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Singh K, Singh VK, Mishra R, Sharma A, Pandey A, Srivastava SK, Chaurasia H. Design, Synthesis, DFT, docking Studies, and antimicrobial evaluation of novel benzimidazole containing sulphonamide derivatives. Bioorg Chem 2024; 149:107473. [PMID: 38820940 DOI: 10.1016/j.bioorg.2024.107473] [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: 03/26/2024] [Revised: 05/05/2024] [Accepted: 05/16/2024] [Indexed: 06/02/2024]
Abstract
In silico approaches have been employed to design a new series of benzimidazole-containing sulphonamide derivatives and qualified compounds have been synthesized to analyze their potential as antimicrobial agents. Antibacterial screening of all synthesized compounds was done using the broth microdilution method against several human pathogenic bacteria, viz. Gram-positive bacteria [B. cerus (NCIN-2156), B. subtilis (ATCC-6051), S. aureus (NCIM-2079)] and Gram-negative bacteria [P. aeruginosa (NCIM-2036), E. coli (NCIM-2065), and a drug-resistant strain of E. coli (U-621)], and the compounds presented admirable MIC values, ranging between 100-1.56 µg/mL. The combinatorial analysis showed the magnificent inhibitory efficiency of the tested compounds, acquired equipotent to ten-fold more potency compared to original MIC values. An immense synergistic effect was exhibited by the compounds during combination studies with reference drugs chloramphenicol and sulfamethoxazole was presented as fractional inhibitory concentration (∑FIC). Enzyme inhibition studies of all synthesized compounds were done by using peptidyl transferase and dihydropteroate synthase enzymes isolated from E. coli and S. aureus and each of the compound presented the admirable IC50 values, where the lead compound 3 bound to peptidyl transferase (of S. aureus with IC50 363.51 ± 2.54 µM and E. coli IC50 1.04 ± 0.08 µM) & dihydropteroate synthase (of S. aureus IC50 3.51 ± 0.82 µM and E. coli IC50 2.77 ± 0.65 µM), might account for the antimicrobial effect, exhibited excellent inhibition potential. Antifungal screening was also performed employing food poisoning methods against several pathogenic fungal species, viz A. flavus, F. oxysporum, A. niger, and A. brassicae. The obtained result indicated that few compounds can prove to be a potent drug regimen against dreaded MDR strains of microbes. Structural activity relationship (SAR) analysis and docking studies reveal that the presence of electron-withdrawing, polar, and more lipophilic substituents positively favor the antibacterial activity, whereas, electron-withdrawing, more polar, and hydrophilic substituents favor the antifungal activities. A robust coherence has been found in in-silico and in-vitro biological screening results of the compounds.
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Affiliation(s)
- Kajal Singh
- Photophysical and Therapeutic Laboratory, Department of Chemistry, C.M.P. Degree College (A constituent P.G. College of University of Allahabad), Prayagraj 211002, India
| | - Vishal K Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Richa Mishra
- Bio-organic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj 211002, India
| | - Ashwani Sharma
- Photophysical and Therapeutic Laboratory, Department of Chemistry, C.M.P. Degree College (A constituent P.G. College of University of Allahabad), Prayagraj 211002, India
| | - Archana Pandey
- Photophysical and Therapeutic Laboratory, Department of Chemistry, C.M.P. Degree College (A constituent P.G. College of University of Allahabad), Prayagraj 211002, India
| | - Santosh K Srivastava
- Photophysical and Therapeutic Laboratory, Department of Chemistry, C.M.P. Degree College (A constituent P.G. College of University of Allahabad), Prayagraj 211002, India
| | - Himani Chaurasia
- Photophysical and Therapeutic Laboratory, Department of Chemistry, C.M.P. Degree College (A constituent P.G. College of University of Allahabad), Prayagraj 211002, India.
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Singh VK, Kumari P, Som A, Rai S, Mishra R, Singh RK. Design, synthesis and antimicrobial activity of novel quinoline derivatives: an in silico and in vitro study. J Biomol Struct Dyn 2024; 42:6904-6924. [PMID: 37477261 DOI: 10.1080/07391102.2023.2236716] [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: 04/24/2023] [Accepted: 07/10/2023] [Indexed: 07/22/2023]
Abstract
A series of new quinoline derivatives has been designed, synthesized and evaluated as antibacterial and antifungal agents functioning as peptide deformylase enzyme (PDF) inhibitors and fungal cell wall disruptors on the basis of computational and experimental methods. The molecular docking and ADMET assessment aided in the synthesis of quinoline derivatives starting from 6-amino-4-methyl-1H-quinoline-2-one substituted with different types of sulfonyl/benzoyl/propargyl moieties. These newly synthesized compounds were evaluated for their in vitro antibacterial and antifungal activity. Antibacterial screening of all compounds showed excellent MIC value (MIC, 50 - 3.12 µg/mL) against bacterial strains, viz. Bacillus cerus, Staphylococcus, Pseudomonas and Escherichia coli. Compounds 2 and 6 showed better activity. Fractional inhibitory concentration (FIC) values of compounds were lowered by 1/2 to 1/128 of the original MIC values when a combinatorial screening with reference drugs was performed. Further, antifungal screening against fungal strains, viz. A. flavus, A. niger, F. oxysporum and C. albicans also showed that all compounds were potentially active and compound 6 being the most potent. Further, the cytotoxicity experiments revealed that compound 6 was the least toxic molecule. The molecular dynamics (MD) simulation investigations elucidated the conformational stability of compound 6-PDF complex with flexible binding pocket residues. The highest number of stable hydrogen bonds with the PDF residues during the entire simulation time illustrated strong binding affinity of compound 6 with PDF.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vishal K Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj, India
| | - Priyanka Kumari
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj, India
| | - Anup Som
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj, India
| | - Shivangi Rai
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj, India
| | - Richa Mishra
- 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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Das NC, Gorai S, Gupta PSS, Panda SK, Rana MK, Mukherjee S. Immune targeting of filarial glutaredoxin through a multi-epitope peptide-based vaccine: A reverse vaccinology approach. Int Immunopharmacol 2024; 133:112120. [PMID: 38657497 DOI: 10.1016/j.intimp.2024.112120] [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: 01/14/2024] [Revised: 04/07/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024]
Abstract
Despite the efforts of global programme to eliminate lymphatic filariasis (GPELF), the threat of lymphatic filariasis (LF) still looms over humanity in terms of long-term disabilities, and morbidities across the globe. In light of this situation, investigators have chosen to focus on the development of immunotherapeutics targeting the physiologically important filarial-specific proteins. Glutaredoxin (16.43 kDa) plays a pivotal role in filarial redox biology, serving as a vital contributor. In the context of the intra-host survival of filarial parasites, this antioxidant helps in mitigating the oxidative stress imposed by the host immune system. Given its significant contribution, the development of a vaccine targeting glutaredoxin holds promise as a new avenue for achieving a filaria-free world. Herein, multi-epitope-based vaccine was designed using advanced immunoinformatics approach. Initially, 4B-cell epitopes and 6 T-cell epitopes (4 MHC I and 2 MHC II) were identified from the 146 amino acid long sequence of glutaredoxin of the human filarid, Wuchereria bancrofti. Subsequent clustering of these epitopes with linker peptides finalized the vaccine structure. To boost TLR-mediated innate immunity, TLR-specific adjuvants were incorporated into the designed vaccine. After that, experimental analyses confirm the designed vaccine, Vac4 as anefficient ligand of human TLR5 to elicit protective innate immunity against filarial glutaredoxin. Immune simulation further demonstrated abundant levels of IgG and IgM as crucial contributors in triggering vaccine-induced adaptive responses in the recipients. Hence, to facilitate the validation of immunogenicity of the designed vaccine, Vac4 was cloned in silico in pET28a(+) expression vector for recombinant production. Taken together, our findings suggest that vaccine-mediated targeting of filarial glutaredoxin could be a future option for intervening LF on a global scale.
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Affiliation(s)
- Nabarun Chandra Das
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol 713 340, West Bengal, India
| | - Sampa Gorai
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol 713 340, West Bengal, India
| | - Parth Sarthi Sen Gupta
- School of Biosciences & Bioengineering, D. Y. Patil International University, Akurdi, Pune 411044, India
| | - Saroj Kumar Panda
- Department of Chemistry, Indian Institute of Science Education and Research, Berhampur, India
| | - Malay Kumar Rana
- Department of Chemistry, Indian Institute of Science Education and Research, Berhampur, India
| | - Suprabhat Mukherjee
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol 713 340, West Bengal, India.
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Shakour N, Hoseinpoor S, Rajabian F, Azimi SG, Iranshahi M, Sadeghi-Aliabadi H, Hadizadeh F. Discovery of non-peptide GLP-1r natural agonists for enhancing coronary safety in type 2 diabetes patients. J Biomol Struct Dyn 2024:1-18. [PMID: 38165453 DOI: 10.1080/07391102.2023.2298734] [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: 09/21/2023] [Accepted: 12/17/2023] [Indexed: 01/03/2024]
Abstract
This study explores the computational discovery of non-peptide agonists targeting the Glucagon-Like Peptide-1 Receptor (GLP-1R) to enhance the safety of major coronary outcomes in individuals affected by Type 2 Diabetes. The objective is to identify novel compounds that can activate the GLP-1R pathway without the limitations associated with peptide agonists. Type 2 diabetes mellitus (T2DM) is associated with an increased risk of cardiovascular disease (CVD) and mortality, which is attributed to the accumulation of fat in organs, including the heart. Glucagon-like peptide-1 receptor agonists (GLP-1RAs) are frequently used to manage T2DM and could potentially offer cardiovascular benefits. Therefore, this study examines non-peptide agonists of GLP-1R to improve coronary safety in type 2 diabetes patients. After rigorous assessments, two standout candidates were identified, with natural compound 12 emerging as the most promising. This study represents a notable advancement in enhancing the management of coronary outcomes among individuals with type 2 diabetes. The computational methodology employed successfully pinpointed potential GLP-1R natural agonists, providing optimism for the development of safer and more effective therapeutic interventions. Although computational methodologies have provided crucial insights, realizing the full potential of these compounds requires extensive experimental investigations, crucial in advancing therapeutic strategies for this critical patient population.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neda Shakour
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saeideh Hoseinpoor
- Department of Biochemistry and Biophysics, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
- International UNESCO Center for Health-Related Basic Sciences and Human Nutrition, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Rajabian
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sabikeh G Azimi
- Department of Chemistry, Faculty of Sciences, University of Birjand, Birjand, Iran
| | - Mehrdad Iranshahi
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hojjat Sadeghi-Aliabadi
- Department of Pharmaceutical Chemistry, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Farzin Hadizadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
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Monga J, Ghosh NS, Rani I, Singh R, Deswal G, Dhingra AK, Grewal AS. Unlocking the Pharmacological Potential of Benzimidazole Derivatives: A Pathway to Drug Development. Curr Top Med Chem 2024; 24:437-485. [PMID: 38311918 DOI: 10.2174/0115680266283641240109080047] [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: 10/19/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 02/06/2024]
Abstract
Heterocyclic molecules have fascinated a massive interest in medicinal chemistry. They are heterocyclic compounds that have gained significance due to their diverse variety of pharmacological activities. Benzimidazole is a heterocyclic compound consisting of benzene and imidazole rings. The ease of synthesis and the structural versatility of benzimidazole make it a promising scaffold for drug development. Many biological actions of benzimidazole derivatives have been well documented, including antibacterial, antiviral, anticancer, anti-inflammatory, antitubercular, and anthelmintic properties. The mechanism of action of benzimidazole derivatives varies with their chemical structure and target enzyme. This review has explored numerous methods for producing benzimidazole derivatives as well as a broad range of pharmacological activities. SAR investigations are also discussed in this review as they provide crucial details regarding the essential structural qualities that benzimidazole derivatives must have in order to be biologically active, which could aid in the rational design of new drug candidates. Benzimidazole scaffold is an exclusive structure in drug design and discovery. Many new pharmaceutical drugs containing benzimidazole are anticipated to be available within the next ten years as a result of the extensive therapeutic applications of benzimidazole and its derivatives. This review inspired many researchers to develop more biologically active compounds bearing benzimidazole, expanding the scope of finding a remedy for other diseases. From this study, we concluded that 2-substituted benzimidazole was considered more extensively by researchers.
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Affiliation(s)
- Jyoti Monga
- Adarsh Vijendra Institute of Pharmaceutical Sciences, Shobhit University, Gangoh, Uttar Pradesh, India
- Ch. Devi Lal College of Pharmacy, Jagadhri, Yamuna Nagar, Haryana, India
| | - Niladry S Ghosh
- Faculty of Pharmaceutical Sciences, Assam down town University, Guwahati, Assam, India
| | - Isha Rani
- Spurthy College of Pharmacy, Marasur Gate, Bengaluru, Karnataka, India
| | - Ranjit Singh
- Adarsh Vijendra Institute of Pharmaceutical Sciences, Shobhit University, Gangoh, Uttar Pradesh, India
| | - Geeta Deswal
- Guru Gobind Singh College of Pharmacy, Yamuna Nagar, Haryana, India
| | | | - Ajmer S Grewal
- Guru Gobind Singh College of Pharmacy, Yamuna Nagar, Haryana, India
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Suleiman M, Almalki FA, Ben Hadda T, Kawsar SMA, Chander S, Murugesan S, Bhat AR, Bogoyavlenskiy A, Jamalis J. Recent Progress in Synthesis, POM Analyses and SAR of Coumarin-Hybrids as Potential Anti-HIV Agents-A Mini Review. Pharmaceuticals (Basel) 2023; 16:1538. [PMID: 38004404 PMCID: PMC10675815 DOI: 10.3390/ph16111538] [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: 09/12/2023] [Revised: 10/18/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
The human immunodeficiency virus (HIV) is the primary cause of acquired immune deficiency syndrome (AIDS), one of the deadliest pandemic diseases. Various mechanisms and procedures have been pursued to synthesise several anti-HIV agents, but due to the severe side effects and multidrug resistance spawning from the treatment of HIV/AIDS using highly active retroviral therapy (HAART), it has become imperative to design and synthesise novel anti-HIV agents. Literature has shown that natural sources, particularly the plant kingdom, can release important metabolites that have several biological, mechanistic and structural representations similar to chemically synthesised compounds. Certainly, compounds from natural and ethnomedicinal sources have proven to be effective in the management of HIV/AIDS with low toxicity, fewer side effects and affordability. From plants, fungi and bacteria, coumarin can be obtained, which is a secondary metabolite and is well known for its actions in different stages of the HIV replication cycle: protease, integrase and reverse transcriptase (RT) inhibition, cell membrane fusion and viral host attachment. These, among other reasons, are why coumarin moieties will be the basis of a good building block for the development of potent anti-HIV agents. This review aims to outline the synthetic pathways, structure-activity relationship (SAR) and POM analyses of coumarin hybrids with anti-HIV activity, detailing articles published between 2000 and 2023.
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Affiliation(s)
- Mustapha Suleiman
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru 81310, Johor, Malaysia;
- Department of Chemistry, Sokoto State University, Birnin Kebbi Road, Sokoto 852101, Nigeria
| | - Faisal A. Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Mecca 21955, Saudi Arabia; (F.A.A.); (T.B.H.)
| | - Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Mecca 21955, Saudi Arabia; (F.A.A.); (T.B.H.)
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, MB 524, Oujda 60000, Morocco
| | - Sarkar M. A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, University of Chittagong, Chittagong 4331, Bangladesh;
| | - Subhash Chander
- Amity Institute of Phytochemistry & Phytomedicine, Amity University Uttar Pradesh, Noida 201313, India;
| | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory, Birla Institute of Technology & Science Pilani (BITS Pilani), Pilani Campus, Pilani 333031, India;
| | - Ajmal R. Bhat
- Department of Chemistry, R.T.M. Nagpur University, Nagpur 440033, India;
| | - Andrey Bogoyavlenskiy
- Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Joazaizulfazli Jamalis
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru 81310, Johor, Malaysia;
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Srivastava R, Gupta SK, Naaz F, Sen Gupta PS, Yadav M, Singh VK, Panda SK, Biswal S, Rana MK, Gupta SK, Schols D, Singh RK. Exploring antiviral potency of N-1 substituted pyrimidines against HIV-1 and other DNA/RNA viruses: Design, synthesis, characterization, ADMET analysis, docking, molecular dynamics and biological activity. Comput Biol Chem 2023; 106:107910. [PMID: 37422940 DOI: 10.1016/j.compbiolchem.2023.107910] [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: 05/09/2023] [Revised: 06/16/2023] [Accepted: 06/25/2023] [Indexed: 07/11/2023]
Abstract
A novel series of pyrimidine derivatives, bearing modified benzimidazoles at N-1 position, has been designed, synthesized and screened as NNRTIs against HIV and as broad-spectrum antiviral agents. The molecules were screened against different HIV targets using molecular docking experiment. The docking results indicated that the molecules interacted well with the residues Lys101, Tyr181, Tyr188, Trp229, Phe227 and Tyr318 present in NNIBP of HIV-RT protein, formed quite stable complexes and, thus, behaved as probable NNRTIs. Among these compounds, 2b and 4b showed anti-HIV activity with IC50 values as 6.65 µg/mL (SI = 15.50) and 15.82 µg/mL (SI = 14.26), respectively. Similarly, compound 1a showed inhibitory property against coxsackie virus B4 and compound 3b against different viruses. Molecular dynamics simulation results unequivocally demonstrated the higher stability of the complex HIV-RT:2b than the HIV-RT:nevirapine complex. The MM/PBSA-based binding free energy (-) 114.92 kJ/mol of HIV-RT:2b complex in comparison to that of HIV-RT:nevirapine complex (-) 88.33 kJ/mol, further demonstrated the higher binding strength of 2b and thus, established the potential of compound 2b as a lead molecule as an HIV-RT inhibitor.
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Affiliation(s)
- Ritika Srivastava
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad 211002, India; Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Odisha 760010, India
| | - Sunil K Gupta
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad 211002, India
| | - Farha Naaz
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad 211002, India
| | - Parth Sarthi Sen Gupta
- School of Biosciences and Bioengineering, D Y Patil International University, Akurdi, Pune, India
| | - Madhu Yadav
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad 211002, India
| | - Vishal Kumar Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad 211002, India
| | - Saroj Kumar Panda
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Odisha 760010, India
| | - Satyaranjan Biswal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Odisha 760010, India
| | - Malay Kumar Rana
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Odisha 760010, India
| | | | | | - Ramendra K Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad 211002, India.
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Stachowicz-Kuśnierz A, Korchowiec B, Korchowiec J. Nucleoside Analog Reverse-Transcriptase Inhibitors in Membrane Environment: Molecular Dynamics Simulations. Molecules 2023; 28:6273. [PMID: 37687102 PMCID: PMC10488468 DOI: 10.3390/molecules28176273] [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: 07/26/2023] [Revised: 08/15/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
The behavior of four drugs from the family of nucleoside analog reverse-transcriptase inhibitors (zalcitabine, stavudine, didanosine, and apricitabine) in a membrane environment was traced using molecular dynamics simulations. The simulation models included bilayers and monolayers composed of POPC and POPG phospholipids. It was demonstrated that the drugs have a higher affinity towards POPG membranes than POPC membranes due to attractive long-range electrostatic interactions. The results obtained for monolayers were consistent with those obtained for bilayers. The drugs accumulated in the phospholipid polar headgroup region. Two adsorption modes were distinguished. They differed in the degree of penetration of the hydrophilic headgroup region. Hydrogen bonds between drug molecules and phospholipid heads were responsible for adsorption. It was shown that apricitabine penetrated the hydrophilic part of the POPC and POPG membranes more effectively than the other drugs. Van der Waals interactions between S atoms and lipids were responsible for this.
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Affiliation(s)
| | | | - Jacek Korchowiec
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; (A.S.-K.); (B.K.)
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da Costa APL, Cardoso FJB, Molfetta FAD. An in silico molecular modeling approach of halolactone derivatives as potential inhibitors for human immunodeficiency virus type-1 reverse transcriptase enzyme. J Biomol Struct Dyn 2023; 41:1715-1729. [PMID: 34996334 DOI: 10.1080/07391102.2021.2024256] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Acquired Immune Deficiency Syndrome (AIDS) is an infectious disease caused by Human Immunodeficiency Virus (HIV) infection and its replication requires the Reverse Transcriptase (RT) enzyme. RT plays a key role in the HIV life cycle, making it one of the most important targets for designing new drugs. Thus, in order to increase therapeutic options against AIDS, halolactone derivatives (D-halolactone) that have been showed as potential non-nucleoside inhibitors of the RT enzyme were studied. In the present work, a series of D-halolactone were investigated by molecular modeling studies, combining Three-dimensional Quantitative Structure-Activity Relationship (3 D-QSAR), molecular docking and Molecular Dynamics (MD) techniques, to understand the molecular characteristics that promote biological activity. The internal and external validation parameters indicated that the 3 D-QSAR model has good predictive capacity and statistical significance. Contour maps provided useful information on the structural characteristics of compounds for anti-HIV-1 activity. The docking results showed that D-halolactone present good complementarity by the RT allosteric site. In MD simulations it was observed that the formation of enzyme-ligand complexes were favorable, and from the free energy decomposition it was found that Leu100, Val106, Tyr181, Try188, and Trp229 are key residues for stabilization in the enzymatic site. Thus, the results showed that the proposed models can be used to design promising HIV-1 RT inhibitors. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ana Paula Lima da Costa
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Fábio José Bonfim Cardoso
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Fábio Alberto de Molfetta
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
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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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11
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Deng C, Yan H, Wang J, Liu K, Liu BS, Shi YM. Current scenario on non-nucleoside reverse transcriptase inhibitors (2018-present). ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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12
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Kumar A, Wahan SK, Virendra SA, Chawla PA. Recent Advances on the Role of Nitrogen‐Based Heterocyclic Scaffolds in Targeting HIV through Reverse Transcriptase Inhibition. ChemistrySelect 2022. [DOI: 10.1002/slct.202202637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ankur Kumar
- Department of Pharmaceutical Chemistry ISF College of Pharmacy GT Road Ghal Kalan Moga 142001 India
| | - Simranpreet K. Wahan
- Department of Pharmaceutical Chemistry ISF College of Pharmacy GT Road Ghal Kalan Moga 142001 India
| | - Sharma Arvind Virendra
- Department of Pharmaceutical Chemistry ISF College of Pharmacy GT Road Ghal Kalan Moga 142001 India
| | - Pooja A. Chawla
- Department of Pharmaceutical Chemistry ISF College of Pharmacy GT Road Ghal Kalan Moga 142001 India
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13
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Singh VK, Mishra R, Kumari P, Som A, Yadav AK, Ram NK, Kumar P, Schols D, Singh RK. In Silico Design, Synthesis and Anti-HIV Activity of Quinoline Derivatives as Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs)r. Comput Biol Chem 2022; 98:107675. [DOI: 10.1016/j.compbiolchem.2022.107675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 12/23/2022]
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14
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Tiwari G, Chauhan MS, Sharma D. Estimation of Binding Sites of Efavirenz with 3EO9 Receptor: In Silico Molecular Docking and Molecular Dynamics Studies. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1998148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Gargi Tiwari
- Department of Physics, Patna University, Patna, India
| | | | - Dipendra Sharma
- Department of Physics, DDU Gorakhpur University, Gorakhpur, India
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15
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Chaurasia H, Singh VK, Mishra R, Yadav AK, Ram NK, Singh P, Singh RK. Molecular modelling, synthesis and antimicrobial evaluation of benzimidazole nucleoside mimetics. Bioorg Chem 2021; 115:105227. [PMID: 34399320 DOI: 10.1016/j.bioorg.2021.105227] [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: 05/26/2021] [Revised: 07/20/2021] [Accepted: 07/28/2021] [Indexed: 01/23/2023]
Abstract
A series of new N-1-(β-d-ribofuranosyl) benzimidazole derivatives has been designed using in silico methods and synthesized as probable antimicrobial agents. Further, the compounds were assessed for their antibacterial and antifungal activity. Antibacterial screening was done by employing broth micro-dilution method and compounds exhibited excellent inhibitory activity (MIC, 50-1.56 µg/mL) against different human pathogenic bacteria, viz. B. cerus, B. subtilis, S. aureus, E. coli and P. aeruginosa and drug resistant strain (DRS) of E. coli. A great synergistic effect was observed during evaluation of ∑FIC, where a combination study was performed using standard references, viz. chloramphenicol and kanamycin. The MIC data obtained from different methods of combination approach revealed 4-128 fold more potency compared to compounds tested alone. The results clearly indicated the possibility of these compounds as active ingredients of drug regimen used against MDR strains. Antifungal screening were also performed employing two different methods, viz. serial dilution method and zone inhibition method, clearly indicated that compounds were also potentially active against several species of pathogenic fungal strains, viz. A. flavus, A. niger, F. oxysporum and C. albicans. The assessment of structure activity relationship (SAR) clearly revealed that presence of less polar and more hydrophobic substituents positively favours the antibacterial activity, conversely, more polar and hydrophilic substituents favours the antifungal activities. Thus, the results positively endorsed the compounds as potent antibacterial and antifungal agents which could be developed as possible drug regimens.
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Affiliation(s)
- Himani Chaurasia
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj 211002, India
| | - Vishal K Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj 211002, India
| | - Richa Mishra
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj 211002, India
| | - Aditya K Yadav
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj 211002, India
| | - Nand K Ram
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj 211002, India
| | - Prashant Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj 211002, India
| | - Ramendra K Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj 211002, India.
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16
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Crisan L, Bora A. Small Molecules of Natural Origin as Potential Anti-HIV Agents: A Computational Approach. Life (Basel) 2021; 11:722. [PMID: 34357094 PMCID: PMC8303883 DOI: 10.3390/life11070722] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/26/2021] [Accepted: 07/15/2021] [Indexed: 12/20/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1), one of the leading causes of infectious death globally, generates severe damages to people's immune systems and makes them susceptible to serious diseases. To date, there are no drugs that completely remove HIV from the body. This paper focuses on screening 224,205 natural compounds of ZINC15 NPs subset to identify those with bioactivity similar to non-nucleoside reverse transcriptase inhibitors (NNRTIs) as promising candidates to treat HIV-1. To reach the goal, an in silico approach involving 3D-similarity search, ADMETox, HIV protein-inhibitor prediction, docking, and MM-GBSA free-binding energies was trained. The FDA-approved HIV drugs, efavirenz, etravirine, rilpivirine, and doravirine, were used as queries. The prioritized compounds were subjected to ADMETox, docking, and MM-GBSA studies against HIV-1 reverse transcriptase (RT). Lys101, Tyr181, Tyr188, Trp229, and Tyr318 residues and free-binding energies have proved that ligands can stably bind to HIV-1 RT. Three natural products (ZINC37538901, ZINC38321654, and ZINC67912677) containing oxan and oxolan rings with hydroxyl substituents and one (ZINC2103242) having 3,6,7,8-tetrahydro-2H-pyrido[1,2-a]pyrazine-1,4-dione core exhibited comparable profiles to etravirine and doravirine, with ZINC2103242 being the most promising anti-HIV candidate in terms of drug metabolism and safety profile. These findings may open new avenues to guide the rational design of novel HIV-1 NNRTIs.
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Affiliation(s)
- Luminita Crisan
- “Coriolan Dragulescu” Institute of Chemistry, 24 M. Viteazu Avenue, 300223 Timisoara, Romania
| | - Alina Bora
- “Coriolan Dragulescu” Institute of Chemistry, 24 M. Viteazu Avenue, 300223 Timisoara, Romania
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17
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Panda SK, Sen Gupta PS, Biswal S, Ray AK, Rana MK. ACE-2-Derived Biomimetic Peptides for the Inhibition of Spike Protein of SARS-CoV-2. J Proteome Res 2021; 20:1296-1303. [PMID: 33472369 PMCID: PMC7839414 DOI: 10.1021/acs.jproteome.0c00686] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Indexed: 12/16/2022]
Abstract
SARS-CoV-2, a novel coronavirus causing overwhelming death and infection worldwide, has emerged as a pandemic. Compared to its predecessor SARS-CoV, SARS-CoV-2 is more infective for being highly contagious and exhibiting tighter binding with host angiotensin-converting enzyme 2 (hACE-2). The entry of the virus into host cells is mediated by the interaction of its spike protein with hACE-2. Thus, a peptide that has a resemblance to hACE-2 but can overpower the spike protein-hACE-2 interaction will be a potential therapeutic to contain this virus. The non-interacting residues in the receptor-binding domain of hACE-2 have been mutated to generate a library of 136 new peptides. Out of this library, docking and virtual screening discover seven peptides that can exert a stronger interaction with the spike protein than hACE-2. A peptide derived from simultaneous mutation of all the non-interacting residues of hACE-2 yields almost three-fold stronger interaction than hACE-2 and thus turns out here to be the best peptide inhibitor of the novel coronavirus. The binding of the best peptide inhibitor with the spike protein is explored further by molecular dynamics, free energy, and principal component analysis, which demonstrate its efficacy compared to hACE-2. The delivery of the screened inhibitors with nanocarriers like metal-organic frameworks will be worthy of further consideration to boost their efficacy.
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Affiliation(s)
| | | | | | - Abhik Kumar Ray
- Department of Chemical Sciences, Indian
Institute of Science Education and Research (IISER) Berhampur, Berhampur
760010 Odisha, India
| | - Malay Kumar Rana
- Department of Chemical Sciences, Indian
Institute of Science Education and Research (IISER) Berhampur, Berhampur
760010 Odisha, India
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18
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Yu Z, Kan R, Ji H, Wu S, Zhao W, Shuian D, Liu J, Li J. Identification of tuna protein-derived peptides as potent SARS-CoV-2 inhibitors via molecular docking and molecular dynamic simulation. Food Chem 2020; 342:128366. [PMID: 33092925 PMCID: PMC7553880 DOI: 10.1016/j.foodchem.2020.128366] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 12/11/2022]
Abstract
The present study aimed to identify potential SARS-CoV-2 inhibitory peptides from tuna protein by virtual screening. The molecular docking was performed to elicit the interaction mechanism between targets (Mpro and ACE2) and peptides. As a result, a potential antiviral peptide EEAGGATAAQIEM (E-M) was identified. Molecular docking analysis revealed that E-M could interact with residues Thr190, Thr25, Thr26, Ala191, Leu50, Met165, Gln189, Glu166, His164, His41, Cys145, Gly143, and Asn119 of Mpro via 11 conventional hydrogen bonds, 9 carbon hydrogen bonds, and one alkyl interaction. The formation of hydrogen bonds between peptide E-M and the residues Gly143 and Gln189 of Mpro may play important roles in inhibiting the activity of Mpro. Besides, E-M could bind with the residues His34, Phe28, Thr27, Ala36, Asp355, Glu37, Gln24, Ser19, Tyr83, and Tyr41 of ACE2. Hydrogen bonds and electrostatic interactions may play vital roles in blocking the receptor ACE2 binding with SARS-CoV-2.
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Affiliation(s)
- Zhipeng Yu
- College of Food Science and Engineering, Bohai University, Jinzhou 121013, PR China
| | - Ruotong Kan
- College of Food Science and Engineering, Bohai University, Jinzhou 121013, PR China
| | - Huizhuo Ji
- College of Food Science and Engineering, Bohai University, Jinzhou 121013, PR China
| | - Sijia Wu
- College of Food Science and Engineering, Bohai University, Jinzhou 121013, PR China
| | - Wenzhu Zhao
- College of Food Science and Engineering, Bohai University, Jinzhou 121013, PR China.
| | - David Shuian
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, PR China
| | - Jingbo Liu
- Lab of Nutrition and Functional Food, Jilin University, Changchun 130062, PR China
| | - Jianrong Li
- College of Food Science and Engineering, Bohai University, Jinzhou 121013, PR China
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19
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Cardoso WB, Mendanha SA. Molecular dynamics simulation of docking structures of SARS-CoV-2 main protease and HIV protease inhibitors. J Mol Struct 2020; 1225:129143. [PMID: 32863430 PMCID: PMC7443253 DOI: 10.1016/j.molstruc.2020.129143] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/20/2020] [Accepted: 08/22/2020] [Indexed: 12/12/2022]
Abstract
We consider possible repurposed-drugs candidates against SARS-CoV-2. 10 different HIV protease inhibitors were investigated. In silico simulations were used to study protease inhibitors for SARS-CoV-2.
In this paper we investigate 10 different HIV protease inhibitors (HPIs) as possible repurposed-drugs candidates against SARS-CoV-2. To this end, we execute molecular docking and molecular dynamics simulations. The in silico data demonstrated that, despite their molecular differences, all HPIs presented a similar behavior for the parameters analyzed, with the exception of Nelfinavir that showed better results for most of the molecular dynamics parameters in comparison with the N3 inhibitor.
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Affiliation(s)
- Wesley B Cardoso
- Instituto de Física, Universidade Federal de Goiás, 74.690-900, Goiânia, Goiás, Brazil
| | - Sebastião A Mendanha
- Instituto de Física, Universidade Federal de Goiás, 74.690-900, Goiânia, Goiás, Brazil
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