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Chan KYY, Chung PY, Zhang C, Poon ENY, Leung AWK, Leung KT. R4 RGS proteins as fine tuners of immature and mature hematopoietic cell trafficking. J Leukoc Biol 2022; 112:785-797. [PMID: 35694792 DOI: 10.1002/jlb.1mr0422-475r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/28/2022] [Indexed: 11/08/2022] Open
Abstract
G-protein-coupled receptors (GPCRs) are the largest and most diverse group of membrane receptors. They are involved in almost every physiologic process and consequently have a pivotal role in an extensive number of pathologies, including genetic, neurologic, and immune system disorders. Indeed, the vast array of GPCRs mechanisms have led to the development of a tremendous number of drug therapies and already account for about a third of marketed drugs. These receptors mediate their downstream signals primarily via G proteins. The regulators of G-protein signaling (RGS) proteins are now in the spotlight as the critical modulatory factors of active GTP-bound Gα subunits of heterotrimeric G proteins to fine-tune the biologic responses driven by the GPCRs. Also, they possess noncanonical functions by multiple mechanisms, such as protein-protein interactions. Essential roles and impacts of these RGS proteins have been revealed in physiology, including hematopoiesis and immunity, and pathologies, including asthma, cancers, and neurologic disorders. This review focuses on the largest subfamily of R4 RGS proteins and provides a brief overview of their structures and G-proteins selectivity. With particular interest, we explore and highlight, their expression in the hematopoietic system and the regulation in the engraftment of hematopoietic stem/progenitor cells (HSPCs). Distinct expression patterns of R4 RGS proteins in the hematopoietic system and their pivotal roles in stem cell trafficking pave the way for realizing new strategies for enhancing the clinical performance of hematopoietic stem cell transplantation. Finally, we discuss the exciting future trends in drug development by targeting RGS activity and expression with small molecules inhibitors and miRNA approaches.
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Affiliation(s)
- Kathy Yuen Yee Chan
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Po Yee Chung
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Chi Zhang
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Ellen Ngar Yun Poon
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Alex Wing Kwan Leung
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong, China.,Department of Paediatrics & Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong SAR, China
| | - Kam Tong Leung
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong, China.,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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2
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Andrzejczyk J, Jovic K, Brown LM, Pascetta VG, Varga K, Vashisth H. Molecular interactions and inhibition of the SARS‐CoV‐2 main protease by a thiadiazolidinone derivative. Proteins 2022; 90:1896-1907. [PMID: 35567429 PMCID: PMC9347825 DOI: 10.1002/prot.26385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 04/17/2022] [Accepted: 05/10/2022] [Indexed: 11/15/2022]
Abstract
We report molecular interactions and inhibition of the main protease (MPro) of SARS‐CoV‐2, a key enzyme involved in the viral life cycle. By using a thiadiazolidinone (TDZD) derivative as a chemical probe, we explore the conformational dynamics of MPro via docking protocols and molecular dynamics simulations in all‐atom detail. We reveal the local and global dynamics of MPro in the presence of this inhibitor and confirm the inhibition of the enzyme with an IC50 value of 1.39 ± 0.22 μM, which is comparable to other known inhibitors of this enzyme.
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Affiliation(s)
- Jacob Andrzejczyk
- Department of Chemical Engineering University of New Hampshire Durham New Hampshire USA
| | - Katarina Jovic
- Department of Molecular, Cellular, and Biomedical Services University of New Hampshire Durham New Hampshire USA
| | - Logan M. Brown
- Department of Molecular, Cellular, and Biomedical Services University of New Hampshire Durham New Hampshire USA
| | - Valerie G. Pascetta
- Department of Molecular, Cellular, and Biomedical Services University of New Hampshire Durham New Hampshire USA
| | - Krisztina Varga
- Department of Molecular, Cellular, and Biomedical Services University of New Hampshire Durham New Hampshire USA
| | - Harish Vashisth
- Department of Chemical Engineering University of New Hampshire Durham New Hampshire USA
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3
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Hao J, Yang Y. Theoretical Investigation of the Excited-State Dynamics Mechanism of the Asymmetric Two-Way Proton Transfer Molecule BTHMB. J Phys Chem A 2021; 125:10280-10290. [PMID: 34846887 DOI: 10.1021/acs.jpca.1c05530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An asymmetric two-way proton transfer molecule 3-(benzo[d]-thiazol-2-yl)-2-hydroxy-5-methoxybenzaldehyde (BTHMB) with the function of white-light emission was synthesized in a recent experiment (Bhattacharyya, A.; Mandal, S. K.; Guchhait, N. J. Phys. Chem. A 2019, 123, 10246). The particularity of this molecule is that there are two possible forms, one of which contained a six-membered H-bonded network toward a N atom (BTHMB-NH) present in the molecule as a proton acceptor and the other was toward an O atom (BTHMB-OH). Unfortunately, the experimental work lacked the theoretical explanation about the determination of the BTHMB-NH form and its excited-state intramolecular proton transfer (ESIPT) process under different solvents. Therefore, this study has explored these two points by means of the time-dependent density functional theory (TDDFT) method. The calculated relative energy and potential energy profile (PEP) of the transformation between BTHMB-NH and BTHMB-OH forms illustrated that BTHMB-NH was more stable, and the transfer from BTHMB-NH to BTHMB-OH was almost impossible at both S0 and S1 states under all solvents due to high potential energy barriers (PEBs) (11.67-21.59 kcal/mol). These calculated results provided the theoretical explanation and verification for the conclusion that the BTHMB molecule exists in the BTHMB-NH form in the experiment. Subsequently, the constructed PEPs of the ESIPT process for BTHMB-NH have proved that it was prone to the ESIPT process due to low PEBs (0.11-0.28 kcal/mol) at the S1 state. In particular, as the solvent polarity increased, the intensity of the intramolecular hydrogen bond (IHB) (O3-H4···N5) increased and the ESIPT process was more likely to occur. In addition, the twisted intramolecular charge-transfer (TICT) process was studied to explore the possible fluorescence quenching pathway of BTHMB-NH. Based on the PEPs of BTHMB-NH-T as a function of the N5-C6-C7-C8 dihedral angle at the S0 and S1 states, it is seen that the S0 state TICT process was inhibited due to the large PEBs (16.45-23.93 kcal/mol). Although the S1 state PEBs have been greatly reduced, they were still maintained at about 3.60 kcal/mol (3.60-3.84 kcal/mol), and hence, this process was still relatively difficult to occur. Due to the fact that BTHMB can be regarded as a standard in future designs involving red light and solvent-specific white-light emitters, a certain amount of investigative work on the ESIPT process was done in detail, and it paved the way for future research on the directionality of ESIPT in double ESIPT probes.
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Affiliation(s)
- Jiaojiao Hao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yang Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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4
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RGS4 inhibition and the effects of adrenoceptor and cholinoceptor agonists on isolated left atrium and aorta of normal and diabetic rats. PHYSIOLOGY AND PHARMACOLOGY 2021. [DOI: 10.52547/phypha.26.2.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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5
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Obeng S, Hiranita T, León F, McMahon LR, McCurdy CR. Novel Approaches, Drug Candidates, and Targets in Pain Drug Discovery. J Med Chem 2021; 64:6523-6548. [PMID: 33956427 DOI: 10.1021/acs.jmedchem.1c00028] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Because of the problems associated with opioids, drug discovery efforts have been employed to develop opioids with reduced side effects using approaches such as biased opioid agonism, multifunctional opioids, and allosteric modulation of opioid receptors. Receptor targets such as adrenergic, cannabinoid, P2X3 and P2X7, NMDA, serotonin, and sigma, as well as ion channels like the voltage-gated sodium channels Nav1.7 and Nav1.8 have been targeted to develop novel analgesics. Several enzymes, such as soluble epoxide hydrolase, sepiapterin reductase, and MAGL/FAAH, have also been targeted to develop novel analgesics. In this review, old and recent targets involved in pain signaling and compounds acting at these targets are summarized. In addition, strategies employed to reduce side effects, increase potency, and efficacy of opioids are also elaborated. This review should aid in propelling drug discovery efforts to discover novel analgesics.
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Affiliation(s)
- Samuel Obeng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States.,Department Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Takato Hiranita
- Department Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Francisco León
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia 29208, United States
| | - Lance R McMahon
- Department Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Christopher R McCurdy
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States.,Translational Drug Development Core, Clinical and Translational Sciences Institute, University of Florida, Gainesville, Florida 32610, United States
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6
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Liu Y, Vashisth H. Allosteric Pathways Originating at Cysteine Residues in Regulators of G-Protein Signaling Proteins. Biophys J 2020; 120:517-526. [PMID: 33347886 PMCID: PMC7895990 DOI: 10.1016/j.bpj.2020.12.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/07/2020] [Accepted: 12/14/2020] [Indexed: 12/23/2022] Open
Abstract
Regulators of G-protein signaling (RGS) proteins play a central role in modulating signaling via G-protein coupled receptors (GPCRs). Specifically, RGS proteins bind to activated Gα subunits in G-proteins, accelerate the GTP hydrolysis, and thereby rapidly dampen GPCR signaling. Therefore, covalent molecules targeting conserved cysteine residues among RGS proteins have emerged as potential candidates to inhibit the RGS/Gα protein-protein interaction and enhance GPCR signaling. Although these inhibitors bind to conserved cysteine residues among RGS proteins, we have previously suggested [J. Am. Chem. Soc. 2018;140:3454–3460] that their potencies and specificities are related to differential protein dynamics among RGS proteins. Using data from all-atom molecular dynamics simulations, we reveal these differences in dynamics of RGS proteins by partitioning the protein structural space into a network of communities that allow allosteric signals to propagate along unique pathways originating at inhibitor binding sites and terminating at the RGS/Gα protein-protein interface.
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Affiliation(s)
- Yong Liu
- Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire.
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7
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Karvar S, Ansa-Addo EA, Suda J, Singh S, Zhu L, Li Z, Rockey DC. Moesin, an Ezrin/Radixin/Moesin Family Member, Regulates Hepatic Fibrosis. Hepatology 2020; 72:1073-1084. [PMID: 31860744 PMCID: PMC7437180 DOI: 10.1002/hep.31078] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 12/06/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS Moesin, an ezrin/radixin/moesin family member, is involved in the regulation of cell adhesion, polarity, and migration by cross-linking between the actin cytoskeleton and plasma membrane. The primary effector cell in hepatic fibrosis is the hepatic stellate cell (HSC), which undergoes activation during liver injury leading to increased extracellular matrix production. APPROACH AND RESULTS Here, we have hypothesized that moesin plays a critical role in linking the HSC cytoskeleton to the fibrogenic cascade during HSC activation. Moesin phosphorylation was up-regulated during HSC activation and fibrogenesis. Using moesin wild-type (WT) and mutant constructs (phosphomimicking T558D and nonphosphorylatable T558A), we found that cellular motility and contraction were increased in moesin WT-infected and T558D-infected cells, paralleled by an increase in smooth muscle α-actin and collagen 1 expression. In contrast, overexpression of nonphosphorylatable moesin and moesin knockout (KO) decreased cellular motility and contraction. Most importantly, moesin KO led to abrogation of liver fibrosis. The mechanism of moesin's effect was a reduction in myocardin-related transcription factor-A and serum-response factor (SRF)-mediated changes in the actin cytoskeleton, which in turn modulated the expression of matrix genes. CONCLUSIONS Taken together, our findings suggest that the linkage between cytoskeletal dynamics and the correlated MRTF/SRF signaling pathway has a pivotal role in HSC activation and fibrogenesis.
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Affiliation(s)
- Serhan Karvar
- Division of Gastroenterology and Hepatology, Department of
Medicine, Medical University of South Carolina, Charleston, SC, USA
| | | | - Jo Suda
- Department of Biomedical Sciences, Cedars-Sinai Medical
Center, Los Angeles, CA
| | | | - Lixin Zhu
- Guangdong Institute of Gastroenterology, Guangdong
Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Department of
Colorectal Surgery, the Sixth Affiliated Hospital, Sun Yat-sen University,
Guangzhou, China. Department of Biochemistry and Department of Pediatrics,
University at Buffalo, Buffalo, NY
| | - Zihai Li
- Department of Microbiology and Immunology, Hollings Cancer
Center
| | - Don C. Rockey
- Division of Gastroenterology and Hepatology, Department of
Medicine, Medical University of South Carolina, Charleston, SC, USA
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8
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Tang Z, Zhou P. New Insights into the Excited State Dynamics of Quinoline–Pyrazole Isomerism. J Phys Chem B 2020; 124:3400-3407. [DOI: 10.1021/acs.jpcb.0c01624] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Zhe Tang
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, P.R. China
| | - Panwang Zhou
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, P.R. China
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9
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Senese NB, Kandasamy R, Kochan KE, Traynor JR. Regulator of G-Protein Signaling (RGS) Protein Modulation of Opioid Receptor Signaling as a Potential Target for Pain Management. Front Mol Neurosci 2020; 13:5. [PMID: 32038168 PMCID: PMC6992652 DOI: 10.3389/fnmol.2020.00005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/09/2020] [Indexed: 12/23/2022] Open
Abstract
Opioid drugs are the gold standard for the management of pain, but their use is severely limited by dangerous and unpleasant side effects. All clinically available opioid analgesics bind to and activate the mu-opioid receptor (MOR), a heterotrimeric G-protein-coupled receptor, to produce analgesia. The activity of these receptors is modulated by a family of intracellular RGS proteins or regulators of G-protein signaling proteins, characterized by the presence of a conserved RGS Homology (RH) domain. These proteins act as negative regulators of G-protein signaling by serving as GTPase accelerating proteins or GAPS to switch off signaling by both the Gα and βγ subunits of heterotrimeric G-proteins. Consequently, knockdown or knockout of RGS protein activity enhances signaling downstream of MOR. In this review we discuss current knowledge of how this activity, across the different families of RGS proteins, modulates MOR activity, as well as activity of other members of the opioid receptor family, and so pain and analgesia in animal models, with particular emphasis on RGS4 and RGS9 families. We discuss inhibition of RGS proteins with small molecule inhibitors that bind to sensitive cysteine moieties in the RH domain and the potential for targeting this family of intracellular proteins as adjuncts to provide an opioid sparing effect or as standalone analgesics by promoting the activity of endogenous opioid peptides. Overall, we conclude that RGS proteins may be a novel drug target to provide analgesia with reduced opioid-like side effects, but that much basic work is needed to define the roles for specific RGS proteins, particularly in chronic pain, as well as a need to develop newer inhibitors.
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Affiliation(s)
- Nicolas B Senese
- Department of Pharmacology, Edward F. Domino Research Center, University of Michigan Medical School, Ann Arbor, MI, United States.,Department of Psychiatry, Chicago, IL, United States
| | - Ram Kandasamy
- Department of Pharmacology, Edward F. Domino Research Center, University of Michigan Medical School, Ann Arbor, MI, United States.,Department of Psychology, California State University, East Bay, Hayward, CA, United States
| | - Kelsey E Kochan
- Department of Pharmacology, Edward F. Domino Research Center, University of Michigan Medical School, Ann Arbor, MI, United States
| | - John R Traynor
- Department of Pharmacology, Edward F. Domino Research Center, University of Michigan Medical School, Ann Arbor, MI, United States.,Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, United States
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10
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Kieninger S, Donati L, Keller BG. Dynamical reweighting methods for Markov models. Curr Opin Struct Biol 2020; 61:124-131. [PMID: 31958761 DOI: 10.1016/j.sbi.2019.12.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/13/2019] [Accepted: 12/26/2019] [Indexed: 12/21/2022]
Abstract
Conformational dynamics is essential to biomolecular processes. Markov State Models (MSMs) are widely used to elucidate dynamic properties of molecular systems from unbiased Molecular Dynamics (MD). However, the implementation of reweighting schemes for MSMs to analyze biased simulations is still at an early stage of development. Several dynamical reweighing approaches have been proposed, which can be classified as approaches based on (i) Kramers rate theory, (ii) rescaling of the probability density flux, (iii) reweighting by formulating a likelihood function, (iv) path reweighting. We present the state-of-the-art and discuss the methodological differences of these methods, their limitations and recent applications.
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Affiliation(s)
- Stefanie Kieninger
- Freie Universität Berlin, Department of Biology, Chemistry, Pharmacy, Arnimallee 22, D-14194 Berlin, Germany
| | - Luca Donati
- Freie Universität Berlin, Department of Biology, Chemistry, Pharmacy, Arnimallee 22, D-14194 Berlin, Germany
| | - Bettina G Keller
- Freie Universität Berlin, Department of Biology, Chemistry, Pharmacy, Arnimallee 22, D-14194 Berlin, Germany.
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11
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Naderi M, Lemoine JM, Govindaraj RG, Kana OZ, Feinstein WP, Brylinski M. Binding site matching in rational drug design: algorithms and applications. Brief Bioinform 2019; 20:2167-2184. [PMID: 30169563 PMCID: PMC6954434 DOI: 10.1093/bib/bby078] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/18/2018] [Accepted: 07/29/2018] [Indexed: 01/06/2023] Open
Abstract
Interactions between proteins and small molecules are critical for biological functions. These interactions often occur in small cavities within protein structures, known as ligand-binding pockets. Understanding the physicochemical qualities of binding pockets is essential to improve not only our basic knowledge of biological systems, but also drug development procedures. In order to quantify similarities among pockets in terms of their geometries and chemical properties, either bound ligands can be compared to one another or binding sites can be matched directly. Both perspectives routinely take advantage of computational methods including various techniques to represent and compare small molecules as well as local protein structures. In this review, we survey 12 tools widely used to match pockets. These methods are divided into five categories based on the algorithm implemented to construct binding-site alignments. In addition to the comprehensive analysis of their algorithms, test sets and the performance of each method are described. We also discuss general pharmacological applications of computational pocket matching in drug repurposing, polypharmacology and side effects. Reflecting on the importance of these techniques in drug discovery, in the end, we elaborate on the development of more accurate meta-predictors, the incorporation of protein flexibility and the integration of powerful artificial intelligence technologies such as deep learning.
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Affiliation(s)
- Misagh Naderi
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jeffrey Mitchell Lemoine
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
- Division of Computer Science and Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | | | - Omar Zade Kana
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Wei Pan Feinstein
- High-Performance Computing, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Michal Brylinski
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
- Center for Computation & Technology, Louisiana State University, Baton Rouge, LA 70803, USA
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12
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O'Brien JB, Wilkinson JC, Roman DL. Regulator of G-protein signaling (RGS) proteins as drug targets: Progress and future potentials. J Biol Chem 2019; 294:18571-18585. [PMID: 31636120 DOI: 10.1074/jbc.rev119.007060] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
G protein-coupled receptors (GPCRs) play critical roles in regulating processes such as cellular homeostasis, responses to stimuli, and cell signaling. Accordingly, GPCRs have long served as extraordinarily successful drug targets. It is therefore not surprising that the discovery in the mid-1990s of a family of proteins that regulate processes downstream of GPCRs generated great excitement in the field. This finding enhanced the understanding of these critical signaling pathways and provided potentially new targets for pharmacological intervention. These regulators of G-protein signaling (RGS) proteins were viewed by many as nodes downstream of GPCRs that could be targeted with small molecules to tune signaling processes. In this review, we provide a brief overview of the discovery of RGS proteins and of the gradual and continuing discovery of their roles in disease states, focusing particularly on cancer and neurological disorders. We also discuss high-throughput screening efforts that have led to the discovery first of peptide-based and then of small-molecule inhibitors targeting a subset of the RGS proteins. We explore the unique mechanisms of RGS inhibition these chemical tools have revealed and highlight the most up-to-date studies using these tools in animal experiments. Finally, we discuss the future opportunities in the field, as there are clearly more avenues left to be explored and potentials to be realized.
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Affiliation(s)
- Joseph B O'Brien
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, Iowa 52242
| | - Joshua C Wilkinson
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, Iowa 52242
| | - David L Roman
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, Iowa 52242; Iowa Neuroscience Institute, Iowa City, Iowa 52242; Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242.
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13
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Shaw VS, Mohammadi M, Quinn JA, Vashisth H, Neubig RR. An Interhelical Salt Bridge Controls Flexibility and Inhibitor Potency for Regulators of G-protein Signaling Proteins 4, 8, and 19. Mol Pharmacol 2019; 96:683-691. [PMID: 31543506 DOI: 10.1124/mol.119.117176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/14/2019] [Indexed: 12/13/2022] Open
Abstract
Regulators of G-protein signaling (RGS) proteins modulate receptor signaling by binding to activated G-protein α-subunits, accelerating GTP hydrolysis. Selective inhibition of RGS proteins increases G-protein activity and may provide unique tissue specificity. Thiadiazolidinones (TDZDs) are covalent inhibitors that act on cysteine residues to inhibit RGS4, RGS8, and RGS19. There is a correlation between protein flexibility and potency of inhibition by the TDZD 4-[(4- fluorophenyl)methyl]-2-(4-methylphenyl)-1,2,4-thiadiazolidine-3,5-dione (CCG-50014). In the context of a single conserved cysteine residue on the α 4 helix, RGS19 is the most flexible and most potently inhibited by CCG-50014, followed by RGS4 and RGS8. In this work, we identify residues responsible for differences in both flexibility and potency of inhibition among RGS isoforms. RGS19 lacks a charged residue on the α 4 helix that is present in RGS4 and RGS8. Introducing a negative charge at this position (L118D) increased the thermal stability of RGS19 and decreased the potency of inhibition of CCG-50014 by 8-fold. Mutations eliminating salt bridge formation in RGS8 and RGS4 decreased thermal stability in RGS8 and increased potency of inhibition of both RGS4 and RGS8 by 4- and 2-fold, respectively. Molecular dynamics simulations with an added salt bridge in RGS19 (L118D) showed reduced RGS19 flexibility. Hydrogen-deuterium exchange studies showed striking differences in flexibility in the α 4 helix of RGS4, 8, and 19 with salt bridge-modifying mutations. These results show that the α 4 salt bridge-forming residue controls flexibility in several RGS isoforms and supports a causal relationship between RGS flexibility and the potency of TDZD inhibitors. SIGNIFICANCE STATEMENT: Inhibitor potency is often viewed in relation to the static structure of a target protein binding pocket. Using both experimental and computation studies we assess determinants of dynamics and inhibitor potency for three different RGS proteins. A single salt bridge-forming residue determines differences in flexibility between RGS isoforms; mutations either increase or decrease protein motion with correlated alterations in inhibitor potency. This strongly suggests a causal relationship between RGS protein flexibility and covalent inhibitor potency.
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Affiliation(s)
- Vincent S Shaw
- Department of Pharmacology and Toxicology (V.S.S., J.A.Q., R.R.N.) and Nicholas V. Perricone, M.D., Division of Dermatology, Department of Medicine (R.R.N.), Michigan State University, East Lansing, Michigan; and Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire (M.M., H.V.)
| | - Mohammadjavad Mohammadi
- Department of Pharmacology and Toxicology (V.S.S., J.A.Q., R.R.N.) and Nicholas V. Perricone, M.D., Division of Dermatology, Department of Medicine (R.R.N.), Michigan State University, East Lansing, Michigan; and Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire (M.M., H.V.)
| | - Josiah A Quinn
- Department of Pharmacology and Toxicology (V.S.S., J.A.Q., R.R.N.) and Nicholas V. Perricone, M.D., Division of Dermatology, Department of Medicine (R.R.N.), Michigan State University, East Lansing, Michigan; and Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire (M.M., H.V.)
| | - Harish Vashisth
- Department of Pharmacology and Toxicology (V.S.S., J.A.Q., R.R.N.) and Nicholas V. Perricone, M.D., Division of Dermatology, Department of Medicine (R.R.N.), Michigan State University, East Lansing, Michigan; and Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire (M.M., H.V.)
| | - Richard R Neubig
- Department of Pharmacology and Toxicology (V.S.S., J.A.Q., R.R.N.) and Nicholas V. Perricone, M.D., Division of Dermatology, Department of Medicine (R.R.N.), Michigan State University, East Lansing, Michigan; and Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire (M.M., H.V.)
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14
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Jagtap PKA, Asami S, Sippel C, Kaila VRI, Hausch F, Sattler M. Selective Inhibitors of FKBP51 Employ Conformational Selection of Dynamic Invisible States. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902994] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Pravin Kumar Ankush Jagtap
- Lehrstuhl für Biomolekulare NMR-SpektroskopieTechnische Universität München Lichtenbergstr. 4 85747 Garching Germany
| | - Sam Asami
- Lehrstuhl für Biomolekulare NMR-SpektroskopieTechnische Universität München Lichtenbergstr. 4 85747 Garching Germany
| | - Claudia Sippel
- Max Planck Institute of Psychiatry Kraepelinstr. 2–10 80804 Munich Germany
| | - Ville R. I. Kaila
- Department ChemieTechnische Universität München Lichtenbergstr. 4 85747 Garching Germany
| | - Felix Hausch
- Max Planck Institute of Psychiatry Kraepelinstr. 2–10 80804 Munich Germany
- Present address: Structure-Based Drug ResearchTechnische Universität Darmstadt Alarich-Weiss-Str. 4 64287 Darmstadt Germany
| | - Michael Sattler
- Lehrstuhl für Biomolekulare NMR-SpektroskopieTechnische Universität München Lichtenbergstr. 4 85747 Garching Germany
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15
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Bełdowski P, Mazurkiewicz A, Topoliński T, Małek T. Hydrogen and Water Bonding between Glycosaminoglycans and Phospholipids in the Synovial Fluid: Molecular Dynamics Study. MATERIALS (BASEL, SWITZERLAND) 2019; 12:E2060. [PMID: 31252519 PMCID: PMC6651827 DOI: 10.3390/ma12132060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 11/17/2022]
Abstract
Synovial fluid is a lubricant of the synovial joint that shows remarkable tribological properties. These properties originate in the synergy between its components, with two of its major components, glycosaminoglycans (GAGs) and phospholipids (PLs), playing a major role in boundary and mixed lubrication regimes. All-atom molecular dynamic simulations were performed to investigate the way these components bond. Hyaluronic acid (HA) and chondroitin sulphate (CS) bonding with three types of lipids was tested. The results show that both glycosaminoglycans bind lipids at a similar rate, except for 1,2-d-ipalmitoyl-sn-glycero-3-phosphoethanolamine lipids, which bind to chondroitin at a much higher rate than to hyaluronan. The results suggest that different synovial fluid lipids may play a different role when binding to both hyaluronan and chondroitin sulphate. The presented results may help in understanding a process of lubrication of articular cartilage at a nanoscale level.
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Affiliation(s)
- Piotr Bełdowski
- Institute for Multiscale Simulation, Cluster of Excellence "Engineering of Advanced Materials", Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstrasse 3, 91058 Erlangen, Germany
- Institute of Mathematics and Physics, UTP University of Science and Technology, Kaliskiego 7 Street, 85-796 Bydgoszcz, Poland
| | - Adam Mazurkiewicz
- Mechanical Engineering Department, UTP University of Science and Technology, Kaliskiego 7 Street, 85-796 Bydgoszcz, Poland.
| | - Tomasz Topoliński
- Mechanical Engineering Department, UTP University of Science and Technology, Kaliskiego 7 Street, 85-796 Bydgoszcz, Poland
| | - Tomasz Małek
- Student Scientific Club "BioMed", Mechanical Engineering Department, UTP University of Science and Technology, Kaliskiego 7 Street, 85-796 Bydgoszcz, Poland
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16
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Jagtap PKA, Asami S, Sippel C, Kaila VRI, Hausch F, Sattler M. Selective Inhibitors of FKBP51 Employ Conformational Selection of Dynamic Invisible States. Angew Chem Int Ed Engl 2019; 58:9429-9433. [PMID: 31100184 DOI: 10.1002/anie.201902994] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/24/2019] [Indexed: 12/26/2022]
Abstract
The recently discovered SAFit class of inhibitors against the Hsp90 co-chaperone FKBP51 show greater than 10 000-fold selectivity over its closely related paralogue FKBP52. However, the mechanism underlying this selectivity remained unknown. By combining NMR spectroscopy, biophysical and computational methods with mutational analysis, we show that the SAFit molecules bind to a transient pocket in FKBP51. This represents a weakly populated conformation resembling the inhibitor-bound state of FKBP51, suggesting conformational selection rather than induced fit as the major binding mechanism. The inhibitor-bound conformation of FKBP51 is stabilized by an allosteric network of residues located away from the inhibitor-binding site. These residues stabilize the Phe67 side chain in a dynamic outward conformation and are distinct in FKBP52, thus rationalizing the basis for the selectivity of SAFit inhibitors. Our results represent a paradigm for the selective inhibition of transient binding pockets.
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Affiliation(s)
- Pravin Kumar Ankush Jagtap
- Lehrstuhl für Biomolekulare NMR-Spektroskopie, Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Sam Asami
- Lehrstuhl für Biomolekulare NMR-Spektroskopie, Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Claudia Sippel
- Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany
| | - Ville R I Kaila
- Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Felix Hausch
- Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany.,Present address: Structure-Based Drug Research, Technische Universität Darmstadt, Alarich-Weiss-Str. 4, 64287, Darmstadt, Germany
| | - Michael Sattler
- Lehrstuhl für Biomolekulare NMR-Spektroskopie, Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany
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17
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The Symmetric Difference Distance: A New Way to Evaluate the Evolution of Interfaces along Molecular Dynamics Trajectories; Application to Influenza Hemagglutinin. Symmetry (Basel) 2019. [DOI: 10.3390/sym11050662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We propose a new and easy approach to evaluate structural dissimilarities between frames issued from molecular dynamics, and we test this methodology on human hemagglutinin. This protein is responsible for the entry of the influenza virus into the host cell by endocytosis, and this virus causes seasonal epidemics of infectious disease, which can be estimated to result in hundreds of thousands of deaths each year around the world. We computed the three interfaces between the three protomers of the hemagglutinin H1 homotrimer (PDB code: 1RU7) for each of its conformations generated from molecular dynamics simulation. For each conformation, we considered the set of residues involved in the union of these three interfaces. The dissimilarity between each pair of conformations was measured with our new methodology, the symmetric difference distance between the associated set of residues. The main advantages of the full procedure are: (i) it is parameter free; (ii) no spatial alignment is needed and (iii) it is simple enough so that it can be implemented by a beginner in programming. It is shown to be a relevant tool to follow the evolution of the conformation along the molecular dynamics trajectories.
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18
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Mohammadi M, Mohammadiarani H, Shaw VS, Neubig RR, Vashisth H. Interplay of cysteine exposure and global protein dynamics in small-molecule recognition by a regulator of G-protein signaling protein. Proteins 2018; 87:146-156. [PMID: 30521141 DOI: 10.1002/prot.25642] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/07/2018] [Accepted: 11/29/2018] [Indexed: 02/06/2023]
Abstract
Regulator of G protein signaling (RGS) proteins play a pivotal role in regulation of G protein-coupled receptor (GPCR) signaling and are therefore becoming an increasingly important therapeutic target. Recently discovered thiadiazolidinone (TDZD) compounds that target cysteine residues have shown different levels of specificities and potencies for the RGS4 protein, thereby suggesting intrinsic differences in dynamics of this protein upon binding of these compounds. In this work, we investigated using atomistic molecular dynamics (MD) simulations the effect of binding of several small-molecule inhibitors on perturbations and dynamical motions in RGS4. Specifically, we studied two conformational models of RGS4 in which a buried cysteine residue is solvent-exposed due to side-chain motions or due to flexibility in neighboring helices. We found that TDZD compounds with aromatic functional groups perturb the RGS4 structure more than compounds with aliphatic functional groups. Moreover, small-molecules with aromatic functional groups but lacking sulfur atoms only transiently reside within the protein and spontaneously dissociate to the solvent. We further measured inhibitory effects of TDZD compounds using a protein-protein interaction assay on a single-cysteine RGS4 protein showing trends in potencies of compounds consistent with our simulation studies. Thermodynamic analyses of RGS4 conformations in the apo-state and on binding to TDZD compounds revealed links between both conformational models of RGS4. The exposure of cysteine side-chains appears to facilitate initial binding of TDZD compounds followed by migration of the compound into a bundle of four helices, thereby causing allosteric perturbations in the RGS/Gα protein-protein interface.
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Affiliation(s)
| | | | - Vincent S Shaw
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Richard R Neubig
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire
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19
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Senese NB, Rasenick MM, Traynor JR. The Role of G-proteins and G-protein Regulating Proteins in Depressive Disorders. Front Pharmacol 2018; 9:1289. [PMID: 30483131 PMCID: PMC6244039 DOI: 10.3389/fphar.2018.01289] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/22/2018] [Indexed: 11/29/2022] Open
Abstract
Progress toward new antidepressant therapies has been relatively slow over the past few decades, with the result that individuals suffering from depression often struggle to find an effective treatment – a process often requiring months. Furthermore, the neural factors that contribute to depression remain poorly understood, and there are many open questions regarding the mechanism of action of existing antidepressants. A better understanding of the molecular processes that underlie depression and contribute to antidepressant efficacy is therefore badly needed. In this review we highlight research investigating the role of G-proteins and the regulators of G-protein signaling (RGS) proteins, two protein families that are intimately involved in both the genesis of depressive states and the action of antidepressant drugs. Many antidepressants are known to indirectly affect the function of these proteins. Conversely, dysfunction of the G-protein and RGS systems can affect antidepressant efficacy. However, a great deal remains unknown about how these proteins interact with antidepressants. Findings pertinent to each individual G-protein and RGS protein are summarized from in vitro, in vivo, and clinical studies.
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Affiliation(s)
- Nicolas B Senese
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL, United States.,Jesse Brown VA Medical Center, Chicago, IL, United States.,Department of Pharmacology and Edward F. Domino Research Center, University of Michigan, Ann Arbor, MI, United States
| | - Mark M Rasenick
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL, United States.,Jesse Brown VA Medical Center, Chicago, IL, United States.,Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, United States
| | - John R Traynor
- Department of Pharmacology and Edward F. Domino Research Center, University of Michigan, Ann Arbor, MI, United States
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20
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Mohammadiarani H, Shaw VS, Neubig RR, Vashisth H. Interpreting Hydrogen-Deuterium Exchange Events in Proteins Using Atomistic Simulations: Case Studies on Regulators of G-Protein Signaling Proteins. J Phys Chem B 2018; 122:9314-9323. [PMID: 30222348 PMCID: PMC6430106 DOI: 10.1021/acs.jpcb.8b07494] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Hydrogen-deuterium exchange (HDX) experiments are widely used in studies of protein dynamics. To predict the propensity of amide hydrogens for exchange with deuterium, several models have been reported in which computations of amide-hydrogen protection factors are carried out using molecular dynamics (MD) simulations. Given significant variation in the criteria used in different models, the robustness and broader applicability of these models to other proteins, especially homologous proteins showing distinct amide-exchange patterns, remains unknown. The sensitivity of the predictions when MD simulations are conducted with different force-fields is yet to tested and quantified. Using MD simulations and experimental HDX data on three homologous signaling proteins, we report detailed studies quantifying the performance of seven previously reported models (M1-M7) of two general types: empirical and fractional-population models. We find that the empirical models show inconsistent predictions but predictions of the fractional population models are robust. Contrary to previously reported work, we find that the solvent-accessible surface area of amide hydrogens is a useful metric when combined with a new metric defining the distances of amide hydrogens from the first polar atoms in proteins. On the basis of this, we report two new models, one empirical (M8) and one population-based (M9). We find strong protection of amide hydrogens from solvent exchange both within the stable helical motifs and also in the interhelical loops. We further observe that the exchange-competent states of amide hydrogens occur on the sub 100 ps time-scale via localized fluctuations, and such states among amides of a given protein do not appear to show any cooperativity or allosteric coupling.
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Affiliation(s)
- Hossein Mohammadiarani
- Department of Chemical Engineering , University of New Hampshire , Durham , New Hampshire 03824 , United States
| | - Vincent S Shaw
- Department of Pharmacology and Toxicology , Michigan State University , East Lansing , Michigan 48825 , United States
| | - Richard R Neubig
- Department of Pharmacology and Toxicology , Michigan State University , East Lansing , Michigan 48825 , United States
| | - Harish Vashisth
- Department of Chemical Engineering , University of New Hampshire , Durham , New Hampshire 03824 , United States
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21
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Hao J, Yang Yang YY. The effects of different heterocycles and solvents on the ESIPT mechanisms of three novel photoactive mono-formylated benzoxazole derivatives. Org Chem Front 2018. [DOI: 10.1039/c8qo00349a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The detailed effects of different heterocycles and solvents on the dynamical ESIPT mechanisms of three novel mono-formylated benzoxazole derivatives A–C in two different surroundings have been expounded by the TDDFT method at the B3LYP/TZVP level.
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Affiliation(s)
- Jiaojiao Hao
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - Yang Yang Yang Yang
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
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