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Chakraborty A, Ghosh R, Soumya Mohapatra S, Barik S, Biswas A, Chowdhuri S. Repurposing of antimycobacterium drugs for COVID-19 treatment by targeting SARS CoV-2 main protease: An in-silico perspective. Gene 2024; 922:148553. [PMID: 38734190 DOI: 10.1016/j.gene.2024.148553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/27/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
The global mortality rate has been significantly impacted by the COVID-19 pandemic, caused by the SARS CoV-2 virus. Although the pursuit for a potent antiviral is still in progress, experimental therapies based on repurposing of existing drugs is being attempted. One important therapeutic target for COVID-19 is the main protease (Mpro) that cleaves the viral polyprotein in its replication process. Recently minocycline, an antimycobacterium drug, has been successfully implemented for the treatment of COVID-19 patients. But it's mode of action is still far from clear. Furthermore, it remains unresolved whether alternative antimycobacterium drugs can effectively regulate SARS CoV-2 by inhibiting the enzymatic activity of Mpro. To comprehend these facets, eight well-established antimycobacterium drugs were put through molecular docking experiments. Four of the antimycobacterium drugs (minocycline, rifampicin, clofazimine and ofloxacin) were selected by comparing their binding affinities towards Mpro. All of the four drugs interacted with both the catalytic residues of Mpro (His41 and Cys145). Additionally, molecular dynamics experiments demonstrated that the Mpro-minocyline complex has enhanced stability, experiences reduced conformational fluctuations and greater compactness than other three Mpro-antimycobacterium and Mpro-N3/lopinavir complexes. This research furnishes evidences for implementation of minocycline against SARS CoV-2. In addition, our findings also indicate other three antimycobacterium/antituberculosis drugs (rifampicin, clofazimine and ofloxacin) could potentially be evaluated for COVID-19 therapy.
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Affiliation(s)
- Ayon Chakraborty
- University Institute of Biotechnology, University Centre for Research & Development, Chandigarh University, Mohali, India
| | - Rajesh Ghosh
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | | | - Subhashree Barik
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India.
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India.
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2
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Parida C, Chowdhuri S. Effects of Hydrogen Peroxide on the Hydrogen Bonding Structure and Dynamics of Water and Its Influence on the Aqueous Solvation of the Insulin Monomer. J Phys Chem B 2023; 127:10814-10823. [PMID: 38055728 DOI: 10.1021/acs.jpcb.3c05107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
The hydrogen bond structure and dynamics of water and hydrogen peroxide (H2O2) in their binary mixtures have been studied at 298 K by classical molecular dynamics simulations. Twelve different concentrations of aqueous-H2O2 solutions are considered for this study. We have analyzed the interactions between water and H2O2 by site-site pair correlation functions and observed that the probability of formation of OW···HP hydrogen bonds are higher compared to OP···HW. The second solvation shell of water is strongly affected by increasing H2O2 concentrations (XP > 0.50), which signifies the destruction of the tetrahedral network structure of water. The translational and rotational dynamics of water and H2O2 do not significantly change up to 25% of H2O2 in aqueous mixtures. The hydrogen bond lifetime of water-water, water-H2O2, and H2O2-H2O2 in the aqueous-H2O2 solutions shows a very minimal change with increasing H2O2 concentrations. In addition to this, we also investigated the effect of H2O2 on the insulin monomer and observed that higher concentrations of H2O2 (XP = 0.10) change the secondary structure. The influence of H2O2 is more on chain-B than that on chain-A in the insulin monomer. The H2O2 occupancy at the protein surface is higher for negatively charged (GLU) and polar (ASN and THR) amino acid residues compared with that for positively charged and neutral residues in the solutions.
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Affiliation(s)
- Chinmay Parida
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar 752050, India
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar 752050, India
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Ghosh R, Badavath VN, Chowdhuri S, Sen A. Identification of Alkaloids from
Terminalia chebula
as Potent SARS‐ CoV‐2 Main Protease Inhibitors: An
In Silico
Perspective. ChemistrySelect 2022; 7:e202200055. [PMID: 35600910 PMCID: PMC9111116 DOI: 10.1002/slct.202200055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/28/2022] [Indexed: 11/12/2022]
Abstract
Natural compounds in medicinal plants are best remedies for different diseases and are important to develop new drugs. This work was dedicated to understand the role of different natural compounds of Terminalia Chebula, a well‐known herbal plant, in the treating of Covid 19. In this article, we have investigated interactions of such natural compounds from Terminalia Chebula with the main protease (Mpro) of the SARS‐CoV‐2, which is a key component for cleavage of viral polyprotein, and an important target for the development of drugs towards COVID‐19. We have performed molecular docking study on 22 different molecules of Terminalia Chebula and proposed that 7 of the natural compounds (triterpenoids and sterols) interacts with a comparable or stronger interactions than the inhibitor N3. Molecular dynamics simulations (100 ns) revealed that 7 Mpro‐Terminalia Chebula complexes are stable, conformationally less fluctuated, slightly less compact, and marginally expanded than ligand‐free conformation of Mpro. The intermolecular H‐bonding and detailed MM/PBSA and MM‐GBSA analysis showed Daucosterol interaction to be the most strong, whereas comparable interactions were observed for Arjunetin, Maslinic acid, and Bellericoside. Our study suggested that these natural compounds can act as potent Mpro inhibitors for SARS‐CoV‐2, and may evolve as promising anti‐COVID‐19 drugs in the near future.
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Affiliation(s)
- Rajesh Ghosh
- School of Basic Sciences Indian Institute of Technology Bhubaneswar Bhubaneswar India
| | | | - Snehasis Chowdhuri
- School of Basic Sciences Indian Institute of Technology Bhubaneswar Bhubaneswar India
| | - Anik Sen
- Department of Chemistry Institute of Science GITAM (Deemed to be University) Visakhapatnam 530045 Andhra Pradesh India
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Ghosh R, Chakraborty A, Biswas A, Chowdhuri S. Computer aided identification of potential SARS CoV-2 main protease inhibitors from diterpenoids and biflavonoids of Torreya nucifera leaves. J Biomol Struct Dyn 2022; 40:2647-2662. [PMID: 33140695 PMCID: PMC7663460 DOI: 10.1080/07391102.2020.1841680] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 10/19/2020] [Indexed: 12/23/2022]
Abstract
SARS CoV-2 is the causative agent of the pandemic disease COVID-19. There is an urgent need for effective drugs or vaccines which can effectively combat this outbreak. The main protease (Mpro), a key component for the SARS CoV-2 replication, is considered to be one of the important drug targets for developing anti-COVID-19 drugs. This SARS CoV-2 Mpro/cysteine protease has high sequence similarity with the same protease from SARS CoV-1. Previously, it has been shown experimentally that eight diterpenoids and four biflavonoids derived from the leaf of Torreya nucifera show inhibitory effect on the cleavage/catalytic activity of the SARS CoV-1 Mpro. But whether these phytochemicals exhibit any inhibitory effect on SARS CoV-2 Mpro is unclear. To understand this fact, here, we have adopted various in-silico approaches. Diterpenoids and biflavonoids those qualified pharmacological test (hinokiol, amentoflavone, bilobetin and ginkgetin) and two well-known Mpro inhibitors (N3 and lopinavir) were subjected for molecular docking studies. Only three biflavonoids (amentoflavone, bilobetin and ginkgetin) were selected by comparing their binding affinities with N3 and lopinavir. They interacted with two most important catalytic residues of Mpro (His41 and Cys145). Molecular dynamics studies further revealed that these three Mpro-biflavonoid complexes are highly stable and share a similar degree of compactness. Besides, these complexes experience less conformational fluctuations and more expansion than Mpro-N3 and/or Mpro-lopinavir complex. MM-GBSA and H-bond analysis further corroborated these findings. Altogether, our study suggested that these three biflavonoids could possibly inhibit the proteolytic/catalytic activity of SARS CoV-2 Mpro and might be useful for COVID-19 treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rajesh Ghosh
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ayon Chakraborty
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
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Rastogi R, Morgan BJ, Badr MS, Chowdhuri S. Hypercapnia-induced vasodilation in the cerebral circulation is reduced in older adults with sleep-disordered breathing. J Appl Physiol (1985) 2022; 132:14-23. [PMID: 34709067 PMCID: PMC8721948 DOI: 10.1152/japplphysiol.00347.2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The prevalence of sleep-disordered breathing (SDB) is higher in older adults compared with younger individuals. The increased propensity for ventilatory control instability in older adults may contribute to the increased prevalence of central apneas. Reductions in the cerebral vascular response to CO2 may exacerbate ventilatory overshoots and undershoots during sleep. Thus, we hypothesized that hypercapnia-induced cerebral vasodilation (HCVD) will be reduced in older compared with younger adults. In 11 older and 10 younger adults with SDB, blood flow velocity in the middle cerebral artery (MCAV) was measured using Doppler transcranial ultrasonography during multiple steady-state hyperoxic hypercapnic breathing trials while awake, interspersed with room air breathing. Changes in ventilation, MCAV, and mean arterial pressure (MAP) via finger plethysmography during the trials were compared with baseline eupneic values. For each hyperoxic hypercapnic trial, the change (Δ) in MCAV for a corresponding change in end-tidal CO2 and the HCVD or the change in cerebral vascular conductance (MCAV divided by MAP) for a corresponding change in end-tidal CO2 was determined. The hypercapnic ventilatory response was similar between the age groups, as was ΔMCAV/Δ[Formula: see text]. However, compared with young, older adults had a significantly smaller HCVD (1.3 ± 0.7 vs. 2.1 ± 0.6 units/mmHg, P = 0.004). Multivariable analyses demonstrated that age and nadir oxygen saturation during nocturnal polysomnography were significant predictors of HCVD. Thus, our data indicate that older age and SDB-related hypoxia are associated with diminished HCVD. We hypothesize that this impairment in vascular function may contribute to breathing instability during sleep in these individuals.NEW & NOTEWORTHY This study demonstrates, for the first time, in individuals with sleep-disordered breathing (SDB) that aging is associated with decreased hypercapnia-induced cerebral vasodilation (HCVD). In addition to advanced age, the magnitude of nocturnal oxygen desaturation due to SDB is an equal independent predictor of HCVD.
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Affiliation(s)
- R. Rastogi
- 1Medical Service, Sleep Medicine Section, John D. Dingell Veterans Affairs Medical Center, Detroit, Michigan,2Division of Pulmonary/Critical Care and Sleep Medicine, Department of Medicine, Wayne State University School of Medicine, Detroit, Michigan
| | - B. J. Morgan
- 3Department of Orthopedics and Rehabilitation, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - M. S. Badr
- 1Medical Service, Sleep Medicine Section, John D. Dingell Veterans Affairs Medical Center, Detroit, Michigan,2Division of Pulmonary/Critical Care and Sleep Medicine, Department of Medicine, Wayne State University School of Medicine, Detroit, Michigan
| | - S. Chowdhuri
- 1Medical Service, Sleep Medicine Section, John D. Dingell Veterans Affairs Medical Center, Detroit, Michigan,2Division of Pulmonary/Critical Care and Sleep Medicine, Department of Medicine, Wayne State University School of Medicine, Detroit, Michigan
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Ghosh R, Chakraborty A, Biswas A, Chowdhuri S. Identification of alkaloids from Justicia adhatoda as potent SARS CoV-2 main protease inhibitors: An in silico perspective. J Mol Struct 2021; 1229:129489. [PMID: 33100380 PMCID: PMC7571971 DOI: 10.1016/j.molstruc.2020.129489] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/17/2020] [Accepted: 10/18/2020] [Indexed: 01/08/2023]
Abstract
The COVID-19 pandemic, caused by SARS CoV-2, is responsible for millions of death worldwide. No approved/proper therapeutics is currently available which can effectively combat this outbreak. Several attempts have been undertaken in the search of effective drugs to control the spread of SARS CoV-2 infection. The main protease (Mpro), key component for the cleavage of the viral polyprotein, is considered to be one of the important drug targets for treating COVID-19. Various phytochemicals, including polyphenols and alkaloids, have been proposed as potent inhibitors of Mpro. The alkaloids from leaf extracts of Justicia adhatoda have also been reported to possess anti-viral activity. But whether these alkaloids exhibit any inhibitory effect on SARS CoV-2 Mpro is far from clear. To explore this in detail, we have adopted computational approaches. Justicia adhatoda alkaloids possessing proper drug-likeness properties and two anti-HIV drugs (lopinavir and darunavir; having binding affinity -7.3 to -7.4 kcal/mol) were docked against SARS CoV-2 Mpro to study their binding properties. Only one alkaloid (anisotine) had interaction with both the catalytic residues (His41 and Cys145) of Mpro and exhibited good binding affinity (-7.9 kcal/mol). Molecular dynamic simulations (100 ns) revealed that Mpro-anisotine complex is more stable, conformationally less fluctuated; slightly less compact and marginally expanded than Mpro-darunavir/lopinavir complex. Even the number of intermolecular H-bonds and MM-GBSA analysis suggested that anisotine is a more potent Mpro inhibitor than the two previously recommended antiviral drugs (lopinavir and darunavir) and may evolve as a promising anti-COVID-19 drug if proven in animal experiments and on patients.
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Affiliation(s)
- Rajesh Ghosh
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ayon Chakraborty
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
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7
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Ghosh R, Chakraborty A, Biswas A, Chowdhuri S. Depicting the inhibitory potential of polyphenols from Isatis indigotica root against the main protease of SARS CoV-2 using computational approaches. J Biomol Struct Dyn 2020; 40:4110-4121. [PMID: 33292085 PMCID: PMC7738210 DOI: 10.1080/07391102.2020.1858164] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The pandemic disease COVID-19, caused by SARS CoV-2, has created a global crisis. Presently, researchers across the globe are in a quest to identify/develop drugs or vaccines by targeting different non-structural proteins (Nsps) of SARS CoV-2. One such important drug target is Nsp5/main protease (Mpro) which plays a critical role in the viral replication. This cysteine protease/Mpro of SARS CoV-2 has high sequence similarity with the same protease from SARS CoV-1. Previously, it has been shown experimentally that eight polyphenols derived from the root of Isatis indigotica show inhibitory effect on the cleavage/catalytic activity of the SARS CoV-1 Mpro. But whether these polyphenols exhibit any inhibitory effect on SARS CoV-2 Mpro is unclear. To explore this possibility, here, we have adopted various computational approaches. Polyphenols that qualified the pharmacological parameters (indigo, sinigrin, hesperetin and daidzein) and two well-known Mpro inhibitors (N3 and lopinavir) were subjected to molecular docking studies. Two of them (sinigrin and hesperetin) were selected by comparing their binding affinities with N3 and lopinavir. Sinigrin and hesperetin interacted with the two most important catalytic residues of Mpro (His41 and Cys145). Molecular dynamics studies further revealed that these two Mpro-polyphenol complexes are more stable and experience less conformational fluctuations than Mpro-N3/lopinavir complex. The Mpro-hesperetin complex was more compact and less expanded than Mpro-sinigrin complex. These findings were additionally validated by MM-GBSA analysis. As a whole, our study revealed that these two polyphenols may be potent SARS CoV-2 Mpro inhibitors and may possibly be considered for COVID-19 treatment.
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Affiliation(s)
- Rajesh Ghosh
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ayon Chakraborty
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
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8
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Ghosh R, Chakraborty A, Biswas A, Chowdhuri S. Potential therapeutic use of corticosteroids as SARS CoV-2 main protease inhibitors: a computational study. J Biomol Struct Dyn 2020; 40:2053-2066. [PMID: 33094701 PMCID: PMC7596904 DOI: 10.1080/07391102.2020.1835728] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The outbreak of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), represents a pandemic threat to global public health. To date, ∼530,000 people died of this disease worldwide. Presently, researchers/clinicians are adopting the drug repurposing strategy to combat this disease. It has also been observed that some repurposed anti-viral drugs may serve as potent inhibitors of SARS CoV-2 Mpro, a key component of viral replication. Apart from these anti-viral drugs, recently dexamethasone (an important corticosteroid) is effectively used to treat COVID-19 patients. However, the mechanism behind the mode of its action is not so clear. Additionally, the effect of other well-known corticosteroids to control this disease by inhibiting the proteolytic activity of Mpro is ambiguous. In this study, we have adopted computational approaches to understand these aspects. Six well-known corticosteroids (cortisone, hydrocortisone, prednisolone, methylprednisolone, betamethasone and dexamethasone) and two repurposed drugs (darunavir and lopinavir) against COVID-19 were subjected for molecular docking studies. Two of them (betamethasone and dexamethasone) were selected by comparing their binding affinities with selected repurposed drugs toward Mpro. Betamethasone and dexamethasone interacted with both the catalytic residues of Mpro (His41 and Cys145). Molecular dynamics studies further revealed that these two Mpro-corticosteroid complexes are more stable, experience less conformational fluctuations and more compact than Mpro-darunavir/lopinavir complexes. These findings were additionally validated by MM-GBSA analysis. This study provides corroboration for execution of anti-COVID-19 activity of dexamethasone. Our study also emphasizes on the use of another important corticosteroid (betamethasone) as potential therapeutic agent for COVID-19 treatment.
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Affiliation(s)
- Rajesh Ghosh
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ayon Chakraborty
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
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9
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Abstract
Elderly adults demonstrate increased propensity for breathing instability during sleep compared with younger adults, and this may contribute to increased prevalence of sleep-disordered breathing (SDB) in this population. Hence, in older adults with SDB, we examined whether addition of supplemental oxygen (O2) will stabilize breathing during sleep and alleviate SDB. We hypothesized that exposure to supplemental O2 during non-rapid eye movement (NREM) sleep will stabilize breathing and will alleviate SDB by reducing ventilatory chemoresponsiveness and by widening the carbon dioxide (CO2) reserve. We studied 10 older adults with mild-to-moderate SDB who were randomized to undergo noninvasive bilevel mechanical ventilation with exposure to room air or supplemental O2 (Oxy) to determine the CO2 reserve, apneic threshold (AT), and controller and plant gains. Supplemental O2 was introduced during sleep to achieve a steady-state O2 saturation ≥95% and fraction of inspired O2 at 40%-50%. The CO2 reserve increased significantly during Oxy versus room air (-4.2 ± 0.5 mmHg vs. -3.2 ± 0.5 mmHg, P = 0.03). Compared with room air, Oxy was associated with a significant decline in the controller gain (1.9 ± 0.4 L/min/mmHg vs. 2.5 ± 0.5 L/min/mmHg, P = 0.04), with reductions in the apnea-hypopnea index (11.8 ± 2.0/h vs. 24.4 ± 5.6/h, P = 0.006) and central apnea-hypopnea index (1.7 ± 0.6/h vs. 6.9 ± 3.9/h, P = 0.03). The AT and plant gain were unchanged. Thus, a reduced slope of CO2 response resulted in an increased CO2 reserve. In conclusion, supplemental O2 reduced SDB in older adults during NREM sleep via reduction in chemoresponsiveness and central respiratory events.NEW & NOTEWORTHY This study demonstrates for the first time in elderly adults without heart disease that intervention with supplemental oxygen in the clinical range will ameliorate central apneas and hypopneas by decreasing the propensity to central apnea through decreased chemoreflex sensitivity, even in the absence of a reduction in the plant gain. Thus, the study provides physiological evidence for use of supplemental oxygen as therapy for mild-to-moderate SDB in this vulnerable population.
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Affiliation(s)
- Ruchi Rastogi
- Medical Service, Sleep Medicine Section, John D. Dingell Veterans Affairs Medical Center, Detroit, Michigan.,Division of Pulmonary/Critical Care and Sleep Medicine, Department of Medicine, Wayne State University School of Medicine, Detroit, Michigan
| | - M S Badr
- Medical Service, Sleep Medicine Section, John D. Dingell Veterans Affairs Medical Center, Detroit, Michigan.,Division of Pulmonary/Critical Care and Sleep Medicine, Department of Medicine, Wayne State University School of Medicine, Detroit, Michigan
| | - A Ahmed
- Division of Pulmonary/Critical Care and Sleep Medicine, Department of Medicine, Wayne State University School of Medicine, Detroit, Michigan
| | - S Chowdhuri
- Medical Service, Sleep Medicine Section, John D. Dingell Veterans Affairs Medical Center, Detroit, Michigan.,Division of Pulmonary/Critical Care and Sleep Medicine, Department of Medicine, Wayne State University School of Medicine, Detroit, Michigan
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Ghosh R, Chakraborty A, Biswas A, Chowdhuri S. Identification of polyphenols from Broussonetia papyrifera as SARS CoV-2 main protease inhibitors using in silico docking and molecular dynamics simulation approaches. J Biomol Struct Dyn 2020; 39:6747-6760. [PMID: 32762411 PMCID: PMC7484588 DOI: 10.1080/07391102.2020.1802347] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The current COVID-19 pandemic is caused by SARS CoV-2. To date, ∼463,000 people died
worldwide due to this disease. Several attempts have been taken in search of effective
drugs to control the spread of SARS CoV-2 infection. The main protease (Mpro) from SARS
CoV-2 plays a vital role in viral replication and thus serves as an important drug target.
This Mpro shares a high degree of sequence similarity (>96%) with the same protease
from SARS CoV-1 and MERS. It was already reported that Broussonetia
papyrifera polyphenols efficiently inhibit the catalytic activity of SARS CoV-1
and MERS Mpro. But whether these polyphenols exhibit any inhibitory effect on SARS CoV-2
Mpro is far from clear. To understand this fact, here we have adopted computational
approaches. Polyphenols having proper drug-likeness properties and two repurposed drugs
(lopinavir and darunavir; having binding affinity −7.3 to −7.4 kcal/mol) were docked
against SARS CoV-2 Mpro to study their binding properties. Only six polyphenols
(broussochalcone A, papyriflavonol A, 3'-(3-methylbut-2-enyl)-3',4',7-trihydroxyflavane,
broussoflavan A, kazinol F and kazinol J) had interaction with both the
catalytic residues (His41 and Cys145) of Mpro and exhibited good binding affinity (−7.6 to
−8.2 kcal/mol). Molecular dynamic simulations (100 ns) revealed that all Mpro-polyphenol
complexes are more stable, conformationally less fluctuated; slightly less compact and
marginally expanded than Mpro-darunavir/lopinavir complex. Even the number of
intermolecular H-bond and MM-GBSA analysis suggested that these six polyphenols are more
potent Mpro inhibitors than the two repurposed drugs (lopinavir and darunavir) and may
serve as promising anti-COVID-19 drugs. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Rajesh Ghosh
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ayon Chakraborty
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
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11
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Ghosh R, Chakraborty A, Biswas A, Chowdhuri S. Evaluation of green tea polyphenols as novel corona virus (SARS CoV-2) main protease (Mpro) inhibitors - an in silico docking and molecular dynamics simulation study. J Biomol Struct Dyn 2020; 39:4362-4374. [PMID: 32568613 PMCID: PMC7332865 DOI: 10.1080/07391102.2020.1779818] [Citation(s) in RCA: 143] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a viral respiratory disease which caused global health emergency and announced as pandemic disease by World Health Organization. Lack of specific drug molecules or treatment strategy against this disease makes it more devastating. Thus, there is an urgent need of effective drug molecules to fight against COVID-19. The main protease (Mpro) of SARS CoV-2, a key component of this viral replication, is considered as a prime target for anti-COVID-19 drug development. In order to find potent Mpro inhibitors, we have selected eight polyphenols from green tea, as these are already known to exert antiviral activity against many RNA viruses. We have elucidated the binding affinities and binding modes between these polyphenols including a well-known Mpro inhibitor N3 (having binding affinity -7.0 kcal/mol) and Mpro using molecular docking studies. All eight polyphenols exhibit good binding affinity toward Mpro (-7.1 to -9.0 kcal/mol). However, only three polyphenols (epigallocatechin gallate, epicatechingallate and gallocatechin-3-gallate) interact strongly with one or both catalytic residues (His41 and Cys145) of Mpro. Molecular dynamics simulations (100 ns) on these three Mpro-polyphenol systems further reveal that these complexes are highly stable, experience less conformational fluctuations and share similar degree of compactness. Estimation of total number of intermolecular H-bond and MM-GBSA analysis affirm the stability of these three Mpro-polyphenol complexes. Pharmacokinetic analysis additionally suggested that these polyphenols possess favorable drug-likeness characteristics. Altogether, our study shows that these three polyphenols can be used as potential inhibitors against SARS CoV-2 Mpro and are promising drug candidates for COVID-19 treatment.
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Affiliation(s)
- Rajesh Ghosh
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ayon Chakraborty
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
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Chettiyankandy P, Chowdhuri S. Ion solvation scenario in an aqueous solution mixture of counteracting osmolytes: Urea and trimethylamine-N-oxide (TMAO). J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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13
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Chand A, Chettiyankandy P, Chowdhuri S. Behaviour of cis- and trans-N-methylformamide in liquid mixture: Dynamical properties at varying pressure and temperature, and ion solvation scenario. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Singh S, Ratz D, Badr SM, Chowdhuri S. 0602 Determinants and Clinical Consequences of Treatment Emergent Central Sleep Apnea. Sleep 2018. [DOI: 10.1093/sleep/zsy061.601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- S Singh
- John D. Dingell VA Medical Center, Detroit, MI
- Oakland University, Rochester, MI
| | - D Ratz
- VA Center for Clinical Management Research, Ann Arbor, MI
| | - S M Badr
- John D. Dingell VA Medical Center, Detroit, MI
- Wayne State University, Detroit, MI
| | - S Chowdhuri
- John D. Dingell VA Medical Center, Detroit, MI
- Wayne State University, Detroit, MI
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Vaughan S, Arvai K, Jouldjian S, Mitchell M, Salloum A, Chowdhuri S, Shamim-Uzzaman A, Henzel M, Sankari A, Martin J, Badr M. 1043 Pulmonary Function and Sleep Quality in Patients with Spinal Cord Injury and Disease. Sleep 2018. [DOI: 10.1093/sleep/zsy061.1042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - K Arvai
- John D. Dingell VAMC, Detroit, MI
| | - S Jouldjian
- VA Greater Los Angeles Healthcare System, Los Angeles, CA
| | - M Mitchell
- VA Greater Los Angeles Healthcare System, Los Angeles, CA
| | | | | | | | - M Henzel
- Louis Stokes Cleveland VA Medical Center, Cleveland, OH
| | | | - J Martin
- VA Greater Los Angeles Healthcare System, Los Angeles, CA
| | - M Badr
- John D. Dingell VAMC, Detroit, MI
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Chand A, Chowdhuri S. A comparative study of hydrogen bonding structure and dynamics in aqueous urea solution of amides with varying hydrophobicity: Effect of addition of trimethylamine N -oxide (TMAO). J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.06.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bakkila K, Axelrod B, Kushida C, Rastogi R, Vogel D, Chowdhuri S. 0619 IMPACT OF OSA AND OSA-COPD OVERLAP SYNDROME ON NEUROCOGNITIVE OUTCOMES. Sleep 2017. [DOI: 10.1093/sleepj/zsx050.618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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Kapur VK, Auckley DH, Chowdhuri S, Kuhlmann DC, Mehra R, Ramar K, Harrod CG. 0478 CLINICAL PRACTICE GUIDELINE FOR DIAGNOSTIC TESTING FOR ADULT OBSTRUCTIVE SLEEP APNEA; AN UPDATE FOR 2016: AN AMERICAN ACADEMY OF SLEEP MEDICINE CLINICAL PRACTICE GUIDELINE. Sleep 2017. [DOI: 10.1093/sleepj/zsx050.477] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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19
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Chand A, Chettiyankandy P, Pattanayak SK, Chowdhuri S. Effects of trimethylamine-N-oxide (TMAO) on aqueous N-methylacetamide solution: A comparison of different force fields of TMAO. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2016.05.044] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Chand A, Chowdhuri S. Behaviour of aqueous N-methylacetamide solution in presence of ethanol and 2,2,2 tri-fluoroethanol: Hydrogen bonding structure and dynamics. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.10.129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Pattanayak SK, Chettiyankandy P, Chowdhuri S. Effects of co-solutes on the hydrogen bonding structure and dynamics in aqueous N-methylacetamide solution: a molecular dynamics simulations study. Mol Phys 2014. [DOI: 10.1080/00268976.2014.916822] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Pattanayak SK, Chowdhuri S. Effects of concentrated NaCl and KCl solutions on the behaviour of aqueous peptide bond environment: single-particle dynamics and H-bond structural relaxation. Mol Phys 2013. [DOI: 10.1080/00268976.2013.783240] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Pattanayak SK, Chowdhuri S. A molecular dynamics simulations study on the behavior of liquid N-methylacetamide in presence of NaCl: Structure, dynamics and H-bond properties. J Mol Liq 2012. [DOI: 10.1016/j.molliq.2012.05.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Chowdhuri S, Pattanayak SK. Pressure dependence on the single-particle dynamics and hydrogen-bond structural relaxation of water–DMSO mixtures under ambient and cold conditions. Mol Phys 2012. [DOI: 10.1080/00268976.2012.707692] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Pattanayak SK, Chowdhuri S. Effect of Water on Solvation Structure and Dynamics of Ions in the Peptide Bond Environment: Importance of Hydrogen Bonding and Dynamics of the Solvents. J Phys Chem B 2011; 115:13241-52. [DOI: 10.1021/jp206027e] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar 751013, India
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Pattanayak SK, Prashar N, Chowdhuri S. Effect of temperature and pressure on the structure, dynamics, and hydrogen bond properties of liquid N-methylacetamide: A molecular dynamics study. J Chem Phys 2011; 134:154506. [DOI: 10.1063/1.3578467] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Chowdhuri S, Chandra A. Dynamics of halide ion-water hydrogen bonds in aqueous solutions: dependence on ion size and temperature. J Phys Chem B 2007; 110:9674-80. [PMID: 16686518 DOI: 10.1021/jp057544d] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have carried out a series of molecular dynamics simulations to investigate the dynamics of X(-)-water (X = F, Cl, Br, and I) and water-water hydrogen bonds in aqueous alkali halide solutions at room temperature and also of Cl(-)-water and water-water hydrogen bonds at seven different temperatures ranging from 238 to 318 K. The hydrogen bonds are defined by using a set of configurational criteria with respect to the anion(oxygen)-oxygen and anion(oxygen)-hydrogen distances and the anion(oxygen)-oxygen-hydrogen angle for an anion(water)-water pair. The results of the hydrogen bond dynamics are obtained for two different cutoff values for the angular criterion. In both cases, similar dynamical behavior of the hydrogen bonds is found with respect to their dependence on ion size and temperature. The fluoride ion-water hydrogen bonds are found to break at a much slower rate than water-water hydrogen bonds, while the lifetimes of chloride and bromide ion-water hydrogen bonds are found to be shorter than those of fluoride ion-water ones but still longer than water-water hydrogen bonds. The short-time dynamics of iodide ion-water hydrogen bonds is found to be slightly faster, while its long-time dynamics is found to be slightly slower than the corresponding water-water hydrogen bond dynamics. Correlations of the observed dynamics of anion(water)-water hydrogen bonds with those of rotational and translational diffusion and residence times of water molecules in ion(water) hydration shells are also discussed. With variation of temperature, the lifetimes of both Cl(-)-water and water-water hydrogen bonds are found to show Arrhenius behavior with a slightly higher activation energy for the Cl(-)-water hydrogen bonds.
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Affiliation(s)
- Snehasis Chowdhuri
- Department of Chemistry, Indian Institute of Technology, Kanpur, India 208016
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Chowdhuri S, Tan ML, Ichiye T. Dynamical properties of the soft sticky dipole-quadrupole-octupole water model: a molecular dynamics study. J Chem Phys 2007; 125:144513. [PMID: 17042615 DOI: 10.1063/1.2357117] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The dynamical properties of the soft sticky dipole-quadrupole-octupole (SSDQO) water model using SPC/E moments are calculated utilizing molecular dynamics simulations. This new potential for liquid water describes the water-water interactions by a Lennard-Jones term and a sticky potential, which is an approximate moment expansion with point dipole, quadrupole, and octupole moments, and reproduces radial distribution functions of pure liquid water using the moments of SPC/E [Ichiye and Tan, J. Chem. Phys. 124, 134504 (2006)]. The forces and torques of SSDQO water for the dipole-quadrupole, quadrupole-quadrupole, and dipole-octupole interactions are derived here. The simulations are carried out at 298 K in the microcanonical ensemble employing the Ewald method for the long-range dipole-dipole interactions. Here, various dynamical properties associated with translational and rotational motions of SSDQO water using the moments of SPC/E (SSDQO:SPC/E) water are compared with the results from SPC/E and also experiment. The self-diffusion coefficient of SSDQO:SPC/E water is found to be in excellent agreement with both SPC/E and experiment whereas the single particle orientational relaxation time for dipole vector is better than SPC/E water but it is somewhat smaller than experiment. The dielectric constant of SSDQO:SPC/E is essentially identical to SPC/E, and both are slightly lower than experiment. Also, molecular dynamics simulations of the SSDQO water model are found to be about twice as fast as three-site models such as SPC/E.
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Affiliation(s)
- Snehasis Chowdhuri
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
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Chowdhuri S, Chandra A. Solute size effects on the solvation structure and diffusion of ions in liquid methanol under normal and cold conditions. J Chem Phys 2006; 124:084507. [PMID: 16512729 DOI: 10.1063/1.2172598] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We have performed a series of molecular dynamics simulations of alkali metal (Li+, Na+, K+, Rb+, and Cs+) and halide (F-, Cl-, Br-, and I-) ions in liquid methanol at two different temperatures to investigate the effects of ion size on the hydration structure and diffusion of ions in methanol under normal and cold conditions. Simulations are also carried out for some of the larger cations such as I+, (CH3)4N+, and (C2H5)4N+ and also neutral alkali metal atoms in methanol at both temperatures. With the increase of ion size, the diffusion coefficients of both positive and negative ions are found to show anomalous behavior. For cations, it is found that the maximum of the diffusion coefficient versus ion size curve occurs at the rather large cation of (CH3)4N+ unlike in water where the maximum occurs at the relatively smaller ion of Rb+. For halide ions, the anomalous behavior, i.e., the increase of diffusion with ion size, continues up to iodide ion and no maximum is observed. These results are in good agreement with experimental observations. The diffusion coefficients of neutral atoms are found to be greater in methanol than that in water and they decrease monotonically with solute size, whereas the diffusion coefficients of the corresponding ions are found to be smaller in methanol. Accordingly, an ion experiences a smaller Stokes friction and a higher dielectric friction in methanol than in water. These contrasting effects are believed to be responsible for the shift of the maximum of ion diffusion toward a larger ion size when compared with similar anomalous size dependence in liquid water.
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Affiliation(s)
- Snehasis Chowdhuri
- Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India
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Abstract
We have carried out a series of molecular-dynamics simulations of water-methanol mixtures containing either an ionic or a neutral atomic solute to investigate the effects of composition of the mixture on the diffusion of these solutes. Altogether, we have considered 17 different systems of varying composition ranging from pure water to pure methanol. The diffusion coefficients of ionic solutes are found to show nonideal behavior with variation of composition of the solvent mixture. The extent of nonideality of the solute diffusion is found to be similar to the nonideality that is observed for the diffusion and orientational relaxation of water and methanol molecules in these mixtures and is attributed to the enhanced stability of the hydrogen bonds and formation of interspecies complexes in the mixtures. The neutral solute shows characteristics of hydrophobic solvation and its diffusion decreases monotonically with increase of methanol concentration. The present simulation results are compared with those of experiments wherever available.
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Affiliation(s)
- Snehasis Chowdhuri
- Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India
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Chowdhuri S, Chandra A. Tracer diffusion of ionic and hydrophobic solutes in water–dimethyl sulfoxide mixtures: Effects of varying composition. J Chem Phys 2003. [DOI: 10.1063/1.1588997] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Chowdhuri S, Chandra A. Hydrogen bonds in aqueous electrolyte solutions: statistics and dynamics based on both geometric and energetic criteria. Phys Rev E Stat Nonlin Soft Matter Phys 2002; 66:041203. [PMID: 12443187 DOI: 10.1103/physreve.66.041203] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2002] [Indexed: 05/24/2023]
Abstract
We have investigated the statistics and dynamics of hydrogen bonds in a concentrated aqueous electrolyte solution and also in pure water by means of molecular dynamics simulations. Both geometric and energetic definitions are employed for the existence of a hydrogen bond. The present study extends our earlier work on the structure and dynamics of hydrogen bonds where only the geometric definition was used [A. Chandra, Phys. Rev. Lett. 85, 768 (2000)]. In the presence of ions, like the earlier results for geometric definition, the energetic definition is also found to give a lower number of hydrogen bonds per water molecule and a wider distribution, a slightly faster rate of breaking and a slower rate of structural relaxation of hydrogen bonds. The results are explained in terms of a decrease of the potential of mean force between water molecules, an enhanced population of hydrogen bonded water pairs in the vicinity of the dividing surface that separates the hydrogen bonded and nonbonded states and an increase of the friction on translational and rotational motion of water molecules in the presence of ions.
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Affiliation(s)
- Snehasis Chowdhuri
- Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India
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Chandra A, Chowdhuri S. Pressure Effects on the Dynamics and Hydrogen Bond Properties of Aqueous Electrolyte Solutions: The Role of Ion Screening. J Phys Chem B 2002. [DOI: 10.1021/jp020659m] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology, Kanpur, India 208016
| | - Snehasis Chowdhuri
- Department of Chemistry, Indian Institute of Technology, Kanpur, India 208016
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Chowdhuri S, Chandra A. Molecular dynamics simulations of aqueous NaCl and KCl solutions: Effects of ion concentration on the single-particle, pair, and collective dynamical properties of ions and water molecules. J Chem Phys 2001. [DOI: 10.1063/1.1387447] [Citation(s) in RCA: 274] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Guilleminault C, Do Kim Y, Chowdhuri S, Horita M, Ohayon M, Kushida C. Sleep and daytime sleepiness in upper airway resistance syndrome compared to obstructive sleep apnoea syndrome. Eur Respir J 2001; 17:838-47. [PMID: 11488314 DOI: 10.1183/09031936.01.17508380] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
This study has investigated differences in the nocturnal sleep and daytime sleepiness among patients with obstructive sleep apnoea syndrome (OSAS), upper airway resistance (UARS), sleep hypopnoea syndrome, and normal control subjects, using sleep scoring and spectral activity analysis of the electroencephalogram (EEG). Twelve nonobese males with UARS aged 30-60 yrs were recruited. These subjects were strictly matched for age and body mass index with twelve OSAS patients, 12 sleep hypopnoea syndrome patients, and 12 normal controls, all male. Daytime sleepiness was evaluated using the Epworth Sleepiness Scale (ESS) and the Multiple Sleep Latency Test (MSLT). The macrostructure of sleep was determined using international criteria and spectral analysis of the sleep EEG was obtained from a central lead. The sleep macrostructure of OSAS and UARS patients was significantly different from that of controls. These patients were also sleepier during the daytime than controls. Complaints of tiredness and daytime sleepiness, ESS and MSLT scores were similar in the different patient groups. Mild dysmorphia was present in all three patient groups. However, nocturnal sleep was significantly different among the different groups. OSAS patients had significantly more awake time during sleep than the UARS patients. The spectral activity of the total sleep time of the patient groups also differed significantly from that of controls. When the sleep spectral activity of UARS and OSAS patients were compared, OSAS patients had less slow wave sleep activity than UARS patients. UARS patients had a significantly higher absolute power in the 7-9 Hz bandwidth than OSAS patients. The absolute delta power over the different sleep cycles was also different between controls and patients, and between UARS and OSAS patients. There are clear differences in the macrostructure and spectral activity of sleep between upper airway resistance and obstructive sleep apnoea syndrome patients, demonstrated by differences in the cortical activity recorded in the central lead during sleep. Despite these nocturnal sleep differences, the tests of subjective daytime sleepiness are not significantly different.
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Affiliation(s)
- C Guilleminault
- Stanford University Sleep Disorders Clinic and Research Center, 94305, USA
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Abstract
We present a case report of a two and a half-year-old boy who presented with precocious puberty. A clinical diagnosis of congenital adrenal hyperplasia was made. Patient was investigated and found to have an adrenocortical tumor. The tumor was about 7 cms in diameter. The tumor was secreting androgens, 17OHP and cortisol. This is an unusual array of hormones to be secreted by an adrenal tumor.
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Affiliation(s)
- S Chowdhuri
- Dept of Endocrinology, MS Ramaiah Medical College, New BEL Road, Mathikere, Bangalore-560054
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Abstract
Objective: Investigation of daytime sleepiness, blood pressure changes and presence of sleep disordered breathing, in healthy young women during pregnancy.Methods: Young, healthy pregnant women between 18 and 32 years of age, seen in three different prenatal care clinics, were enlisted in a prospective study divided in two parts: part 1 of the study consisted of completing a standardized questionnaire on past and present sleep disorders. It also included filling out visual analog scales (VAS) for daytime sleepiness and snoring by the subject and bed partner. Blood pressure measurement was performed at 9 AM as per the WHO protocol. Similar data were collected again at the 6-month prenatal visit and at the 3-month post-delivery visit. At the 6-month visit, ambulatory monitoring of nocturnal sleep using a portable six-channel recorder (Edentrace((R))) was performed at home. Part 2 involved a subgroup of subjects that were randomly selected after stratification based on results of VAS and ambulatory monitoring. It included 1 night of nocturnal polysomnography with esophageal manometry and 24 h of ambulatory BP monitoring with portable equipment with cuff inflation every 30 min.Results: Of the 267 women who participated in part 1 of the study, only 128 consented to enroll in part 2, from which 26 were selected to undergo polysomnography. At the 6-week prenatal visit 37.45% of the subjects reported daytime sleepiness of variable severity. At the 6-month visit, this was noted in 52% of the subjects. Bed-partners reported chronic, loud snoring prior to pregnancy in 3.7% of the study population, but this increased to 11.8% at the 6-month visit. Blood pressure (BP) remained below the pathological range, i.e. less than 150/95 mm Hg, during the entire pregnancy. However, ambulatory monitoring indicated that 37 women, including the loud chronic snorers, had some minor SaO(2) drops during sleep and this same group presented the largest increase in BP between the 6th week and the 6th month prenatal visits. Part 2 included 26 women, 13 from the above identified 37 women and 13 from the rest of the group, chosen randomly, age and body mass index (BMI) matched. Polysomnography did identify two abnormal breathing patterns during sleep: (1) esophageal pressure 'crescendos' associated predominantly with stage 1 and 2 NREM sleep, and (2) 'abnormal sustained efforts' seen predominantly with delta sleep. These abnormal breathing patterns were noted during a significantly longer time during sleep. This group of women with the abnormal breathing patterns were not only chronic snorers but also had significantly higher systolic and diastolic BP increases when compared to the 13 other non-snorers. Six out of the 13 snorers were 'non-dippers' at the 24-h BP recording.Conclusion: Abnormal breathing during sleep (that is frequently, but not always, associated with loud, chronic snoring, and may be a consequence of edema induced by hormonal changes associated with pregnancy), can be seen in otherwise healthy young pregnant women. It may contribute to the symptom of daytime sleepiness. The changes in blood pressure noted were of no pathological significance in our population but could be an added risk factor in high-risk pregnancies.
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Affiliation(s)
- C Guilleminault
- Stanford University Sleep Disorders Clinic, Suite 3301, 401 Quarry Road, CA 94305, Stanford, USA
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Giakos GC, Pillai B, Vedantham S, Chowdhuri S, Odogba J, Dasgupta A, Vega-Lozada V, Guntupalli R, Suryanarayanan S, Endorf RJ, Passalaqua A, Kollipara S. Electric Field Dependence on Charge Collection of CdZnTe X-Ray Detectors. J Xray Sci Technol 1997; 7:198-210. [PMID: 21307550 DOI: 10.3233/xst-1997-7210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In this study, the electric field dependence on the charge collection process of CdZnTe detectors, at different x-ray tube settings, within the x-ray diagnostic energy range, is investigated. In addition, the detector contrast at different applied bias voltages and x-ray tube settings have been experimentally determined. The experimental results suggest that an efficient charge collection process is obtained by increasing the applied bias voltage. Once the applied bias voltage is sufficiently high, charge collection becomes complete and the detector operates in the saturation region. This is a prerequisite for high contrast and spatial resolution. As a result, the detector contrast is enhanced significantly. Therefore, CdZnTe detectors appear to be potential candidates for digital radiographic applications.
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Affiliation(s)
- G C Giakos
- Department of Biomedical Engineering, University of Akron, Akron, Ohio 44325
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Giakos GC, Pillai B, Vedantham S, Chowdhuri S, Dasgupta A, Richardson RB, Ghotra P, Endorf RJ, Passalaqua A, Davros WJ. Optimization of Cd1-xZnxTe Detectors for Digital Radiography. J Xray Sci Technol 1997; 7:37-49. [PMID: 21307538 DOI: 10.3233/xst-1997-7104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In this study, measurements of the electrical and detection parameters of the Cd1-xZnxTe detectors, within the x-ray diagnostic energy range, have been performed with the aim of optimizing the image quality parameters of these solid-state-ionization detectors. Namely, the leakage current and system capacitance of the x-ray imaging system have been measured as they relate to signal parameters. Similarly, the detected signal and noise contributions were measured and related to the radiation exposure and tube current setting. Furthermore, the detector contrast has been experimentally determined. The experimental results indicate that Cd1-xZnxTe detectors have low leakage current, high resistivity, and high detector contrast resolution. Therefore, they appear to be very attractive for imaging applications with applications in x-ray digital radiography.
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Affiliation(s)
- G C Giakos
- Department of Biomedical Engineering, University of Akron, Akron, Ohio 44325
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Chowdhuri S, Chatterjee PC. Survey of haemagglutinating properties of plant seeds and fungi. Indian J Med Res 1973; 61:1478-84. [PMID: 4781004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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