1
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Cobre ADF, Maia Neto M, de Melo EB, Fachi MM, Ferreira LM, Tonin FS, Pontarolo R. Naringenin-4'-glucuronide as a new drug candidate against the COVID-19 Omicron variant: a study based on molecular docking, molecular dynamics, MM/PBSA and MM/GBSA. J Biomol Struct Dyn 2024; 42:5881-5894. [PMID: 37394802 DOI: 10.1080/07391102.2023.2229446] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/19/2023] [Indexed: 07/04/2023]
Abstract
This study aimed to identify natural bioactive compounds (NBCs) as potential inhibitors of the spike (S1) receptor binding domain (RBD) of the COVID-19 Omicron variant using computer simulations (in silico). NBCs with previously proven biological in vitro activity were obtained from the ZINC database and analyzed through virtual screening, molecular docking, molecular dynamics (MD), molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA), and molecular mechanics/generalized Born surface area (MM/GBSA). Remdesivir was used as a reference drug in docking and MD calculations. A total of 170,906 compounds were analyzed. Molecular docking screening revealed the top four NBCs with a high affinity with the spike (affinity energy <-7 kcal/mol) to be ZINC000045789238, ZINC000004098448, ZINC000008662732, and ZINC000003995616. In the MD analysis, the four ligands formed a complex with the highest dynamic equilibrium S1 (mean RMSD <0.3 nm), lowest fluctuation of the complex amino acid residues (RMSF <1.3), and solvent accessibility stability. However, the ZINC000045789238-spike complex (naringenin-4'-O glucuronide) was the only one that simultaneously had minus signal (-) MM/PBSA and MM/GBSA binding free energy values (-3.74 kcal/mol and -15.65 kcal/mol, respectively), indicating favorable binding. This ligand (naringenin-4'-O glucuronide) was also the one that produced the highest number of hydrogen bonds in the entire dynamic period (average = 4601 bonds per nanosecond). Six mutant amino acid residues formed these hydrogen bonds from the RBD region of S1 in the Omicron variant: Asn417, Ser494, Ser496, Arg403, Arg408, and His505. Naringenin-4'-O-glucuronide showed promising results as a potential drug candidate against COVID-19. In vitro and preclinical studies are needed to confirm these findings.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Moisés Maia Neto
- Department of Pharmacy, Fametro University Centre (UNIFAMETRO), Fortaleza-Ceará, Brazil
| | - Eduardo Borges de Melo
- Department of Pharmacy, Universidade Estadual do Oeste do Paraná (UNIOESTE), Cascavel-PR, Brazil
| | - Mariana Millan Fachi
- Pharmaceutical Sciences Postgraduate Programme, Universidade Federal do Paraná, Curitiba, Brazil
| | | | - Fernanda Stumpf Tonin
- H&TRC - Health & Technology Research Centre, ESTeSL, Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Roberto Pontarolo
- Department of Pharmacy, Universidade Federal do Paraná, Curitiba, Brazil
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2
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Shu VA, Eni DB, Ntie-Kang F. A survey of isatin hybrids and their biological properties. Mol Divers 2024:10.1007/s11030-024-10883-z. [PMID: 38833124 DOI: 10.1007/s11030-024-10883-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/15/2024] [Indexed: 06/06/2024]
Abstract
The emergence of diverse infections worldwide, which is a serious global threat to human existence, necessitates the urgent development of novel therapeutic candidates that can combat these diseases with efficacy. Molecular hybridization has been established as an efficient technique in designing bioactive molecules capable of fighting infections. Isatin, a core nucleus of an array of compounds with diverse biological properties can be modified at different positions leading to the creation of novel drug targets, is an active area of medicinal chemistry. This review containing published articles from 2005 to 2022 highlights isatin hybrids which have been synthesized and reported in the literature alongside a discussion on their biological properties. The enriched structure-activity relationship studies discussed provides insights for the rational design of novel isatin hybrids with tailored biological properties as effective therapeutic candidates inspired by nature.
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Affiliation(s)
- Vanessa Asoh Shu
- Center for Drug Discovery, Faculty of Science, University of Buea, Buea, Cameroon
| | - Donatus Bekindaka Eni
- Center for Drug Discovery, Faculty of Science, University of Buea, Buea, Cameroon.
- Department of Chemistry, Faculty of Science, University of Buea, Buea, Cameroon.
| | - Fidele Ntie-Kang
- Center for Drug Discovery, Faculty of Science, University of Buea, Buea, Cameroon.
- Department of Chemistry, Faculty of Science, University of Buea, Buea, Cameroon.
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany.
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3
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Rasul HO, Thomas NV, Ghafour DD, Aziz BK, Salgado M G, Mendoza-Huizar LH, Candia LG. Searching possible SARS-CoV-2 main protease inhibitors in constituents from herbal medicines using in silico studies. J Biomol Struct Dyn 2024; 42:4234-4248. [PMID: 37349945 DOI: 10.1080/07391102.2023.2220040] [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: 04/01/2023] [Accepted: 05/23/2023] [Indexed: 06/24/2023]
Abstract
The largest threat to civilization since the Second World War is the spread of the new coronavirus disease (COVID-19). Therefore, there is an urgent need for innovative therapeutic medicines to treat COVID-19. Reusing bio-actives is a workable and efficient strategy in the battle against new epidemics because the process of developing new drugs is time-consuming. This research aimed to identify which herbal remedies had the highest affinity for the receptor and assess a variety of them for potential targets to suppress the SARS-CoV-2 Mpro. The use of AutoDock Vina for structure-based virtual screening was done first due to the importance of protein interactions in the development of drugs. Molecular docking was used in the comparative study to assess 89 different chemicals from medicinal herbs. To anticipate their effectiveness against the primary protease of SARS-CoV-2, more analysis was done on the ADMET profile, drug-likeness, and Lipinski's rule of five. The next step involved three replicas of 100 ns-long molecular dynamics simulations on the potential candidates, which were preceded by calculations of the binding free energy of MM-GBSA. The outcomes showed that Achyrodimer A, Cinchonain Ib, Symphonone F, and Lupeol acetate all performed well and had the highest 6LU7 binding affinities. Using RMSD, RMSF, and protein-ligand interactions, the stability of the protein-ligand complex was assessed. The studies indicate that bioactive substances obtained from herbal medicines may function as a COVID-19 therapeutic agent, necessitating additional wet lab research to confirm their therapeutic potential, efficacy, and pharmacological capacity against the condition.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hezha O Rasul
- Department of Pharmaceutical Chemistry, College of Science, Charmo University, Chamchamal, Sulaimani, Iraq
| | - Noel Vinay Thomas
- Department of BioMedical Science, College of Science, Komar University of Science and Technology, Sulaimani, Iraq
| | - Dlzar D Ghafour
- Department of Medical Laboratory Science, College of Science, Komar University of Science and Technology, Sulaimani, Iraq
- Department of Chemistry, College of Science, University of Sulaimani, Sulaimani, Iraq
| | - Bakhtyar K Aziz
- Department of Nanoscience and Applied Chemistry, College of Science, Charmo University, Chamchamal, Sulaimani, Iraq
| | | | - L H Mendoza-Huizar
- Academic Area of Chemistry, Mineral de la Reforma, Autonomous University of Hidalgo State, Hidalgo, México
| | - Lorena Gerli Candia
- Departamento de Química Ambiental, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile
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4
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Huang CY, Metz A, Lange R, Artico N, Potot C, Hazemann J, Müller M, Dos Santos M, Chambovey A, Ritz D, Eris D, Meyer S, Bourquin G, Sharpe M, Mac Sweeney A. Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket. Acta Crystallogr D Struct Biol 2024; 80:123-136. [PMID: 38289714 PMCID: PMC10836397 DOI: 10.1107/s2059798324000329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/09/2024] [Indexed: 02/01/2024] Open
Abstract
To identify starting points for therapeutics targeting SARS-CoV-2, the Paul Scherrer Institute and Idorsia decided to collaboratively perform an X-ray crystallographic fragment screen against its main protease. Fragment-based screening was carried out using crystals with a pronounced open conformation of the substrate-binding pocket. Of 631 soaked fragments, a total of 29 hits bound either in the active site (24 hits), a remote binding pocket (three hits) or at crystal-packing interfaces (two hits). Notably, two fragments with a pose that was sterically incompatible with a more occluded crystal form were identified. Two isatin-based electrophilic fragments bound covalently to the catalytic cysteine residue. The structures also revealed a surprisingly strong influence of the crystal form on the binding pose of three published fragments used as positive controls, with implications for fragment screening by crystallography.
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Affiliation(s)
- Chia Ying Huang
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Alexander Metz
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | - Roland Lange
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | - Nadia Artico
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | - Céline Potot
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | | | - Manon Müller
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | | | | | - Daniel Ritz
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | - Deniz Eris
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Solange Meyer
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | | | - May Sharpe
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
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5
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Rudrapal M, Kirboga KK, Abdalla M, Maji S. Explainable artificial intelligence-assisted virtual screening and bioinformatics approaches for effective bioactivity prediction of phenolic cyclooxygenase-2 (COX-2) inhibitors using PubChem molecular fingerprints. Mol Divers 2024:10.1007/s11030-023-10782-9. [PMID: 38200203 DOI: 10.1007/s11030-023-10782-9] [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: 07/11/2023] [Accepted: 11/22/2023] [Indexed: 01/12/2024]
Abstract
Cyclooxygenase-2 (COX-2) inhibitors are nonsteroidal anti-inflammatory drugs that treat inflammation, pain and fever. This study determined the interaction mechanisms of COX-2 inhibitors and the molecular properties needed to design new drug candidates. Using machine learning and explainable AI methods, the inhibition activity of 1488 molecules was modelled, and essential properties were identified. These properties included aromatic rings, nitrogen-containing functional groups and aliphatic hydrocarbons. They affected the water solubility, hydrophobicity and binding affinity of COX-2 inhibitors. The binding mode, stability and ADME properties of 16 ligands bound to the Cyclooxygenase active site of COX-2 were investigated by molecular docking, molecular dynamics simulation and MM-GBSA analysis. The results showed that ligand 339,222 was the most stable and effective COX-2 inhibitor. It inhibited prostaglandin synthesis by disrupting the protein conformation of COX-2. It had good ADME properties and high clinical potential. This study demonstrated the potential of machine learning and bioinformatics methods in discovering COX-2 inhibitors.
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Affiliation(s)
- Mithun Rudrapal
- Department of Pharmaceutical Sciences, School of Biotechnology and Pharmaceutical Sciences, Vignan's Foundation for Science, Technology & Research (Deemed to Be University), Guntur, 522213, India.
| | - Kevser Kübra Kirboga
- Informatics Institute, Istanbul Technical University, 34469, Maslak, Istanbul, Turkey.
- Bioengineering Department, BilecikSeyhEdebali University, 11230, Bilecik, Turkey.
| | - Mohnad Abdalla
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University, Jinan, 250022, Shandong, People's Republic of China
| | - Siddhartha Maji
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA
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6
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Fegade BS, Jadhav SB, Chaudhari SY, T Tandale D, Shantaram Uttekar P, Tabrez S, Khan MS, Zaidi SK, Mukerjee N, Ghosh A. Synthesis and computational insights of flavone derivatives as potential estrogen receptor alpha (ER-α) antagonist. J Biomol Struct Dyn 2023:1-10. [PMID: 38006310 DOI: 10.1080/07391102.2023.2278746] [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: 05/24/2023] [Accepted: 10/01/2023] [Indexed: 11/27/2023]
Abstract
Hormone-related breast cancer is mostly caused by interactions with estrogen receptor alpha (ER-α), which functions as a transcription factor to control the transcription of numerous genes. Flavones are considered a good substrate for the estrogen receptor. Substitution of the N-heterocyclic ring on the flavon structure may potentiate its anticancer effect. A series of flavon derivatives with an N-heteroaryl ring at the 4' position of the B ring of flavon were designed, prepared and evaluated for in vitro breast cancer activity. Binding interactions of the PzFL, PzF, PiFL, PiF and IFL compounds with ER-α were studied by molecular docking. Molecular dynamics simulation studies were carried out in order to determine the stability and convergence of protein-ligand complexes. The compounds were produced by cyclizing chalcones and chalcones were produced by Claisen-Schmidt condensation of substituted aldehydes and 2-hydroxy acetophenone. Breast cancer activity was evaluated by the MTT assay on MCF-7 cell lines. Also, compounds were studied for their estrogen receptor binding potential on the same cell lines. Molecular docking of compounds showed a good docking score. The molecular dynamics of these compounds expressed stable root mean square deviation, stable radius of gyration and low binding energy, suggesting that ligand bound to protein is quite stable in the complex. MTT assay on MCF-7 cell lines reported PzF and IFL were the most active compounds with lower IC50 values. ER-α binding assay of these compounds revealed the presence of binding interactions with receptors. This study offers a viable reference point for the design of flavon-incorporated N-heterocyclic ring derivatives as breast cancer compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bharti S Fegade
- Department of Pharmaceutical Chemistry, Modern College of Pharmacy, Nigdi, Pune, Maharashtra, India
- Department of Pharmaceutical Chemistry, Gahlot Institute of Pharmacy, Koparkhairane, Navi Mumbai, Maharashtra, India
| | - Shailaja B Jadhav
- Department of Pharmaceutical Chemistry, Modern College of Pharmacy, Nigdi, Pune, Maharashtra, India
| | - Somdatta Y Chaudhari
- Department of Pharmaceutical Chemistry, Modern College of Pharmacy, Nigdi, Pune, Maharashtra, India
| | - Deepak T Tandale
- Department of Pharmaceutics, Gahlot Institute of Pharmacy, Koparkhairane, Navi Mumbai, Maharashtra, India
| | | | - Shams Tabrez
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohd Shahnawaz Khan
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Syed Kashif Zaidi
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nobendu Mukerjee
- Center for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute Of Medical and Technical Sciences, India
- Department of Microbiology, West Bengal State University, Kolkata, Barasat, India
| | - Arabinda Ghosh
- Department of Computational Biology and Biotechnology, Mahapurusha Srimanta Sankaradeva Viswavidyalaya, Assam, India
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7
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Güngör SA. Synthesis, DNA Binding Properties, Molecular Docking and ADME Studies of Schiff Base Compound Containing Pyridine-Propargyl Group. Chem Biodivers 2023; 20:e202300752. [PMID: 37782576 DOI: 10.1002/cbdv.202300752] [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: 05/24/2023] [Revised: 09/15/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023]
Abstract
The structure of the pyridine-based Schiff base compound containing the propargyl group was characterized by NMR spectroscopy. Binding of compound 2 with double-stranded fish sperm DNA (Fsds-DNA) was investigated using viscosity measurement studies and UV/VIS and fluorescence spectral techniques. Binding of compound 2 with Fsds-DNA results in minor hypochromism with no change in absorption maxima and fluorescence quenching with almost no shift in emission maxima, which can be attributed to the groove-binding mode of the interaction. The binding constant was found to be 4.7×104 M-1 . The Fsds-DNA viscosity measurement, KI quenching and NaCl quenching studies and the competitive interaction between compound 2 and ethidium bromide with DNA confirm the proposed binding mode. In addition, interactions between compound 2 and the DNA double helix were analysed by molecular docking study in order to determine the binding mode and binding affinity. As a result of molecular docking, the binding affinity of the 2-DNA complex, which has the most stable conformation -8.10 kcal/mol and it is located in its minor groove. In addition, molecular docking and ADME studies for compound 2 were also performed.
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Affiliation(s)
- Seyit Ali Güngör
- Chemistry Department, Faculty of Science, Kahramanmaras Sütcü Imam University, 46100, Kahramanmaras, Turkey
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8
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Rocha Aguiar G, Leda Gomes de Lemos T, Braz-Filho R, Marques da Fonseca A, Silva Marinho E, Vasconcelos Ribeiro PR, Marques Canuto K, Queiroz Monte FJ. Synthesis and in silico study of chenodeoxycholic acid and its analogues as an alternative inhibitor of spike glycoprotein of SARS-CoV-2. J Biomol Struct Dyn 2023; 41:8334-8348. [PMID: 36218138 DOI: 10.1080/07391102.2022.2133010] [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: 06/07/2022] [Accepted: 09/30/2022] [Indexed: 10/17/2022]
Abstract
COVID-19, caused by SARS-CoV-2, is a viral infection that has generated one of the most significant health problems in the world. Spike glycoprotein is a crucial enzyme in viral replication and transcription mediation. There are reports in the literature on using bile acid in the fight against this virus through in vitro tests. This work presents the synthesis of nine chenodeoxycholic acid derivatives (1-9), which were prepared by oxidation, acetylation, formylation, and esterification reactions, and the analogs 6-9 have not yet been reported in the literature and the possibility of conducting an in silico study of bile acid derivatives as a therapeutic alternative to combat the virus using glycoprotein as a macromolecular target. As a result, five compounds (1, 6-9) possessed favorable competitive interactions with the lowest energies compared to the native ligand (BLA), and the highlighted compound 9 got the best scores. At the same time, analog 1 presented the best ADME filter result. Molecular dynamics also simulated these compounds to verify their stability within the active protein site to seek new therapeutic propositions to fight against the pandemic. Physical and spectroscopic data have fully characterized all the compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gisele Rocha Aguiar
- Departamento de Química Orgânica, Universidade Federal do Ceará, Fortaleza-CE, Brazil
| | | | - Raimundo Braz-Filho
- Laboratório de Ciências Químicas, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro-RJ, Brazil
| | - Aluísio Marques da Fonseca
- Instituto de Ciências Exatas e Naturais, Universidade da Integração Internacional da Lusofonia Afro-Brasileira, Redenção-CE, Brazil
| | - Emmanuel Silva Marinho
- Faculdade de Filosofia Dom Aureliano Matos, Universidade Estadual do Ceará, Limoeiro do Norte-CE, Brazil
| | | | - Kirley Marques Canuto
- Laboratório multiusuário de Química de Produtos Naturais, Embrapa Agroindústria Tropical, Fortaleza-CE, Brazil
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9
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Saramago LC, Santana MV, Gomes BF, Dantas RF, Senger MR, Oliveira Borges PH, Ferreira VNDS, dos Santos Rosa A, Tucci AR, Dias Miranda M, Lukacik P, Strain-Damerell C, Owen CD, Walsh MA, Ferreira SB, Silva-Junior FP. AI-Driven Discovery of SARS-CoV-2 Main Protease Fragment-like Inhibitors with Antiviral Activity In Vitro. J Chem Inf Model 2023; 63:2866-2880. [PMID: 37058135 PMCID: PMC10124747 DOI: 10.1021/acs.jcim.3c00409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Indexed: 04/15/2023]
Abstract
SARS-CoV-2 is the causative agent of COVID-19 and is responsible for the current global pandemic. The viral genome contains 5 major open reading frames of which the largest ORF1ab codes for two polyproteins, pp1ab and pp1a, which are subsequently cleaved into 16 nonstructural proteins (nsp) by two viral cysteine proteases encoded within the polyproteins. The main protease (Mpro, nsp5) cleaves the majority of the nsp's, making it essential for viral replication and has been successfully targeted for the development of antivirals. The first oral Mpro inhibitor, nirmatrelvir, was approved for treatment of COVID-19 in late December 2021 in combination with ritonavir as Paxlovid. Increasing the arsenal of antivirals and development of protease inhibitors and other antivirals with a varied mode of action remains a priority to reduce the likelihood for resistance emerging. Here, we report results from an artificial intelligence-driven approach followed by in vitro validation, allowing the identification of five fragment-like Mpro inhibitors with IC50 values ranging from 1.5 to 241 μM. The three most potent molecules (compounds 818, 737, and 183) were tested against SARS-CoV-2 by in vitro replication in Vero E6 and Calu-3 cells. Compound 818 was active in both cell models with an EC50 value comparable to its measured IC50 value. On the other hand, compounds 737 and 183 were only active in Calu-3, a preclinical model of respiratory cells, showing selective indexes twice as high as those for compound 818. We also show that our in silico methodology was successful in identifying both reversible and covalent inhibitors. For instance, compound 818 is a reversible chloromethylamide analogue of 8-methyl-γ-carboline, while compound 737 is an N-pyridyl-isatin that covalently inhibits Mpro. Given the small molecular weights of these fragments, their high binding efficiency in vitro and efficacy in blocking viral replication, these compounds represent good starting points for the development of potent lead molecules targeting the Mpro of SARS-CoV-2.
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Affiliation(s)
- Luiz Carlos Saramago
- LaBECFar-Laboratório de Bioquímica
Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz,
Fundação Oswaldo Cruz, 21040-900 Rio de
Janeiro, Brazil
| | - Marcos V. Santana
- LaBECFar-Laboratório de Bioquímica
Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz,
Fundação Oswaldo Cruz, 21040-900 Rio de
Janeiro, Brazil
| | - Bárbara Figueira Gomes
- LaBECFar-Laboratório de Bioquímica
Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz,
Fundação Oswaldo Cruz, 21040-900 Rio de
Janeiro, Brazil
| | - Rafael Ferreira Dantas
- LaBECFar-Laboratório de Bioquímica
Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz,
Fundação Oswaldo Cruz, 21040-900 Rio de
Janeiro, Brazil
| | - Mario R. Senger
- LaBECFar-Laboratório de Bioquímica
Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz,
Fundação Oswaldo Cruz, 21040-900 Rio de
Janeiro, Brazil
| | - Pedro Henrique Oliveira Borges
- LaBECFar-Laboratório de Bioquímica
Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz,
Fundação Oswaldo Cruz, 21040-900 Rio de
Janeiro, Brazil
- LaSOPB-Laboratório de Síntese
Orgânica e Prospecção Biológica, Instituto de Química,
Universidade Federal do Rio de Janeiro, 21040-900 Rio de
Janeiro, Brazil
| | - Vivian Neuza dos Santos Ferreira
- LMMV-Laboratório de Morfologia e
Morfogênese Viral (LMMV), Instituto Oswaldo Cruz,
Fundação Oswaldo Cruz, 21040-900 Rio de
Janeiro, Brazil
| | - Alice dos Santos Rosa
- LMMV-Laboratório de Morfologia e
Morfogênese Viral (LMMV), Instituto Oswaldo Cruz,
Fundação Oswaldo Cruz, 21040-900 Rio de
Janeiro, Brazil
| | - Amanda Resende Tucci
- LMMV-Laboratório de Morfologia e
Morfogênese Viral (LMMV), Instituto Oswaldo Cruz,
Fundação Oswaldo Cruz, 21040-900 Rio de
Janeiro, Brazil
| | - Milene Dias Miranda
- LMMV-Laboratório de Morfologia e
Morfogênese Viral (LMMV), Instituto Oswaldo Cruz,
Fundação Oswaldo Cruz, 21040-900 Rio de
Janeiro, Brazil
| | - Petra Lukacik
- Diamond Light Source, Harwell Science and
Innovation Campus, OX11 0DE Didcot, U.K.
- Research Complex at Harwell, Harwell
Science & Innovation Campus, OX11 0FA Didcot,
U.K.
| | - Claire Strain-Damerell
- Diamond Light Source, Harwell Science and
Innovation Campus, OX11 0DE Didcot, U.K.
- Research Complex at Harwell, Harwell
Science & Innovation Campus, OX11 0FA Didcot,
U.K.
| | - C. David Owen
- Diamond Light Source, Harwell Science and
Innovation Campus, OX11 0DE Didcot, U.K.
- Research Complex at Harwell, Harwell
Science & Innovation Campus, OX11 0FA Didcot,
U.K.
| | - Martin Austin Walsh
- Diamond Light Source, Harwell Science and
Innovation Campus, OX11 0DE Didcot, U.K.
- Research Complex at Harwell, Harwell
Science & Innovation Campus, OX11 0FA Didcot,
U.K.
| | - Sabrina Baptista Ferreira
- LaSOPB-Laboratório de Síntese
Orgânica e Prospecção Biológica, Instituto de Química,
Universidade Federal do Rio de Janeiro, 21040-900 Rio de
Janeiro, Brazil
| | - Floriano Paes Silva-Junior
- LaBECFar-Laboratório de Bioquímica
Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz,
Fundação Oswaldo Cruz, 21040-900 Rio de
Janeiro, Brazil
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10
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Mudi PK, Mahanty AK, Kotakonda M, Prasad S, Bhattacharyya S, Biswas B. A benzimidazole scaffold as a promising inhibitor against SARS-CoV-2. J Biomol Struct Dyn 2023; 41:1798-1810. [PMID: 35000553 DOI: 10.1080/07391102.2021.2024448] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The manuscript reports the green-chemical synthesis of a new diindole-substituted benzimidazole compound, B1 through a straightforward route in coupling between indolyl-3-carboxaldehyde and o-phenylenediamine in water medium under the aerobic condition at 75 ºC. The single crystal X-ray structural analysis of B1 suggests that the disubstituted benzimidazole compound crystallizes in a monoclinic system and the indole groups exist in a perpendicular fashion with respect to benzimidazole moiety. The SARS-CoV-2 screening activity has been studied against 1 × 10e4 VeroE6 cells in a dose-dependent manner following Hoechst 33342 and nucleocapsid staining activity with respect to remdesivir. The compound exhibits 92.4% cell viability for 30 h and 35.1% inhibition against VeroE6 cells at non-cytotoxic concentration. Molecular docking studies predict high binding propensities of B1 with the main protease (Mpro) and non-structural (nsp2 and nsp7-nsp8) proteins of SARS-CoV-2 through a number of non-covalent interactions. Molecular dynamics (MD) simulation analysis for 100 ns confirms the formation of stable conformations of B1-docked proteins with significant changes of binding energy, attributing the potential inhibition properties of the synthetic benzimidazole scaffold against SARS-CoV-2. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prafullya Kumar Mudi
- Department of Chemistry, Department of Biotechnology, University of North Bengal, Darjeeling, India
| | - Ayan Kumar Mahanty
- Department of Chemistry, Department of Biotechnology, University of North Bengal, Darjeeling, India
| | | | - Sunnapu Prasad
- Department of Pharmaceutical Chemistry, Sri Ramakrishna Institute of Paramedical Science, Coimbatore, India
| | - Subires Bhattacharyya
- Department of Chemistry, Department of Biotechnology, University of North Bengal, Darjeeling, India
| | - Bhaskar Biswas
- Department of Chemistry, Department of Biotechnology, University of North Bengal, Darjeeling, India
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11
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Rharmili N, Thiruvalluvar AA, Anouar EH, Rodi YK, Chahdi FO, Haoudi A, Mague JT, Mazzah A, Sebbar NK, Essassi EM. Synthesis, X-Ray, Spectroscopic Characterization, Hirshfeld Surface Analysis, Molecular Docking, and DFT Calculations of a New Series of 3-Hydrazono and 3-Phenylhydrazono Isatin Derivatives. Polycycl Aromat Compd 2023. [DOI: 10.1080/10406638.2022.2157454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Nohaila Rharmili
- Laboratory of Applied Organic Chemistry, Faculty of Science and Techniques, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | | | - El Hassane Anouar
- Department of Chemistry, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al Kharj, Saudi Arabia
| | - Youssef Kandri Rodi
- Laboratory of Applied Organic Chemistry, Faculty of Science and Techniques, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Fouad Ouazzani Chahdi
- Laboratory of Applied Organic Chemistry, Faculty of Science and Techniques, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Amal Haoudi
- Laboratory of Applied Organic Chemistry, Faculty of Science and Techniques, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Joel T. Mague
- Department of Chemistry, Tulane University, New Orleans, LA, USA
| | - Ahmed Mazzah
- University of Lille, CNRS, USR 3290, MSAP, Miniaturization for Synthesis, Analysis and Proteomics, Lille, France
| | - Nada Kheira Sebbar
- Laboratory of Organic and Physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
- Laboratory of Heterocyclic Organic Chemistry, Mohammed V University in Rabat, Rabat, BP, Morocco
| | - El Mokhtar Essassi
- Laboratory of Heterocyclic Organic Chemistry, Mohammed V University in Rabat, Rabat, BP, Morocco
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12
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Naidu SAG, Tripathi YB, Shree P, Clemens RA, Naidu AS. Phytonutrient Inhibitors of SARS-CoV-2/NSP5-Encoded Main Protease (M pro) Autocleavage Enzyme Critical for COVID-19 Pathogenesis. J Diet Suppl 2023; 20:284-311. [PMID: 34821532 DOI: 10.1080/19390211.2021.2006388] [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] [Indexed: 12/23/2022]
Abstract
The genomic reshuffling, mutagenicity, and high transmission rate of the SARS-CoV-2 pathogen highlights an urgent need for effective antiviral interventions for COVID-19 control. Targeting the highly conserved viral genes and/or gene-encoded viral proteins such as main proteinase (Mpro), RNA-dependent RNA polymerase (RdRp) and helicases are plausible antiviral approaches to prevent replication and propagation of the SARS-CoV-2 infection. Coronaviruses (CoVs) are prone to extensive mutagenesis; however, any genetic alteration to its highly conserved Mpro enzyme is often detrimental to the viral pathogen. Therefore, inhibitors that target the Mpro enzyme could reduce the risk of mutation-mediated drug resistance and provide effective antiviral protection. Several existing antiviral drugs and dietary bioactives are currently repurposed to treat COVID-19. Dietary bioactives from three ayurvedic medicinal herbs, 18 β-glycyrrhetinic acid (ΔG = 8.86 kcal/mol), Solanocapsine (ΔG = 8.59 kcal/mol), and Vasicoline (ΔG = 7.34 kcal/mol), showed high-affinity binding to Mpro enzyme than the native N3 inhibitor (ΔG = 5.41 kcal/mol). Flavonoids strongly inhibited SARS-CoV-2 Mpro with comparable or higher potency than the antiviral drug, remdesivir. Several tannin hydrolysates avidly bound to the receptor-binding domain and catalytic dyad (His41 and Cys145) of SARS-CoV-2 Mpro through H-bonding forces. Quercetin binding to Mpro altered the thermostability of the viral protein through redox-based mechanism and inhibited the viral enzymatic activity. Interaction of quercetin-derivatives with the Mpro seem to be influenced by the 7-OH group and the acetoxylation of sugar moiety on the ligand molecule. Based on pharmacokinetic and ADMET profiles, several phytonutrients could serve as a promising redox nutraceutical for COVID-19 management.
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Affiliation(s)
- Sreus A G Naidu
- N-terminus Research Laboratory, Yorba Linda, California, USA
| | - Yamini B Tripathi
- Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Priya Shree
- Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Roger A Clemens
- Department of International Regulatory Science, University of Southern California School of Pharmacy, Los Angeles, California, USA
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13
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Singh VK, Chaurasia H, Kumari P, Som A, Mishra R, Srivastava R, Naaz F, Singh A, Singh RK. Design, synthesis, and molecular dynamics simulation studies of quinoline derivatives as protease inhibitors against SARS-CoV-2. J Biomol Struct Dyn 2022; 40:10519-10542. [PMID: 34253149 DOI: 10.1080/07391102.2021.1946716] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A new series of quinoline derivatives has been designed and synthesized as probable protease inhibitors (PIs) against severe acute respiratory syndrome coronavirus 2. In silico studies using DS v20.1.0.19295 software have shown that these compounds behaved as PIs while interacting at the allosteric site of target Mpro enzyme (6LU7). The designed compounds have shown promising docking results, which revealed that all compounds formed hydrogen bonds with His41, His164, Glu166, Tyr54, Asp187, and showed π-interaction with His41, the highly conserved amino acids in the target protein. Toxicity Prediction by Komputer Assisted Technology results confirmed that the compounds were found to be less toxic than the reference drug. Further, molecular dynamics simulations were performed on compound 5 and remdesivir with protease enzyme. Analysis of conformational stability, residue flexibility, compactness, hydrogen bonding, solvent accessible surface area (SASA), and binding free energy revealed comparable stability of protease:5 complex to the protease: remdesivir complex. The result of hydrogen bonding showed a large number of intermolecular hydrogen bonds formed between protein residues (Glu166 and Gln189) and ligand 5, indicating strong interaction, which validated the docking result. Further, compactness analysis, SASA and interactions like hydrogen-bonding demonstrated inhibitory properties of compound 5 similar to the existing reference drug. Thus, the designed compound 5 might act as a potential inhibitor against the protease enzyme.Communicated by Ramaswamy H. SarmaHighlightsQuinoline derivatives have been designed as protease inhibitors against SARS-CoV-2.The compounds were docked at the allosteric site of SARS-CoV-2-Mpro enzyme (PDB ID: 6LU7) to study the stability of protein-ligand complex.Docking studies indicated the stable ligand-protein complexes for all designed compounds.The Toxicity Prediction by Komputer Assisted Technology protocol in DS v20.1.0.19295 software was used to evaluate the toxicity of the designed quinoline derivatives.Molecular dynamics studies indicated the formation of stable ligand-Mpro complexes.
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Affiliation(s)
- Vishal K Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj, India
| | - Himani Chaurasia
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj, India
| | - Priyanka Kumari
- Centre of Bioinformatics, University of Allahabad, Prayagraj, India
| | - Anup Som
- Centre of Bioinformatics, University of Allahabad, Prayagraj, India
| | - Richa Mishra
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj, India
| | - Ritika Srivastava
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj, India
| | - Farha Naaz
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj, India
| | - Anuradha Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj, India
| | - Ramendra K Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj, India
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14
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Barakat A, Mostafa A, Ali M, Al-Majid AM, Domingo LR, Kutkat O, Moatasim Y, Zia K, Ul-Haq Z, Elshaier YAMM. Design, Synthesis and In Vitro Evaluation of Spirooxindole-Based Phenylsulfonyl Moiety as a Candidate Anti-SAR-CoV-2 and MERS-CoV-2 with the Implementation of Combination Studies. Int J Mol Sci 2022; 23:ijms231911861. [PMID: 36233160 PMCID: PMC9569468 DOI: 10.3390/ijms231911861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 09/27/2022] [Accepted: 09/30/2022] [Indexed: 12/03/2022] Open
Abstract
The search for an effective anti-viral to inhibit COVID-19 is a challenge for the specialized scientific research community. This work investigated the anti-coronavirus activity for spirooxindole-based phenylsulfone cycloadducts in a single and combination protocols. The newly designed anti-SARS-CoV-2 therapeutics spirooxindoles synthesized by [3 + 2] cycloaddition reactions represent an efficient approach. One-pot multicomponent reactions between phenyl vinyl sulfone, substituted isatins, and amines afforded highly stereoselective anti-SARS-CoV-2 therapeutics spirooxindoles with three stereogenic centers. Herein, the newly synthesized spirooxindoles were assessed individually against the highly pathogenic human coronaviruses and proved to be highly potent and safer. Interestingly, the synergistic effect by combining the potent, tested spirooxindoles resulted in an improved antiviral activity as well as better host-cell safety. Compounds 4i and 4d represented the most potent activity against MERS-CoV with IC50 values of 11 and 23 µM, respectively. Both compounds 4c and 4e showed equipotent activity with the best IC50 against SARS-CoV-2 with values of 17 and 18 µM, respectively, then compounds 4d and 4k with IC50 values of 24 and 27 µM, respectively. Then, our attention oriented to perform a combination protocol as anti-SARS-CoV-2 for the best compounds with a different binding mode and accompanied with different pharmacophores. Combination of compound 4k with 4c and combination of compounds 4k with 4i proved to be more active and safer. Compounds 4k with 4i displayed IC50 = 3.275 µM and half maximal cytotoxic-concentration CC50 = 11832 µM. MD simulation of the most potential compounds as well as in silico ADMET properties were investigated. This study highlights the potential drug-like properties of spirooxindoles as a cocktail anti-coronavirus protocol.
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Affiliation(s)
- Assem Barakat
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
- Correspondence: (A.B.); (Y.A.M.M.E.); Tel.: +966-11467-5901 (A.B.); Fax: +966-11467-5992 (A.B.)
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt
| | - M. Ali
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdullah Mohammed Al-Majid
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Luis R. Domingo
- Department of Organic Chemistry, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Valencia, Spain
| | - Omnia Kutkat
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt
| | - Yassmin Moatasim
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt
| | - Komal Zia
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Yaseen A. M. M. Elshaier
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Sadat City, Menoufiya 32958, Egypt
- Correspondence: (A.B.); (Y.A.M.M.E.); Tel.: +966-11467-5901 (A.B.); Fax: +966-11467-5992 (A.B.)
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15
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Mudi PK, Mahato RK, Verma H, Panda SJ, Purohit CS, Silakari O, Biswas B. In silico anti-SARS-CoV-2 activities of five-membered heterocycle-substituted benzimidazoles. J Mol Struct 2022; 1261:132869. [PMID: 35340531 PMCID: PMC8934690 DOI: 10.1016/j.molstruc.2022.132869] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/10/2022] [Accepted: 03/17/2022] [Indexed: 12/16/2022]
Abstract
The manuscript deals with cost-effective synthesis, structural characterization and in silico SARS-CoV-2 screening activity of 5-membered heterocycle-substituted benzimidazole derivatives, 1-((1H-pyrrol-2-yl)methyl)-2-(1H-pyrrol-2-yl)-1H-benzo[d]imidazole (L1), 2-(furan-2-yl)-1-(furan-2-ylmethyl)-1H-benzo[d]imidazole (L2), 2-(thiophen-2-yl)-1-(thiophen-2-ylmethyl)-1H-benzo[d]imidazole (L3). The benzimidazole compounds were synthesized through a green-synthetic approach by coupling of 5-membered heterocyclic-carboxaldehyde and o-phenylenediamine in water under an aerobic condition. The compounds were characterized by various spectroscopic methods and X-ray structural analysis. The suitable single-crystals of the methyl derivative of L3 were grown as L3' which crystallized in a monoclinic system and the thiophene groups co-existed in a nearly a perpendicular orientation. Further, in silico anti-SARS-CoV-2 proficiency of the synthetic derivatives is evaluated against main protease (Mpro) and non-structural proteins (nsp2 and nsp7) of SARS-CoV-2. Molecular docking and molecular dynamics analysis of the ligands (L1-L3) against Mpro and nsp2 and nsp7 for 50 ns reveal that L3 turns out to be the superlative antiviral candidate against Mpro, nsp2 and nsp7 of SARS-CoV-2 as evident from the binding score and stability of the ligand-docked complexes with considerable binding energy changes.
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Affiliation(s)
| | - Rajani Kanta Mahato
- Department of Chemistry, University of North Bengal, Darjeeling 734013, India
| | - Himanshu Verma
- Molecular Modeling Lab, Department Pharmaceutical Sciences and Drug Research, Punjabi University, India
| | - Subhra Jyoti Panda
- Department of Chemical Sciences, National School of Science Education and Research, Bhubaneswar 752050, India
| | - Chandra Sekhar Purohit
- Department of Chemical Sciences, National School of Science Education and Research, Bhubaneswar 752050, India
| | - Om Silakari
- Molecular Modeling Lab, Department Pharmaceutical Sciences and Drug Research, Punjabi University, India
| | - Bhaskar Biswas
- Department of Chemistry, University of North Bengal, Darjeeling 734013, India,Corresponding author
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16
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Alici H, Tahtaci H, Demir K. Design and various in silico studies of the novel curcumin derivatives as potential candidates against COVID-19 -associated main enzymes. Comput Biol Chem 2022; 98:107657. [PMID: 35259661 PMCID: PMC8881819 DOI: 10.1016/j.compbiolchem.2022.107657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 02/04/2022] [Accepted: 02/25/2022] [Indexed: 01/18/2023]
Abstract
The novel coronavirus disease (COVID-19) is a highly contagious disease caused by the SARS-CoV-2 virus, leading severe acute respiratory syndrome in patients. Although various antiviral drugs and their combinations have been tried so far against SARS-CoV-2 and they have shown some effectiveness, there is still a need for safe and cost-effective binding inhibitors in the fight against COVID-19. Therefore, phytochemicals in nature can be a quick solution due to their wide therapeutic spectrum and strong antiviral, anti-inflammatory, and antioxidant properties. In this context, the low toxicity, and high pharmacokinetic properties of curcumin, which is a natural phytochemical, as well as the easy synthesizing of its derivatives reveal the need for investigation of its various derivatives as inhibitors against coronaviruses. The present study focused on curcumin derivatives with reliable ADME profile and high molecular binding potency to different SARS-CoV-2 target enzymes (3CLPro, PLpro, NSP7/8/12, NSP7/8/12 +RNA, NSP15, NSP16, Spike, Spike+ACE). In the molecular docking studies, the best binding scores for the 22 proposed curcumin derivatives were obtained for the PLpro protein. Furthermore, MD simulations were performed for high-affinity ligand-PLpro protein complexes and subsequently, Lys157, Glu161, Asp164, Arg166, Glu167, Met208, Pro247, Pro248, Tyr264, Tyr273 and Asp302 residues of PLpro was determined to play key role for ligand binding by Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) analysis. The results of the study promise that the proposed curcumin derivatives can be potent inhibitors against SARS-CoV-2 and be converted into pharmaceutical drugs. It is also expected that the findings may provide guiding insights to future design studies for synthesizing different antiviral derivatives of phytochemicals.
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Affiliation(s)
- Hakan Alici
- Department of Physics, Faculty of Arts and Sciences, Zonguldak Bulent Ecevit University, 67100 Zonguldak, Turkey.
| | - Hakan Tahtaci
- Department of Chemistry, Faculty of Science, Karabuk University, 78050 Karabuk, Turkey
| | - Kadir Demir
- Department of Physics, Faculty of Arts and Sciences, Zonguldak Bulent Ecevit University, 67100 Zonguldak, Turkey
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17
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Tatlidil D, Raza MA, Dege N, Agar AA, Farwa U, Rehman SU. Therapeutical Potential of Imines; Synthesis, Single Crystal Structure, Computational, Molecular Modeling, and ADMET Evaluation. ACS OMEGA 2022; 7:10568-10579. [PMID: 35382330 PMCID: PMC8973114 DOI: 10.1021/acsomega.2c00102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/28/2022] [Indexed: 05/15/2023]
Abstract
Imines are multipurpose pharmacophores, simply accessible compounds, and have a broad range of usage in several areas of chemistry especially in medicine. Two novel compound imines, (E)-4-methyl-2-((o-tolylimino)methyl)phenol (1) and (E)-2-(((4-methoxybenzyl)imino)methyl)-4-methylphenol (2), were synthesized with effective product via reported protocol in the literature. Single crystal X-ray diffraction (SCXRD) was employed for structural exposition, disclosing that both compounds are orthorhombic. To optimize the newly designed imines, a B3LYP functional with a basis set 6-31G(d,p) was mainly considered. DFT results were utilized to check correlation between the data recovered from SCXRD outcomes and also to measure the energy difference. Hirshfeld surface study was done to demonstrate the intermolecular contacts along the percentage of interaction in the overall crystalline compound. Molecular operating environment program was tested against AChE and BChE enzymes to perform a modeling study of the compounds. The docking score and binding affinity of the compounds revealed that 2 showed comparatively more inhibition than 1. In silico ADMET studies exposed the physiochemical nature of these novel compounds, and it also unveiled that both compounds behaved as drug-like candidates.
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Affiliation(s)
- Digdem Tatlidil
- Faculty
of Arts and Sciences, Department of Chemistry, Ondokuz Mayıs University, Samsun 55020, Turkey
| | - Muhammad Asam Raza
- Department
of Chemistry, Hafiz Hayat Campus, University
of Gujrat, Gujrat 54000, Pakistan
| | - Necmi Dege
- Faculty
of Arts and Sciences, Department of Physics, Ondokuz Mayıs University, Samsun 55200, Turkey
| | - Aysen Alaman Agar
- Faculty
of Arts and Sciences, Department of Chemistry, Ondokuz Mayıs University, Samsun 55020, Turkey
| | - Umme Farwa
- Department
of Chemistry, Hafiz Hayat Campus, University
of Gujrat, Gujrat 54000, Pakistan
| | - Shafiq Ur Rehman
- Department
of Chemistry, University of Central Punjab, Lahore 54590, Pakistan
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18
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Elsaman T, Mohamed MS, Eltayib EM, Abdel-aziz HA, Abdalla AE, Munir MU, Mohamed MA. Isatin derivatives as broad-spectrum antiviral agents: the current landscape. Med Chem Res 2022; 31:244-273. [PMID: 35039740 PMCID: PMC8754539 DOI: 10.1007/s00044-021-02832-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/02/2021] [Indexed: 01/09/2023]
Abstract
In recent decades, several viruses have resulted in large outbreaks with serious health, economic and social consequences. The current unprecedented outbreak of the new coronavirus, SARS-COV-2, necessitates intensive efforts for delivering effective therapies to eradicate such a deadly virus. Isatin is an opulent heterocycle that has been proven to provide tremendous opportunities in the area of drug discovery. Over the last fifty years, suitably functionalized isatin has shown remarkable and broad-spectrum antiviral properties. The review herein is an attempt to compile all of the reported information about the antiviral activity of isatin derivatives with an emphasis on their structure-activity relationships (SARs) along with mechanistic and molecular modeling studies. In this regard, we are confident that the review will afford the scientific community a valuable platform to generate more potent and cost-effective antiviral therapies based on isatin templates.
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Affiliation(s)
- Tilal Elsaman
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Malik Suliman Mohamed
- Department of Pharmaceutics, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Eyman Mohamed Eltayib
- Department of Pharmaceutics, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Hatem A. Abdel-aziz
- Department of Applied Organic Chemistry, National Research Center, Dokki, Cairo, 12622 Egypt
| | - Abualgasim Elgaili Abdalla
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Muhammad Usman Munir
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Magdi Awadalla Mohamed
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
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19
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Gangireddy MSR, Badavath VN, Velez C, Loeanurit N, Thakur A, Maddipati VC, Katari NK, Acevedo O, Boonyasuppayakorn S, Gundla R. Discovery of 3-chlorobenzyl-linked 1,9-diazaspiro[5.5]undecane derivatives, a lead for dengue virus type 2 infection. NEW J CHEM 2022. [DOI: 10.1039/d1nj02453a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dengue virus is a worldwide health threat with 400 million yearly infections. Given a lack in specific therapeutics, the current work reports DENV2 inhibitory activity in newly designed compounds that are more potent than the standard drug ribavirin.
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Affiliation(s)
| | - Vishnu Nayak Badavath
- Department of Microbiology, Applied Medical Virology Research Unit, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok-10330, Thailand
- Chitkara College of Pharmacy, Chitkara University, Punjab, 140401, India
| | - Caroline Velez
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, USA
| | - Naphat Loeanurit
- Department of Microbiology, Applied Medical Virology Research Unit, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok-10330, Thailand
- Interdisciplinary Program in Microbiology, Graduate School, Chulalongkorn University, Pathumwan, Bangkok-10330, Thailand
| | - Abhishek Thakur
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, USA
| | | | - Naresh Kumar Katari
- Department of Chemistry, School of Science, GITAM Deemed to be University, Hyderabad 502329, Telangana, India
| | - Orlando Acevedo
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, USA
| | - Siwaporn Boonyasuppayakorn
- Department of Microbiology, Applied Medical Virology Research Unit, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok-10330, Thailand
| | - Rambabu Gundla
- Department of Chemistry, School of Science, GITAM Deemed to be University, Hyderabad 502329, Telangana, India
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20
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Alzahrani AY, Ammar YA, Abu-Elghait M, Salem MA, Assiri MA, Ali TE, Ragab A. Development of novel indolin-2-one derivative incorporating thiazole moiety as DHFR and quorum sensing inhibitors: Synthesis, antimicrobial, and antibiofilm activities with molecular modelling study. Bioorg Chem 2021; 119:105571. [PMID: 34959177 DOI: 10.1016/j.bioorg.2021.105571] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/03/2021] [Accepted: 12/15/2021] [Indexed: 12/17/2022]
Abstract
Nowadays, it's imperative to develop novel antimicrobial agents active against both drug-sensitive and drug-resistant bacterial infections with favorable profiles as high efficacy, low toxicity, and short therapy duration. Accordingly, a series of new thiazolo-indolin-2-one derivatives were synthesized based on acid and base catalyzed condensation or reaction of thiosemicarbazone 8 with different electrophilic reagents. The structure of the new compounds was confirmed based on elemental analysis and spectral data. Based on the MIC results, the most active thiazolo-indoline derivatives 2, 4, 7a, and 12 exhibited promising antibacterial activity against gram-positive and gram-negative bacteria with weak to moderate antifungal activities. Surprisingly, the N-(thiazol-2-yl)benzenesulfonamide derivative 4 was found to be most active on antibiofilm activity against both S. aureus (ATCC 29213) with BIC50 (1.95 ± 0.01 µg/mL), while 5-(2-oxoindolin-3-ylidene)-thiazol-4(5H)-one derivative 7a exhibited the strongest antibiofilm activity against P. aeruginosa pathogens with BIC50 (3.9 ± 0.16 µg/mL). Further, the thiazole derivatives 2, 4 and 12 exhibited a significant inhibition activity against the fsr system in a dose-dependent manner without affecting bacterial growth. The target derivatives behaved synergistic and additively effect against MDR p. aeruginosa, and thiazole derivative 12 exhibited a high synergistic effect with most tested antibiotics except Cefepime with FIC value ranging between 0.249 and 1.0, reducing their MICs. Interestingly, the 3-(2-(4-thiazol-2-yl)hydrazono)indolin-2-one derivative 12 displayed the highest selectivity to DHFR inhibitory with IC50 value 40.71 ± 1.86 nM superior to those of the reference Methotrexate. Finally, in silico molecular modeling simulation, some physicochemical properties and toxicity predictions were performed for the most active derivatives.
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Affiliation(s)
- Abdullah Y Alzahrani
- Department of Chemistry, Faculty of Science and Arts, King Khalid University, Mohail, Assir, Saudi Arabia
| | - Yousry A Ammar
- Department of Chemistry, Faculty of Science, Al-Azhar University, 11884 Nasr City, Cairo, Egypt
| | - Mohammed Abu-Elghait
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Nasr City, Cairo 11884, Egypt.
| | - Mohamed A Salem
- Department of Chemistry, Faculty of Science and Arts, King Khalid University, Mohail, Assir, Saudi Arabia; Department of Chemistry, Faculty of Science, Al-Azhar University, 11884 Nasr City, Cairo, Egypt.
| | - Mohammed A Assiri
- Department of Chemistry, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Tarik E Ali
- Department of Chemistry, Faculty of Science, King Khalid University, Abha, Saudi Arabia; Department of Chemistry, Faculty of Education, Ain Shams University, Egypt
| | - Ahmed Ragab
- Department of Chemistry, Faculty of Science, Al-Azhar University, 11884 Nasr City, Cairo, Egypt.
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21
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Mahato RK, Mahanty AK, Kotakonda M, Prasad S, Bhattacharyya S, Biswas B. A hydrated 2,3-diaminophenazinium chloride as a promising building block against SARS-CoV-2. Sci Rep 2021; 11:23122. [PMID: 34848758 PMCID: PMC8633378 DOI: 10.1038/s41598-021-02280-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 11/08/2021] [Indexed: 12/14/2022] Open
Abstract
Phenazine scaffolds are the versatile secondary metabolites of bacterial origin. It functions in the biological control of plant pathogens and contributes to the producing strains ecological fitness and pathogenicity. In the light of the excellent therapeutic properties of phenazine, we have synthesized a hydrated 2,3-diaminophenazinium chloride (DAPH+Cl-·3H2O) through direct catalytic oxidation of o-phenylenediamine with an iron(III) complex, [Fe(1,10-phenanthroline)2Cl2]NO3 in ethanol under aerobic condition. The crystal structure, molecular complexity and supramolecular aspects of DAPH+Cl- were confirmed and elucidated with different spectroscopic methods and single crystal X-ray structural analysis. Crystal engineering study on DAPH+Cl- exhibits a fascinating formation of (H2O)2…Cl-…(H2O) cluster and energy framework analysis of defines the role of chloride ions in the stabilization of DAPH+Cl-. The bactericidal efficiency of the compound has been testified against few clinical bacteria like Streptococcus pneumoniae, Escherichia coli, K. pneumoniae using the disc diffusion method and the results of high inhibition zone suggest its excellent antibacterial properties. The phenazinium chloride exhibits a significant percentage of cell viability and a considerable inhibition property against SARS-CoV-2 at non-cytotoxic concentration compared to remdesivir. Molecular docking studies estimate a good binding propensity of DAPH+Cl- with non-structural proteins (nsp2 and nsp7-nsp-8) and the main protease (Mpro) of SARS-CoV-2. The molecular dynamics simulation studies attribute the conformationally stable structures of the DAPH+Cl- bound Mpro and nsp2, nsp7-nsp8 complexes as evident from the considerable binding energy values, - 19.2 ± 0.3, - 25.7 ± 0.1, and - 24.5 ± 0.7 kcal/mol, respectively.
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Affiliation(s)
- Rajani Kanta Mahato
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India
| | - Ayan Kumar Mahanty
- Department of Biotechnology, University of North Bengal, Darjeeling, 734013, India
| | | | - Sunnapu Prasad
- Department of Pharmaceutical Chemistry, Sri Ramakrishna Institute of Paramedical Science, Coimbatore, 641044, India
| | | | - Bhaskar Biswas
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India.
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Determination the binding ability of N-acetyl cysteine and its derivatives with SARS-COV-2 main protease using molecular docking and molecular dynamics studies. UKRAINIAN BIOCHEMICAL JOURNAL 2021. [DOI: 10.15407/ubj93.05.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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23
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Bisht B, Imandi V, Pant S, Sen A. Solvent-Dependent Spectral Properties in Diverse Solvents, Light Harvesting and Antiviral Properties of Mono-Azo Dye (Direct Yellow-27): A Combined Experimental and Theoretical Study. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416521500368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In this paper, we have discussed for the first time a detailed electronic absorption study of the mono-azo dye Direct Yellow 27 [C[Formula: see text]H[Formula: see text]N4Na2O9S3] (DY-27) with five different homogeneous media by applying experimental and theoretical techniques along with some new characteristics of DY-27 in the field of solar cells as well as antiviral activities. A clear absorption band in the UV-visible region was observed, although the absorption maxima lie in the visible region. The electronic absorption transitions observed in our study were fully spin and symmetry allowed transitions with [Formula: see text]–[Formula: see text] character. Time-dependent density functional theory (TD-DFT) analysis has been done for understanding the electronic and the charge transfer performance. Moreover, the impacts of polar protic and polar aprotic solvents in the structural variation of DY-27 have been reported here. Further, applications of the dye in the field of solar cell, as well as antiviral activity, were performed using molecular modeling approaches. The dye exhibited a D–[Formula: see text]–A–A structure with a high light-harvesting efficiency (LHE) and good injection efficiency acts as an effective dye sensitized solar cell (DSSC). Molecular docking studies of the dye DY-27 performed with M-protease of the different corona viruses, MERS, SARS-CoV-1 and SARS-CoV-2 indicated comparable binding energies with the controlled inhibitors and best interactions are observed for the SARS-CoV-1.
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Affiliation(s)
- Babita Bisht
- Photophysics Laboratory, Department of Physics, Centre of Advance Study, DSB Campus, Kumaun University, Nainital 263002, India
| | - Venkataramana Imandi
- Center for Computational Biology and Bioinformatics School of Computational & Integrative Sciences (SCIS), Jawaharlal Nehru University, New Delhi, India
| | - Sanjay Pant
- Photophysics Laboratory, Department of Physics, Centre of Advance Study, DSB Campus, Kumaun University, Nainital 263002, India
| | - Anik Sen
- Department of Chemistry, GITAM Institute of Science, GITAM (Deemed to be University), Gandhi Nagar, Rushikonda, Visakhapatnam, Andhra Pradesh 530045, India
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24
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Sallam HH, Mohammed YHE, Al-Ostoot FH, Sridhar M, Khanum SA. Synthesis, structure analysis, DFT calculations, Hirshfeld surface studies, and energy frameworks of 6-Chloro-3-[(4-chloro-3-methylphenoxy)methyl][1,2,4]triazolo[4,3-b]pyridazine. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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25
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Ghosh S, Ramarao TA, Samanta PK, Jha A, Satpati P, Sen A. Triazole based isatin derivatives as potential inhibitor of key cancer promoting kinases- insight from electronic structure, docking and molecular dynamics simulations. J Mol Graph Model 2021; 107:107944. [PMID: 34091175 DOI: 10.1016/j.jmgm.2021.107944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 04/07/2021] [Accepted: 05/11/2021] [Indexed: 01/22/2023]
Abstract
Computer Aided Drug Design approaches have been applied to predict potential inhibitors for two different kinases, namely, cyclin-dependent kinase 2 (CDK2) and Epidermal Growth Factor Receptor (EGFR) which are known to play crucial role in cancer growth. We have designed alkyl and aryl substituted isatin-triazole ligands and performed molecular docking to rank and predict possible binding pockets in CDK2 and EGFR kinases. Best-scoring ligands in the kinase-binding pocket were selected from the docking study and subjected to molecular dynamics simulation. Absolute binding affinities were estimated from the MD trajectories using the MM/PBSA approach. The results suggest that aryl substituted isatin-triazole ligands are better binder to the kinases relative to its alkyl analogue. Furthermore, aryl substituted isatin-triazole ligands prefer binding to EGFR kinases relative to CDK2. The ligand binding pockets of the kinases are primarily hydrophobic in nature. Ligand-kinase binding is favoured by electrostatic and Van der Waals interactions, later being the major contributor. Large estimated negative binding affinities (~ -10 to -25 kcal/mol) indicate that the ligands might inhibit the kinases. Physicochemical property analysis suggests that the proposed ligands could be orally bio-available.
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Affiliation(s)
- Suvankar Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - T Atchuta Ramarao
- Department of Chemistry, GIS, GITAM Deemed to Be University, Rushikonda, Visakhapatnam, 530045, AP, India
| | - Pralok K Samanta
- Department of Chemistry, GSS, GITAM Deemed to Be University, Rudaram, Hyderabad, 502329, Telangana, India
| | - Anjali Jha
- Department of Chemistry, GIS, GITAM Deemed to Be University, Rushikonda, Visakhapatnam, 530045, AP, India.
| | - Priyadarshi Satpati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
| | - Anik Sen
- Department of Chemistry, GIS, GITAM Deemed to Be University, Rushikonda, Visakhapatnam, 530045, AP, India.
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26
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Qureshi S, Khandelwal R, Madhavi M, Khurana N, Gupta N, Choudhary SK, Suresh RA, Hazarika L, Srija CD, Sharma K, Hindala MR, Hussain T, Nayarisseri A, Singh SK. A Multi-target Drug Designing for BTK, MMP9, Proteasome and TAK1 for the Clinical Treatment of Mantle Cell Lymphoma. Curr Top Med Chem 2021; 21:790-818. [PMID: 33463471 DOI: 10.2174/1568026621666210119112336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Mantle cell lymphoma (MCL) is a type of non-Hodgkin lymphoma characterized by the mutation and overexpression of the cyclin D1 protein by the reciprocal chromosomal translocation t(11;14)(q13:q32). AIM The present study aims to identify potential inhibition of MMP9, Proteasome, BTK, and TAK1 and determine the most suitable and effective protein target for the MCL. METHODOLOGY Nine known inhibitors for MMP9, 24 for proteasome, 15 for BTK and 14 for TAK1 were screened. SB-3CT (PubChem ID: 9883002), oprozomib (PubChem ID: 25067547), zanubrutinib (PubChem ID: 135565884) and TAK1 inhibitor (PubChem ID: 66760355) were recognized as drugs with high binding capacity with their respective protein receptors. 41, 72, 102 and 3 virtual screened compounds were obtained after the similarity search with compound (PubChem ID:102173753), PubChem compound SCHEMBL15569297 (PubChem ID:72374403), PubChem compound SCHEMBL17075298 (PubChem ID:136970120) and compound CID: 71814473 with best virtual screened compounds. RESULT MMP9 inhibitors show commendable affinity and good interaction profile of compound holding PubChem ID:102173753 over the most effective established inhibitor SB-3CT. The pharmacophore study of the best virtual screened compound reveals its high efficacy based on various interactions. The virtual screened compound's better affinity with the target MMP9 protein was deduced using toxicity and integration profile studies. CONCLUSION Based on the ADMET profile, the compound (PubChem ID: 102173753) could be a potent drug for MCL treatment. Similar to the established SB-3CT, the compound was non-toxic with LD50 values for both the compounds lying in the same range.
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Affiliation(s)
- Shahrukh Qureshi
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Ravina Khandelwal
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Maddala Madhavi
- Department of Zoology, Nizam College, Osmania University, Hyderabad - 500001, Telangana State, India
| | - Naveesha Khurana
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Neha Gupta
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Saurav K Choudhary
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Revathy A Suresh
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Lima Hazarika
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Chillamcherla D Srija
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Khushboo Sharma
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Mali R Hindala
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Tajamul Hussain
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Sanjeev K Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
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27
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Rossi FV, Gentili D, Marcantoni E. Metal-Promoted Heterocyclization: A Heterosynthetic Approach to Face a Pandemic Crisis. Molecules 2021; 26:2620. [PMID: 33947170 PMCID: PMC8124705 DOI: 10.3390/molecules26092620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 11/25/2022] Open
Abstract
The outbreak of SARS-CoV-2 has drastically changed our everyday life and the life of scientists from all over the world. In the last year, the scientific community has faced this worldwide threat using any tool available in order to find an effective response. The recent formulation, production, and ongoing administration of vaccines represent a starting point in the battle against SARS-CoV-2, but they cannot be the only aid available. In this regard, the use of drugs capable to mitigate and fight the virus is a crucial aspect of the pharmacological strategy. Among the plethora of approved drugs, a consistent element is a heterocyclic framework inside its skeleton. Heterocycles have played a pivotal role for decades in the pharmaceutical industry due to their high bioactivity derived from anticancer, antiviral, and anti-inflammatory capabilities. In this context, the development of new performing and sustainable synthetic strategies to obtain heterocyclic molecules has become a key focus of scientists. In this review, we present the recent trends in metal-promoted heterocyclization, and we focus our attention on the construction of heterocycles associated with the skeleton of drugs targeting SARS-CoV-2 coronavirus.
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Affiliation(s)
- Federico Vittorio Rossi
- Chemistry Division, School of Science and Technology, University of Camerino, 62032 Camerino, Italy; (D.G.); (E.M.)
- Laboratori Alchemia Srl, Via San Faustino, 20134 Milano, Italy
| | - Dario Gentili
- Chemistry Division, School of Science and Technology, University of Camerino, 62032 Camerino, Italy; (D.G.); (E.M.)
| | - Enrico Marcantoni
- Chemistry Division, School of Science and Technology, University of Camerino, 62032 Camerino, Italy; (D.G.); (E.M.)
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28
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Miroshnychenko KV, Shestopalova AV. Combined use of the hepatitis C drugs and amentoflavone could interfere with binding of the spike glycoprotein of SARS-CoV-2 to ACE2: the results of a molecular simulation study. J Biomol Struct Dyn 2021; 40:8672-8686. [PMID: 33896392 PMCID: PMC8074653 DOI: 10.1080/07391102.2021.1914168] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 04/05/2021] [Indexed: 12/14/2022]
Abstract
The worldwide rapid spread of the COVID-19 disease necessitates the search for fast and effective treatments. The repurposing of existing drugs seems to be the best solution in this situation. In this study, the molecular docking method was used to test 248 drugs against the receptor-binding domain (RBD) of spike glycoprotein of SARS-CoV-2, which is responsible for viral entry into the host cell. Among the top-ranked ligands are drugs that are used for hepatitis C virus (HCV) treatments (paritaprevir, ledipasvir, simeprevir) and a natural biflavonoid amentoflavone. The binding sites of the HCV drugs and amentoflavone are different. Therefore, the ternary complexes of the HCV drug, amentoflavone, and RBD can be created. For the 5 top-ranked ligands, the validating molecular dynamics simulations of binary and ternary complexes with RBD were performed. According to the MMPBSA-binding free energies, the HCV drugs ledipasvir and paritaprevir (in a neutral form) are the most efficient binders of the RBD when used in combination with amentoflavone.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Anna V. Shestopalova
- O. Ya. Usikov Institute for Radiophysics and Electronics of NAS of Ukraine, Kharkiv, Ukraine
- V. N. Karazin Kharkiv National University, Kharkiv, Ukraine
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29
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Gangadevi S, Badavath VN, Thakur A, Yin N, De Jonghe S, Acevedo O, Jochmans D, Leyssen P, Wang K, Neyts J, Yujie T, Blum G. Kobophenol A Inhibits Binding of Host ACE2 Receptor with Spike RBD Domain of SARS-CoV-2, a Lead Compound for Blocking COVID-19. J Phys Chem Lett 2021; 12:1793-1802. [PMID: 33577324 PMCID: PMC7901140 DOI: 10.1021/acs.jpclett.0c03119] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/04/2021] [Indexed: 05/03/2023]
Abstract
In the search for inhibitors of COVID-19, we have targeted the interaction between the human angiotensin-converting enzyme 2 (ACE2) receptor and the spike receptor binding domain (S1-RBD) of SARS-CoV-2. Virtual screening of a library of natural compounds identified Kobophenol A as a potential inhibitor. Kobophenol A was then found to block the interaction between the ACE2 receptor and S1-RBD in vitro with an IC50 of 1.81 ± 0.04 μM and inhibit SARS-CoV-2 viral infection in cells with an EC50 of 71.6 μM. Blind docking calculations identified two potential binding sites, and molecular dynamics simulations predicted binding free energies of -19.0 ± 4.3 and -24.9 ± 6.9 kcal/mol for Kobophenol A to the spike/ACE2 interface and the ACE2 hydrophobic pocket, respectively. In summary, Kobophenol A, identified through docking studies, is the first compound that inhibits SARS-CoV-2 binding to cells through blocking S1-RBD to the host ACE2 receptor and thus may serve as a good lead compound against COVID-19.
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Affiliation(s)
- Suresh Gangadevi
- Anhui
Provincial Engineering Laboratory of Silicon-Based Materials, Bengbu University, Caoshan Road 1866, Bengbu, Anhui 233030, PR China
| | | | - Abhishek Thakur
- Department
of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Na Yin
- Anhui
Provincial Engineering Laboratory of Silicon-Based Materials, Bengbu University, Caoshan Road 1866, Bengbu, Anhui 233030, PR China
| | - Steven De Jonghe
- Department
of Microbiology, Immunology and Transplantation, Rega Institute for
Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Orlando Acevedo
- Department
of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Dirk Jochmans
- Department
of Microbiology, Immunology and Transplantation, Rega Institute for
Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Pieter Leyssen
- Department
of Microbiology, Immunology and Transplantation, Rega Institute for
Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Ke Wang
- College
of Material and Chemical Engineering, Bengbu
University, Bengbu 233030, China
| | - Johan Neyts
- Department
of Microbiology, Immunology and Transplantation, Rega Institute for
Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Tao Yujie
- East China
University of Political Science and Law, Shanghai 20042 China
| | - Galia Blum
- Institute
for Drug Research, The Hebrew University, Jerusalem 9112001, Israel
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Vougogiannopoulou K, Corona A, Tramontano E, Alexis MN, Skaltsounis AL. Natural and Nature-Derived Products Targeting Human Coronaviruses. Molecules 2021; 26:448. [PMID: 33467029 PMCID: PMC7831024 DOI: 10.3390/molecules26020448] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 01/18/2023] Open
Abstract
The ongoing pandemic of severe acute respiratory syndrome (SARS), caused by the SARS-CoV-2 human coronavirus (HCoV), has brought the international scientific community before a state of emergency that needs to be addressed with intensive research for the discovery of pharmacological agents with antiviral activity. Potential antiviral natural products (NPs) have been discovered from plants of the global biodiversity, including extracts, compounds and categories of compounds with activity against several viruses of the respiratory tract such as HCoVs. However, the scarcity of natural products (NPs) and small-molecules (SMs) used as antiviral agents, especially for HCoVs, is notable. This is a review of 203 publications, which were selected using PubMed/MEDLINE, Web of Science, Scopus, and Google Scholar, evaluates the available literature since the discovery of the first human coronavirus in the 1960s; it summarizes important aspects of structure, function, and therapeutic targeting of HCoVs as well as NPs (19 total plant extracts and 204 isolated or semi-synthesized pure compounds) with anti-HCoV activity targeting viral and non-viral proteins, while focusing on the advances on the discovery of NPs with anti-SARS-CoV-2 activity, and providing a critical perspective.
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Affiliation(s)
- Konstantina Vougogiannopoulou
- Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece;
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Biomedical Section, Laboratory of Molecular Virology, E block, Cittadella Universitaria di Monserrato, SS55409042 Monserrato, Italy; (A.C.); (E.T.)
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Biomedical Section, Laboratory of Molecular Virology, E block, Cittadella Universitaria di Monserrato, SS55409042 Monserrato, Italy; (A.C.); (E.T.)
| | - Michael N. Alexis
- Molecular Endocrinology Team, Inst of Chemical Biology, National Hellenic Research Foundation (NHRF), 48 Vassileos Constantinou Ave., 11635 Athens, Greece;
| | - Alexios-Leandros Skaltsounis
- Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece;
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Nagoor Meeran M, Seenipandi A, Javed H, Sharma C, Hashiesh HM, Goyal SN, Jha NK, Ojha S. Can limonene be a possible candidate for evaluation as an agent or adjuvant against infection, immunity, and inflammation in COVID-19? Heliyon 2021; 7:e05703. [PMID: 33490659 PMCID: PMC7810623 DOI: 10.1016/j.heliyon.2020.e05703] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 09/16/2020] [Accepted: 12/08/2020] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease (COVID-19) caused by novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an ongoing pandemic and presents a public health emergency. It has affected millions of people and continues to affect more, despite the tremendous social preventive measures. The therapeutic strategy relies on suppressing infectivity and inflammation, along with immune modulation. The identification of candidate drugs effective for COVID-19 is crucial, thus many natural products including phytochemicals are also being proposed for repurposing and evaluated for their potential in COVID-19. Among numerous phytochemicals, limonene (LMN), a dietary terpene of natural origin has been recently showed to target viral proteins in the in-silico studies. LMN is one of the main compounds identified in many citrus plants, available and accessible in diets and well-studied for its therapeutic benefits. Due to dietary nature, relative safety and efficacy along with favorable physicochemical properties, LMN has been suggested to be a fascinating candidate for further investigation in COVID-19. LMN showed to modulate numerous signaling pathways and inhibits inflammatory mediators, including cytokines, chemokines, adhesion molecules, prostanoids, and eicosanoids. We hypothesized that given the pathogenesis of COVID-19 involving infection, inflammation, and immunity, LMN may have potential to limit the severity and progression of the disease owing to its immunomodulatory, anti-inflammatory, and antiviral properties. The present article discusses the possibilities of LMN in SARS-CoV-2 infections based on its immunomodulatory, anti-inflammatory, and antiviral properties. Though, the suggestion on the possible use of LMN in COVID-19 remains inconclusive until the in-silico effects confirmed in the experimental studies and further proof of the concept studies. The candidature of LMN in COVID-19 treatment somewhat appear speculative but cannot be overlooked provided favorable physiochemical and druggable properties. The safety and efficacy of LMN are necessary to be established in preclinical and clinical studies before making suggestions for use in humans.
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Affiliation(s)
- M.F. Nagoor Meeran
- Department of Pharmacology and Therapeutics, College of Medicine and Health Sciences, PO Box - 17666, United Arab Emirates University, Al Ain, United Arab Emirates
| | - A. Seenipandi
- Department of Pharmacology and Therapeutics, College of Medicine and Health Sciences, PO Box - 17666, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Hayate Javed
- Department of Anatomy, College of Medicine and Health Sciences, PO Box - 17666, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Charu Sharma
- Department of Internal Medicine, College of Medicine and Health Sciences, PO Box - 17666, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Hebaallah Mamdouh Hashiesh
- Department of Pharmacology and Therapeutics, College of Medicine and Health Sciences, PO Box - 17666, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Sameer N. Goyal
- Shri Vile Parle Kelvani Mandal's Institute of Pharmacy, Dhule 424001, Maharashtra, India
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering & Technology, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh 201310, India
| | - Shreesh Ojha
- Department of Pharmacology and Therapeutics, College of Medicine and Health Sciences, PO Box - 17666, United Arab Emirates University, Al Ain, United Arab Emirates
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