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Balaji E V, Satarker S, Kumar BH, Pandey S, Birangal SR, Nayak UY, Pai KSR. In-silico lead identification of the pan-mutant IDH1 and IDH2 inhibitors to target glioblastoma. J Biomol Struct Dyn 2024; 42:3764-3789. [PMID: 37227789 DOI: 10.1080/07391102.2023.2215884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023]
Abstract
Glioblastoma (GBM) is an aggressive malignant type of brain tumor. Targeting one single intracellular pathway might not alleviate the disease, rather it activates the other molecular pathways that lead to the worsening of the disease condition. Therefore, in this study, we attempted to target both isocitrate dehydrogenase 1 (IDH1) and IDH2, which are one of the most commonly mutated proteins in GBM and other cancer types. Here, standard precision and extra precision docking, IFD, MM-GBSA, QikProp, and molecular dynamics (MD) simulation were performed to identify the potential dual inhibitor for IDH1 and IDH2 from the enamine database containing 59,161 ligands. Upon docking the ligands with IDH1 (PDB: 6VEI) and IDH2 (PDB: 6VFZ), the top eight ligands were selected, based on the XP Glide score. These ligands produced favourable MMGBSA scores and ADME characteristics. Finally, the top four ligands 12953, 44825, 51295, and 53210 were subjected to MD analysis. Interestingly, 53210 showed maximum interaction with Gln 277 for 99% in IDH1 and Gln 316 for 100% in IDH2, which are the crucial amino acids for the inhibitory function of IDH1 and IDH2 to target GBM. Therefore, the present study attempts to identify the novel molecules which could possess a pan-inhibitory action on both IDH1 and IDH that could be crucial in the management of GBM. Yet further evaluation involving in vitro and in vivo studies is warranted to support the data in our current study.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vignesh Balaji E
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sairaj Satarker
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - B Harish Kumar
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Samyak Pandey
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sumit Raosaheb Birangal
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Usha Y Nayak
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - K Sreedhara Ranganath Pai
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
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2
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Nayak SS, Sundararajan V. Robust anti-inflammatory activity of genistein against neutrophil elastase: a microsecond molecular dynamics simulation study. J Biomol Struct Dyn 2023; 41:11612-11628. [PMID: 36705087 DOI: 10.1080/07391102.2023.2170919] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/26/2022] [Indexed: 01/28/2023]
Abstract
Human Neutrophil Elastase (HNE) is one of the major causes of tissue destruction in numerous chronic and inflammatory disorders and has been reported as a therapeutic target for inflammatory diseases. Overexpression of this enzyme plays a critical role in the pathogenesis of rheumatoid arthritis (RA). The focus of this study is to identify potent natural inhibitors that could target the active site of the HNE through the use of computational methods. The molecular structure of small molecules was retrieved from several natural compound databases. This was followed by structure-based virtual screening, molecular docking, ADMET property predictions and molecular dynamic simulation studies to screen potential HNE inhibitors. In total, 1881 natural compounds were extracted and subjected to molecular docking studies, and 10 compounds were found to have good interactions, exhibiting the best docking scores. Genistein showed higher binding efficacy (-10.28 Kcal/mol) to HNE in comparison to other natural compounds. The conformational stability of the docked complex of the ELANE gene (HNE) with genistein was assessed using 1-microsecond molecular dynamic simulation (MDs), which reliably revealed the unique stereochemical alteration of the complex, indicating its conformational stability and flexibility. Alterations in the enzyme structure upon complex formation were further characterized through clustering analysis and linear interaction energy (LIE) calculation. The outcomes of this research propose novel potential candidates against target HNE.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Smruti Sudha Nayak
- Department of Bio-Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, India
| | - Vino Sundararajan
- Department of Bio-Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, India
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3
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Saleem U, Khalid S, Zaib S, Anwar F, Akhtar MF, Hussain L, Saleem A, Ahmad B. Wound Healing Potential and In Silico Appraisal of Convolvulus arvensis L. Methanolic Extract. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1373160. [PMID: 36467883 PMCID: PMC9715325 DOI: 10.1155/2022/1373160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/21/2022] [Accepted: 10/28/2022] [Indexed: 10/29/2023]
Abstract
Convolvulus arvensis L. is rich in phenolic compounds and traditionally used to treat wounds, skin ulcer, and inflammation. The current study is aimed at scientifically potentiating its traditional wound healing use. The methanolic extract of C. arvensis stem (CaME) was analyzed for HPLC and GC-MS analyses. The binding modes of active compounds were investigated against protein targets glycogen synthase kinase-3β (GSK-3β), transforming growth factor-beta (TGF-β), c-myc, and β-catenin by molecular docking followed by molecular dynamic simulations which revealed some conserved mode of binding as reported in crystal structures. The antioxidant potential of CaME was evaluated by in vitro methods such as 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging, hydrogen peroxide scavenging, and ferric reducing power assays. Ointment formulations of 10 and 20% CaME were applied topically and evaluated for wound healing potency against the excisional wound on the skin of Wistar rats. Gentamycin (0.1%) served as standard therapy. The healing process was observed for 20 days in the form of wound size and epithelialization followed by histopathological evaluation of the wound area. Chemical characterization showed the presence of 7-hexadecenoic acid, 2-hexadecylicosan-1-ol, quercetin, gallic acid, ferulic acid, and other compounds. The plant extract exhibited significant in vitro antioxidant activity. The animals treated with 10% ointment showed moderate healing, whereas the treatment with 20% CaME revealed healing potential comparable to the standard 0.1% gentamycin as coevidenced from histopathological evaluation of skin. The study corroborates promising potential of C. arvensis on the healing of wounds, which possibly will be attributed to its antioxidant activity, fatty acids, quercetin, and gallic and caffeic acids, and binding potential of its phytoconstituents (phenolic acids) with wound healing targets.
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Affiliation(s)
- Uzma Saleem
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad 38000, Pakistan
| | - Sana Khalid
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad 38000, Pakistan
| | - Shingraf Zaib
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad 38000, Pakistan
| | - Fareeha Anwar
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Lahore, Pakistan
| | - Muhammad Furqan Akhtar
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Lahore, Pakistan
| | - Liaqat Hussain
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad 38000, Pakistan
| | - Ammara Saleem
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad 38000, Pakistan
| | - Bashir Ahmad
- Hamza College of Pharmaceutical and Allied Health Sciences, Lahore, Pakistan
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4
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Islam S, Hosen MA, Ahmad S, ul Qamar MT, Dey S, Hasan I, Fujii Y, Ozeki Y, Kawsar SM. Synthesis, antimicrobial, anticancer activities, PASS prediction, molecular docking, molecular dynamics and pharmacokinetic studies of designed methyl α-D-glucopyranoside esters. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132761] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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5
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Pagilla S, Anagani Kanaka Durga B, Vodnala S, Kamutam R, Mudiraj A, Phanithi PB, Chetti P. Identification of novel quinazolinone hybrids as cytotoxic agents against
C6
glioma cell lines. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | | | - Sumathi Vodnala
- Department of Chemistry, Nizam College, Basheerbhag Osmania University Hyderabad India
| | | | - Anwita Mudiraj
- Department of Biotechnology and Bioinformatics, School of Life Sciences University of Hyderabad Hyderabad India
| | - Prakash Babu Phanithi
- Department of Biotechnology and Bioinformatics, School of Life Sciences University of Hyderabad Hyderabad India
| | - Prabhakar Chetti
- Department of Chemistry National Institute of Technology Kurukshetra India
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6
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Fatima I, Ahmad S, Alamri MA, Mirza MU, Tahir Ul Qamar M, Rehman A, Shahid F, Alatawi EA, Alkhayl FFA, Al-Megrin WA, Almatroudi A. Discovery of Rift Valley fever virus natural pan-inhibitors by targeting its multiple key proteins through computational approaches. Sci Rep 2022; 12:9260. [PMID: 35662263 PMCID: PMC9163866 DOI: 10.1038/s41598-022-13267-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 05/18/2022] [Indexed: 12/14/2022] Open
Abstract
The Rift Valley fever virus (RVFV) is a zoonotic arbovirus and pathogenic to both humans and animals. Currently, no proven effective RVFV drugs or licensed vaccine are available for human or animal use. Hence, there is an urgent need to develop effective treatment options to control this viral infection. RVFV glycoprotein N (GN), glycoprotein C (GC), and nucleocapsid (N) proteins are attractive antiviral drug targets due to their critical roles in RVFV replication. In present study, an integrated docking-based virtual screening of more than 6000 phytochemicals with known antiviral activities against these conserved RVFV proteins was conducted. The top five hit compounds, calyxin C, calyxin D, calyxin J, gericudranins A, and blepharocalyxin C displayed optimal binding against all three target proteins. Moreover, multiple parameters from the molecular dynamics (MD) simulations and MM/GBSA analysis confirmed the stability of protein-ligand complexes and revealed that these compounds may act as potential pan-inhibitors of RVFV replication. Our computational analyses may contribute toward the development of promising effective drugs against RVFV infection.
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Affiliation(s)
- Israr Fatima
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Mubarak A Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Canada
| | | | - Abdur Rehman
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Farah Shahid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Eid A Alatawi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, 71491, Saudi Arabia
| | - Faris F Aba Alkhayl
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, 51452, Saudi Arabia.,Department of Pharmaceutical Chemistry and Pharmacognosy, College of Dentistry and Pharmacy, Buraydah Colleges, Buraydah, 51418, Saudi Arabia
| | - Wafa Abdullah Al-Megrin
- Department of Biology, Faculty of Science, Princess Nourah Bint Abdulrahman University, Riyadh, 11671, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, 51452, Saudi Arabia.
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7
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Mirza MU, Alanko I, Vanmeert M, Muzzarelli KM, Salo-Ahen OMH, Abdullah I, Kovari IA, Claes S, De Jonghe S, Schols D, Schinazi RF, Kovari LC, Trant JF, Ahmad S, Froeyen M. The discovery of Zika virus NS2B-NS3 inhibitors with antiviral activity via an integrated virtual screening approach. Eur J Pharm Sci 2022; 175:106220. [PMID: 35618201 DOI: 10.1016/j.ejps.2022.106220] [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: 03/22/2022] [Revised: 05/18/2022] [Accepted: 05/23/2022] [Indexed: 11/15/2022]
Abstract
With expanding recent outbreaks and a lack of treatment options, the Zika virus (ZIKV) poses a severe health concern. The availability of ZIKV NS2B-NS3 co-crystallized structures paved the way for rational drug discovery. A computer-aided structure-based approach was used to screen a diverse library of compounds against ZIKV NS2B-NS3 protease. The top hits were selected based on various binding free energy calculations followed by per-residue decomposition analysis. The selected hits were then evaluated for their biological potential with ZIKV protease inhibition assay and antiviral activity. Among 26 selected compounds, 8 compounds showed promising activity against ZIKV protease with a percentage inhibition of greater than 25 and 3 compounds displayed ∼50% at 10 µM, which indicates an enrichment rate of approximately 36% (threshold IC50 < 10 µM) in the ZIKV-NS2B-NS3 protease inhibition assay. Of these, only one compound (23) produced whole-cell anti-ZIKV activity, and the binding mode of 23 was extensively analyzed through long-run molecular dynamics simulations. The current study provides a promising starting point for the further development of novel compounds against ZIKV.
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Affiliation(s)
- Muhammad Usman Mirza
- KU Leuven, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, Medicinal Chemistry, Herestraat 49, box 1041, Leuven 3000, Belgium; Department of Chemistry and Biochemistry, University of Windsor, Windsor N9B 3P4, ON, Canada
| | - Ida Alanko
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland; Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
| | - Michiel Vanmeert
- KU Leuven, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, Medicinal Chemistry, Herestraat 49, box 1041, Leuven 3000, Belgium
| | - Kendall M Muzzarelli
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit 48201, MI, USA
| | - Outi M H Salo-Ahen
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland; Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
| | - Iskandar Abdullah
- Drug Design Development Research Group, Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Iulia A Kovari
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit 48201, MI, USA
| | - Sandra Claes
- KU Leuven, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Herestraat 49, box 1043, Leuven, Belgium
| | - Steven De Jonghe
- KU Leuven, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Herestraat 49, box 1043, Leuven, Belgium
| | - Dominique Schols
- KU Leuven, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Herestraat 49, box 1043, Leuven, Belgium
| | - Raymond F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta 30322, GA, USA
| | - Ladislau C Kovari
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit 48201, MI, USA
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, Windsor N9B 3P4, ON, Canada
| | - Sarfraz Ahmad
- Drug Design Development Research Group, Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Matheus Froeyen
- KU Leuven, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, Medicinal Chemistry, Herestraat 49, box 1041, Leuven 3000, Belgium.
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8
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Folate Conjugated Polyethylene Glycol Probe for Tumor-Targeted Drug Delivery of 5-Fluorouracil. Molecules 2022; 27:molecules27061780. [PMID: 35335144 PMCID: PMC8954791 DOI: 10.3390/molecules27061780] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/25/2022] [Accepted: 03/04/2022] [Indexed: 01/01/2023] Open
Abstract
A targeted delivery system is primarily intended to carry a potent anticancer drug to specific tumor sites within the bodily tissues. In the present study, a carrier system has been designed using folic acid (FA), bis-amine polyethylene glycol (PEG), and an anticancer drug, 5-fluorouracil (5-FU). FA and PEG were joined via an amide bond, and the resulting FA-PEG-NH2 was coupled to 5-FU producing folate-polyethylene glycol conjugated 5-fluorouracil (FA-PEG-5-FU). Spectroscopic techniques (UV-Vis, 1HNMR, FTIR, and HPLC) were used for the characterization of products. Prodrug (FA-PEG-5-FU) was analyzed for drug release profile (in vitro) up to 10 days and compared to a standard anticancer drug (5-FU). Folate conjugate was also analyzed to study its folate receptors (FR) mediated transport and in vitro cytotoxicity assays using HeLa cancer cells/Vero cells, respectively, and antitumor activity in tumor-bearing mice models. Folate conjugate showed steady drug release patterns and improved uptake in the HeLa cancer cells than Vero cells. Folate conjugate treated mice group showed smaller tumor volumes; specifically after the 15th day post-treatment, tumor sizes were decreased significantly compared to the standard drug group (5-FU). Molecular docking findings demonstrated importance of Trp138, Trp140, and Lys136 in the stabilization of flexible loop flanking the active site. The folic acid conjugated probe has shown the potential of targeted drug delivery and sustained release of anticancer drug to tumor lesions with intact antitumor efficacy.
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9
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Ahmad S, Usman Mirza M, Yean Kee L, Nazir M, Abdul Rahman N, Trant JF, Abdullah I. Fragment-based in silico design of SARS-CoV-2 main protease inhibitors. Chem Biol Drug Des 2021; 98:604-619. [PMID: 34148292 PMCID: PMC8444677 DOI: 10.1111/cbdd.13914] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/16/2021] [Accepted: 06/06/2021] [Indexed: 11/27/2022]
Abstract
3CLpro is essential for SARS-CoV-2 replication and infection; its inhibition using small molecules is a potential therapeutic strategy. In this study, a comprehensive crystallography-guided fragment-based drug discovery approach was employed to design new inhibitors for SARS-CoV-2 3CLpro. All small molecules co-crystallized with SARS-CoV-2 3CLpro with structures deposited in the Protein Data Bank were used as inputs. Fragments sitting in the binding pocket (87) were grouped into eight geographical types. They were interactively coupled using various synthetically reasonable linkers to generate larger molecules with divalent binding modes taking advantage of two different fragments' interactions. In total, 1,251 compounds were proposed, and 7,158 stereoisomers were screened using Glide (standard precision and extra precision), AutoDock Vina, and Prime MMGBSA. The top 22 hits having conformations approaching the linear combination of their constituent fragments were selected for MD simulation on Desmond. MD simulation suggested 15 of these did adopt conformations very close to their constituent pieces with far higher binding affinity than either constituent domain alone. These structures could provide a starting point for the further design of SARS-CoV-2 3CLpro inhibitors with improved binding, and structures are provided.
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Affiliation(s)
- Sarfraz Ahmad
- Drug Design Development Research GroupDepartment of ChemistryFaculty of ScienceUniversiti MalayaKuala LumpurMalaysia
| | | | - Lee Yean Kee
- Drug Design Development Research GroupDepartment of ChemistryFaculty of ScienceUniversiti MalayaKuala LumpurMalaysia
| | - Mamoona Nazir
- Department of PharmacyThe University of LahoreLahorePakistan
| | - Noorsaadah Abdul Rahman
- Drug Design Development Research GroupDepartment of ChemistryFaculty of ScienceUniversiti MalayaKuala LumpurMalaysia
| | - John F. Trant
- Department of Chemistry and BiochemistryUniversity of WindsorWindsorONCanada
| | - Iskandar Abdullah
- Drug Design Development Research GroupDepartment of ChemistryFaculty of ScienceUniversiti MalayaKuala LumpurMalaysia
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10
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Alamri MA, Tahir ul Qamar M, Mirza MU, Bhadane R, Alqahtani SM, Muneer I, Froeyen M, Salo-Ahen OMH. Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CL pro. J Biomol Struct Dyn 2021; 39:4936-4948. [PMID: 32579061 PMCID: PMC7332866 DOI: 10.1080/07391102.2020.1782768] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/08/2020] [Indexed: 12/22/2022]
Abstract
The SARS-CoV-2 was confirmed to cause the global pandemic of coronavirus disease 2019 (COVID-19). The 3-chymotrypsin-like protease (3CLpro), an essential enzyme for viral replication, is a valid target to combat SARS-CoV and MERS-CoV. In this work, we present a structure-based study to identify potential covalent inhibitors containing a variety of chemical warheads. The targeted Asinex Focused Covalent (AFCL) library was screened based on different reaction types and potential covalent inhibitors were identified. In addition, we screened FDA-approved protease inhibitors to find candidates to be repurposed against SARS-CoV-2 3CLpro. A number of compounds with significant covalent docking scores were identified. These compounds were able to establish a covalent bond (C-S) with the reactive thiol group of Cys145 and to form favorable interactions with residues lining the substrate-binding site. Moreover, paritaprevir and simeprevir from FDA-approved protease inhibitors were identified as potential inhibitors of SARS-CoV-2 3CLpro. The mechanism and dynamic stability of binding between the identified compounds and SARS-CoV-2 3CLpro were characterized by molecular dynamics (MD) simulations. The identified compounds are potential inhibitors worthy of further development as COVID-19 drugs. Importantly, the identified FDA-approved anti-hepatitis-C virus (HCV) drugs paritaprevir and simeprevir could be ready for clinical trials to treat infected patients and help curb COVID-19. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mubarak A. Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkarj, Saudi Arabia
| | | | - Muhammad Usman Mirza
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, Leuven, Belgium
| | - Rajendra Bhadane
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku, Finland
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, Turku, Finland
| | - Safar M. Alqahtani
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkarj, Saudi Arabia
| | - Iqra Muneer
- School of Life Sciences, University of Science and Technology of China, Hefei, P. R. China
| | - Matheus Froeyen
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, Leuven, Belgium
| | - Outi M. H. Salo-Ahen
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku, Finland
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, Turku, Finland
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11
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Naheed N, Maher S, Saleem F, Khan A, Wadood A, Rasheed S, Choudhary MI, Froeyen M, Abdullah I, Mirza MU, Trant JF, Ahmad S. New isolate from Salvinia molesta with antioxidant and urease inhibitory activity. Drug Dev Res 2021; 82:1169-1181. [PMID: 33983647 DOI: 10.1002/ddr.21831] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/16/2021] [Accepted: 04/23/2021] [Indexed: 11/10/2022]
Abstract
Urease plays a significant role in the pathogenesis of urolithiasis pyelonephritis, urinary catheter encrustation, hepatic coma, hepatic encephalopathy, and peptic acid duodenal ulcers. Salvinia molesta was explored to identify new bioactive compounds with particular emphasis on urease inhibitors. The aqueous methanol extract was fractionated using solvents of increasing polarity. A series of column chromatography and later HPLC were performed on butanol extract. The structures of the resulting pure compounds were resolved using NMR (1D and 2D), infrared, and mass spectroscopy. The novel isolate was evaluated for antioxidant activity (using DPPH, superoxide anion radical scavenging, oxidative burst, and Fe+2 chelation assays), anti-glycation behavior, anticancer activity, carbonic anhydrase inhibition, phosphodiesterase inhibition, and urease inhibition. One new glucopyranose derivative 6'-O-(3,4-dihydroxybenzoyl)-4'-O-(4-hydroxybenzoyl)-α/β-D-glucopyranoside (1) and four known glycosides were identified. Glycoside 1 demonstrated promising antioxidant potential with IC50 values of 48.2 ± 0.3, 60.3 ± 0.6, and 42.1 ± 1.8 μM against DPPH, superoxide radical, and oxidative burst, respectively. Its IC50 in the Jack bean urease inhibition assay was 99.1 ± 0.8 μM. The mechanism-based kinetic studies presented that compound 1 is a mixed-type inhibitor of urease with a Ki value of 91.8 ± 0.1 μM. Finally, molecular dynamic simulations exploring the binding mode of compound 1 with urease provided quantitative agreement between estimated binding free energies and the experimental results. The studies corroborate the use of compound 1 as a lead for QSAR studies as an antioxidant and urease inhibitor. Moreover, it needs to be further evaluated through the animal model, that is, in vivo or tissue culture-based ex-vivo studies, to establish their therapeutic potential against oxidative stress phosphodiesterase-II and urease-induced pathologies.
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Affiliation(s)
- Nadra Naheed
- H.E.J. Research Institute of Chemistry, International Centre for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Saima Maher
- Department of Chemistry, Sardar Bahadur Khan Women University, Quetta, Pakistan
| | - Farooq Saleem
- Faculty of Pharmacy, The University of Lahore, Lahore, Pakistan
| | - Ajmal Khan
- H.E.J. Research Institute of Chemistry, International Centre for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.,Department of Chemistry, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Shankar Campus, Abdul Wali Khan University, Mardan, Pakistan
| | - Saima Rasheed
- Department of Chemistry, Sardar Bahadur Khan Women University, Quetta, Pakistan
| | - M Iqbal Choudhary
- H.E.J. Research Institute of Chemistry, International Centre for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.,Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Matheus Froeyen
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, Leuven, Belgium
| | - Iskandar Abdullah
- Drug Design Development Research Group, Department of Chemistry, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Sarfraz Ahmad
- Drug Design Development Research Group, Department of Chemistry, Universiti Malaya, Kuala Lumpur, Malaysia
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Gurushankar K, Rimac H, Potemkin V, Grishina M. Investigation of the newly characterized baimantuoluoamide a and baimantuoluoamide b alkaloids as potential cyclin-dependent kinase 4 (CDK4) inhibitors using molecular docking and molecular dynamics simulations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.129925] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Alamri MA, Tahir ul Qamar M, Mirza MU, Alqahtani SM, Froeyen M, Chen LL. Discovery of human coronaviruses pan-papain-like protease inhibitors using computational approaches. J Pharm Anal 2020; 10:546-559. [PMID: 32874702 PMCID: PMC7453225 DOI: 10.1016/j.jpha.2020.08.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 08/23/2020] [Accepted: 08/24/2020] [Indexed: 12/22/2022] Open
Abstract
The papain-like protease (PLpro) is vital for the replication of coronaviruses (CoVs), as well as for escaping innate-immune responses of the host. Hence, it has emerged as an attractive antiviral drug-target. In this study, computational approaches were employed, mainly the structure-based virtual screening coupled with all-atom molecular dynamics (MD) simulations to computationally identify specific inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) PLpro, which can be further developed as potential pan-PLpro based broad-spectrum antiviral drugs. The sequence, structure, and functional conserveness of most deadly human CoVs PLpro were explored, and it was revealed that functionally important catalytic triad residues are well conserved among SARS-CoV, SARS-CoV-2, and middle east respiratory syndrome coronavirus (MERS-CoV). The subsequent screening of a focused protease inhibitors database composed of ∼7,000 compounds resulted in the identification of three candidate compounds, ADM_13083841, LMG_15521745, and SYN_15517940. These three compounds established conserved interactions which were further explored through MD simulations, free energy calculations, and residual energy contribution estimated by MM-PB(GB)SA method. All these compounds showed stable conformation and interacted well with the active residues of SARS-CoV-2 PLpro, and showed consistent interaction profile with SARS-CoV PLpro and MERS-CoV PLpro as well. Conclusively, the reported SARS-CoV-2 PLpro specific compounds could serve as seeds for developing potent pan-PLpro based broad-spectrum antiviral drugs against deadly human coronaviruses. Moreover, the presented information related to binding site residual energy contribution could lead to further optimization of these compounds.
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Affiliation(s)
- Mubarak A. Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkarj, Saudi Arabia
| | | | - Muhammad Usman Mirza
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000, Leuven, Belgium
| | - Safar M. Alqahtani
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkarj, Saudi Arabia
| | - Matheus Froeyen
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000, Leuven, Belgium
| | - Ling-Ling Chen
- College of Life Science and Technology, Guangxi University, Nanning, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
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Anwar F, Saleem U, Ahmad B, Ashraf M, Rehman AU, Froeyen M, Kee LY, Abdullah I, Mirza MU, Ahmad S. New naphthalene derivative for cost-effective AChE inhibitors for Alzheimer’s treatment: In silico identification, in vitro and in vivo validation. Comput Biol Chem 2020; 89:107378. [DOI: 10.1016/j.compbiolchem.2020.107378] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/16/2020] [Accepted: 09/15/2020] [Indexed: 12/11/2022]
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Mirza MU, Ahmad S, Abdullah I, Froeyen M. Identification of novel human USP2 inhibitor and its putative role in treatment of COVID-19 by inhibiting SARS-CoV-2 papain-like (PLpro) protease. Comput Biol Chem 2020; 89:107376. [PMID: 32979815 PMCID: PMC7487165 DOI: 10.1016/j.compbiolchem.2020.107376] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/07/2020] [Accepted: 09/10/2020] [Indexed: 02/07/2023]
Abstract
Human ubiquitin carboxyl-terminal hydrolase-2 (USP2) inhibitors, such as thiopurine analogs, have been reported to inhibit SARS-CoV papain-like proteases (PLpro). The PLpro have significant functional implications in the innate immune response during SARS-CoV-2 infection and considered an important antiviral target. Both proteases share strikingly similar USP fold with right-handed thumb-palm-fingers structural scaffold and conserved catalytic triad Cys-His-Asp/Asn. In this urgency situation of COVID-19 outbreak, there is a lack of in-vitro facilities readily available to test SARS-CoV-2 inhibitors in whole-cell assays. Therefore, we adopted an alternate route to identify potential USP2 inhibitor through integrated in-silico efforts. After an extensive virtual screening protocol, the best compounds were selected and tested. The compound Z93 showed significant IC50 value against Jurkat (9.67 μM) and MOTL-4 cells (11.8 μM). The binding mode of Z93 was extensively analyzed through molecular docking, followed by MD simulations, and molecular interactions were compared with SARS-CoV-2. The relative binding poses of Z93 fitted well in the binding site of both proteases and showed consensus π-π stacking and H-bond interactions with histidine and aspartate/asparagine residues of the catalytic triad. These results led us to speculate that compound Z93 might be the first potential chemical lead against SARS-CoV-2 PLpro, which warrants in-vitro evaluations.
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Affiliation(s)
- Muhammad Usman Mirza
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000, Leuven, Belgium
| | - Sarfraz Ahmad
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Iskandar Abdullah
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Matheus Froeyen
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000, Leuven, Belgium.
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16
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Rehman HM, Mirza MU, Ahmad MA, Saleem M, Froeyen M, Ahmad S, Gul R, Alghamdi HA, Aslam MS, Sajjad M, Bhinder MA. A Putative Prophylactic Solution for COVID-19: Development of Novel Multiepitope Vaccine Candidate against SARS-COV-2 by Comprehensive Immunoinformatic and Molecular Modelling Approach. BIOLOGY 2020; 9:E296. [PMID: 32962156 PMCID: PMC7563440 DOI: 10.3390/biology9090296] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/04/2020] [Accepted: 09/05/2020] [Indexed: 12/13/2022]
Abstract
The outbreak of 2019-novel coronavirus (SARS-CoV-2) that causes severe respiratory infection (COVID-19) has spread in China, and the World Health Organization has declared it a pandemic. However, no approved drug or vaccines are available, and treatment is mainly supportive and through a few repurposed drugs. The urgency of the situation requires the development of SARS-CoV-2-based vaccines. Immunoinformatic and molecular modelling are time-efficient methods that are generally used to accelerate the discovery and design of the candidate peptides for vaccine development. In recent years, the use of multiepitope vaccines has proved to be a promising immunization strategy against viruses and pathogens, thus inducing more comprehensive protective immunity. The current study demonstrated a comprehensive in silico strategy to design stable multiepitope vaccine construct (MVC) from B-cell and T-cell epitopes of essential SARS-CoV-2 proteins with the help of adjuvants and linkers. The integrated molecular dynamics simulations analysis revealed the stability of MVC and its interaction with human Toll-like receptors (TLRs), which trigger an innate and adaptive immune response. Later, the in silico cloning in a known pET28a vector system also estimated the possibility of MVC expression in Escherichia coli. Despite that this study lacks validation of this vaccine construct in terms of its efficacy, the current integrated strategy encompasses the initial multiple epitope vaccine design concepts. After validation, this MVC can be present as a better prophylactic solution against COVID-19.
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Affiliation(s)
- Hafiz Muzzammel Rehman
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan; (H.M.R.); (M.S.A.)
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan; (M.A.A.); (M.A.B.)
| | - Muhammad Usman Mirza
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000 Leuven, Belgium; (M.U.M.); (M.F.)
| | - Mian Azhar Ahmad
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan; (M.A.A.); (M.A.B.)
- Department of Health, Government of the Punjab, Lahore 54590, Punjab, Pakistan
| | - Mahjabeen Saleem
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan; (H.M.R.); (M.S.A.)
| | - Matheus Froeyen
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000 Leuven, Belgium; (M.U.M.); (M.F.)
| | - Sarfraz Ahmad
- Drug Design and Development Research Group (DDDRG), Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - Roquyya Gul
- Faculty of Life Sciences, Gulab Devi Educational Complex, Lahore 54590, Punjab, Pakistan;
| | - Huda Ahmed Alghamdi
- Department of Biology, College of Sciences, King Khalid University, Abha 61413, Saudi Arabia;
| | - Muhammad Shahbaz Aslam
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan; (H.M.R.); (M.S.A.)
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Quaid e Azam Campus, Lahore 54590, Punjab, Pakistan;
| | - Munir Ahmad Bhinder
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan; (M.A.A.); (M.A.B.)
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Mirza MU, Saadabadi A, Vanmeert M, Salo-Ahen OMH, Abdullah I, Claes S, De Jonghe S, Schols D, Ahmad S, Froeyen M. Discovery of HIV entry inhibitors via a hybrid CXCR4 and CCR5 receptor pharmacophore-based virtual screening approach. Eur J Pharm Sci 2020; 155:105537. [PMID: 32890663 PMCID: PMC7467125 DOI: 10.1016/j.ejps.2020.105537] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/10/2020] [Accepted: 08/30/2020] [Indexed: 12/30/2022]
Abstract
Chemokine receptors are key regulators of cell migration in terms of immunity and inflammation. Among these, CCR5 and CXCR4 play pivotal roles in cancer metastasis and HIV-1 transmission and infection. They act as essential co-receptors for HIV and furnish a route to the cell entry. In particular, inhibition of either CCR5 or CXCR4 leads very often the virus to shift to a more virulent dual-tropic strain. Therefore, dual receptor inhibition might improve the therapeutic strategies against HIV. In this study, we aimed to discover selective CCR5, CXCR4, and dual CCR5/CXCR4 antagonists using both receptor- and ligand-based computational methods. We employed this approach to fully incorporate the interaction attributes of the binding pocket together with molecular dynamics (MD) simulations and binding free energy calculations. The best hits were evaluated for their anti-HIV-1 activity against CXCR4- and CCR5-specific NL4.3 and BaL strains. Moreover, the Ca2+ mobilization assay was used to evaluate their antagonistic activity. From the 27 tested compounds, three were identified as inhibitors: compounds 27 (CCR5), 6 (CXCR4) and 3 (dual) with IC50 values ranging from 10.64 to 64.56 μM. The binding mode analysis suggests that the active compounds form a salt bridge with the glutamates and π-stacking interactions with the aromatic side chains binding site residues of the respective co-receptor. The presented hierarchical virtual screening approach provides essential aspects in identifying potential antagonists in terms of selectivity against a specific co-receptor. The compounds having multiple heterocyclic nitrogen atoms proved to be relatively more specific towards CXCR4 inhibition as compared to CCR5. The identified compounds serve as a starting point for further development of HIV entry inhibitors through synthesis and quantitative structure-activity relationship studies.
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Affiliation(s)
- Muhammad Usman Mirza
- Medicinal Chemistry, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| | - Atefeh Saadabadi
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland; Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
| | - Michiel Vanmeert
- Medicinal Chemistry, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| | - Outi M H Salo-Ahen
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland; Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
| | - Iskandar Abdullah
- Department of Chemistry, Faculty of Sciences, University Malaya, Kuala Lumpur 59100, Malaysia
| | - Sandra Claes
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| | - Steven De Jonghe
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| | - Sarfraz Ahmad
- Department of Chemistry, Faculty of Sciences, University Malaya, Kuala Lumpur 59100, Malaysia
| | - Matheus Froeyen
- Medicinal Chemistry, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium.
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Mirza MU, Froeyen M. Structural elucidation of SARS-CoV-2 vital proteins: Computational methods reveal potential drug candidates against main protease, Nsp12 polymerase and Nsp13 helicase. J Pharm Anal 2020; 10:320-328. [PMID: 32346490 PMCID: PMC7187848 DOI: 10.1016/j.jpha.2020.04.008] [Citation(s) in RCA: 175] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/23/2020] [Accepted: 04/26/2020] [Indexed: 01/07/2023] Open
Abstract
Recently emerged SARS-CoV-2 caused a major outbreak of coronavirus disease 2019 (COVID-19) and instigated a widespread fear, threatening global health safety. To date, no licensed antiviral drugs or vaccines are available against COVID-19 although several clinical trials are under way to test possible therapies. During this urgent situation, computational drug discovery methods provide an alternative to tiresome high-throughput screening, particularly in the hit-to-lead-optimization stage. Identification of small molecules that specifically target viral replication apparatus has indicated the highest potential towards antiviral drug discovery. In this work, we present potential compounds that specifically target SARS-CoV-2 vital proteins, including the main protease, Nsp12 RNA polymerase and Nsp13 helicase. An integrative virtual screening and molecular dynamics simulations approach has facilitated the identification of potential binding modes and favourable molecular interaction profile of corresponding compounds. Moreover, the identification of structurally important binding site residues in conserved motifs located inside the active site highlights relative importance of ligand binding based on residual energy decomposition analysis. Although the current study lacks experimental validation, the structural information obtained from this computational study has paved way for the design of targeted inhibitors to combat COVID-19 outbreak.
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Affiliation(s)
- Muhammad Usman Mirza
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000, Leuven, Belgium
| | - Matheus Froeyen
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000, Leuven, Belgium
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Maher S, Choudhary MI, Saleem F, Rasheed S, Waheed I, Halim SA, Azeem M, Abdullah IB, Froeyen M, Mirza MU, Ahmad S. Isolation of Antidiabetic Withanolides from Withania coagulans Dunal and Their In Vitro and In Silico Validation. BIOLOGY 2020; 9:biology9080197. [PMID: 32751610 PMCID: PMC7464911 DOI: 10.3390/biology9080197] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/06/2020] [Accepted: 06/17/2020] [Indexed: 12/11/2022]
Abstract
Withania coagulans (W. coagulans) is well-known in herbal medicinal systems for its high biological potential. Different parts of the plant are used against insomnia, liver complications, asthma, and biliousness, as well as it is reported to be sedative, emetic, diuretic, antidiabetic antimicrobial, anti-inflammatory, antitumor, hepatoprotective, antihyperglycemic, cardiovascular, immuno-suppressive and central nervous system depressant. Withanolides present in W. coagulans have attracted an immense interest in the scientific field due to their diverse therapeutic applications. The current study deals with chemical and biological evaluation of chloroform, and n-butanol fractions of W. coagulans. The activity-guided fractionation of both extracts via multiple chromatographic steps and structure elucidation of pure isolates using spectroscopies (NMR, mass spectrometry, FTIR and UV-Vis) led to the identification of a new withanolide glycoside, withacogulanoside-B (1) from n-butanol extract and five known withanolides from chloroform extract [withanolid J (2), coagulin E (3), withaperuvin C (4), 27-hydroxywithanolide I (5), and ajugin E (6)]. Among the tested compounds, compound 5 was the most potent α-glucosidase inhibitor with IC50 = 66.7 ± 3.6 µM, followed by compound 4 (IC50: 407 ± 4.5 µM) and compound 2 (IC50: 683 ± 0.94 µM), while no antiglycation activity was observed with the six isolated compounds. Molecular docking was used to predict the binding potential and binding site interactions of these compounds as α-glucosidase inhibitors. Consequently, this study provides basis to discover specific antidiabetic compounds from W. coagulans.
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Affiliation(s)
- Saima Maher
- Department of Chemistry, Sardar Bahadur Khan Woman University, Quetta 95000, Pakistan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; (M.I.C.); (S.R.)
- Correspondence: (S.M.); (S.A.)
| | - M. Iqbal Choudhary
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; (M.I.C.); (S.R.)
- Department of Chemistry, College of Science, King Saud University, Riyadh-11451, Saudi Arabia
| | - Farooq Saleem
- Faculty of Pharmacy, The University of Lahore, Lahore 54000, Pakistan; (F.S.); (M.A.)
| | - Saima Rasheed
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; (M.I.C.); (S.R.)
| | - Imran Waheed
- Akhtar Saeed College of Pharmaceutical Sciences, Bahria Town, Lahore 54000, Pakistan;
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman;
| | - Muhammad Azeem
- Faculty of Pharmacy, The University of Lahore, Lahore 54000, Pakistan; (F.S.); (M.A.)
| | - Iskandar Bin Abdullah
- Department of Chemistry, Faculty of Sciences, University Malaya, Kuala Lumpur 50603, Malaysia;
| | - Matheus Froeyen
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000 Leuven, Belgium; (M.F.); (M.U.M.)
| | - Muhammad Usman Mirza
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000 Leuven, Belgium; (M.F.); (M.U.M.)
| | - Sarfraz Ahmad
- Department of Chemistry, Faculty of Sciences, University Malaya, Kuala Lumpur 50603, Malaysia;
- Correspondence: (S.M.); (S.A.)
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Khalid H, Landry KB, Ijaz B, Ashfaq UA, Ahmed M, Kanwal A, Froeyen M, Mirza MU. Discovery of novel Hepatitis C virus inhibitor targeting multiple allosteric sites of NS5B polymerase. INFECTION GENETICS AND EVOLUTION 2020; 84:104371. [PMID: 32485331 DOI: 10.1016/j.meegid.2020.104371] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 05/13/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023]
Abstract
HCV is a viral infection posing a severe global threat when left untreated progress to end-stage liver disease, including cirrhosis and HCC. The NS5B polymerase of HCV is the most potent target that harbors four allosteric binding sites that could interfere with the HCV infection. We present the discovery of a novel synthetic compound that harbors the potential of NS5B polymerase inhibition. All eight compounds belonging to the benzothiazine family of heterocycles displayed no cellular cytotoxicity in HepG2 cells at nontoxic dose concentration (200 μM). Subsequently, among eight compounds of the series, merely compound 5b exhibited significant inhibition of the expression of the HCV NS5B gene as compared to DMSO control in semi-quantitative PCR. Based on our western blot result, 5b at the range of 50, 100 and 200 μM induced 20, 40, and 70% inhibition of NS5B protein respectively. To estimate the binding potential, 5b was docked at respective allosteric sites followed by molecular dynamics (MD) simulations for a period of 20 ns. In addition, binding free energy calculation by MM-GB/PBSA method revealed a conserved interaction profile of residues lining the allosteric sites in agreement with the reported NS5B co-crystallized inhibitors. The presented results provide important information about a novel compound 5b which may facilitate the the discovery of novel inhibitors that tends to target multiple sites on NS5B polymerase.
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Affiliation(s)
- Hina Khalid
- Department of Bioinformatics and Biotechnology, Government College University, 38000 Faisalabad, Pakistan
| | - Koloko Brice Landry
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Bushra Ijaz
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, 38000 Faisalabad, Pakistan.
| | - Matloob Ahmed
- Department of Chemistry, Government College University, 38000 Faisalabad, Pakistan
| | - Afshan Kanwal
- Department of Chemistry, Government College University, 38000 Faisalabad, Pakistan
| | - Matheus Froeyen
- Department of Pharmaceutical Sciences, REGA Institute for Medical Research, Medicinal Chemistry, University of Leuven, 3000 Leuven, Belgium
| | - Muhammad Usman Mirza
- Department of Pharmaceutical Sciences, REGA Institute for Medical Research, Medicinal Chemistry, University of Leuven, 3000 Leuven, Belgium
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In Vitro Antidiabetic, Anti-Obesity and Antioxidant Analysis of Ocimum basilicum Aerial Biomass and in Silico Molecular Docking Simulations with Alpha-Amylase and Lipase Enzymes. BIOLOGY 2019; 8:biology8040092. [PMID: 31817095 PMCID: PMC6955989 DOI: 10.3390/biology8040092] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 10/13/2019] [Accepted: 10/30/2019] [Indexed: 12/11/2022]
Abstract
The present study explored phytochemicals, porcine pancreatic α-amylase (PPA) and lipase (PPL) inhibitory activities and antioxidant potential of polar and nonpolar extracts of the leaves and flowers of Ocimum basilicum and the in-silico mode of interaction between these enzymes and the major chemical constituents of the herb. The hexane extract (HE) and hydro-ethanolic extract (EE) obtained sequentially were used to estimate PPA and PPL inhibitory and antioxidant activities, total phenolic content (TPC) and total flavonoid content (TFC). Chemical constituents of the essential oils and HE were determined by GC-MS (Gas Chromatography-Mass Spectrometry). For PPA inhibition, IC50 (µg/mL) of the extracts were 0.27-0.37, which were close to 0.24 of acarbose, while for PPL inhibition, IC50 (µg/mL) of the extracts were 278.40-399.65, and that of Orlistat 145.72. The flowers EE was most potent antioxidant followed by leaves EE. The leaves EE had highest TPC and TFC followed of flowers EE. The essential oil of flowers had higher estragole (55%) than linalool (37%), while the essential oil of the leaves had higher linalool (42%) than estragole (38%). The HE of the flowers contained higher estragole (42%) than linalool (23%), while of the HE of the leaves too had higher estragole (65%) than linalool (18%). The in-silico molecular docking study showed linalool and estragole to have considerable PPA and PPL binding potential, which were further investigated through molecular dynamics simulations and binding free energy calculations. The PPA and PPL inhibitory activities of O. basilicum extracts and their notable antioxidant potential propose the herb as a multi-target complimentary medicine for diabetes, obesity and oxidative stress.
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Ahmad S, Hussain A, Hussain A, Abdullah I, Ali MS, Froeyen M, Mirza MU. Quantification of Berberine in Berberis vulgaris L. Root Extract and Its Curative and Prophylactic Role in Cisplatin-Induced In Vivo Toxicity and In Vitro Cytotoxicity. Antioxidants (Basel) 2019; 8:E185. [PMID: 31248160 PMCID: PMC6616455 DOI: 10.3390/antiox8060185] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/10/2019] [Accepted: 06/12/2019] [Indexed: 01/16/2023] Open
Abstract
Cisplatin is amongst the most potent chemotherapeutic drugs with applications in more than 50% of cancer treatments, but dose-dependent side effects limit its usefulness. Berberis vulgaris L. (B. vulgaris) has a proven role in several therapeutic applications in the traditional medicinal system. High-performance liquid chromatography was used to quantify berberine, a potent alkaloid in the methanolic root extract of B. vulgaris (BvRE). Berberine chloride in BvRE was found to be 10.29% w/w. To assess the prophylactic and curative protective effects of BvRE on cisplatin-induced nephrotoxicity, hepatotoxicity, and hyperlipidemia, in vivo toxicity trials were carried out on 25 healthy male albino Wistar rats (130-180 g). Both prophylactic and curative trials included a single dose of cisplatin (4 mg/kg, i.p.) and nine doses of BvRE (500 mg/kg/day, orally). An array of marked toxicity effects appeared in response to cisplatin dosage evident by morphological condition, biochemical analysis of serum (urea, creatinine, total protein, alanine transaminase, aspartate transaminase, total cholesterol, and triglyceride), and organ tissue homogenates (malondialdehyde and catalase). Statistically-significant (p < 0.05) variations were observed in various parameters. Moreover, histological studies of liver and kidney tissues revealed that the protective effect of BvRE effectively minimized and reversed nephrotoxic, hepatotoxic, and hyperlipidemic effects caused by cisplatin in both prophylactic and curative groups with relatively promising ameliorative effects in the prophylactic regimen. The in vitro cell viability effect of cisplatin, BvRE, and their combination was determined on HeLa cells using the tetrazolium (MTT) assay. MTT clearly corroborated that HeLa cells appeared to be less sensitive to cisplatin and berberine individually, while the combination of both at the same concentrations resulted in growth inhibition of HeLa cells in a remarkable synergistic way. The present study validated the use of BvRE as a protective agent in combination therapy with cisplatin.
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Affiliation(s)
- Sarfraz Ahmad
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - Amina Hussain
- Department of Biochemistry, Institute of Molecular Biology and Biotechnology (IMBB), University of Lahore, Lahore 54000, Pakistan.
| | - Aroosha Hussain
- Department of Biochemistry, Institute of Molecular Biology and Biotechnology (IMBB), University of Lahore, Lahore 54000, Pakistan.
| | - Iskandar Abdullah
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - Muhammad Sajjad Ali
- Department of Biochemistry, Institute of Molecular Biology and Biotechnology (IMBB), University of Lahore, Lahore 54000, Pakistan.
| | - Matheus Froeyen
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000 Leuven, Belgium.
| | - Muhammad Usman Mirza
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000 Leuven, Belgium.
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