Repurposing benzimidazole and benzothiazole derivatives as potential inhibitors of SARS-CoV-2: DFT, QSAR, molecular docking, molecular dynamics simulation, and in-silico pharmacokinetic and toxicity studies

Mohapatra, Ranjan K.; Dhama, Kuldeep; El‐Arabey, Amr Ahmed; Sarangi, Ashish K.; Tiwari, Ruchi; Emran, Talha Bin; Azam, Mohammad; Al‐Resayes, Saud I.; Raval, Mukesh Kumar; Seidel, Véronique; Abdalla, Mohnad

doi:10.1016/j.jksus.2021.101637

Cited by 43 publications

(14 citation statements)

References 36 publications

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“…While its absorption via both the gastro-intestinal tract and the skin were low (Log Kp = − 10.51 cm/s), it was not categorized as blood–brain–barrier (BBB) permeant but it was a substrate of the p-glycoprotein. Cytochrome P450 (CYP) isoforms, such as CYP1A2, CYP2C19, CYP2C9, CYP2D6 and CYP3A4, are commonly used in biotransformation of drugs and xenobiotics [ 30 , 33 , 61 ]. In this study, the screened CYP enzyme isoforms data indicate that the compound is inhibiting none of these isoenzymes.…”

Section: Resultsmentioning

confidence: 99%

“…Several biological-related parameters were assessed. The analyses include the lipophilicity, druggability, medicinal chemistry and pharmacokinetics based on ADMET (for absorption, distribution, metabolism, excretion and toxicity) properties as previously described [ 30 , 33 ].…”

Section: In Silico Molecular Docking Druggability and Pharmacokineticsmentioning

confidence: 99%

“…The crystal structure of COVID-19 main protease (PDB 6LU7) in complex with an inhibitor N3 was also used. All proteins were preprocessed than targeted for molecular binding with the compound as previously described [30][31][32]. Preprocessing includes removing water molecules and adding polar hydrogen and Coleman charges [33,34].…”

Section: In Silico Molecular Docking Druggability and Pharmacokineticsmentioning

confidence: 99%

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Vibrational Spectroscopies, Global Reactivity, Molecular Docking, Thermodynamic Properties and Linear and Nonlinear Optical Parameters of Monohydrate Arsenate Salt of 4-Aminopyridine

et al. 2023

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In this work, a structural and electronic properties of a novel organic arsenate template by 4-aminopyridine, with the general formula (C 5 H 7 N 2 )(C 5 H 8 N 2 )[AsO 4 ]·H 2 O ((4-APH)(4-APH 2 )[AsO 4 ]·H 2 O) have been presented. The density functional theory (DFT) along with B3LYP hybrid functional is employed. The optimized structure was found to be in well consistent with the X-ray diffraction geometry. The examination of the vibrational spectrum was correlated by DFT calculation using the unit cell parameters obtained from the experiment data. Besides, the thermodynamic functions (heat capacity, entropy, enthalpy) from spectroscopic data by statistical methods were obtained for the range of temperature 100–1000 K. In addition, the molecular orbital calculations such as Natural Bond Orbitals (NBOs), AIM approach, HOMO–LUMO energy gap, NLO characteristic and Hirshfeld surface analysis were also performed with the same level of DFT. Electronic stability of the compound arising from hyper conjugative interactions and charge delocalization were also investigated based on the natural bond orbital (NBO) analysis. Molecular docking studies were also conducted as part of this study. The theoretical results showed an excellent agreement with the experimental values. Supplementary Information The online version contains supplementary material available at 10.1007/s42250-023-00620-8.

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Section: Resultsmentioning

confidence: 99%

Section: In Silico Molecular Docking Druggability and Pharmacokineticsmentioning

confidence: 99%

Section: In Silico Molecular Docking Druggability and Pharmacokineticsmentioning

confidence: 99%

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Vibrational Spectroscopies, Global Reactivity, Molecular Docking, Thermodynamic Properties and Linear and Nonlinear Optical Parameters of Monohydrate Arsenate Salt of 4-Aminopyridine

et al. 2023

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“…The unwanted COVID‐19 outbreak after its possible emergence from Wuhan Seafood market of China, spread to the whole world, and has taken millions of people under its cover with successive hits (Abdalla et al, 2021 ; Mohapatra, Das, et al, 2020 ; Mohapatra et al, 2021a , 2021b ; Mohapatra & Rahman, 2021 ). As reported, the causative virus (SARS‐CoV‐2) emergence from bats and pangolins.…”

Section: Introductionmentioning

confidence: 99%

SARS‐CoV‐2 and its variants of concern including Omicron: A never ending pandemic

Mohapatra¹,

Kuppili

Suvvari

et al. 2022

Chem Biol Drug Des

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The ongoing COVID‐19 pandemic caused by SARS‐CoV‐2 is associated with high morbidity and mortality. This zoonotic virus has emerged in Wuhan of China in December 2019 from bats and pangolins probably and continuing the human‐to‐human transmission globally since last two years. As there is no efficient approved treatment, a number of vaccines were developed at an unprecedented speed to counter the pandemic. Moreover, vaccine hesitancy is observed that may be another possible reason for this never ending pandemic. In the meantime, several variants and mutations were identified and causing multiple waves globally. Now the safety and efficacy of these vaccines are debatable and recommended to determine whether vaccines are able to interrupt transmission of SARS‐CoV‐2 variant of concern (VOC). Moreover, the VOCs continue to emerge that appear more transmissible and less sensitive to virus‐specific immune responses. In this overview, we have highlighted various drugs and vaccines used to counter this pandemic along with their reported side effects. Moreover, the preliminary data for the novel VOC “Omicron” are discussed with the existing animal models.

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“…The disease is manifested with typical [ 5 , 7 ] and atypical [ 8 , 9 ] symptoms. As per reports, the virus infects the upper and lower respiratory parts, heart, kidney, liver, gut, and the nervous system, ultimately causing multiorgan damage [ 10 , 11 ]. It causes severe health problems in the immunocompromised with diabetes, obesity, hypertension, cardiovascular disorder, psychiatric disorder, etc.…”

Section: Introductionmentioning

confidence: 99%

Symptom-Based COVID-19 Prognosis through AI-Based IoT: A Bioinformatics Approach

Pal¹,

Parija²,

Mohapatra³

et al. 2022

BioMed Research International

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Objective. Internet of Things (IoT) integrates several technologies where devices learn from the experience of each other thereby reducing human-intervened likely errors. Modern technologies like IoT and machine learning enable the conventional to patient-specific approach transition in healthcare. In conventional approach, the biggest challenge faced by healthcare professionals is to predict a disease by observing the symptoms, monitoring the remote area patient, and also attending to the patient all the time after being hospitalised. IoT provides real-time data, makes decision-making smarter, and provides far superior analytics, and all these to help improve the quality of healthcare. The main objective of the work was to create an IoT-based automated system using machine learning models for symptom-based COVID-19 prognosis. Methods. Comparative analysis of predictive microbiology of COVID-19 from case symptoms using various machine learning classifiers like logistics regression, k-nearest neighbor, support vector machine, random forest, decision trees, Naïve Bayes, and gradient booster is reported here. For the sake of the validation and verification of the models, performance of each model based on the retrieved cloud-stored data was measured for accuracy. Results. From the accuracy plot, it was concluded that k-NN was more accurate (97.97%) followed by decision tree (97.79), support vector machine (97.42), logistics regression (96.50), random forest (90.66), gradient boosting classifier (87.77), and Naïve Bayes (73.50) in COVID-19 prognosis. Conclusion. The paper presents a health monitoring IoT framework having high clinical significance in real-time and remote healthcare monitoring. The findings reported here and the lessons learnt shall enable the healthcare system worldwide to counter not only this ongoing COVID but many other such global pandemics the humanity may suffer from time to come.

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Repurposing benzimidazole and benzothiazole derivatives as potential inhibitors of SARS-CoV-2: DFT, QSAR, molecular docking, molecular dynamics simulation, and in-silico pharmacokinetic and toxicity studies

Cited by 43 publications

References 36 publications

Vibrational Spectroscopies, Global Reactivity, Molecular Docking, Thermodynamic Properties and Linear and Nonlinear Optical Parameters of Monohydrate Arsenate Salt of 4-Aminopyridine

Vibrational Spectroscopies, Global Reactivity, Molecular Docking, Thermodynamic Properties and Linear and Nonlinear Optical Parameters of Monohydrate Arsenate Salt of 4-Aminopyridine

SARS‐CoV‐2 and its variants of concern including Omicron: A never ending pandemic

Symptom-Based COVID-19 Prognosis through AI-Based IoT: A Bioinformatics Approach

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