1
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Wang Q, Song Y, Kim M, Hahn SK, Jiang G. Effect of chitooligosaccharide on the inhibition of SARS-CoV-2 main protease. Biomater Res 2023; 27:13. [PMID: 36797775 PMCID: PMC9935244 DOI: 10.1186/s40824-023-00351-4] [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: 11/16/2022] [Accepted: 02/05/2023] [Indexed: 02/18/2023] Open
Abstract
BACKGROUND The main protease (Mpro) is a crucial target for severe acute respiratory syndrome coronavirus (SARS-CoV-2). Chitooligosaccharide (CS) has broad-spectrum antiviral activity and can effectively inhibit the activity of SARS-CoV. Here, based on the high homology between SARS-CoV-2 and SARS-CoV, this study explores the effect and mechanism of CS with various molecular weights on the activity of SARS-CoV-2 Mpro. METHODS We used fluorescence resonance energy transfer (FRET), UV-Vis, synchronous fluorescence spectroscopy, circular dichroism (CD) spectroscopy and computational simulation to investigate the molecular interaction and the interaction mechanism between CS and SARS-CoV-2 Mpro. RESULTS Four kinds of CS with different molecular weights significantly inhibited the activity of Mpro by combining the hydrogen bonding and the salt bridge interaction to form a stable complex. Glu166 appeared to be the key amino acid. Among them, chitosan showed the highest inhibition effect on Mpro enzyme activity and the greatest impact on the spatial structure of protein. Chitosan would be one of the most potential anti-viral compounds. CONCLUSION This study provides the theoretical basis to develop targeted Mpro inhibitors for the screening and application of anti-novel coronavirus drugs.
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Affiliation(s)
- Qian Wang
- grid.440706.10000 0001 0175 8217Bioengineering College, Dalian University, 10 Xuefu Street, Jinzhou District, Dalian, 116600 Liaoning China
| | - Yuanyuan Song
- grid.440706.10000 0001 0175 8217Bioengineering College, Dalian University, 10 Xuefu Street, Jinzhou District, Dalian, 116600 Liaoning China
| | - Mungu Kim
- grid.49100.3c0000 0001 0742 4007Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, 790-784 Gyeongbuk Korea
| | - Sei Kwang Hahn
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, 790-784, Gyeongbuk, Korea.
| | - Ge Jiang
- Bioengineering College, Dalian University, 10 Xuefu Street, Jinzhou District, Dalian, 116600, Liaoning, China.
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2
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Natural Products from Plants and Algae for Treatment of Alzheimer’s Disease: A Review. Biomolecules 2022; 12:biom12050694. [PMID: 35625622 PMCID: PMC9139049 DOI: 10.3390/biom12050694] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 12/14/2022] Open
Abstract
Neurodegenerative disorders including Parkinson’s disease (PD), Huntington’s disease (HD) and the most frequent, Alzheimer’s disease (AD), represent one of the most urgent medical needs worldwide. Despite a significantly developed understanding of disease development and pathology, treatments that stop AD progression are not yet available. The recent approval of sodium oligomannate (GV-971) for AD treatment in China emphasized the potential value of natural products for the treatment of neurodegenerative disorders. Many current clinical studies include the administration of a natural compound as a single and combination treatment. The most prominent mechanisms of action are anti-inflammatory and anti-oxidative activities, thus preserving cellular survival. Here, we review current natural products that are either approved or are in testing for a treatment of neurodegeneration in AD. In addition to the most important compounds of plant origin, we also put special emphasis on compounds from algae, given their neuroprotective activity and their underlying mechanisms of neuroprotection.
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Duarte Y, Márquez-Miranda V, Miossec MJ, González-Nilo F. Integration of target discovery, drug discovery and drug delivery: A review on computational strategies. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 11:e1554. [PMID: 30932351 DOI: 10.1002/wnan.1554] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/14/2018] [Accepted: 01/23/2019] [Indexed: 12/22/2022]
Abstract
Most of the computational tools involved in drug discovery developed during the 1980s were largely based on computational chemistry, quantitative structure-activity relationship (QSAR) and cheminformatics. Subsequently, the advent of genomics in the 2000s gave rise to a huge number of databases and computational tools developed to analyze large quantities of data, through bioinformatics, to obtain valuable information about the genomic regulation of different organisms. Target identification and validation is a long process during which evidence for and against a target is accumulated in the pursuit of developing new drugs. Finally, the drug delivery system appears as a novel approach to improve drug targeting and releasing into the cells, leading to new opportunities to improve drug efficiency and avoid potential secondary effects. In each area: target discovery, drug discovery and drug delivery, different computational strategies are being developed to accelerate the process of selection and discovery of new tools to be applied to different scientific fields. Research on these three topics is growing rapidly, but still requires a global view of this landscape to detect the most challenging bottleneck and how computational tools could be integrated in each topic. This review describes the current state of the art in computational strategies for target discovery, drug discovery and drug delivery and how these fields could be integrated. Finally, we will discuss about the current needs in these fields and how the continuous development of databases and computational tools will impact on the improvement of those areas. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.
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Affiliation(s)
- Yorley Duarte
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Valeria Márquez-Miranda
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Matthieu J Miossec
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Fernando González-Nilo
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,Centro Interdisciplinario de Neurociencias de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
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4
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Grove LE, Vajda S, Kozakov D. Computational Methods to Support Fragment-based Drug Discovery. FRAGMENT-BASED DRUG DISCOVERY LESSONS AND OUTLOOK 2016. [DOI: 10.1002/9783527683604.ch09] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
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5
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Wasko MJ, Pellegrene KA, Madura JD, Surratt CK. A Role for Fragment-Based Drug Design in Developing Novel Lead Compounds for Central Nervous System Targets. Front Neurol 2015; 6:197. [PMID: 26441817 PMCID: PMC4566055 DOI: 10.3389/fneur.2015.00197] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 08/24/2015] [Indexed: 01/12/2023] Open
Abstract
Hundreds of millions of U.S. dollars are invested in the research and development of a single drug. Lead compound development is an area ripe for new design strategies. Therapeutic lead candidates have been traditionally found using high-throughput in vitro pharmacological screening, a costly method for assaying thousands of compounds. This approach has recently been augmented by virtual screening (VS), which employs computer models of the target protein to narrow the search for possible leads. A variant of VS is fragment-based drug design (FBDD), an emerging in silico lead discovery method that introduces low-molecular weight fragments, rather than intact compounds, into the binding pocket of the receptor model. These fragments serve as starting points for “growing” the lead candidate. Current efforts in virtual FBDD within central nervous system (CNS) targets are reviewed, as is a recent rule-based optimization strategy in which new molecules are generated within a 3D receptor-binding pocket using the fragment as a scaffold. This process not only places special emphasis on creating synthesizable molecules but also exposes computational questions worth addressing. Fragment-based methods provide a viable, relatively low-cost alternative for therapeutic lead discovery and optimization that can be applied to CNS targets to augment current design strategies.
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Affiliation(s)
- Michael J Wasko
- Mylan School of Pharmacy, Graduate School of Pharmaceutical Sciences, Duquesne University , Pittsburgh, PA , USA
| | - Kendy A Pellegrene
- Mylan School of Pharmacy, Graduate School of Pharmaceutical Sciences, Duquesne University , Pittsburgh, PA , USA
| | - Jeffry D Madura
- Department of Chemistry and Biochemistry, Center for Computational Sciences, Bayer School of Natural and Environmental Sciences, Duquesne University , Pittsburgh, PA , USA
| | - Christopher K Surratt
- Mylan School of Pharmacy, Graduate School of Pharmaceutical Sciences, Duquesne University , Pittsburgh, PA , USA
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6
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Successful generation of structural information for fragment-based drug discovery. Drug Discov Today 2015; 20:1104-11. [DOI: 10.1016/j.drudis.2015.04.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/12/2015] [Accepted: 04/20/2015] [Indexed: 12/25/2022]
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7
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Millan MJ, Goodwin GM, Meyer-Lindenberg A, Ove Ögren S. Learning from the past and looking to the future: Emerging perspectives for improving the treatment of psychiatric disorders. Eur Neuropsychopharmacol 2015; 25:599-656. [PMID: 25836356 DOI: 10.1016/j.euroneuro.2015.01.016] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 01/28/2015] [Indexed: 02/06/2023]
Abstract
Modern neuropsychopharmacology commenced in the 1950s with the serendipitous discovery of first-generation antipsychotics and antidepressants which were therapeutically effective yet had marked adverse effects. Today, a broader palette of safer and better-tolerated agents is available for helping people that suffer from schizophrenia, depression and other psychiatric disorders, while complementary approaches like psychotherapy also have important roles to play in their treatment, both alone and in association with medication. Nonetheless, despite considerable efforts, current management is still only partially effective, and highly-prevalent psychiatric disorders of the brain continue to represent a huge personal and socio-economic burden. The lack of success in discovering more effective pharmacotherapy has contributed, together with many other factors, to a relative disengagement by pharmaceutical firms from neuropsychiatry. Nonetheless, interest remains high, and partnerships are proliferating with academic centres which are increasingly integrating drug discovery and translational research into their traditional activities. This is, then, a time of transition and an opportune moment to thoroughly survey the field. Accordingly, the present paper, first, chronicles the discovery and development of psychotropic agents, focusing in particular on their mechanisms of action and therapeutic utility, and how problems faced were eventually overcome. Second, it discusses the lessons learned from past successes and failures, and how they are being applied to promote future progress. Third, it comprehensively surveys emerging strategies that are (1), improving our understanding of the diagnosis and classification of psychiatric disorders; (2), deepening knowledge of their underlying risk factors and pathophysiological substrates; (3), refining cellular and animal models for discovery and validation of novel therapeutic agents; (4), improving the design and outcome of clinical trials; (5), moving towards reliable biomarkers of patient subpopulations and medication efficacy and (6), promoting collaborative approaches to innovation by uniting key partners from the regulators, industry and academia to patients. Notwithstanding the challenges ahead, the many changes and ideas articulated herein provide new hope and something of a framework for progress towards the improved prevention and relief of psychiatric and other CNS disorders, an urgent mission for our Century.
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Affiliation(s)
- Mark J Millan
- Pole for Innovation in Neurosciences, IDR Servier, 125 chemin de ronde, 78290 Croissy sur Seine, France.
| | - Guy M Goodwin
- University Department of Psychiatry, Oxford University, Warneford Hospital, Oxford OX3 7JX, England, UK
| | - Andreas Meyer-Lindenberg
- Central Institute of Mental Health, University of Heidelberg/Medical Faculty Mannheim, J5, D-68159 Mannheim, Germany
| | - Sven Ove Ögren
- Department of Neuroscience, Karolinska Institutet, Retzius väg 8, S-17177 Stockholm, Sweden
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8
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Xu D, Wang B, Meroueh SO. Structure-based computational approaches for small-molecule modulation of protein-protein interactions. Methods Mol Biol 2015; 1278:77-92. [PMID: 25859944 DOI: 10.1007/978-1-4939-2425-7_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Three-dimensional structures of proteins offer an opportunity for the rational design of small molecules to modulate protein-protein interactions. The presence of a well-defined binding pocket on the surface of protein complexes, particularly at their interface, can be used for docking-based virtual screening of chemical libraries. Several approaches have been developed to identify binding pockets that are implemented in programs such as SiteMap, fpocket, and FTSite. These programs enable the scoring of these pockets to determine whether they are suitable to accommodate high-affinity small molecules. Virtual screening of commercial or combinatorial libraries can be carried out to enrich these libraries and select compounds for further experimental validation. In virtual screening, a compound library is docked to the target protein. The resulting structures are scored and ranked for the selection and experimental validation of top candidates. Molecular docking has been implemented in a number of computer programs such as AutoDock Vina. We select a set of protein-protein interactions that have been successfully inhibited with small molecules in the past. Several computer programs are applied to identify pockets on the surface, and molecular docking is conducted in an attempt to reproduce the binding pose of the inhibitors. The results highlight the strengths and limitations of computational methods for the design of PPI inhibitors.
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Affiliation(s)
- David Xu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 W. 10th Street, Indianapolis, IN, 46202, USA
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9
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Li Q, Bian L, Zhao X, Gao X, Zheng J, Li Z, Zhang Y, Jiang R, Zheng X. Immobilised histidine tagged β2-adrenoceptor oriented by a diazonium salt reaction and its application in exploring drug-protein interaction using ephedrine and pseudoephedrine as probes. PLoS One 2014; 9:e94955. [PMID: 24747442 PMCID: PMC3991622 DOI: 10.1371/journal.pone.0094955] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 03/21/2014] [Indexed: 02/06/2023] Open
Abstract
A new oriented method using a diazonium salt reaction was developed for linking β2-adrenoceptor (β2-AR) on the surface of macroporous silica gel. Stationary phase containing the immobilised receptor was used to investigate the interaction between β2-AR and ephedrine plus pseudoephedrine by zonal elution. The isotherms of the two drugs best fit the Langmuir model. Only one type of binding site was found for ephedrine and pseudoephedrine targeting β2-AR. At 37 °C, the association constants during the binding were (5.94±0.05)×103/M for ephedrine and (3.80±0.02) ×103/M for pseudoephedrine, with the binding sites of (8.92±0.06) ×10−4 M. Thermodynamic studies showed that the binding of the two compounds to β2-AR was a spontaneous reaction with exothermal processes. The ΔGθ, ΔHθ and ΔSθ for the interaction between ephedrine and β2-AR were −(22.33±0.04) kJ/mol, −(6.51±0.69) kJ/mol and 50.94±0.31 J/mol·K, respectively. For the binding of pseudoephedrine to the receptor, these values were −(21.17±0.02) kJ/mol, −(7.48±0.56) kJ/mol and 44.13±0.01 J/mol·K. Electrostatic interaction proved to be the driving force during the binding of the two drugs to β2-AR. The proposed immobilised method will have great potential for attaching protein to solid substrates and realizing the interactions between proteins and drugs.
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Affiliation(s)
- Qian Li
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Liujiao Bian
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Xinfeng Zhao
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Xiaokang Gao
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Jianbin Zheng
- Institute of Analytical Science, Northwest University, Xi'an, Shaanxi, China
| | - Zijian Li
- Institute of Vascular Medicine, Peking University; Third Hospital and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Beijing, China
| | - Youyi Zhang
- Institute of Vascular Medicine, Peking University; Third Hospital and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Beijing, China
- * E-mail: (YZ); (XZ)
| | - Ru Jiang
- School of Pharmacy, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
- * E-mail: (YZ); (XZ)
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10
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Dalet FGE, Guadalupe TFJ, María del Carmen CH, Humberto GAC, Antonio SUM. Insights into the structural biology of G-protein coupled receptors impacts drug design for central nervous system neurodegenerative processes. Neural Regen Res 2013; 8:2290-302. [PMID: 25206539 PMCID: PMC4146033 DOI: 10.3969/j.issn.1673-5374.2013.24.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 06/25/2013] [Indexed: 02/05/2023] Open
Abstract
In the last few years, there have been important new insights into the structural biology of G-protein coupled receptors. It is now known that allosteric binding sites are involved in the affinity and selectivity of ligands for G-protein coupled receptors, and that signaling by these receptors involves both G-protein dependent and independent pathways. The present review outlines the physiological and pharmacological implications of this perspective for the design of new drugs to treat disorders of the central nervous system. Specifically, new possibilities are explored in relation to allosteric and orthosteric binding sites on dopamine receptors for the treatment of Parkinson's disease, and on muscarinic receptors for Alzheimer's disease. Future research can seek to identify ligands that can bind to more than one site on the same receptor, or simultaneously bind to two receptors and form a dimer. For example, the design of bivalent drugs that can reach homo/hetero-dimers of D2 dopamine receptor holds promise as a relevant therapeutic strategy for Parkinson's disease. Regarding the treatment of Alzheimer's disease, the design of dualsteric ligands for mono-oligomeric rinic receptors could increase therapeutic effectiveness by generating potent compounds that could activate more than one signaling pathway.
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Affiliation(s)
- Farfán-García Eunice Dalet
- Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Del. Benito Juárez, Mexico City 11340, Mexico
| | - Trujillo-Ferrara José Guadalupe
- Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Del. Benito Juárez, Mexico City 11340, Mexico
| | - Castillo-Hernández María del Carmen
- Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Del. Benito Juárez, Mexico City 11340, Mexico
| | - Guerra-Araiza Christian Humberto
- Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Del. Benito Juárez, Mexico City 11340, Mexico
| | - Soriano-Ursúa Marvin Antonio
- Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Del. Benito Juárez, Mexico City 11340, Mexico
- Corresponding author: Soriano-Ursúa Marvin Antonio, Professor/Researcher, Departamento de Fisiología y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Del. Benito Juárez, Mexico City 11340, Mexico, , (N201304028)
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11
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McNeely PM, Naranjo AN, Robinson AS. Structure-function studies with G protein-coupled receptors as a paradigm for improving drug discovery and development of therapeutics. Biotechnol J 2013; 7:1451-61. [PMID: 23213015 DOI: 10.1002/biot.201200076] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 10/07/2012] [Accepted: 10/10/2012] [Indexed: 12/21/2022]
Abstract
There are a great variety of human membrane proteins, and these currently form the largest group of targets for marketed drugs. Despite the advances in drug design, however, promiscuity between drug molecules and targets often leads to undesired signaling effects, which result in unintended side effects. In this review, one family of membrane proteins - the G protein-coupled receptors (GPCRs) - is used as a model to review experimental techniques that may be used to examine the activity of membrane proteins. As these receptors are highly relevant to healthy human physiology and represent the largest family of drug targets, they represent an excellent model for membrane proteins in general. We also review experimental evidence that suggests there may be multiple ways to target a GPCR - and by extension, membrane proteins - to more effectively target unhealthy phenotypes while reducing the occurrence and severity of side effects.
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Affiliation(s)
- Patrick M McNeely
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
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12
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Abstract
The concept of chemoisosterism of protein environments is introduced as the complementary property to bioisosterism of chemical fragments. In the same way that two chemical fragments are considered bioisosteric if they can bind to the same protein environment, two protein environments will be considered chemoisosteric if they can interact with the same chemical fragment. The basis for the identification of chemoisosteric relationships among protein environments was the increasing amount of crystal structures available currently for protein-ligand complexes. It is shown that one can recover the right location and orientation of chemical fragments constituting the native ligand in a nuclear receptor structure by using only chemoisosteric environments present in enzyme structures. Examples of the potential applicability of chemoisosterism in fragment-based drug discovery are provided.
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Affiliation(s)
- Xavier Jalencas
- Chemogenomics Laboratory, Research Programme on Biomedical Informatics (GRIB), IMIM Hospital del Mar Research Institute and University Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
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13
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Lahti JL, Tang GW, Capriotti E, Liu T, Altman RB. Bioinformatics and variability in drug response: a protein structural perspective. J R Soc Interface 2012; 9:1409-37. [PMID: 22552919 DOI: 10.1098/rsif.2011.0843] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Marketed drugs frequently perform worse in clinical practice than in the clinical trials on which their approval is based. Many therapeutic compounds are ineffective for a large subpopulation of patients to whom they are prescribed; worse, a significant fraction of patients experience adverse effects more severe than anticipated. The unacceptable risk-benefit profile for many drugs mandates a paradigm shift towards personalized medicine. However, prior to adoption of patient-specific approaches, it is useful to understand the molecular details underlying variable drug response among diverse patient populations. Over the past decade, progress in structural genomics led to an explosion of available three-dimensional structures of drug target proteins while efforts in pharmacogenetics offered insights into polymorphisms correlated with differential therapeutic outcomes. Together these advances provide the opportunity to examine how altered protein structures arising from genetic differences affect protein-drug interactions and, ultimately, drug response. In this review, we first summarize structural characteristics of protein targets and common mechanisms of drug interactions. Next, we describe the impact of coding mutations on protein structures and drug response. Finally, we highlight tools for analysing protein structures and protein-drug interactions and discuss their application for understanding altered drug responses associated with protein structural variants.
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Affiliation(s)
- Jennifer L Lahti
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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14
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Heifetz A, Morris GB, Biggin PC, Barker O, Fryatt T, Bentley J, Hallett D, Manikowski D, Pal S, Reifegerste R, Slack M, Law R. Study of Human Orexin-1 and -2 G-Protein-Coupled Receptors with Novel and Published Antagonists by Modeling, Molecular Dynamics Simulations, and Site-Directed Mutagenesis. Biochemistry 2012; 51:3178-97. [DOI: 10.1021/bi300136h] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Alexander Heifetz
- Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - G. Benjamin Morris
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Philip C. Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Oliver Barker
- Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Tara Fryatt
- Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Jonathan Bentley
- Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - David Hallett
- Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | | | - Sandeep Pal
- Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Rita Reifegerste
- Evotec AG, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | - Mark Slack
- Evotec AG, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | - Richard Law
- Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
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15
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Combinatorial support vector machines approach for virtual screening of selective multi-target serotonin reuptake inhibitors from large compound libraries. J Mol Graph Model 2012; 32:49-66. [DOI: 10.1016/j.jmgm.2011.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 08/30/2011] [Accepted: 09/01/2011] [Indexed: 12/13/2022]
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16
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Janero DR, Lindsley L, Vemuri VK, Makriyannis A. Cannabinoid 1 G protein-coupled receptor (periphero-)neutral antagonists: emerging therapeutics for treating obesity-driven metabolic disease and reducing cardiovascular risk. Expert Opin Drug Discov 2011; 6:995-1025. [DOI: 10.1517/17460441.2011.608063] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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17
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Sun C, Petros AM, Hajduk PJ. Fragment-based lead discovery: challenges and opportunities. J Comput Aided Mol Des 2011; 25:607-10. [DOI: 10.1007/s10822-011-9451-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 06/17/2011] [Indexed: 01/28/2023]
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18
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Fan J, Heng J, Dai S, Shaw N, Zhou B, Huang B, He Z, Wang Y, Jiang T, Li X, Liu Z, Wang X, Zhang XC. An efficient strategy for high throughput screening of recombinant integral membrane protein expression and stability. Protein Expr Purif 2011; 78:6-13. [PMID: 21354311 DOI: 10.1016/j.pep.2011.02.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 02/14/2011] [Accepted: 02/18/2011] [Indexed: 02/05/2023]
Abstract
Membrane proteins account for about 30% of the genomes sequenced to date and play important roles in a variety of cellular functions. However, determining the three-dimensional structures of membrane proteins continues to pose a major challenge for structural biologists due to difficulties in recombinant expression and purification. We describe here a high throughput pipeline for Escherichia coli based membrane protein expression and purification. A ligation-independent cloning (LIC)-based vector encoding a C-terminal green fluorescence protein (GFP) tag was used for cloning in a high throughput mode. The GFP tag facilitated expression screening in E. coli through both cell culture fluorescence measurements and in-gel fluorescence imaging. Positive candidates from the GFP screening were subsequently sub-cloned into a LIC-based, GFP free vector for further expression and purification. The expressed, C-terminal His-tagged membrane proteins were purified via membrane enrichment and Ni-affinity chromatography. Thermofluor technique was applied to screen optimal buffers and detergents for the purified membrane proteins. This pipeline has been successfully tested for membrane proteins from E. coli and can be potentially expanded to other prokaryotes.
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Affiliation(s)
- Junping Fan
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
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Spedding M. Resolution of controversies in drug/receptor interactions by protein structure. Limitations and pharmacological solutions. Neuropharmacology 2010; 60:3-6. [PMID: 20709088 DOI: 10.1016/j.neuropharm.2010.08.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Accepted: 08/05/2010] [Indexed: 11/29/2022]
Abstract
Structural biology offers breakthroughs for key issues in receptors, ion channels and transporters. Unfortunately, while knowledge is growing exponentially about receptors and drug targets, there is also an exponential knowledge of all the variables involved. A key issue for structure-based drug design is if there are distinct outcomes from a single structurally defined site. The ways in which drugs can interact with G-protein-coupled receptors (GPCRs) at the orthosteric site can be multiple, and ligands can also interact with allosteric sites. Receptors may exist as homo- or heterodimers, with the potential for distinct pharmacology, and NC-IUPHAR has proposed stringent criteria for recognition of heterodimers (Pin et al., 2007). Furthermore, some drugs have the capacity for activating different signalling cascades from a single receptor (Urban et al., 2007) indicating unique pharmacology. Thus although specific drugs were the main tool by which receptors were (and still can be, if appropriate precautions are taken) classified, drugs may also have distinct pharmacology at certain receptors depending on their chemical structure, showing drug-specific pharmacology rather than the specific-drug pharmacology which had been used in the past to define (and limit) drug classes. Primary structure is an essential but occasionally treacherous tool for defining receptors because distinct primary structures may evolve to perform similar function. This has immense implications in drug screening, and development - which also entails much testing, and selection, in pathophysiological situations.
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Affiliation(s)
- Michael Spedding
- Experimental Sciences, Institute of Research Servier, 11 Rue des Moulineaux, 92150 Suresnes, France.
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