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Paul S, Nair NN, Vashisth H. Phase space and collective variable based simulation methods for studies of rare events. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1634268] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Sanjib Paul
- Department of Chemical Engineering, University of New Hampshire, Durham, NH, USA
| | - Nisanth N. Nair
- Department of Chemistry, Indian Institute of Technology, Kanpur, India
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham, NH, USA
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2
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Investigating targets for neuropharmacological intervention by molecular dynamics simulations. Biochem Soc Trans 2019; 47:909-918. [PMID: 31085614 DOI: 10.1042/bst20190048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/11/2019] [Accepted: 04/23/2019] [Indexed: 01/09/2023]
Abstract
Medical research has identified over 500 brain disorders. Among these, there are still only very few neuropathologies whose causes are fully understood and, consequently, very few drugs whose mechanism of action is known. No FDA drug has been identified for major neurodegenerative diseases, such as Alzheimer's and Parkinson's. We still lack effective treatments and strategies for modulating progression or even early neurodegenerative disease onset diagnostic tools. A great support toward the highly needed identification of neuroactive drugs comes from computer simulation methods and, in particular, from molecular dynamics (MD). This provides insight into structure-function relationship of a target and predicts structure, dynamics and energetics of ligand/target complexes under biologically relevant conditions like temperature and physiological saline concentration. Here, we present examples of the predictive power of MD for neuroactive ligands/target complexes. This brief survey from our own research shows the usefulness of partnerships between academia and industry, and from joint efforts between experimental and theoretical groups.
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Awasthi S, Nair NN. Exploring high‐dimensional free energy landscapes of chemical reactions. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1398] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Shalini Awasthi
- Department of Chemistry Indian Institute of Technology Kanpur Uttar Pradesh India
| | - Nisanth N. Nair
- Department of Chemistry Indian Institute of Technology Kanpur Uttar Pradesh India
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Stefanucci A, Novellino E, Mirzaie S, Macedonio G, Pieretti S, Minosi P, Szűcs E, Erdei AI, Zádor F, Benyhe S, Mollica A. Opioid Receptor Activity and Analgesic Potency of DPDPE Peptide Analogues Containing a Xylene Bridge. ACS Med Chem Lett 2017; 8:449-454. [PMID: 28435535 DOI: 10.1021/acsmedchemlett.7b00044] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/14/2017] [Indexed: 11/29/2022] Open
Abstract
d-Pen2,d-Pen5 enkephalin (DPDPE) is one of the most selective synthetic peptide agonists targeting the δ-opioid receptor. Three cyclic analogues of DPDPE containing a xylene bridge in place of disulfide bond have been synthesized and fully characterized as opioid receptors agonists. The in vitro activity was investigated showing a good affinity of 7a-c for μ- and δ-receptors. In vivo biological assays revealed that 7b is the most potent analogue with the ability to maintain high level of analgesia from 15 to 60 min following intracerebroventricular (i.c.v.) administration, whereas DPDPE was slightly active until 45 min. Compound 7b induced long lasting analgesia also after subcutaneous administration, whereas DPDPE was inactive.
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Affiliation(s)
- Azzurra Stefanucci
- Dipartimento
di Farmacia, Università di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, 66100 Chieti, Italy
| | - Ettore Novellino
- Dipartimento
di Farmacia, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Naples, Italy
| | - Sako Mirzaie
- Department
of Biochemistry, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
| | - Giorgia Macedonio
- Dipartimento
di Farmacia, Università di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, 66100 Chieti, Italy
| | - Stefano Pieretti
- Istituto Superiore di Sanità, Centro Nazionale
per la Ricerca e la Valutazione Preclinica dei Farmaci, Viale Regina Elena 299, 00161 Rome, Italy
| | - Paola Minosi
- Istituto Superiore di Sanità, Centro Nazionale
per la Ricerca e la Valutazione Preclinica dei Farmaci, Viale Regina Elena 299, 00161 Rome, Italy
| | - Edina Szűcs
- Institute
of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary
| | - Anna I. Erdei
- Institute
of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary
| | - Ferenc Zádor
- Institute
of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary
| | - Sándor Benyhe
- Institute
of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary
| | - Adriano Mollica
- Dipartimento
di Farmacia, Università di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, 66100 Chieti, Italy
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Abstract
This paper is the thirty-seventh consecutive installment of the annual review of research concerning the endogenous opioid system. It summarizes papers published during 2014 that studied the behavioral effects of molecular, pharmacological and genetic manipulation of opioid peptides, opioid receptors, opioid agonists and opioid antagonists. The particular topics that continue to be covered include the molecular-biochemical effects and neurochemical localization studies of endogenous opioids and their receptors related to behavior (endogenous opioids and receptors), and the roles of these opioid peptides and receptors in pain and analgesia (pain and analgesia); stress and social status (human studies); tolerance and dependence (opioid mediation of other analgesic responses); learning and memory (stress and social status); eating and drinking (stress-induced analgesia); alcohol and drugs of abuse (emotional responses in opioid-mediated behaviors); sexual activity and hormones, pregnancy, development and endocrinology (opioid involvement in stress response regulation); mental illness and mood (tolerance and dependence); seizures and neurologic disorders (learning and memory); electrical-related activity and neurophysiology (opiates and conditioned place preferences (CPP)); general activity and locomotion (eating and drinking); gastrointestinal, renal and hepatic functions (alcohol and drugs of abuse); cardiovascular responses (opiates and ethanol); respiration and thermoregulation (opiates and THC); and immunological responses (opiates and stimulants). This paper is the thirty-seventh consecutive installment of the annual review of research concerning the endogenous opioid system. It summarizes papers published during 2014 that studied the behavioral effects of molecular, pharmacological and genetic manipulation of opioid peptides, opioid receptors, opioid agonists and opioid antagonists. The particular topics that continue to be covered include the molecular-biochemical effects and neurochemical localization studies of endogenous opioids and their receptors related to behavior (endogenous opioids and receptors), and the roles of these opioid peptides and receptors in pain and analgesia (pain and analgesia); stress and social status (human studies); tolerance and dependence (opioid mediation of other analgesic responses); learning and memory (stress and social status); eating and drinking (stress-induced analgesia); alcohol and drugs of abuse (emotional responses in opioid-mediated behaviors); sexual activity and hormones, pregnancy, development and endocrinology (opioid involvement in stress response regulation); mental illness and mood (tolerance and dependence); seizures and neurologic disorders (learning and memory); electrical-related activity and neurophysiology (opiates and conditioned place preferences (CPP)); general activity and locomotion (eating and drinking); gastrointestinal, renal and hepatic functions (alcohol and drugs of abuse); cardiovascular responses (opiates and ethanol); respiration and thermoregulation (opiates and THC); and immunological responses (opiates and stimulants).
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Affiliation(s)
- Richard J Bodnar
- Department of Psychology and Neuropsychology Doctoral Sub-Program, Queens College, City University of New York, Flushing, NY 11367, United States.
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Rossetti G, Dibenedetto D, Calandrini V, Giorgetti A, Carloni P. Structural predictions of neurobiologically relevant G-protein coupled receptors and intrinsically disordered proteins. Arch Biochem Biophys 2015; 582:91-100. [DOI: 10.1016/j.abb.2015.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 01/05/2023]
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