Computational Chemistry and Molecular Biophysics Section – Publications

@article{pmid35483373,

title = {GPCR-mediated β-arrestin activation deconvoluted with single-molecule precision},

author = {Wesley B Asher and Daniel S Terry and G Glenn A Gregorio and Alem W Kahsai and Alessandro Borgia and Bing Xie and Arnab Modak and Ying Zhu and Wonjo Jang and Alekhya Govindaraju and Li-Yin Huang and Asuka Inoue and Nevin A Lambert and Vsevolod V Gurevich and Lei Shi and Robert J Lefkowitz and Scott C Blanchard and Jonathan A Javitch},

url = {https://pubmed.ncbi.nlm.nih.gov/35483373/},

doi = {10.1016/j.cell.2022.03.042},

issn = {1097-4172},

year  = {2022},

date = {2022-04-01},

urldate = {2022-04-01},

journal = {Cell},

abstract = {β-arrestins bind G protein-coupled receptors to terminate G protein signaling and to facilitate other downstream signaling pathways. Using single-molecule fluorescence resonance energy transfer imaging, we show that β-arrestin is strongly autoinhibited in its basal state. Its engagement with a phosphopeptide mimicking phosphorylated receptor tail efficiently releases the β-arrestin tail from its N domain to assume distinct conformations. Unexpectedly, we find that β-arrestin binding to phosphorylated receptor, with a phosphorylation barcode identical to the isolated phosphopeptide, is highly inefficient and that agonist-promoted receptor activation is required for β-arrestin activation, consistent with the release of a sequestered receptor C tail. These findings, together with focused cellular investigations, reveal that agonism and receptor C-tail release are specific determinants of the rate and efficiency of β-arrestin activation by phosphorylated receptor. We infer that receptor phosphorylation patterns, in combination with receptor agonism, synergistically establish the strength and specificity with which diverse, downstream β-arrestin-mediated events are directed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid34420294,

title = {Toward Reducing hERG Affinities for DAT Inhibitors with a Combined Machine Learning and Molecular Modeling Approach},

author = {Kuo Hao Lee and Andrew D Fant and Jiqing Guo and Andy Guan and Joslyn Jung and Mary Kudaibergenova and Williams E Miranda and Therese Ku and Jianjing Cao and Soren Wacker and Henry J Duff and Amy Hauck Newman and Sergei Y Noskov and Lei Shi},

url = {https://pubmed.ncbi.nlm.nih.gov/34420294/},

doi = {10.1021/acs.jcim.1c00856},

issn = {1549-960X},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {J Chem Inf Model},

volume = {61},

number = {9},

pages = {4266--4279},

abstract = {Psychostimulant drugs, such as cocaine, inhibit dopamine reuptake via blockading the dopamine transporter (DAT), which is the primary mechanism underpinning their abuse. Atypical DAT inhibitors are dissimilar to cocaine and can block cocaine- or methamphetamine-induced behaviors, supporting their development as part of a treatment regimen for psychostimulant use disorders. When developing these atypical DAT inhibitors as medications, it is necessary to avoid off-target binding that can produce unwanted side effects or toxicities. In particular, the blockade of a potassium channel, human  (hERG), can lead to potentially lethal ventricular tachycardia. In this study, we established a counter screening platform for DAT and against hERG binding by combining machine learning-based quantitative structure-activity relationship (QSAR) modeling, experimental validation, and molecular modeling and simulations. Our results show that the available data are adequate to establish robust QSAR models, as validated by chemical synthesis and pharmacological evaluation of a validation set of DAT inhibitors. Furthermore, the QSAR models based on subsets of the data according to experimental approaches used have predictive power as well, which opens the door to target specific functional states of a protein. Complementarily, our molecular modeling and simulations identified the structural elements responsible for a pair of DAT inhibitors having opposite binding affinity trends at DAT and hERG, which can be leveraged for rational optimization of lead atypical DAT inhibitors with desired pharmacological properties.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Plenge:2020aab,

title = {The mechanism of a high-affinity allosteric inhibitor of the serotonin transporter},

author = {Per Plenge and Ara M Abramyan and Gunnar Sørensen and Arne Mørk and Pia Weikop and Ulrik Gether and Benny Bang-Andersen and Lei Shi and Claus J Loland},

url = {https://pubmed.ncbi.nlm.nih.gov/32198394/},

doi = {10.1038/s41467-020-15292-y},

isbn = {2041-1723},

year  = {2020},

date = {2020-01-01},

journal = {Nature Communications},

volume = {11},

number = {1},

pages = {1491},

abstract = {The serotonin transporter (SERT) terminates serotonin signaling by rapid presynaptic reuptake. SERT activity is modulated by antidepressants, e.g., S-citalopram and imipramine, to alleviate symptoms of depression and anxiety. SERT crystal structures reveal two S-citalopram binding pockets in the central binding (S1) site and the extracellular vestibule (S2 site). In this study, our combined in vitro and in silico analysis indicates that the bound S-citalopram or imipramine in S1 is allosterically coupled to the ligand binding to S2 through altering protein conformations. Remarkably, SERT inhibitor Lu AF60097, the first high-affinity S2-ligand reported and characterized here, allosterically couples the ligand binding to S1 through a similar mechanism. The SERT inhibition by Lu AF60097 is demonstrated by the potentiated imipramine binding and increased hippocampal serotonin level in rats. Together, we reveal a S1-S2 coupling mechanism that will facilitate rational design of high-affinity SERT allosteric inhibitors.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.7554/eLife.52189,

title = {Distinct inactive conformations of the dopamine D2 and D3 receptors correspond to different extents of inverse agonism},

author = {Robert J Lane and Ara M Abramyan and Pramisha Adhikari and Alastair C Keen and Kuo-Hao Lee and Julie Sanchez and Ravi Kumar Verma and Herman D Lim and Hideaki Yano and Jonathan A Javitch and Lei Shi},

editor = {Yibing Shan and Richard W Aldrich},

url = {https://pubmed.ncbi.nlm.nih.gov/31985399/},

doi = {10.7554/eLife.52189},

issn = {2050-084X},

year  = {2020},

date = {2020-01-01},

journal = {eLife},

volume = {9},

pages = {e52189},

publisher = {eLife Sciences Publications, Ltd},

abstract = {By analyzing and simulating inactive conformations of the highly homologous dopamine Dtextsubscript2 and Dtextsubscript3 receptors (Dtextsubscript2R and Dtextsubscript3R), we find that eticlopride binds Dtextsubscript2R in a pose very similar to that in the Dtextsubscript3R/eticlopride structure but incompatible with the Dtextsubscript2R/risperidone structure. In addition, risperidone occupies a sub-pocket near the Natextsuperscript+ binding site, whereas eticlopride does not. Based on these findings and our experimental results, we propose that the divergent receptor conformations stabilized by Natextsuperscript+-sensitive eticlopride and Natextsuperscript+-insensitive risperidone correspond to different degrees of inverse agonism. Moreover, our simulations reveal that the extracellular loops are highly dynamic, with spontaneous transitions of extracellular loop 2 from the helical conformation in the Dtextsubscript2R/risperidone structure to an extended conformation similar to that in the Dtextsubscript3R/eticlopride structure. Our results reveal previously unappreciated diversity and dynamics in the inactive conformations of Dtextsubscript2R. These findings are critical for rational drug discovery, as limiting a virtual screen to a single conformation will miss relevant ligands.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ABRAMYAN2019107411,

title = {Computation-guided analysis of paroxetine binding to hSERT reveals functionally important structural elements and dynamics},

author = {Ara M Abramyan and Rachel D Slack and Sitaram Meena and Bruce A Davis and Amy Hauck Newman and Satinder K Singh and Lei Shi},

url = {https://pubmed.ncbi.nlm.nih.gov/30391505/},

doi = {https://doi.org/10.1016/j.neuropharm.2018.10.040},

issn = {0028-3908},

year  = {2019},

date = {2019-01-01},

journal = {Neuropharmacology},

volume = {161},

pages = {107411},

abstract = {The serotonin transporter (SERT) is one of the primary targets for medications to treat neuropsychiatric disorders and functions by exploiting pre-existing ion gradients of Na+, Cl−, and K+ to translocate serotonin from the synaptic cleft into the presynaptic neuron. Although recent hSERT crystal structures represent a milestone for structure-function analyses of mammalian neurotransmitter:sodium symporters, they are all derived from thermostabilized but transport-deficient constructs. Two of these structures are in complex with paroxetine, the most potent selective serotonin reuptake inhibitor known. In this study, by carrying out and analyzing the results of extensive and comparative molecular dynamics simulations while also re-evaluating the transport and binding properties of the thermostabilized constructs, we identified functionally important structural elements that are perturbed by these mutations, revealed unexpected dynamics in the central primary binding site of SERT, and uncovered a conceivable ambiguity in paroxetine's binding orientation. We propose that the favored entropy contribution plays a significant role in paroxetine's extraordinarily high affinity for SERT. Our findings lay the foundation for future mechanistic studies and rational design of high-affinity SERT inhibitors. This article is part of the issue entitled `Special Issue on Neurotransmitter Transporters'.},

note = {Neurotransmitter Transporters},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN9711,

title = {The E2.65A mutation disrupts dynamic binding poses of SB269652 at the dopamine D2 and D3 receptors},

author = {R K Verma and A M Abramyan and M Michino and R B Free and D R Sibley and J A Javitch and J R Lane and L Shi},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29337986},

doi = {10.1371/journal.pcbi.1005948},

issn = {1553-7358 (Electronic) 1553-734X (Linking)},

year  = {2018},

date = {2018-01-01},

journal = {PLoS Comput Biol},

volume = {14},

number = {1},

pages = {e1005948},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN9724,

title = {Pharmacological profiling of sigma 1 receptor ligands by novel receptor homomer assays},

author = {H Yano and A Bonifazi and M Xu and D A Guthrie and S N Schneck and A M Abramyan and A D Fant and W C Hong and Amy Hauck Newman and L Shi},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29407216},

doi = {10.1016/j.neuropharm.2018.01.042},

issn = {1873-7064 (Electronic) 0028-3908 (Linking)},

year  = {2018},

date = {2018-01-01},

urldate = {2018-01-01},

journal = {Neuropharmacology},

volume = {133},

pages = {264-275},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN9683,

title = {The Isomeric Preference of an Atypical Dopamine Transporter Inhibitor Contributes to Its Selection of the Transporter Conformation},

author = {A M Abramyan and S Stolzenberg and Z Li and C J Loland and F Noe and L Shi},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28441487},

doi = {10.1021/acschemneuro.7b00094},

issn = {1948-7193 (Electronic) 1948-7193 (Linking)},

year  = {2017},

date = {2017-01-01},

journal = {ACS Chem Neurosci},

volume = {8},

number = {8},

pages = {1735-1746},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN9670,

title = {Toward Understanding the Structural Basis of Partial Agonism at the Dopamine D3 Receptor},

author = {M Michino and C A Boateng and P Donthamsetti and H Yano and O M Bakare and A Bonifazi and M P Ellenberger and T M Keck and V Kumar and C Zhu and R Verma and J R Deschamps and J A Javitch and Amy Hauck Newman and L Shi},

url = {https://www.ncbi.nlm.nih.gov/pubmed/27983845},

doi = {10.1021/acs.jmedchem.6b01148},

issn = {1520-4804 (Electronic) 0022-2623 (Linking)},

year  = {2017},

date = {2017-01-01},

urldate = {2017-01-01},

journal = {J Med Chem},

volume = {60},

number = {2},

pages = {580-593},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN9684,

title = {The role of transmembrane segment 5 (TM5) in Na2 release and the conformational transition of neurotransmitter:sodium symporters toward the inward-open state},

author = {S Stolzenberg and Z Li and M Quick and L Malinauskaite and P Nissen and H Weinstein and J A Javitch and L Shi},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28320858},

doi = {10.1074/jbc.M116.757153},

issn = {1083-351X (Electronic) 0021-9258 (Linking)},

year  = {2017},

date = {2017-01-01},

journal = {J Biol Chem},

volume = {292},

number = {18},

pages = {7372-7384},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN8556,

title = {Computational approaches to detect allosteric pathways in transmembrane molecular machines},

author = {S Stolzenberg and M Michino and M V LeVine and H Weinstein and L Shi},

url = {https://www.ncbi.nlm.nih.gov/pubmed/26806157},

doi = {10.1016/j.bbamem.2016.01.010},

issn = {0006-3002 (Print) 0006-3002 (Linking)},

year  = {2016},

date = {2016-01-01},

journal = {Biochim Biophys Acta},

volume = {1858},

number = {7 Pt B},

pages = {1652-62},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN9885,

title = {A new era of rationally designed antipsychotics},

author = {D R Sibley and L Shi},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29517027},

doi = {10.1038/d41586-018-02328-z},

issn = {1476-4687 (Electronic) 0028-0836 (Linking)},

year  = {2018},

date = {2018-01-01},

journal = {Nature},

volume = {555},

number = {7695},

pages = {170-172},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN9713,

title = {Editorial: Computer Aided Structure-based Lead Optimization},

author = {T Beuming and L Shi},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28889794},

doi = {10.2174/156802661723170808161306},

issn = {1873-4294 (Electronic) 1568-0266 (Linking)},

year  = {2017},

date = {2017-01-01},

journal = {Curr Top Med Chem},

volume = {17},

number = {23},

pages = {2575-2576},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Michino2015b,

title = {What can crystal structures of aminergic receptors tell us about designing subtype-selective ligands?},

author = {Michino, M. and Beuming, T. and Donthamsetti, P. and Amy Hauck Newman and Javitch, J. A. and Shi, L.},

url = {https://www.ncbi.nlm.nih.gov/pubmed/25527701},

doi = {10.1124/pr.114.009944},

issn = {1521-0081 (Electronic); 0031-6997 (Linking)},

year  = {2015},

date = {2015-12-20},

urldate = {2015-12-20},

journal = {Pharmacol Rev},

volume = {67},

number = {1},

pages = {198--213},

abstract = {G protein-coupled receptors (GPCRs) are integral membrane proteins that represent an important class of drug targets. In particular, aminergic GPCRs interact with a significant portion of drugs currently on the market. However, most drugs that target these receptors are associated with undesirable side effects, which are due in part to promiscuous interactions with close homologs of the intended target receptors. Here, based on a systematic analysis of all 37 of the currently available high-resolution crystal structures of aminergic GPCRs, we review structural elements that contribute to and can be exploited for designing subtype-selective compounds. We describe the roles of secondary binding pockets (SBPs), as well as differences in ligand entry pathways to the orthosteric binding site, in determining selectivity. In addition, using the available crystal structures, we have identified conformational changes in the SBPs that are associated with receptor activation and explore the implications of these changes for the rational development of selective ligands with tailored efficacy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}