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Pradhan S, Mishra DK, Gurung P, Chettri A, Singha UK, Dutta T, Sinha B. An In-Silico Drug Designing Approach Attempted on a Newly Synthesized Co(II) Complex along with its Other Biological Activities: A Combined Investigation of both Experimental and Theoretical Aspects. J Fluoresc 2024:10.1007/s10895-024-03852-0. [PMID: 39031237 DOI: 10.1007/s10895-024-03852-0] [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: 05/07/2024] [Accepted: 07/15/2024] [Indexed: 07/22/2024]
Abstract
A new Co (II) complex incorporating a novel Schiff base ligand acquired from the condensation of 3,3'-Methylenedianiline and 2-Hydroxy-5-bromobenzaldehyde was synthesized and characterized. The synthesized complex was air and moisture stable, monomeric, and non-electrolytic in nature. Based on physical and spectral studies, tetrahedral conformation was ascribed to the synthesized Co (II) complex.Density Functional Theory (DFT) was used to analysis different electronic parameters of the optimized structure of Co(II) complex to reveal its stability.Using different analytic and spectroscopic techniques, the new Co (II) complex was established to interact with DNA quite effectively and works as an efficient metallo intercalators. The synthesized complex was discovered to cleave DNA significantly, so it can be inferred that the complex will inhibit the growth of pathogens. Molecular docking was performed to check the binding affinity of the cobalt complex with different receptors, responsible for different diseases. Proteins like progesterone receptor and induced myeloid leukemia cell differentiation Mcl-1 protein showed high binding affinity with this complex, and hence the complex might have some implications for inhibition of progesterone hormones in biological systems. Biological activity of the Co (II) complex was also predicted through computational analysis with SwissADME.Using strains of Escherichia coli, Klebsiella pneumoniae, Bacillus subtilis, and Staphylococcus aureus, an in vitro antibacterial activity of the ligand and Co (II) complex was carried out. This activity was further validated by a molecular docking investigation.
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Affiliation(s)
- Sudarshan Pradhan
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India
| | - Dipu Kumar Mishra
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India
| | - Pritika Gurung
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India
| | - Anmol Chettri
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India
| | - Uttam Kumar Singha
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India
| | - Tanmoy Dutta
- Department of Chemistry, JIS College of Engineering, Kalyani, 741235, India
| | - Biswajit Sinha
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India.
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2
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Liu D, Leung KY, Lam HY, Zhang R, Fan Y, Xie X, Chan KH, Hung IFN. Interaction and antiviral treatment of coinfection between SARS-CoV-2 and influenza in vitro. Virus Res 2024; 345:199371. [PMID: 38621598 PMCID: PMC11047751 DOI: 10.1016/j.virusres.2024.199371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/18/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has lasted for three years. Coinfection with seasonal influenza may occur resulting in more severe diseases. The interaction between these two viruses for infection and the effect of antiviral treatment remains unclear. METHODS A SARS-CoV-2 and influenza H1N1 coinfection model on Calu-3 cell line was established, upon which the simultaneous and sequential coinfection was evaluated by comparing the viral load. The efficacy of molnupiravir and baloxavir against individual virus and coinfection were also studied. RESULTS The replication of SARS-CoV-2 was significantly interfered when the influenza virus was infected simultaneously or in advance (p < 0.05). On the contrary, the replication of the influenza virus was not affected by the SARS-CoV-2. Molnupiravir monotherapy had significant inhibitory effect on SARS-CoV-2 when the concentration reached to 6.25 μM but did not show any significant anti-influenza activity. Baloxavir was effective against influenza within the dosage range and showed significant effect of anti-SARS-CoV-2 at 16 μM. In the treatment of coinfection, molnupiravir had significant effect for SARS-CoV-2 from 6.25 μM to 100 μM and inhibited H1N1 at 100 μM (p < 0.05). The tested dosage range of baloxavir can inhibit H1N1 significantly (p < 0.05), while at the highest concentration of baloxavir did not further inhibit SARS-CoV-2, and the replication of SARS-CoV-2 significantly increased in lower concentrations. Combination treatment can effectively inhibit influenza H1N1 and SARS-CoV-2 replication during coinfection. Compared with molnupiravir or baloxavir monotherapy, combination therapy was more effective in less dosage to inhibit the replication of both viruses. CONCLUSIONS In coinfection, the replication of SARS-CoV-2 would be interfered by influenza H1N1. Compared with molnupiravir or baloxavir monotherapy, treatment with a combination of molnupiravir and baloxavir should be considered for early treatment in patients with SARS-CoV-2 and influenza coinfection.
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Affiliation(s)
- Danlei Liu
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Ka-Yi Leung
- Department of Microbiology, Li Ka Shing faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Hoi-Yan Lam
- Department of Microbiology, Li Ka Shing faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Ruiqi Zhang
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Yujing Fan
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Xiaochun Xie
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Kwok-Hung Chan
- Department of Microbiology, Li Ka Shing faculty of Medicine, University of Hong Kong, Hong Kong, China; State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, Li Ka Shing faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Ivan Fan-Ngai Hung
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China; State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, Li Ka Shing faculty of Medicine, University of Hong Kong, Hong Kong, China.
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3
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Singha UK, Pradhan S, Gurung P, Chhetri P, Chettri A, Dutta T, Sinha B. Synthesis and Characterization of Zn(II) Complex of 4-chloro-2-(((2-phenoxyphenyl)imino)methyl)phenol and its Biological Efficacies: DNA Interaction, ADMET, DFT and Molecular Docking Study. J Fluoresc 2024:10.1007/s10895-024-03687-9. [PMID: 38613713 DOI: 10.1007/s10895-024-03687-9] [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: 02/07/2024] [Accepted: 03/22/2024] [Indexed: 04/15/2024]
Abstract
Condensing 2-phenoxyaniline with 5-chlorosalicyldehyde under reflux conditions, a 4-chloro-2-(((2-phenoxyphenyl)imino)methyl)phenol Schiff base has been Synthesized. A zinc complex was synthesized by combining the ligand in a 1:1 molar ratio with zinc sulphateheptahydrate. Mass spectroscopy, NMR, infrared, and elemental analysis were used to characterize the ligand and zinc complex. By measuring the molar conductance, the non-electrolytic character of the complex was confirmed. The zinc ion is coordinated in a pentadentate manner, according to an IR and NMR investigation. Viscosity measurements, absorption and fluorescence spectroscopy were utilized to examine the complex's interaction with CT (calf thymus) DNA. Furthermore, the ligand and complex's ADMET characteristics were ascertained through the use of ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) study. Calculation of the different electronic parameters of the optimized structure through Density Functional Theory (DFT) indicated the stability of the Zn(II) complex. Molecular docking study reflected the future opportunity for the consideration of Zn(II) complex to fight against Alzheimer and Glaucoma diseases.
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Affiliation(s)
- Uttam Kumar Singha
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India
| | - Sudarshan Pradhan
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India
| | - Pritika Gurung
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India
| | - Prajal Chhetri
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India
| | - Anmol Chettri
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India
| | - Tanmoy Dutta
- Department of Chemistry, JIS College of Engineering, Kalyani, 741235, India
| | - Biswajit Sinha
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India.
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4
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Sheikhi N, Bahraminejad M, Saeedi M, Mirfazli SS. A review: FDA-approved fluorine-containing small molecules from 2015 to 2022. Eur J Med Chem 2023; 260:115758. [PMID: 37657268 DOI: 10.1016/j.ejmech.2023.115758] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023]
Abstract
Fluorine-containing small molecules have occupied a special position in drug discovery research. The successful clinical use of fluorinated corticosteroids in the 1950s and fluoroquinolones in the 1980s led to an ever-increasing number of approved fluorinated compounds over the last 50 years. They have shown various biological properties such as antitumor, antimicrobial, and anti-inflammatory activities. Fluoro-pharmaceuticals have been considered a strong and practical tool in the rational drug design approach due to their benefits from potency and ADME (absorption, distribution, metabolism, and excretion) points of view. Herein, approved fluorinated drugs from 2015 to 2022 were reviewed.
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Affiliation(s)
- Negar Sheikhi
- Department of Medicinal Chemistry, School of Pharmacy, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Bahraminejad
- Department of Medicinal Chemistry, School of Pharmacy, Iran University of Medical Sciences, Tehran, Iran
| | - Mina Saeedi
- Medicinal Plants Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; Persian Medicine and Pharmacy Research Center, Tehran University of Medical Sciences, Tehran, Iran.
| | - Seyedeh Sara Mirfazli
- Department of Medicinal Chemistry, School of Pharmacy, Iran University of Medical Sciences, Tehran, Iran.
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5
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Shehzadi K, Saba A, Yu M, Liang J. Structure-Based Drug Design of RdRp Inhibitors against SARS-CoV-2. Top Curr Chem (Cham) 2023; 381:22. [PMID: 37318607 DOI: 10.1007/s41061-023-00432-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide pandemic since 2019, spreading rapidly and posing a significant threat to human health and life. With over 6 billion confirmed cases of the virus, the need for effective therapeutic drugs has become more urgent than ever before. RNA-dependent RNA polymerase (RdRp) is crucial in viral replication and transcription, catalysing viral RNA synthesis and serving as a promising therapeutic target for developing antiviral drugs. In this article, we explore the inhibition of RdRp as a potential treatment for viral diseases, analysing the structural information of RdRp in virus proliferation and summarizing the reported inhibitors' pharmacophore features and structure-activity relationship profiles. We hope that the information provided by this review will aid in structure-based drug design and aid in the global fight against SARS-CoV-2 infection.
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Affiliation(s)
- Kiran Shehzadi
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Afsheen Saba
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Mingjia Yu
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China.
| | - Jianhua Liang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China.
- Yangtze Delta Region Academy of Beijing Institute of Technology, Jiaxing, 314019, China.
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6
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Seyedi SH, Alhagh MS, Ahmadizad M, Ardalan N, Hosseininezhadian Koushki E, Farshadfar C, Amjadi B. Structural screening into the recognition of a potent inhibitor against non-structural protein 16: a molecular simulation to inhibit SARS-CoV-2 infection. J Biomol Struct Dyn 2022; 40:14115-14130. [PMID: 34762019 DOI: 10.1080/07391102.2021.2001374] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
COVID-19 infection is caused by endemic crown infection (SARS-CoV-2) and is associated with lung damage and severe immune response. Non-Structural Proteins are the central components of coronaviral transcription and replication machinery in SARS-CoV-2 and also stimulate mRNA cap methylation to avoid the immune response. Non-Structural Protein 16 (NSP16) is one of the primary targets for the drug discovery of coronaviruses. Discovering an effective inhibitor against the NSP16 in comparison with Sinefungin was the main purpose of this investigation. Binding free-energy calculations, computational methods of molecular dynamics, docking, and virtual screening were utilized in this study. The ZINC and PubChem databases were applied to screen some chemical compounds regarding Sinefungin as a control inhibitor. Based on structural similarity to Sinefungin, 355 structures were obtained from the mentioned databases. Subsequently, this set of compounds were monitored by AutoDock Vina software, and ultimately the potent inhibitor (PUBCHEM512713) was chosen. At the next stage, molecular dynamics were carried out by GROMACS software to evaluate the potential elected compounds in a simulated environment and in a timescale of 100 nanoseconds. MM-PBSA investigation exhibited that the value of binding free energy for PUBCHEM512713 (-30.829 kJ.mol-1) is more potent than Sinefungin (-11.941 kJ.mol-1). Furthermore, the results of ADME analysis illustrated that the pharmacokinetics, drug-likeness, and lipophilicity parameters of PUBCHEM512713 are admissible for human utilization. Finally, our data suggested that PUBCHEM512713 is an effective drug candidate for inhibiting the NSP16 and is suitable for in vitro and in vivo studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Seyed Hamid Seyedi
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | - Mohammad Shakib Alhagh
- Department of Microbiology, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Mehran Ahmadizad
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | - Noeman Ardalan
- Department of Microbiology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Chiako Farshadfar
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | - Barzan Amjadi
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
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7
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Ávila-Gálvez MÁ, Rafael-Pita C, Fernández N, Baixinho J, Anastácio JD, Cankar K, Bosch D, Nunes Dos Santos C. Targeting proteases involved in the viral replication of SARS-CoV-2 by sesquiterpene lactones from chicory ( Cichorium intybus L.). Food Funct 2022; 13:8977-8988. [PMID: 35938740 DOI: 10.1039/d2fo00933a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
SARS-CoV-2 is a highly transmissible and pathogenic coronavirus causing a respiratory disease that emerged in 2019, leading to a public health emergency situation which continues to date. The treatment options are still very limited and vaccines available are less effective against new variants. SARS-CoV-2 enzymes, namely main protease (Mpro) and papain-like protease (PLpro), play a pivotal role in the viral life cycle, making them a putative drug target. Here, we described for the first time the potential inhibitory activity of chicory extract against both proteases. Besides, we have identified that the four most abundant sesquiterpene lactones in chicory inhibited these proteases, showing an effective binding in the active sites of Mpro and PLpro. This paper provides new insight for further drug development or food-based strategies for the prevention of SARS-CoV-2 by targeting viral proteases.
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Affiliation(s)
- María Ángeles Ávila-Gálvez
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
- NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal.
| | - Carlos Rafael-Pita
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
- NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal.
| | - Naiara Fernández
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
| | - João Baixinho
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - José D Anastácio
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
- NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal.
| | - Katarina Cankar
- Wageningen University and Research, Wageningen Plant Research, BU Bioscience, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Dirk Bosch
- Wageningen University and Research, Wageningen Plant Research, BU Bioscience, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Cláudia Nunes Dos Santos
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
- NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal.
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8
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Tan A. Synthesis, spectroscopic characterization of novel phthalimides derivatives bearing a 1,2,3-triazole unit and examination as potential SARS-CoV-2 inhibitors via in silico studies. J Mol Struct 2022; 1261:132915. [PMID: 35345413 PMCID: PMC8942404 DOI: 10.1016/j.molstruc.2022.132915] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/08/2022] [Accepted: 03/22/2022] [Indexed: 12/16/2022]
Abstract
In the present study, novel phthalimide derivatives 8(a-f) and 9(a-f) bearing a 1,2,3-triazole subunit were synthesized via CuAAC reactions and characterized by 1H, 13C NMR, HR-MS, and FT-IR analyses. To support the fight against SARS-CoV-2, in silico molecular docking studies were carried out to examine their interactions with the proteins of SARS-CoV-2 (Mpro and PLpro) and the protein-protein interactions (PPI) between the ACE2-spike (S1) in comparison with various inhibitors reported to be active by in vitro experiments. The ligand-protein stabilities of compounds 8a-Mpro, 8b-PLpro, and 9a-'ACE2-S1' showing the best binding energy and predicted inhibition constant values (Ki) were examined by molecular dynamics simulation studies. Finally, in silico ADMET properties of the target compounds were investigated using the Swiss ADME and ProTox-II web tools. According to in silico results, all phthalimide analogs may block the PPI between S1 and ACE2. The compounds may also inhibit the progression of the Mpro, and PLpro proteins of SARS-CoV-2. Additionally, it has been estimated that the compounds are suitable for oral administration and exhibit low levels of toxicity.
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Affiliation(s)
- Ayse Tan
- Vocational School of Technical Sciences, Mus Alparslan University, Mus 49250, Turkey
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9
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Tabbiche A, Bouchama A, Chafai N, Zaidi F, Chiter C, Yahiaoui M, Abiza A. New bis hydrazone: Synthesis, X-ray crystal structure, DFT computations, conformational study and in silico study of the inhibition activity of SARS-CoV-2. J Mol Struct 2022; 1261:132865. [PMID: 35345533 PMCID: PMC8934244 DOI: 10.1016/j.molstruc.2022.132865] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 12/16/2022]
Abstract
The aim of this work was to synthesize new bis hydrazone derived from benzil in good yield, namely: (1Z,2Z)-1,2-bis (3-Chlorophenyl Hydrazino) Benzil, encoded by 3-Cl BHB. The benzil (or 1,2-diphenyl ethanedione) reacts with 3-Cl phenyl hydrazine by reflux method using ethanol as solvent to obtain the target compound. The obtained product is depicted by UV-Vis, IR spectroscopy and XRD-crystals analysis. All various contacts intra and intermolecular found in 3-Cl BHB were determined by the X-ray diffraction technique performed on single crystals. On the other hand, the optimized geometric structure of 3-Cl BHB was computed by the DFT/B3LYP method with 6-31 G (d, p) level. So, the bond lengths and angles, frontier molecular orbitals (FMO), surface electrostatic potential of the molecule (MEP), global reactivity descriptors, Mulliken atomic charges, computed vibrational analysis and electronic absorption spectrum were determined to get a good understanding of the electronic properties and the active sites of 3-Cl BHB, then to compare them with experimental data. Additionally, a conformational study was carried out using the same method (DFT). The structure-activity relationships established through molecular docking studies showed that 3-Cl BHB structure strongly binds to the receptors Mpro (-8.90 Kcal/mol) and RdRp (-8.60 Kcal/mol) which confirm its inhibition activity against COVID-19.
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Affiliation(s)
- Abdelkader Tabbiche
- Laboratoire de Chimie, Ingénierie Moléculaire et Nanostructures, Université Ferhat Abbas Sétif 1, Sétif 19000, Algeria,Département de chimie, Faculté des sciences, Université Ferhat Abbas-Sétif-1, Algeria
| | - Abdelaziz Bouchama
- Département de chimie, Faculté des sciences, Université Ferhat Abbas-Sétif-1, Algeria
| | - Nadjib Chafai
- Department of Process Engineering, Faculty of Technology, Laboratory of Electrochemistry of Molecular Materials and Complex (LEMMC). University of Ferhat ABBAS Setif-1, El-Mabouda campus, Sétif 19000, Algeria,Corresponding author
| | - Farouk Zaidi
- Département de chimie, Faculté des sciences, Université Ferhat Abbas-Sétif-1, Algeria
| | - Chaabane Chiter
- Department of Process Engineering, Faculty of Technology, Laboratory of Electrochemistry of Molecular Materials and Complex (LEMMC). University of Ferhat ABBAS Setif-1, El-Mabouda campus, Sétif 19000, Algeria
| | - Messaoud Yahiaoui
- Department of Process Engineering, Faculty of Technology, Laboratory of Electrochemistry of Molecular Materials and Complex (LEMMC). University of Ferhat ABBAS Setif-1, El-Mabouda campus, Sétif 19000, Algeria
| | - Abdellah Abiza
- Laboratoire de Chimie, Ingénierie Moléculaire et Nanostructures, Université Ferhat Abbas Sétif 1, Sétif 19000, Algeria
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10
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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11
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Baildya N, Ghosh NN, Chattopadhyay AP, Mandal V, Majumdar S, Ansary D, Sarkar MM. Inhibitory effect of compounds extracted from Monochoria hastata (L.) Solms on SARS-CoV-2 main protease: An insight from molecular docking and MD-simulation studies. J Mol Struct 2022; 1257:132644. [PMID: 35185220 PMCID: PMC8846558 DOI: 10.1016/j.molstruc.2022.132644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 02/06/2022] [Accepted: 02/15/2022] [Indexed: 11/29/2022]
Abstract
Using molecular docking and other studies, 20 compounds extracted from Monochoria hastata (L.) Solms were screened, and their inhibitory efficiency examined against main protease (3CLpro) of SARS CoV-2. All the compounds were found to binding with 3CLpro through van der Waals and electrostatic forces of attractions. Among them, Azelaic dihydrazide (ADZ) was found to have the highest docking score. 3CLpro-ADZ complex was studied by MD simulation. ADZ was found to disrupt the structure of 3CLpro after 2 ns. RMSD and RMSF analysis along with sequence and binding energy analysis suggest that ADZ can be a potential drug against SARS CoV-2.
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Affiliation(s)
- Nabajyoti Baildya
- Department of Chemistry, University of Kalyani, Kalyani 741235, India
| | - Narendra Nath Ghosh
- Department of Chemistry, University of Gour Banga, Mokdumpur, Malda 732103, India
| | | | - Vivekananda Mandal
- Plant and Microbial Physiology and Biochemistry Laboratory, Department of Botany, University of Gour Banga, Mokdumpur, Malda 732103, India
| | - Sourav Majumdar
- Department of Chemistry, Kandi Raj College, Kandi, Murshidabad, 742137, India
| | - Delwar Ansary
- Department of Chemistry, Dumkal College, Murshidabad, Domkal 742406, India
| | - Md Muttakin Sarkar
- Department of Chemistry, Dumkal College, Murshidabad, Domkal 742406, India
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Reza R, Dutta T, Baildya N, Ghosh NN, Khan AA, Das RK. Repurposing of anti-lung cancer drugs as multi-target inhibitors of SARS-CoV-2 proteins: An insight from molecular docking and MD-simulation study. Microb Pathog 2022; 169:105615. [PMID: 35690231 PMCID: PMC9174081 DOI: 10.1016/j.micpath.2022.105615] [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: 10/04/2021] [Revised: 06/02/2022] [Accepted: 06/02/2022] [Indexed: 11/20/2022]
Abstract
Herein we have selected seventeen anti-lung cancer drugs to screen against Mpro, PLpro and spike glycoproteins of SARS-CoV-2to ascertain the potential therapeutic agent against COVID-19. ADMET profiling were employed to evaluate their pharmacokinetic properties. Molecular docking studies revealed that Capmatinib (CAP) showed highest binding affinity against the selected proteins of SARS-CoV-2. Molecular Dynamics (MD) simulation and the analysis of RMSD, RMSF, and binding energy confirmed the abrupt conformational changes of the proteins due to the presence of this drug. These findings provide an opportunity for doing advanced experimental research to evaluate the potential drug to combat COVID-19.
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13
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Zhou M, Li Y. Modification of PAE-degrading Esterase(CarEW) for Higher Degradation Efficiency Through Integrated Homology Modeling, Molecular Docking, and Molecular Dynamics Simulation. Chem Res Chin Univ 2022. [DOI: 10.1007/s40242-022-1433-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Roy A, Das R, Roy D, Saha S, Ghosh NN, Bhattacharyya S, Roy MN. Encapsulated hydroxychloroquine and chloroquine into cyclic oligosaccharides are the potential therapeutics for COVID-19: insights from first-principles calculations. J Mol Struct 2022; 1247:131371. [PMID: 34462609 PMCID: PMC8387931 DOI: 10.1016/j.molstruc.2021.131371] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/14/2021] [Accepted: 08/23/2021] [Indexed: 01/04/2023]
Abstract
Novel-Coronavirus (COVID-19) outburst has become a worldwide pandemic which threaten the scientific community to design and discover efficient and effective treatment strategies against this deadly virus (SARS-CoV-2). Still now, there is no antiviral therapy or drug available in the market which can efficiently combat the infection caused by this virus. In this respect, using available drugs by screening with molecular docking and molecular dynamics studies not only minimizes lengthy chemical trials but also reduces discovery cost for the pharmaceutical industry. During the COVID-19 pandemic situations hydroxychloroquine, chloroquine known as HCQ and CQ tablets have gained popularity as for the treatment coronavirus (COVID-19) but the main threatening effect of HCQ, CQ use lies on their side effects like blistering, peeling, loosening of the skin, blurred vision stomach pain, diarrhea, chest discomfort, pain, or tightness, cough or hoarseness which require immediate medical attention. Encapsulation of HCQ and CQ drugs by the cyclic macromolecules such as α and β-Cyclodextrin, to form host-guest complexes is very effective strategy to mask the cytotoxicity of certain drugs and alleviating and modulating side effects of drug applications. In the present work, we have encapsulated the HCQ and CQ drugs α and β-Cyclodextrin and made a comprehensive analysis of stability, optical properties. Details analysis verified that between QC and HCQ, HQC showed stronger affinity towards β-Cyclodextrin. This strategy can reduce the side effect of HCQ and CQ thereby offers a new way to use these drugs. We hope the present study should help the researchers to develop potential therapeutics against the novel coronavirus.
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Affiliation(s)
- Aditi Roy
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India
| | - Ranjoy Das
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India
| | - Debadrita Roy
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India
| | - Subhadeep Saha
- Department of Chemistry, Government General Degree College at Pedong, Kalimpong-734311, India
| | - Narendra Nath Ghosh
- Department of Chemistry, University of Gour Banga, Mokdumpur, Malda, 732103, India
| | | | - Mahendra Nath Roy
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India.,Alipurduar University, Alipurduar, 736123, India
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Al-Otaibi JS, Mary YS, Mary YS, Yadav R. Structural and reactivity studies of pravadoline –An ionic liquid, with reference to its wavefunction-relative properties using DFT and MD simulation. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131074] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Synthesis, crystal structural determination and in silco biological studies of 3,3′-ethane-1,2-diylbis(2-benzylidene-1,3-thiazolidin-4-one. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Inhibitory effect of anti-HIV compounds extracted from Indian medicinal plants to retard the replication and transcription process of SARS-CoV-2: an insight from molecular docking and MD-simulation studies. ACTA ACUST UNITED AC 2021; 10:32. [PMID: 33948424 PMCID: PMC8084713 DOI: 10.1007/s13721-021-00309-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 04/19/2021] [Accepted: 04/21/2021] [Indexed: 12/23/2022]
Abstract
Outbreak of Coronavirus (SARS-CoV-2) has thrown a big challenge to the globe by snatching millions of human lives from the world. In this study, inhibitory efficiency of ten anti-HIV compounds from different Indian medicinal plant parts have been virtually screened against Mpro, PLpro and RdRp proteins of SARS-CoV-2. The molecular docking study reflected that among these compounds, Proptine (PTP) has the highest binding affinity for the three cases. Introduction of PTP molecules within the binding pocket of these proteins showed a large structural and conformational changes on the structure of proteins which is revealed from molecular dynamics (MD) simulation studies. RMSD, RMSF and analysis of thermodynamic parameters also revealed that PTP makes a huge impact on the structures of the respective proteins which will pave an opportunity for doing advanced experimental research to evaluate the potential drug to combat COVID-19.
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