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Bharadwaj KK, Ahmad I, Pati S, Ghosh A, Rabha B, Sarkar T, Bhattacharjya D, Patel H, Baishya D. Screening of Phytocompounds for Identification of Prospective Histone Deacetylase 1 (HDAC1) Inhibitor: An In Silico Molecular Docking, Molecular Dynamics Simulation, and MM-GBSA Approach. Appl Biochem Biotechnol 2024; 196:3747-3764. [PMID: 37776441 DOI: 10.1007/s12010-023-04731-3] [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] [Accepted: 09/15/2023] [Indexed: 10/02/2023]
Abstract
The upregulation of HDAC1 facilitate the induction of epigenetic repression of genes responsible for suppressing tumourigenesis, thereby triggering the development of cancer. HDAC1 inhibitors have thus emerged as possible therapeutic approaches against a variety of human malignancies, as they can inhibit the activity of certain HDACs, repair the overexpression of tumour suppressor genes, and induce cell differentiation, cell cycle arrest, and apoptosis. In this study, among 810 virtually screened compounds, Pinocembrin (PHUB000396) had a significant binding affinity (-7.99 kcal/mol). In molecular dynamics simulation (MD) studies for 200 ns time scale, the compound Pinocembrin effectively undergoes conformational optimization, thereby enabling its accommodation within the active site of the receptor. This outcome serves as a rational for the observed binding affinity. The optimal binding free energy calculations using the Molecular Mechanics Generalized Born Surface Area (MM-GBSA) (-35.86 ± 7.52 kcal/mol) showed the significant role of van der Waals forces and Coulomb interactions in the stability of the respective complex. The pharmacokinetic study showed its potential as a lead compound. The in-silico cytotoxicity prediction also confirmed its potential as an active anticancer phytocompound in lung and brain cancer. Therefore, it can be predicted that Pinocembrin could be a useful bioactive compound as an HDAC1 inhibitor and could be used in developing epigenetic therapy in cancer such as brain cancer and lung cancer to regulate gene expression.
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Affiliation(s)
- Kaushik Kumar Bharadwaj
- Department of Bioengineering and Technology, Gauhati University, Guwahati, 781014, Assam, India
| | - Iqrar Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, 425405, Maharashtra, India
| | - Siddhartha Pati
- Skills Innovation & Academic Network (SIAN) Institute-ABC, Balasore, 756001, Odisha, India
- NatNov Bioscience Private Limited, 756001, Balasore, Odisha, India
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, Assam, India, 781014
| | - Bijuli Rabha
- Department of Bioengineering and Technology, Gauhati University, Guwahati, 781014, Assam, India
| | - Tanmay Sarkar
- Department of Food Processing Technology, Malda Polytechnic, West Bengal State Council of Technical Education, Government of West Bengal, Malda, 732102, West Bengal, India
| | - Dorothy Bhattacharjya
- Department of Bioengineering and Technology, Gauhati University, Guwahati, 781014, Assam, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, 425405, Maharashtra, India
| | - Debabrat Baishya
- Department of Bioengineering and Technology, Gauhati University, Guwahati, 781014, Assam, India.
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2
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Bapat RA, Mak KK, Pichika MR, Pang JC, Lin SL, Khoo SP, Daood U. Newly discovered clouting interplay between matrix metalloproteinases structures and novel quaternary Ammonium K21: computational and in-vivo testing. BMC Oral Health 2024; 24:382. [PMID: 38528501 DOI: 10.1186/s12903-024-04069-0] [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: 12/11/2023] [Accepted: 02/24/2024] [Indexed: 03/27/2024] Open
Abstract
AIMS AND OBJECTIVES To analyze anti-MMP mode of action of Quaternary Ammonium Silane (QAS, codenamed as k21) by binding onto specific MMP site using computational molecular simulation and Anti-Sortase A (SrtA) mode of action by binding onto specific site using computational molecular simulation. MATERIALS AND METHODS In silico Molecular Dynamics (MD) was used to determine the interactions of K21 inside the pocket of the targeted protein (crystal structure of fibroblast collagenase-1 complexed to a diphenyl-ether sulphone based hydroxamic acid; PDB ID: 966C; Crystal structure of MMP-2 active site mutant in complex with APP-derived decapeptide inhibitor. MD simulations were accomplished with the Desmond package in Schrödinger Drug Discovery Suite. Blood samples (~ 0.5 mL) collected into K2EDTA were immediately transferred for further processing using the Litron MicroFlow® PLUS micronucleus analysis kit for mouse blood according to the manufacturer's instructions. Bacterial Reverse Mutation Test of K21 Molecule was performed to evaluate K21 and any possible metabolites for their potential to induce point mutations in amino acid-requiring strains of Escherichia coli (E. coli) (WP2 uvrA (tryptophan-deficient)). RESULTS Molecular Simulation depicted that K21 has a specific pocket binding on various MMPs and SrtA surfaces producing a classical clouting effect. K21 did not induce micronuclei, which are the result of chromosomal damage or damage to the mitotic apparatus, in the peripheral blood reticulocytes of male and female CD-1 mice when administered by oral gavage up to the maximum recommended dose of 2000 mg/kg. The test item, K21, was not mutagenic to Salmonella typhimurium (S. typhimurium) strains TA98, TA100, TA1535 and TA1537 and E. coli strain WP2 uvrA in the absence and presence of metabolic activation when tested up to the limit of cytotoxicity or solubility under the conditions of the test. CONCLUSION K21 could serve as a potent protease inhibitor maintaining the physical and biochemical properties of dental structures.
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Affiliation(s)
- Ranjeet Ajit Bapat
- Restorative Dentistry Division, School of Dentistry, International Medical University Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Kit-Kay Mak
- School of Pharmacy, International Medical University Kuala Lumpur, 126, Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Mallikarjuna Rao Pichika
- School of Pharmacy, International Medical University Kuala Lumpur, 126, Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Jia Chern Pang
- School of Postgraduate Studies, International Medical University, 57000, Kuala Lumpur, Malaysia
| | - Seow Liang Lin
- Restorative Dentistry Division, School of Dentistry, International Medical University Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Suan Phaik Khoo
- Division of Clinical Oral Health, School of Dentistry, International Medical University, Kuala Lumpur, Malaysia
| | - Umer Daood
- Restorative Dentistry Division, School of Dentistry, International Medical University Kuala Lumpur, Kuala Lumpur, Malaysia.
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3
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Rabaan AA, Almansour ZH, Al Bshabshe A, Halwani MA, Al-Subaie MF, Al Kaabi NA, Alshamrani SA, Alshehri AA, Nahari MH, Alqahtani AS, Alhajri M, Alissa M. Application of temperature-dependent and steered molecular dynamics simulation to screen anti-dengue compounds against Marburg virus. J Biomol Struct Dyn 2024:1-20. [PMID: 38234048 DOI: 10.1080/07391102.2024.2303386] [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: 06/20/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
Marburg virus infections are extremely fatal with a fatality range of 23% to 90%, therefore there is an urgent requirement to design and develop efficient therapeutic molecules. Here, a comprehensive temperature-dependent molecular dynamics (MD) simulation method was implemented to identify the potential molecule from the anti-dengue compound library that can inhibit the function of the VP24 protein of Marburg. Virtual high throughput screening identified five effective binders of VP24 after screening 484 anti-dengue compounds. These compounds were treated in MD simulation at four different temperatures: 300, 340, 380, and 420 K. Higher temperatures showed dissociation of hit compounds from the protein. Further, triplicates of 100 ns MD simulation were conducted which showed that compounds ID = 118717693, and ID = 5361 showed strong stability with the protein molecule. These compounds were further validated using Δ G binding free energies and they showed: -30.38 kcal/mol, and -67.83 kcal/mol binding free energies, respectively. Later, these two compounds were used in steered MD simulation to detect its dissociation. Compound ID = 5361 showed the maximum pulling force of 199.02 kcal/mol/nm to dissociate the protein-ligand complex while ID = 118717693 had a pulling force of 101.11 kcal/mol/nm, respectively. This ligand highest number of hydrogen bonds with varying occupancies at 89.93%, 69.80%, 57.93%, 52.33%, and 50.63%. This study showed that ID = 5361 can bind with the VP24 strongly and has the potential to inhibit its function which can be validated in the in-vitro experiment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur, Pakistan
| | - Zainab H Almansour
- Biological Science Department, College of Science, King Faisal University, Hofuf, Saudi Arabia
| | - Ali Al Bshabshe
- Adult critical care Department of Medicine, Division of adult critical care, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Muhammad A Halwani
- Department of Medical Microbiology, Faculty of Medicine, Al Baha University, Saudi Arabia
| | - Maha F Al-Subaie
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Research Center, Dr. Sulaiman Alhabib Medical Group, Riyadh, Saudi Arabia
| | - Nawal A Al Kaabi
- College of Medicine and Health Science, Khalifa University, Abu Dhabi, United Arab Emirates
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi, United Arab Emirates
| | - Saleh A Alshamrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Ahmad A Alshehri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Mohammed H Nahari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Ali S Alqahtani
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mashael Alhajri
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
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4
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Tivari S, Kokate SV, Belmonte-Vázquez JL, Pawar TJ, Patel H, Ahmad I, Gayke MS, Bhosale RS, Jain VD, Muteeb G, Delgado-Alvarado E, Jadeja Y. Synthesis and Evaluation of Biological Activities for a Novel 1,2,3,4-Tetrahydroisoquinoline Conjugate with Dipeptide Derivatives: Insights from Molecular Docking and Molecular Dynamics Simulations. ACS OMEGA 2023; 8:48843-48854. [PMID: 38162790 PMCID: PMC10753551 DOI: 10.1021/acsomega.3c05961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/24/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024]
Abstract
Peptide synthesis has opened new frontiers in the quest for bioactive molecules with limitless biological applications. This study presents the synthesis of a series of novel isoquinoline dipeptides using advanced spectroscopic techniques for characterization. These compounds were designed with the goal of discovering unexplored biological activities that could contribute to the development of novel pharmaceuticals. We evaluated the biological activities of novel compounds including their antimicrobial, antibacterial, and antifungal properties. The results show promising activity against Escherichia coli and potent antibacterial activity against MTCC 443 and MTCC 1688. Furthermore, these compounds demonstrate strong antifungal activity, outperforming existing standard drugs. Computational binding affinity studies of tetrahydroisoquinoline-conjugated dipeptides against E. coli DNA gyrase displayed significant binding interactions and binding affinity, which are reflected in antimicrobial activities of compounds. Our integrative significant molecular findings from both wet and dry laboratories would help pave a path for the development of antimicrobial therapeutics. The findings suggest that these isoquinoline-conjugated dipeptides could be excellent candidates for drug development, with potential applications in the fight against bacterial and fungal infections. This research represents an exciting step forward in the field of peptide synthesis and its potential to discover novel bioactive molecules with significant implications for human health.
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Affiliation(s)
- Sunil
R. Tivari
- Department
of Chemistry, Marwadi University, Rajkot, Gujarat 360003, India
| | - Siddhant V. Kokate
- Department
of Chemistry, S.S.C. College, Junnar, Pune, Maharashtra 410502, India
| | - José L. Belmonte-Vázquez
- Facultad
de Química, Universidad Nacional
Autónoma de México, Circuito Escolar s/n, Ciudad Universitaria, Ciudad de México 04510, Mexico
| | - Tushar Janardan Pawar
- Red
de Estudios Moleculares Avanzados, Clúster
Científico y Tecnológico BioMimic del Instituto de Ecología, A.C. Carretera Antigua a Coatepec
351, Xalapa, Veracruz91073, Mexico
| | - Harun Patel
- Department
of Pharmaceutical Chemistry, R. C. Patel
Institute of Pharmaceutical Education and Research, Shirpur, Dhule, Maharashtra 425405, India
| | - Iqrar Ahmad
- Department
of Pharmaceutical Chemistry, R. C. Patel
Institute of Pharmaceutical Education and Research, Shirpur, Dhule, Maharashtra 425405, India
| | - Manoj S. Gayke
- Department
of Chemistry, School of Science, Indrashil
University, Mehsana, Gujarat 382715, India
| | - Rajesh S. Bhosale
- Department
of Chemistry, School of Science, Indrashil
University, Mehsana, Gujarat 382715, India
| | - Vicky D. Jain
- Department
of Chemistry, Marwadi University, Rajkot, Gujarat 360003, India
| | - Ghazala Muteeb
- Department
of Nursing, College of Applied Medical Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Enrique Delgado-Alvarado
- Micro
and Nanotechnology Research Center, Universidad
Veracruzana, Blvd. Av. Ruiz Cortines No. 455 Fracc, Costa Verde, Boca del Río 94294, Mexico
- Facultad
de Ciencias Químicas, Universidad
Veracruzana, Blvd. Av. Ruiz Cortines No. 455 Fracc, Costa Verde, Boca del Río 94294, Mexico
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5
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Shukla D, Alanazi AM, Panda SP, Dwivedi VD, Kamal MA. Unveiling the antiviral potential of Plant compounds from the Meliaceae family against the Zika virus through QSAR modeling and MD simulation analysis. J Biomol Struct Dyn 2023:1-16. [PMID: 37728536 DOI: 10.1080/07391102.2023.2259498] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/11/2023] [Indexed: 09/21/2023]
Abstract
Zika virus (ZIKV) is a flavivirus transmitted by mosquitoes, causing neurological disorders and congenital malformations. RNA-dependent RNA polymerase (RdRp) is one of its essential enzymes and a promising drug target for antiviral therapy due to its involvement in the growth and multiplication of the virus. In this study, we conducted a QSAR-based chemical library screening from the Meliaceae family to identify potential RdRp inhibitors. The QSAR model was built using the known inhibitors of RdRp NS5 of ZIKV and their biological activity (EC50), along with the structural and chemical characteristics of the compounds. The top two hit compounds were selected from QSAR screening for further analysis using molecular docking to evaluate their binding energies and intermolecular interactions with RdRp, including the critical residue Trp485. Furthermore, molecular dynamics (MD) simulations were performed to evaluate their binding stability and flexibility upon binding to RdRp. The MD results showed that the selected compounds formed stable complexes with RdRp, and their binding interactions were similar to those observed for the native ligand. The binding energies of the top two hits (-8.6 and -7.7 kcal/mole) were comparable to those of previously reported ZIKV RdRp inhibitors (-8.9 kcal/mole). The compound IMPHY009135 showed the strongest binding affinity with RdRp, forming multiple hydrogen bonds and hydrophobic interactions with key residues. However, compound IMPHY009276 showed the most stable and consistent RMSD, which was similar to the native ligand. Our findings suggest that IMPHY009135 and IMPHY009276 are potential lead compounds for developing novel antiviral agents against ZIKV.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Divyanshi Shukla
- Department of Chemistry, Lajpat Rai PG College, Sahibabad, Ghaziabad, India
- Computational Chemistry & Drug Discovery Division, Quanta Calculus, Greater Noida, India
| | - Amer M Alanazi
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Siva Prasad Panda
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar, India
| | - Vivek Dhar Dwivedi
- Computational Chemistry & Drug Discovery Division, Quanta Calculus, Greater Noida, India
- Center for Global Health Research, Saveetha Institute of Medical and Technical Sciences, Saveetha Medical College and Hospitals, Saveetha University, Thandalam, Tamil Nadu, India
| | - Mohammad Amjad Kamal
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Enzymoics, Novel Global Community Educational Foundation, Hebersham, New South Wales, Australia
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6
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Alandijany TA, El-Daly MM, Tolah AM, Bajrai LH, Khateb AM, Alsaady IM, Altwaim SA, Dubey A, Dwivedi VD, Azhar EI. Investigating the Mechanism of Action of Anti-Dengue Compounds as Potential Binders of Zika Virus RNA-Dependent RNA Polymerase. Viruses 2023; 15:1501. [PMID: 37515188 PMCID: PMC10384299 DOI: 10.3390/v15071501] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/25/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
The World Health Organization (WHO) has designated the Zika virus (ZIKV) as a significant risk to the general public's health. Currently, there are no vaccinations or medications available to treat or prevent infection with the Zika virus. Thus, it is urgently required to develop a highly efficient therapeutic molecule. In the presented study, a computationally intensive search was carried out to identify potent compounds that have the potential to bind and block the activity of ZIKV NS5 RNA-dependent RNA polymerase (RdRp). The anti-dengue chemical library was subjected to high-throughput virtual screening and MM/GBSA analysis in order to rate the potential candidates. The top three compounds were then chosen. According to the MM/GBSA analysis, compound 127042987 from the database had the highest binding affinity to the protein with a minimum binding free energy of -77.16 kcal/mole. Compound 127042987 had the most stable RMSD trend and the greatest number of hydrogen bond interactions when these chemical complexes were evaluated further under a 100 ns molecular dynamics simulation. Compound 127042987 displayed the best binding free energy (GBind) of -96.50 kcal/mol, surpassing the native ligand binding energy (-66.17 kcal/mole). Thereafter, an MM/GBSA binding free energy study was conducted to validate the stability of selected chemical complexes. Overall, this study illustrated that compound 127042987 showed preferred binding free energies, suggesting a possible inhibitory mechanism against ZIKV-RdRp. As per this study, it was proposed that compound 127042987 could be used as a therapeutic option to prevent Zika virus infection. These compounds need to be tested in experiments for further validation.
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Affiliation(s)
- Thamir A Alandijany
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Mai M El-Daly
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Ahmed M Tolah
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Rabig 25732, Saudi Arabia
| | - Leena H Bajrai
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Aiah M Khateb
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Taibah University, Madinah 42353, Saudi Arabia
| | - Isra M Alsaady
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Sarah A Altwaim
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 20136, Saudi Arabia
| | - Amit Dubey
- Computational Chemistry & Drug Discovery Division, Quanta Calculus, Greater Noida 201310, India
| | - Vivek Dhar Dwivedi
- Bioinformatics Research Division, Quanta Calculus, Greater Noida 201310, India
| | - Esam I Azhar
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
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7
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Jagatap V, Ahmad I, Sriram D, Kumari J, Adu DK, Ike BW, Ghai M, Ansari SA, Ansari IA, Wetchoua PO, Karpoormath R, Patel H. Isoflavonoid and Furanochromone Natural Products as Potential DNA Gyrase Inhibitors: Computational, Spectral, and Antimycobacterial Studies. ACS OMEGA 2023; 8:16228-16240. [PMID: 37179626 PMCID: PMC10173323 DOI: 10.1021/acsomega.3c00684] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/18/2023] [Indexed: 05/15/2023]
Abstract
In pursuit of new antitubercular agents, we here report the antimycobacterial (H37Rv) and DNA gyrase inhibitory potential of daidzein and khellin natural products (NPs). We procured a total of 16 NPs based on their pharmacophoric similarities with known antimycobacterial compounds. The H37Rv strain of M. tuberculosis was found to be susceptible to only two out of the 16 NPs procured; specifically, daidzein and khellin each exhibited an MIC of 25 μg/mL. Moreover, daidzein and khellin inhibited the DNA gyrase enzyme with IC50 values of 0.042 and 0.822 μg/mL, respectively, compared to ciprofloxacin with an IC50 value of 0.018 μg/mL. Daidzein and khellin were found to have lower toxicity toward the vero cell line, with IC50 values of 160.81 and 300.23 μg/mL, respectively. Further, molecular docking study and MD simulation of daidzein indicated that it remained stable inside the cavity of DNA GyrB domain for 100 ns.
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Affiliation(s)
- Vilas
R. Jagatap
- Division
of Computer-Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education
and Research, Shirpur District, Dhule 425405, Maharashtra, India
| | - Iqrar Ahmad
- Division
of Computer-Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education
and Research, Shirpur District, Dhule 425405, Maharashtra, India
| | - Dharmarajan Sriram
- Department
of Pharmacy, Birla Institute of Technology
and Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shameerpet Mandal, R. R. District, Hyderabad 500078, India
| | - Jyothi Kumari
- Department
of Pharmacy, Birla Institute of Technology
and Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shameerpet Mandal, R. R. District, Hyderabad 500078, India
| | - Darko Kwabena Adu
- Department
of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences,
College of Health Sciences, University of
KwaZulu-Natal (Westville), Durban 4000, South Africa
| | - Blessing Wisdom Ike
- Department
of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences,
College of Health Sciences, University of
KwaZulu-Natal (Westville), Durban 4000, South Africa
| | - Meenu Ghai
- Discipline
of Genetics, School of Life Sciences, University
of KwaZulu-Natal, Westville, Durban 4000, South Africa
| | - Siddique Akber Ansari
- Department
of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Irfan Aamer Ansari
- Department
of Drug Science and Technology, University
of Turin, Turin 10124, Italy
| | - Priscille Ornella
Mefotso Wetchoua
- Department
of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences,
College of Health Sciences, University of
KwaZulu-Natal (Westville), Durban 4000, South Africa
| | - Rajshekhar Karpoormath
- Department
of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences,
College of Health Sciences, University of
KwaZulu-Natal (Westville), Durban 4000, South Africa
| | - Harun Patel
- Division
of Computer-Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education
and Research, Shirpur District, Dhule 425405, Maharashtra, India
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8
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Acar Çevik U, Celik I, İnce U, Maryam Z, Ahmad I, Patel H, Özkay Y, Asım Kaplancıklı Z. Synthesis, Biological Evaluation, and Molecular Modeling Studies of New 1,3,4-Thiadiazole Derivatives as Potent Antimicrobial Agents. Chem Biodivers 2023; 20:e202201146. [PMID: 36764924 DOI: 10.1002/cbdv.202201146] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/14/2023] [Accepted: 02/10/2023] [Indexed: 02/12/2023]
Abstract
In this work, the synthesis, characterization, and biological activities of a new series of 1,3,4-thiadiazole derivatives were investigated. The structures of final compounds were identified using 1 H-NMR, 13 C-NMR, elemental analysis, and HRMS. All the new synthesized compounds were then screened for their antimicrobial activity against four types of pathogenic bacteria and one fungal strain, by application of the MIC assays, using Ampicilin, Gentamycin, Vancomycin, and Fluconazole as standards. Among the compounds, the MIC values of 4 and 8 μg/mL of the compounds 3f and 3g, respectively, are remarkable and indicate that these compounds are good candidates for antifungal activity. The docking experiments were used to identify the binding forms of produced ligands with sterol 14-demethylase to acquire insight into relevant proteins. The MD performed about 100 ns simulations to validate selected compounds' theoretical studies. Finally, using density functional theory (DFT) to predict reactivity, the chemical characteristics and quantum factors of synthesized compounds were computed. These results were then correlated with the experimental data. Furthermore, computational estimation was performed to predict the ADME properties of the most active compound 3f.
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Affiliation(s)
- Ulviye Acar Çevik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, 26470, Turkey
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, 38039, Turkey
| | - Ufuk İnce
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Erciyes University, Kayseri, 38039, Turkey
| | - Zahra Maryam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, 26470, Turkey
| | - Iqrar Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R C. Patel Institute of Pharmaceutical Education and Research, Shirpur, 425405, Maharashtra, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R C. Patel Institute of Pharmaceutical Education and Research, Shirpur, 425405, Maharashtra, India
| | - Yusuf Özkay
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, 26470, Turkey
| | - Zafer Asım Kaplancıklı
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, 26470, Turkey
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9
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Acar Çevik U, Celik I, Işık A, Ahmad I, Patel H, Özkay Y, Kaplancıklı ZA. Design, synthesis, molecular modeling, DFT, ADME and biological evaluation studies of some new 1,3,4-oxadiazole linked benzimidazoles as anticancer agents and aromatase inhibitors. J Biomol Struct Dyn 2023; 41:1944-1958. [PMID: 35037830 DOI: 10.1080/07391102.2022.2025906] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Breast cancer is the most frequent female cancer and second cause of cancer-related deaths among women around the world. Two thirds of breast cancer patients have hormone-dependent tumors, which is very likely be treated with hormonal therapy. Aromatase is involved in the biosynthesis of estrogen thus a critical target for breast cancer. In this study, in order to identify new aromatase enzyme inhibitors, a series of benzimidazole-1,3,4-oxadiazole derivatives were synthesized and characterized by 1H NMR, 13C NMR, and MS spectra analyses. In the in vitro anticancer assay, all the compounds tested anticancer activities using MTT-based assay against five cancer cell lines (MCF-7, A549, HeLa, C6, and HepG2). Among them, compound 5a exhibited the most potent activity with IC50 values of 5.165 ± 0.211 μM and 5.995 ± 0.264 μM against MCF-7 and HepG2 cell lines. Compound 5a was included in the BrdU test to determine the DNA synthesis inhibition effects for both cell types. Furthermore, compound 5c was also found to be more effective than doxorubicin on the HeLa cell line. The selectivity of anticancer activity was evaluated in NIH3T3 cell line. In vitro, enzymatic inhibition assays of aromatase enzyme were performed for compound 5a acting on the MCF-7 cell line. For compound 5a, in silico molecular docking and dynamics simulations against aromatase enzyme was performed to determine possible protein-ligand interactions and stability. DFT study was performed to evaluate the quantum mechanical and electronic properties of compound 5a. Finally, the theoretical ADME properties of the potential aromatase inhibitor compound 5a were analyzed by calculations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ulviye Acar Çevik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Doping and Narcotic Compounds Analysis Laboratory, Anadolu University, Eskişehir, Turkey
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Ayşen Işık
- Department of Biochemistry, Faculty of Science, Selçuk University, Konya, Turkey
| | - Iqrar Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Yusuf Özkay
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Doping and Narcotic Compounds Analysis Laboratory, Anadolu University, Eskişehir, Turkey
| | - Zafer Asım Kaplancıklı
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
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10
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Valencia J, Rubio V, Puerto G, Vasquez L, Bernal A, Mora JR, Cuesta SA, Paz JL, Insuasty B, Abonia R, Quiroga J, Insuasty A, Coneo A, Vidal O, Márquez E, Insuasty D. QSAR Studies, Molecular Docking, Molecular Dynamics, Synthesis, and Biological Evaluation of Novel Quinolinone-Based Thiosemicarbazones against Mycobacterium tuberculosis. Antibiotics (Basel) 2022; 12:antibiotics12010061. [PMID: 36671262 PMCID: PMC9854539 DOI: 10.3390/antibiotics12010061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
In this study, a series of novel quinolinone-based thiosemicarbazones were designed in silico and their activities tested in vitro against Mycobacterium tuberculosis (M. tuberculosis). Quantitative structure-activity relationship (QSAR) studies were performed using quinolinone and thiosemicarbazide as pharmacophoric nuclei; the best model showed statistical parameters of R2 = 0.83; F = 47.96; s = 0.31, and was validated by several different methods. The van der Waals volume, electron density, and electronegativity model results suggested a pivotal role in antituberculosis (anti-TB) activity. Subsequently, from this model a new series of quinolinone-thiosemicarbazone 11a-e was designed and docked against two tuberculosis protein targets: enoyl-acyl carrier protein reductase (InhA) and decaprenylphosphoryl-β-D-ribose-2'-oxidase (DprE1). Molecular dynamics simulation over 200 ns showed a binding energy of -71.3 to -12.7 Kcal/mol, suggesting likely inhibition. In vitro antimycobacterial activity of quinolinone-thiosemicarbazone for 11a-e was evaluated against M. bovis, M. tuberculosis H37Rv, and six different strains of drug-resistant M. tuberculosis. All compounds exhibited good to excellent activity against all the families of M. tuberculosis. Several of the here synthesized compounds were more effective than the standard drugs (isoniazid, oxafloxacin), 11d and 11e being the most active products. The results suggest that these compounds may contribute as lead compounds in the research of new potential antimycobacterial agents.
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Affiliation(s)
- Jhesua Valencia
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
| | - Vivian Rubio
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Gloria Puerto
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Luisa Vasquez
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Anthony Bernal
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
| | - José R. Mora
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170157, Ecuador
| | - Sebastian A. Cuesta
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170157, Ecuador
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - José Luis Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Cercado de Lima 15081, Peru
| | - Braulio Insuasty
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Rodrigo Abonia
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Jairo Quiroga
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Alberto Insuasty
- Grupo de Investigación en Materiales Funcionales Nanoestructurados, Universidad CESMAG, Pasto 520003, Colombia
| | - Andres Coneo
- Medicine Department, Division of Health Sciences, Universidad del Norte, Barranquilla 081007, Colombia
| | - Oscar Vidal
- Medicine Department, Division of Health Sciences, Universidad del Norte, Barranquilla 081007, Colombia
| | - Edgar Márquez
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
- Correspondence: (E.M.); (D.I.)
| | - Daniel Insuasty
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
- Correspondence: (E.M.); (D.I.)
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11
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Edwards BD, Field SK. The Struggle to End a Millennia-Long Pandemic: Novel Candidate and Repurposed Drugs for the Treatment of Tuberculosis. Drugs 2022; 82:1695-1715. [PMID: 36479687 PMCID: PMC9734533 DOI: 10.1007/s40265-022-01817-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2022] [Indexed: 12/12/2022]
Abstract
This article provides an encompassing review of the current pipeline of putative and developed treatments for tuberculosis, including multidrug-resistant strains. The review has organized each compound according to its site of activity. To provide context, mention of drugs within current recommended treatment regimens is made, thereafter followed by discussion on recently developed and upcoming molecules at established and novel targets. The review is designed to provide a clinically applicable understanding of the compounds that are deemed most currently relevant, including those already under clinical study and those that have shown promising pre-clinical results. An extensive review of the efficacy and safety data for key contemporary drugs already incorporated into treatment regimens, such as bedaquiline, pretomanid, and linezolid, is provided. The three levels of the bacterial cell wall (mycolic acid, arabinogalactan, and peptidoglycan layers) are highlighted and important compounds designed to target each layer are delineated. Amongst others, the highly optimistic and potent anti-mycobacterial activity of agents such as BTZ-043, PBTZ 169, and OPC-167832 are emphasized. The evolving spectrum of oxazolidinones, such as sutezolid, delpazolid, and TBI-223, all aiming to exceed the efficacy achieved with linezolid yet offer a safer alternative to the potential toxicity, are reviewed. New and exciting prospective agents with novel mechanisms of impact against TB, including 3-aminomethyl benzoxaboroles and telacebec, are underscored. We describe new diaryloquinolines in development, striving to build on the immense success of bedaquiline. Finally, we discuss some of these compounds that have shown encouraging additive or synergistic benefit when used in combination, providing some promise for the future in treating this ancient scourge.
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Affiliation(s)
- Brett D Edwards
- Division of Infectious Diseases and Tuberculosis Services, Alberta Health Services, Department of Medicine, Cumming School of Medicine, University of Calgary, Peter Lougheed Centre, 3500, 26 Avenue NE, Calgary, AB, T1Y6J4, Canada.
| | - Stephen K Field
- Division of Infectious Diseases and Tuberculosis Services, Alberta Health Services, Department of Medicine, Cumming School of Medicine, University of Calgary, Peter Lougheed Centre, 3500, 26 Avenue NE, Calgary, AB, T1Y6J4, Canada
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12
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Zhang Y, Luo M, Wu P, Wu S, Lee TY, Bai C. Application of Computational Biology and Artificial Intelligence in Drug Design. Int J Mol Sci 2022; 23:13568. [PMID: 36362355 PMCID: PMC9658956 DOI: 10.3390/ijms232113568] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/29/2022] [Accepted: 11/03/2022] [Indexed: 08/24/2023] Open
Abstract
Traditional drug design requires a great amount of research time and developmental expense. Booming computational approaches, including computational biology, computer-aided drug design, and artificial intelligence, have the potential to expedite the efficiency of drug discovery by minimizing the time and financial cost. In recent years, computational approaches are being widely used to improve the efficacy and effectiveness of drug discovery and pipeline, leading to the approval of plenty of new drugs for marketing. The present review emphasizes on the applications of these indispensable computational approaches in aiding target identification, lead discovery, and lead optimization. Some challenges of using these approaches for drug design are also discussed. Moreover, we propose a methodology for integrating various computational techniques into new drug discovery and design.
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Affiliation(s)
- Yue Zhang
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Mengqi Luo
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- South China Hospital, Health Science Center, Shenzhen University, Shenzhen 518116, China
| | - Peng Wu
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518055, China
| | - Song Wu
- South China Hospital, Health Science Center, Shenzhen University, Shenzhen 518116, China
| | - Tzong-Yi Lee
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Chen Bai
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Warshel Institute for Computational Biology, Shenzhen 518172, China
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13
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Abdelgawad MA, Oh JM, Parambi DG, Kumar S, Musa A, Ghoneim MM, Nayl A, El-Ghorab AH, Ahmad I, Patel H, Kim H, Mathew B. Development of bromo- and fluoro-based α, β-unsaturated ketones as highly potent MAO-B inhibitors for the treatment of Parkinson's disease. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133545] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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14
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Radwan HA, Ahmad I, Othman IM, Gad-Elkareem MA, Patel H, Aouadi K, Snoussi M, Kadri A. Design, synthesis, in vitro anticancer and antimicrobial evaluation, SAR analysis, molecular docking and dynamic simulation of new pyrazoles, triazoles and pyridazines based isoxazole. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Paul RK, Ahmad I, Patel H, Kumar V, Raza K. Phytochemicals from Amberboa ramosa as potential DPP-IV inhibitors for the management of Type-II Diabetes Mellitus: Inferences from In-silico Investigations. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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16
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Ayipo YO, Alananzeh WA, Ahmad I, Patel H, Mordi MN. Structural modelling and in silico pharmacology of β-carboline alkaloids as potent 5-HT1A receptor antagonists and reuptake inhibitors. J Biomol Struct Dyn 2022:1-17. [PMID: 35881145 DOI: 10.1080/07391102.2022.2104376] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Serotonin (5-HT) antagonists and reuptake inhibitors (SARIs) are atypical antidepressants for managing major depressive disorder. They are oftentimes applied as adjuvants for ameliorating aftereffects of SSRI antidepressants including insomnia and sexual dysfunction. The few available candidates of this class including lorpiprazole and trazodone also display some daunting side effects, making a continuous search for improved alternatives essential. Natural β-carboline alkaloids (NβCs) are interestingly renowned with broad pharmacological spectrum against several neuropsychiatric disorders including depression. However, their potentials as SARIs remain underexplored. In this study, 982 NβCs retrieved from the Ambinter-Greenpharma (Amb) database were virtually screened for potent SARI alternatives using computational and biocheminformatics approaches: homology modelling of 5-HT1A receptor, Glide HTVS, SP and XP molecular docking, molecular dynamics (MD) simulation, ADMET and mutagenicity predictions. The homology receptor was validated as a good representative of human 5HT1A receptor using the RCSB structure validation and quality protocols. From the virtual screening against the 5-HT1A receptor, Amb ligands, Amb18709727 and Amb37857532 showed higher binding affinities by XP scores of -8.725 and -7.976 kcal/mol, and MMGBSA of -87.972 and -107.585 kcal/mol respectively compared to lorpiprazole, a reference SARI with XP score and MMGBSA of -6.512 and -62.788 kcal/mol respectively. They maintained ideal contacts with pharmacologically essential amino acid residues implicated in SARI mechanisms and expressed higher stability and compactness than lorpiprazole throughout the trajectories of 100 ns MD simulation. They also displayed interesting ADME, druggability, low toxicity and mutagenicity profiles, ideal for CNS drug prospects, thus, recommended as putative SARI candidates for further study.
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Affiliation(s)
- Yusuf Oloruntoyin Ayipo
- Centre for Drug Research, Universiti Sains Malaysia, USM, Pulau Pinang, Malaysia.,Department of Chemistry and Industrial Chemistry, Kwara State University, Malete, Ilorin, Nigeria
| | - Waleed A Alananzeh
- Centre for Drug Research, Universiti Sains Malaysia, USM, Pulau Pinang, Malaysia
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Harun Patel
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Mohd Nizam Mordi
- Centre for Drug Research, Universiti Sains Malaysia, USM, Pulau Pinang, Malaysia
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17
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Ahmad I, Pawara RH, Girase RT, Pathan AY, Jagatap VR, Desai N, Ayipo YO, Surana SJ, Patel H. Synthesis, Molecular Modeling Study, and Quantum-Chemical-Based Investigations of Isoindoline-1,3-diones as Antimycobacterial Agents. ACS OMEGA 2022; 7:21820-21844. [PMID: 35785272 PMCID: PMC9244950 DOI: 10.1021/acsomega.2c01981] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/19/2022] [Indexed: 05/25/2023]
Abstract
The condensation of phthalic anhydride afforded structurally modified isoindoline-1,3-dione derivatives with selected amino-containing compounds. The title compounds (2-30) have been characterized by thin-layer chromatography (TLC), infrared spectroscopy, 1H and 13C NMR spectroscopy, and mass spectroscopy. All of the compounds were assessed for their antimycobacterial activity toward the H37Rv strain by a dual read-out assay method. Among the synthesized compounds, compound 27 possessed a significant IC50 of 18 μM, making it the most potent compound of the series. The InhA inhibitory (IC50) activity of compound 27 was 8.65 μM in comparison to Triclosan (1.32 μM). Computational studies like density functional theory (DFT) study, molecular docking, and dynamic simulation studies illustrated the reactivity and stability of the synthesized compounds as InhA inhibitors. A quantum-mechanics-based DFT study was carried out to investigate the molecular and electronic properties, reactivities, and nature of bonding present in the synthesized compounds and theoretical vibrational (IR) and isotropic value (1H and 13C NMR) calculations.
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Affiliation(s)
- Iqrar Ahmad
- Division
of Computer-Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education
and Research, Shirpur 425405, Dhule, Maharashtra, India
| | - Rahul H. Pawara
- Division
of Computer-Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education
and Research, Shirpur 425405, Dhule, Maharashtra, India
| | - Rukaiyya T. Girase
- Division
of Computer-Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education
and Research, Shirpur 425405, Dhule, Maharashtra, India
| | - Asama Y. Pathan
- Division
of Computer-Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education
and Research, Shirpur 425405, Dhule, Maharashtra, India
| | - Vilas R. Jagatap
- Division
of Computer-Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education
and Research, Shirpur 425405, Dhule, Maharashtra, India
| | - Nisheeth Desai
- Division
of Medicinal Chemistry, Department of Chemistry (DST-FIST Sponsored), Maharaja Krishnakumarsinhji Bhavnagar University, Mahatma Gandhi Campus, Bhavnagar 364002, India
| | - Yusuf Oloruntoyin Ayipo
- Centre
for Drug Research, Universiti Sains Malaysia,
USM, 11800 Gelugor, Pulau Pinang, Malaysia
| | - Sanjay J. Surana
- Division
of Computer-Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education
and Research, Shirpur 425405, Dhule, Maharashtra, India
| | - Harun Patel
- Division
of Computer-Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education
and Research, Shirpur 425405, Dhule, Maharashtra, India
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18
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Pawara R, Ahmad I, Nayak D, Belamkar S, Surana S, Kundu CN, Patil C, Patel H. Design and synthesis of the novel, selective WZ4002 analogue as EGFR-L858R/T790M tyrosine kinase inhibitors for targeted drug therapy in non-small-cell lung cancer (NSCLC). J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132313] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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19
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Bendre RS, Patil RD, Patil PN, Patel HM, Sancheti RS. Synthesis and characterization of new Schiff-bases as Methicillin resistant Staphylococcus aureus (MRSA) inhibitors. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Synthesis, molecular modelling study of the methaqualone analogues as anti-convulsant agent with improved cognition activity and minimized neurotoxicity. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131972] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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21
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Girase R, Ahmad I, Pawara R, Patel H. Optimizing cardio, hepato and phospholipidosis toxicity of the Bedaquiline by chemoinformatics and molecular modelling approach. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:215-235. [PMID: 35225110 DOI: 10.1080/1062936x.2022.2041724] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
The FDA granted expedited approval for Johnson and Johnson's Bedaquiline to treat pulmonary multidrug resistant tuberculosis on 28 December 2012 which is more common in China, Russian Federation and India. Bedaquiline is the first anti-tubercular drug approved by the FDA in the last 40 years, and it has become a cynosure in the circles of synthetic chemists researching new anti-tubercular drugs. Bedaquiline's highly lipophilic nature raises major concerns like suppression of the hERG gene, hepatotoxicity, and phospholipidosis despite its potential antitubercular profile. To address these toxicity concerns, in the present work, we have employed the structural optimization of Bedaquiline using the ADMETopt web server, which optimizes lead with scaffold hopping and ADMET screening. The ADMETopt web server yielded the 476 structures through optimization of three sites in Bedaquiline. Further, we have validated the optimized structures for their activity by performing molecular docking and molecular dynamics (MD) simulations against the mycobacterial ATP synthase enzyme and density functional theory (DFT) study further provides insight into the reactivity of the compounds. After screening and analysis, compound #449 was observed to be the most promising mycobacterial ATP synthase inhibitor with minimal cardiotoxicity, hepatotoxicity and phospholipidosis.
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Affiliation(s)
- R Girase
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur Maharashtra, India
| | - I Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur Maharashtra, India
| | - R Pawara
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur Maharashtra, India
| | - H Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur Maharashtra, India
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22
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Boulaamane Y, Ahmad I, Patel H, Das N, Britel MR, Maurady A. Structural exploration of selected C6 and C7-substituted coumarin isomers as selective MAO-B inhibitors. J Biomol Struct Dyn 2022; 41:2326-2340. [PMID: 35168478 DOI: 10.1080/07391102.2022.2033643] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Monoamine Oxidase B is considered a successful target for developing antiparkinsonian drugs. Due to the side effects of current MAO-B inhibitors, there's an urgent need for novel potent and highly selective MAO-B inhibitors. A recent study has shown that coumarins tend to be more selective towards MAO-B than MAO-A when connected to a hex-5-ynyloxy chain at position 6 in contrast to their C7-isomers. The present study describes the mode of interaction of the C6 and C7-substituted coumarin isomers characterized by their difference in selectivity towards MAO-B through molecular docking and molecular dynamics simulations in an effort to elucidate the structural components and molecular interactions that may be responsible for MAO-B selectivity. Three isomeric coumarin pairs connected to ether chain at position 6 or 7 were taken from the literature and modelled according to their IUPAC nomenclature. Molecular docking study revealed one π- π stacking interaction with Tyr-326 in common between the selective coumarin C6-isomers. Resulting complexes of one isomeric coumarin pair that displayed the highest selectivity shift towards MAO-B were subject to 100 ns molecular dynamics simulations study to analyze the stability of the docked complexes. Molecular dynamics revealed that the C7-isomer is relatively stable in both MAO isoforms through the simulation duration, whereas the C6-isomer deemed unstable for MAO-A which may be due to the bulky Phe-208 residue in MAO-A. Our results might be applied for further development and optimization of coumarin derivatives into a successful drug against Parkinson's disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yassir Boulaamane
- Laboratory of Innovative Technologies, National School of Applied Sciences of Tangier, Abdelmalek Essaadi University, Tetouan, Morocco
| | - Iqrar Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Niloy Das
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
| | - Mohammed Reda Britel
- Laboratory of Innovative Technologies, National School of Applied Sciences of Tangier, Abdelmalek Essaadi University, Tetouan, Morocco
| | - Amal Maurady
- Laboratory of Innovative Technologies, National School of Applied Sciences of Tangier, Abdelmalek Essaadi University, Tetouan, Morocco.,Laboratory of Innovative Technologies, Faculty of Sciences and Techniques of Tangier, Abdelmalek Essaadi University, Tetouan, Morocco
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23
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Aljuhani A, Ahmed HEA, Ihmaid SK, Omar AM, Althagfan SS, Alahmadi YM, Ahmad I, Patel H, Ahmed S, Almikhlafi MA, El-Agrody AM, Zayed MF, Turkistani SA, Abulkhair SH, Almaghrabi M, Salama SA, Al-Karmalawy AA, Abulkhair HS. In vitro and computational investigations of novel synthetic carboxamide-linked pyridopyrrolopyrimidines with potent activity as SARS-CoV-2-M Pro inhibitors. RSC Adv 2022; 12:26895-26907. [PMID: 36320844 PMCID: PMC9494209 DOI: 10.1039/d2ra04015h] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/12/2022] [Indexed: 12/14/2022] Open
Abstract
An essential target for COVID-19 is the main protease of SARS-CoV-2 (Mpro). With the objective of targeting this receptor, a novel set of pyrido[1,2-a]pyrrolo[2,3-d]pyrimidines with terminal carboxamide fragments was designed, synthesized, and considered as an initial motif for the creation of effective pan-coronavirus inhibitors. Accordingly, nine derivatives (21–29) have been introduced for in vitro assay to evaluate their antiviral activity and cytotoxicity effect against COVID-19 virus using Vero cells. The obtained data revealed that the majority of these derivatives showed potent cellular anti-COVID-19 activity and prevent viral growth by more than 90% at two different concentrations with weak or even no detectable cytotoxic effect on Vero cells. Extensive molecular docking simulations highlighted proper non-covalent interaction of new compounds within the binding pocket of Mpro as a potential target for their antiviral activity. In vitro assay for all the synthesized derivatives against the viral Mpro target indicated that compounds 25 and 29 have promising inhibitory activity with IC50 values at low micromolar concentrations. The molecular dynamic simulation results predicted the stability of compound 29 in the binding cavity of SARS-CoV-2 Mpro and hence supported the high inhibitory activity shown by the In vitro assay. These results suggested that compounds 25 and 29 merit further investigations as promising drug candidates for the management of SARS-CoV-2. An essential target for COVID-19 is the main protease of SARS-CoV-2 (Mpro).![]()
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Affiliation(s)
- Ateyatallah Aljuhani
- Chemistry Department, College of Sciences, Taibah University, Al-Madinah Al-Munawarah 41477, Saudi Arabia
| | - Hany E. A. Ahmed
- Pharmacognosy and Pharmaceutical Chemistry Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Nasr City 11884, Cairo, Egypt
| | - Saleh K. Ihmaid
- Pharmacognosy and Pharmaceutical Chemistry Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Jadara University, Irbid, Jordan
| | - Abdelsattar M. Omar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia
- Center for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Nasr City 11884, Cairo, Egypt
| | - Sultan S. Althagfan
- Clinical and Hospital Pharmacy Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia
| | - Yaser M. Alahmadi
- Clinical and Hospital Pharmacy Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia
| | - Iqrar Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, 425405, Maharashtra, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, 425405, Maharashtra, India
| | - Sahar Ahmed
- Pharmacognosy and Pharmaceutical Chemistry Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assiut University, Assuit, Egypt
| | - Mohannad A. Almikhlafi
- Pharmacology and Toxicology Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia
| | - Ahmed M. El-Agrody
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo, Egypt
| | - Mohamed F. Zayed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Nasr City 11884, Cairo, Egypt
- Pharmaceutical Sciences Department, Fakeeh College for Medical Sciences, Jeddah 21461, Saudi Arabia
| | | | - Shorouk H. Abulkhair
- Department of Biochemistry, Faculty of Medicine, Al-Azhar University (Girls), Nasr City 11754, Cairo, Egypt
| | - Mohammed Almaghrabi
- Pharmacognosy and Pharmaceutical Chemistry Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia
| | - Samir A. Salama
- Division of Biochemistry, Department of Pharmacology, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ahmed A. Al-Karmalawy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Horus University – Egypt, International Coastal Road, New Damietta 34518, Egypt
| | - Hamada S. Abulkhair
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Nasr City 11884, Cairo, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Horus University – Egypt, International Coastal Road, New Damietta 34518, Egypt
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24
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Snoussi M, Ahmad I, Patel H, Noumi E, Zrieq R, Saeed M, Sulaiman S, Khalifa N, Chabchoub F, De Feo V, M. Gad-Elkareem M, Aouadi K, Kadri A. Lapachol and ( α/ β)-lapachone as inhibitors of SARS-CoV-2 main protease (Mpro) and hACE-2: ADME properties, docking and dynamic simulation approaches. Pharmacogn Mag 2022. [DOI: 10.4103/pm.pm_251_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2022] Open
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25
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Desai NC, Maheta AS, Jethawa AM, Pandit UP, Ahmad I, Patel H. Zeolite (Y‐H)‐based green synthesis, antimicrobial activity, and molecular docking studies of imidazole bearing oxydibenzene hybrid molecules. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Nisheeth C. Desai
- Division of Medicinal Chemistry, Department of Chemistry (DST‐FIST Sponsored) Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University Bhavnagar India
| | - Abhay S. Maheta
- Division of Medicinal Chemistry, Department of Chemistry (DST‐FIST Sponsored) Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University Bhavnagar India
| | - Aratiba M. Jethawa
- Division of Medicinal Chemistry, Department of Chemistry (DST‐FIST Sponsored) Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University Bhavnagar India
| | - Unnat P. Pandit
- Special Centre for Systems Medicine Jawaharlal Nehru University New Delhi India
| | - Iqrar Ahmad
- Division of Computer‐Aided Drug Design, Department of Pharmaceutical Chemistry R.C. Patel Institute of Pharmaceutical Education and Research Shirpur India
| | - Harun Patel
- Division of Computer‐Aided Drug Design, Department of Pharmaceutical Chemistry R.C. Patel Institute of Pharmaceutical Education and Research Shirpur India
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26
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Li P, Niu Y, Li S, Zu X, Xiao M, Yin L, Feng J, He J, Shen Y. Identification of an AXL kinase inhibitor in triple-negative breast cancer by structure-based virtual screening and bioactivity test. Chem Biol Drug Des 2021; 99:222-232. [PMID: 34679238 DOI: 10.1111/cbdd.13977] [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: 07/12/2021] [Revised: 09/27/2021] [Accepted: 10/16/2021] [Indexed: 01/04/2023]
Abstract
Breast cancer is a malignant tumor that occurs in the glandular epithelium of the breast, and more than 15% of the patients are triple-negative breast cancer (TNBC). Therefore, finding new targets and targeted therapeutic drugs for TNBC is urgent. Overexpression of the AXL is associated with motility and invasiveness of the TNBC cells, which is a potential target for breast cancer therapy. A compound Y041-5921 (IC50 = 6.069 μm for AXL kinase and IC50 = 4.1 μm for MDA-MB-231 cell line) was identified through structure-based virtual screening and bioassay test for the first time. The compound Y041-5921 could significantly inhibit the proliferation and invasion of the TNBC cells and the toxicity of Y041-5921 to normal immortalized breast epithelial cells was far lower than that of commonly used clinical chemotherapy drugs. Besides, it also had well inhibitory effect on the proliferation of many other malignant tumor cell lines (the IC50 value are 10.0 m, 7.1 m, 10.3 m, 11.4 m and 5.8 m for U251 cell, COLO cell, PC-9 cell, CAKI-1 cell and MG63 cell, respectively). The interaction mechanism between Y041-5921 and AXL was studied by molecular dynamics (MD) simulations and binding free energy calculation, and the key residues whose energy contribution mainly comes from non-polar solvation interaction (such as Ala565, Lys567, Met598, Leu620, Pro621, Met623, Lys624, Arg676, Asn677 and Met679) were identified. The small molecule inhibitors Y041-5921 targeting AXL reported in this work will lay a foundation and provide a theoretical basis for the development of the TNBC.
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Affiliation(s)
- Pei Li
- The First Affiliated Hospital, Department of Oncology, Hengyang Medical School, University of South China, Hengyang, Hunan, China.,Key Laboratory of Oncology and Molecular Pathology of Hunan Province, The First Affiliated Hospital of University of South China, Hengyang, Hunan, China
| | - Yuzhen Niu
- School of Life Sciences, Shandong University of Technology, Zibo, Shandong, China
| | - Shuyan Li
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, China
| | - Xuyu Zu
- The First Affiliated Hospital, Department of Oncology, Hengyang Medical School, University of South China, Hengyang, Hunan, China.,Key Laboratory of Oncology and Molecular Pathology of Hunan Province, The First Affiliated Hospital of University of South China, Hengyang, Hunan, China
| | - Maoyu Xiao
- The First Affiliated Hospital, Department of Oncology, Hengyang Medical School, University of South China, Hengyang, Hunan, China.,Key Laboratory of Oncology and Molecular Pathology of Hunan Province, The First Affiliated Hospital of University of South China, Hengyang, Hunan, China
| | - Liyang Yin
- The First Affiliated Hospital, Department of Oncology, Hengyang Medical School, University of South China, Hengyang, Hunan, China.,Key Laboratory of Oncology and Molecular Pathology of Hunan Province, The First Affiliated Hospital of University of South China, Hengyang, Hunan, China
| | - Jianbo Feng
- The First Affiliated Hospital, Department of Oncology, Hengyang Medical School, University of South China, Hengyang, Hunan, China.,Key Laboratory of Oncology and Molecular Pathology of Hunan Province, The First Affiliated Hospital of University of South China, Hengyang, Hunan, China
| | - Jun He
- The Nanhua Affiliated Hospital, Department of Spine Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Yingying Shen
- The First Affiliated Hospital, Department of Oncology, Hengyang Medical School, University of South China, Hengyang, Hunan, China.,Key Laboratory of Oncology and Molecular Pathology of Hunan Province, The First Affiliated Hospital of University of South China, Hengyang, Hunan, China
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27
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Computational identification of 2,4-disubstituted amino-pyrimidines as L858R/T790M-EGFR double mutant inhibitors using pharmacophore mapping, molecular docking, binding free energy calculation, DFT study and molecular dynamic simulation. In Silico Pharmacol 2021; 9:54. [PMID: 34631361 DOI: 10.1007/s40203-021-00113-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 09/24/2021] [Indexed: 10/20/2022] Open
Abstract
Pharmacophore modelling studies have been performed for a series of 2,4-disubstituted-pyrimidines derivatives as EGFR L858R/T790M tyrosine kinase inhibitors. The high scoring AARR.15 hypothesis was selected as the best pharmacophore model with the highest survival score of 3.436 having two hydrogen bond acceptors and two aromatic ring features. Pharmacophore-based virtual screening followed by structure-based yielded the six molecules (ZINC17013227, ZINC17013215, ZINC9573324, ZINC9573445, ZINC24023331 and ZINC17013503) from the ZINC database with significant in silico predicted activity and strong binding affinity towords the EGFR L858R/T790M tyrosine kinase. In silico toxicity and cytochrome profiling indicates that all the 06 virtually screened compounds were substrate/inhibitors of the CYP-3A4 metabolizing enzyme and were non-carcinogenic and devoid of Ames mutagenesis. Density functional theory (DFT) and molecular dynamic (MD) simulation further validated the obtained hits. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-021-00113-x.
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28
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Zrieq R, Ahmad I, Snoussi M, Noumi E, Iriti M, Algahtani FD, Patel H, Saeed M, Tasleem M, Sulaiman S, Aouadi K, Kadri A. Tomatidine and Patchouli Alcohol as Inhibitors of SARS-CoV-2 Enzymes (3CLpro, PLpro and NSP15) by Molecular Docking and Molecular Dynamics Simulations. Int J Mol Sci 2021; 22:10693. [PMID: 34639036 PMCID: PMC8509278 DOI: 10.3390/ijms221910693] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 12/24/2022] Open
Abstract
Considering the current dramatic and fatal situation due to the high spreading of SARS-CoV-2 infection, there is an urgent unmet medical need to identify novel and effective approaches for prevention and treatment of Coronavirus disease (COVID 19) by re-evaluating and repurposing of known drugs. For this, tomatidine and patchouli alcohol have been selected as potential drugs for combating the virus. The hit compounds were subsequently docked into the active site and molecular docking analyses revealed that both drugs can bind the active site of SARS-CoV-2 3CLpro, PLpro, NSP15, COX-2 and PLA2 targets with a number of important binding interactions. To further validate the interactions of promising compound tomatidine, Molecular dynamics study of 100 ns was carried out towards 3CLpro, NSP15 and COX-2. This indicated that the protein-ligand complex was stable throughout the simulation period, and minimal backbone fluctuations have ensued in the system. Post dynamic MM-GBSA analysis of molecular dynamics data showed promising mean binding free energy 47.4633 ± 9.28, 51.8064 ± 8.91 and 54.8918 ± 7.55 kcal/mol, respectively. Likewise, in silico ADMET studies of the selected ligands showed excellent pharmacokinetic properties with good absorption, bioavailability and devoid of toxicity. Therefore, patchouli alcohol and especially, tomatidine may provide prospect treatment options against SARS-CoV-2 infection by potentially inhibiting virus duplication though more research is guaranteed and secured.
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Affiliation(s)
- Rafat Zrieq
- Department of Public Health, College of Public Health and Health Informatics, University of Ha’il, Ha’il 81451, Saudi Arabia; (R.Z.); (F.D.A.)
| | - Iqrar Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 425405, India; (I.A.); (H.P.)
| | - Mejdi Snoussi
- Department of Biology, College of Science, University of Ha’il City, P.O. 2440, Ha’il 2440, Saudi Arabia; (E.N.); (M.S.)
- Laboratory of Genetics, Biodiversity and Valorization of Bio-Resources (LR11ES41), University of Monastir, Higher Institute of Biotechnology of Monastir, Avenue Tahar Haddad, BP74, Monastir 5000, Tunisia
| | - Emira Noumi
- Department of Biology, College of Science, University of Ha’il City, P.O. 2440, Ha’il 2440, Saudi Arabia; (E.N.); (M.S.)
- Laboratory of Bioresources: Integrative Biology and Valorization, (LR14-ES06), University of Monastir, Higher Institute of Biotechnology of Monastir, Avenue Tahar Haddad, BP74, Monastir 5000, Tunisia
| | - Marcello Iriti
- Department of Agricultural and Environmental Sciences, Università degli Studi di Milano, 20133 Milano, Italy
- Phytochem Lab., Department of Agricultural and Environmental Sciences, Università degli Studi di Milano, 20133 Milano, Italy
- National Interuniversity Consortium of Materials Science and Technology (INSTM), 50121 Firenze, Italy
- BAT Center—Interuniversity Center for Studies on Bioispired Agro-Environmental Technology, University of Napoli “Federico II”, Portici, 80055 Napoli, Italy
| | - Fahad D. Algahtani
- Department of Public Health, College of Public Health and Health Informatics, University of Ha’il, Ha’il 81451, Saudi Arabia; (R.Z.); (F.D.A.)
- Molecular Diagnostic and Personalized Therapeutics Unit, University of Ha’il, Ha’il 81451, Saudi Arabia
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 425405, India; (I.A.); (H.P.)
| | - Mohd Saeed
- Department of Biology, College of Science, University of Ha’il City, P.O. 2440, Ha’il 2440, Saudi Arabia; (E.N.); (M.S.)
| | - Munazzah Tasleem
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, China;
| | - Shadi Sulaiman
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, University of Ha’il, Ha’il 81451, Saudi Arabia;
| | - Kaïss Aouadi
- Department of Chemistry, College of Science, Qassim University, Buraidah 51452, Saudi Arabia;
- Faculty of Science of Monastir, University of Monastir, Avenue of the Environment, Monastir 5019, Tunisia
| | - Adel Kadri
- Department of Chemistry, Faculty of Science and Arts of Baljurashi, Albaha University, Al Bahah 65731, Saudi Arabia;
- Faculty of Science of Sfax, Department of Chemistry, University of Sfax, B.P. 1171, Sfax 3000, Tunisia
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29
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AYIPO YO, YAHAYA SN, BABAMALE HF, AHMAD I, PATEL H, MORDI MN. β-Carboline alkaloids induce structural plasticity and inhibition of SARS-CoV-2 nsp3 macrodomain more potently than remdesivir metabolite GS-441524: computational approach. Turk J Biol 2021; 45:503-517. [PMID: 34803450 PMCID: PMC8573841 DOI: 10.3906/biy-2106-64] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 07/31/2021] [Indexed: 12/28/2022] Open
Abstract
The nsp3 macrodomain is implicated in the viral replication, pathogenesis and host immune responses through the removal of ADP-ribosylation sites during infections of coronaviruses including the SARS-CoV-2. It has ever been modulated by macromolecules including the ADP-ribose until Ni and co-workers recently reported its inhibition and plasticity enhancement unprecedentedly by remdesivir metabolite, GS-441524, creating an opportunity for investigating other biodiverse small molecules such as β-Carboline (βC) alkaloids. In this study, 1497 βC analogues from the HiT2LEAD chemical database were screened, using computational approaches of Glide XP docking, molecular dynamics simulation and pk-CSM ADMET predictions. Selectively, βC ligands, 129, 584, 1303 and 1323 demonstrated higher binding affinities to the receptor, indicated by XP docking scores of -10.72, -10.01, -9.63 and -9.48 kcal/mol respectively than remdesivir and GS-441524 with -4.68 and -9.41 kcal/mol respectively. Consistently, their binding free energies were -36.07, -23.77, -24.07 and -17.76 kcal/mol respectively, while remdesivir and GS-441524 showed -21.22 and -24.20 kcal/mol respectively. Interestingly, the selected βC ligands displayed better stability and flexibility for enhancing the plasticity of the receptor than GS-441524, especially 129 and 1303. Their predicted ADMET parameters favour druggability and low expressions for toxicity. Thus, they are recommended as promising adjuvant/standalone anti-SARS-CoV-2 candidates for further study.Key words: SARS-CoV-2, nsp3 macrodomain, ADP-ribose, β-carboline, bioinformatics, drug design.
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Affiliation(s)
- Yusuf Oloruntoyin AYIPO
- Centre for Drug Research, Universiti Sains Malaysia, Pulau PinangMalaysia
- Department of Chemical, Geological and Physical Sciences, Kwara State University, IlorinNigeria
| | - Sani Najib YAHAYA
- Centre for Drug Research, Universiti Sains Malaysia, Pulau PinangMalaysia
- Department of Pharmaceutical and Medicinal Chemistry, Bayero University, KanoNigeria
| | - Halimah Funmilayo BABAMALE
- School of Chemical Sciences, Universiti Sains Malaysia, Pulau PinangMalaysia
- Department of Industrial Chemistry, University of Ilorin, IlorinNigeria
| | - Iqrar AHMAD
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, MaharashtraIndia
| | - Harun PATEL
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, MaharashtraIndia
| | - Mohd Nizam MORDI
- Centre for Drug Research, Universiti Sains Malaysia, Pulau PinangMalaysia
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30
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Shinde Y, Ahmad I, Surana S, Patel H. The Mur Enzymes Chink in the Armour of Mycobacterium tuberculosis cell wall. Eur J Med Chem 2021; 222:113568. [PMID: 34118719 DOI: 10.1016/j.ejmech.2021.113568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 02/02/2023]
Abstract
TUBERCULOSIS: (TB) transmitted by Mycobacterium tuberculosis (Mtb) is one of the top 10 causes of death globally. Currently, the widespread occurrence of resistance toward Mtb strains is becoming a significant concern to public health. This scenario exaggerated the need for the discovery of novel targets and their inhibitors. Targeting the "Mtb cell wall peptidoglycan synthesis" is an attractive strategy to overcome drug resistance. Mur enzymes (MurA-MurF) play essential roles in the peptidoglycan synthesis by catalyzing the ligation of key amino acid residues to the stem peptide. These enzymes are unique and confined to the eubacteria and are absent in humans, representing potential targets for anti-tubercular drug discovery. Mtb Mur ligases with the same catalytic mechanism share conserved amino acid regions and structural features that can conceivably exploit for the designing of the inhibitors, which can simultaneously target more than one isoforms (MurC-MurF) of the enzyme. In light of these findings in the current review, we have discussed the recent advances in medicinal chemistry of Mtb Mur enzymes (MurA-MurF) and their inhibitors, offering attractive multi-targeted strategies to combat the problem of drug-resistant in M. tuberculosis.
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Affiliation(s)
- Yashodeep Shinde
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425405, Maharashtra, India
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425405, Maharashtra, India
| | - Sanjay Surana
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425405, Maharashtra, India
| | - Harun Patel
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425405, Maharashtra, India.
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31
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Effect of Aminosilane Coupling Agent-Modified Nano-SiO2 Particles on Thermodynamic Properties of Epoxy Resin Composites. Processes (Basel) 2021. [DOI: 10.3390/pr9050771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
From the perspective of improving the thermodynamic properties of epoxy resin, it has become the focus of research to enhance the operational stability of GIS (Gas Insulated Substation) basin insulators for UHV (Ultra-High Voltage) equipment. In this paper, three aminosilane coupling agents with different chain lengths, (3-Aminopropyl)trimethoxysilane (KH550), Aminoethyl)-γ-aminopropyltrimethoxysilane (KH792) and 3-[2-(2-Aminoethylamino)ethylamino]propyl-trimethoxysilane (TAPS), were used to modify nano-SiO2 and doped into epoxy resin, respectively, using a combination of experimental and molecular dynamics simulations. The experimental results showed that the surface-grafted KH792 model of nano-SiO2 exhibited the most significant improvement in thermal properties compared with the undoped nanoparticle model. The storage modulus increased by 276 MPa and the Tg increased by 61 K. The simulation results also showed that the mechanical properties of the nano-SiO2 surface-grafted KH792 model were about 3 times higher than that of the undoped nanoparticle model, the Tg increased by 36.5 K, and the thermal conductivity increased by 24.5%.
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