Knowledge of the interactions may provide insights into the mechanisms of crucial 'driver' mutations in oncogenesis. They also provide the foundation toward the design of protein-protein interfaces and inhibitors that can abrogate their formation or enhance them. The main features to learn from known 3-D structures of protein-protein complexes and the extensive literature which analyzes them computationally and experimentally include the interaction details which permit undertaking structure-based drug discovery, the evolution of complexes and their interactions, the consequences of alterations such as post-translational modifications, ligand binding, disease causing mutations, host pathogen interactions, oligomerization, aggregation and the roles of disorder, dynamics, allostery and more to the protein and the cell. This review highlights some of the recent advances in these areas, including design, inhibition and prediction of protein-protein complexes. The field is broad, and much work has been carried out in these areas, making it challenging to cover it in its entirety. Much of this is due to the fast increase in the number of molecules whose structures have been determined experimentally and the vast increase in computational power. Here we provide a concise overview.
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Affiliation(s)
- Govindarajan Sudha
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
| | - Ruth Nussinov
- Cancer and Inflammation Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., National Cancer Institute, Frederick, MD 21702, USA; Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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Villoutreix BO, Kuenemann MA, Poyet JL, Bruzzoni-Giovanelli H, Labbé C, Lagorce D, Sperandio O, Miteva MA. Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology. Mol Inform 2014; 33:414-437. [PMID: 25254076 PMCID: PMC4160817 DOI: 10.1002/minf.201400040] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 04/21/2014] [Indexed: 12/13/2022]
Abstract
[Formula: see text] Fundamental processes in living cells are largely controlled by macromolecular interactions and among them, protein-protein interactions (PPIs) have a critical role while their dysregulations can contribute to the pathogenesis of numerous diseases. Although PPIs were considered as attractive pharmaceutical targets already some years ago, they have been thus far largely unexploited for therapeutic interventions with low molecular weight compounds. Several limiting factors, from technological hurdles to conceptual barriers, are known, which, taken together, explain why research in this area has been relatively slow. However, this last decade, the scientific community has challenged the dogma and became more enthusiastic about the modulation of PPIs with small drug-like molecules. In fact, several success stories were reported both, at the preclinical and clinical stages. In this review article, written for the 2014 International Summer School in Chemoinformatics (Strasbourg, France), we discuss in silico tools (essentially post 2012) and databases that can assist the design of low molecular weight PPI modulators (these tools can be found at www.vls3d.com). We first introduce the field of protein-protein interaction research, discuss key challenges and comment recently reported in silico packages, protocols and databases dedicated to PPIs. Then, we illustrate how in silico methods can be used and combined with experimental work to identify PPI modulators.
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Affiliation(s)
- Bruno O Villoutreix
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
- CDithem, Faculté de Pharmacie, 1 rue du Prof Laguesse59000 Lille, France
| | - Melaine A Kuenemann
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
| | - Jean-Luc Poyet
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
- IUH, Hôpital Saint-LouisParis, France
- CDithem, Faculté de Pharmacie, 1 rue du Prof Laguesse59000 Lille, France
| | - Heriberto Bruzzoni-Giovanelli
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
- CIC, Clinical investigation center, Hôpital Saint-LouisParis, France
| | - Céline Labbé
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
| | - David Lagorce
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
| | - Olivier Sperandio
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
- CDithem, Faculté de Pharmacie, 1 rue du Prof Laguesse59000 Lille, France
| | - Maria A Miteva
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
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