1
|
Yamin R, Ahmad I, Khalid H, Perveen A, Abbasi SW, Nishan U, Sheheryar S, Moura AA, Ahmed S, Ullah R, Ali EA, Shah M, Chandra Ojha S. Identifying plant-derived antiviral alkaloids as dual inhibitors of SARS-CoV-2 main protease and spike glycoprotein through computational screening. Front Pharmacol 2024; 15:1369659. [PMID: 39086396 PMCID: PMC11288853 DOI: 10.3389/fphar.2024.1369659] [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: 01/15/2024] [Accepted: 06/04/2024] [Indexed: 08/02/2024] Open
Abstract
COVID-19 is currently considered the ninth-deadliest pandemic, spreading through direct or indirect contact with infected individuals. It has imposed a consistent strain on both the financial and healthcare resources of many countries. To address this challenge, there is a pressing need for the development of new potential therapeutic agents for the treatment of this disease. To identify potential antiviral agents as novel dual inhibitors of SARS-CoV-2, we retrieved 404 alkaloids from 12 selected medicinal antiviral plants and virtually screened them against the renowned catalytic sites and favorable interacting residues of two essential proteins of SARS-CoV-2, namely, the main protease and spike glycoprotein. Based on docking scores, 12 metabolites with dual inhibitory potential were subjected to drug-likeness, bioactivity scores, and drug-like ability analyses. These analyses included the ligand-receptor stability and interactions at the potential active sites of target proteins, which were analyzed and confirmed through molecular dynamic simulations of the three lead metabolites. We also conducted a detailed binding free energy analysis of pivotal SARS-CoV-2 protein inhibitors using molecular mechanics techniques to reveal their interaction dynamics and stability. Overall, our results demonstrated that 12 alkaloids, namely, adouetine Y, evodiamide C, ergosine, hayatinine, (+)-homoaromoline, isatithioetherin C, N,alpha-L-rhamnopyranosyl vincosamide, pelosine, reserpine, toddalidimerine, toddayanis, and zanthocadinanine, are shortlisted as metabolites based on their interactions with target proteins. All 12 lead metabolites exhibited a higher unbound fraction and therefore greater distribution compared with the standards. Particularly, adouetine Y demonstrated high docking scores but exhibited a nonspontaneous binding profile. In contrast, ergosine and evodiamide C showed favorable binding interactions and superior stability in molecular dynamics simulations. Ergosine demonstrated exceptional performance in several key pharmaceutical metrics. Pharmacokinetic evaluations revealed that ergosine exhibited pronounced bioactivity, good absorption, and optimal bioavailability. Additionally, it was predicted not to cause skin sensitivity and was found to be non-hepatotoxic. Importantly, ergosine and evodiamide C emerged as superior drug candidates for dual inhibition of SARS-CoV-2 due to their strong binding affinity and drug-like ability, comparable to known inhibitors like N3 and molnupiravir. This study is limited by its in silico nature and demands the need for future in vitro and in vivo studies to confirm these findings.
Collapse
Affiliation(s)
- Ramsha Yamin
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Iqra Ahmad
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Hira Khalid
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Asia Perveen
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science & Technology, Kohat, Pakistan
| | - Sheheryar Sheheryar
- Department of Animal Science, Federal University of Ceara, Fortaleza, Brazil
| | | | - Sarfraz Ahmed
- Wellman Centre for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Essam A. Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Suvash Chandra Ojha
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| |
Collapse
|
2
|
Khan J, Ali G, Saeed A, Khurshid A, Ahmad S, Kashtoh H, Ataya FS, Bathiha GES, Ullah A, Khan A. Efficacy assessment of novel methanimine derivatives in chronic constriction injury-induced neuropathic model: An in-vivo, ex-vivo and In-Silico approach. Eur J Pharm Sci 2024; 198:106797. [PMID: 38735401 DOI: 10.1016/j.ejps.2024.106797] [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: 03/10/2024] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/14/2024]
Abstract
The multicomponent etiology, complex clinical implications, dose-based side effect and degree of pain mitigation associated with the current pharmacological therapy is incapable in complete resolution of chronic neuropathic pain patients which necessitates the perpetual requirement of novel medication therapy. Therefore, this study explored the ameliorative aptitude of two novel methanimine imitative like (E)-N-(4-nitrobenzylidene)-4‑chloro-2-iodobenzamine (KB 09) and (E)-N-(4-methylbenzylidene)-4‑chloro-2-iodobenzamine (KB 10) in chronic constriction injury (CCI) of sciatic nerve induced neuropathic pain in rat model. Standard behavioral tests like dynamic and static allodynia, cold, thermal and mechanical hyperalgesia along with rotarod activity were performed at various experimental days like 0, 3, 7, 14 and 21. Enzyme linked immunosorbent assay (ELISA) on spinal tissue and antioxidant assays on sciatic nerve were executed accompanied by molecular docking and simulation studies. Prolonged ligation of sciatic nerve expressively induced hyperalgesia as well as allodynia in rats. KB 09 and KB 10 substantially attenuated the CCI elicited hyperalgesia and allodynia. They significantly reduced the biomarkers of pain and inflammation like Interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-α) in ELISA and while enhanced the GSH, SOD and CAT and diminished the MDA levels during antioxidant assays. KB 09 displayed -9.62 kcal/mol with TNF-α and -7.68 kcal/mol binding energy with IL-6 whereas KB 10 exhibited binding energy of -8.20 kcal/mol with IL-6 while -11.68 kcal/mol with TNF-α and hence both trial compounds ensured stable interaction with IL-6 and TNF-α during computational analysis. The results advocated that both methanimine derivatives might be novel candidates for attenuation of CCI-induced neuropathic pain prospects via anti-nociceptive, anti-inflammatory and antioxidant mechanisms.
Collapse
Affiliation(s)
- Jawad Khan
- Department of Pharmacy, University of Peshawar, Peshawar 25120, Pakistan.
| | - Gowhar Ali
- Department of Pharmacy, University of Peshawar, Peshawar 25120, Pakistan.
| | - Aamer Saeed
- Department of Chemistry, Quaid-I-Azam University Islamabad 45320, Pakistan
| | - Asma Khurshid
- Department of Chemistry, Quaid-I-Azam University Islamabad 45320, Pakistan.
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University Peshawar 25000, Pakistan
| | - Hamdy Kashtoh
- Department of Biotechnology, Yeungnam University, Gyeongbuk, Korea.
| | - Farid S Ataya
- Department of Biochemistry, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Gaber El-Saber Bathiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, AlBeheria, Egypt
| | - Aman Ullah
- Department of Pharmacy, Saba Medical Center, Abu Dhabi PO Box 20316, United Arab Emirates
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, P.O Box 33, Postal Code 616, Birkat Al Mauz, Nizwa, Sultanate of Oman
| |
Collapse
|
3
|
Alawam AS, M Alneghery L, Alwethaynani MS, Alamri MA. A hierarchical approach towards identification of novel inhibitors against L, D-transpeptidase YcbB as an anti-bacterial therapeutic target. J Biomol Struct Dyn 2024:1-11. [PMID: 38411016 DOI: 10.1080/07391102.2024.2322619] [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: 10/22/2023] [Accepted: 02/16/2024] [Indexed: 02/28/2024]
Abstract
The bacterial cell wall, being a vital component for cell viability, is regarded as a promising drug target. The L, D-Transpeptidase YcbB enzyme has been implicated for a significant role in cell wall polymers cross linking during typhoid toxin release, β-lactam resistance and outer membrane defect rescue. These observations have been recorded in different bacterial pathogens such as Salmonella Typhimurium, Citrobacter rodentium, and Salmonella typhi. In this work, we have shown structure based virtual screening of diverse natural and synthetic drug libraries against the enzyme and revealed three compounds as LAS_32135590, LAS_34036730 and LAS-51380924. These compounds showed highly stable energies and the findings are very competitive with the control molecule ((1RG or (4 R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid or ertapenem)) used. Compared to control (which has binding energy score of -11.63 kcal/mol), the compounds showed better binding energy. The binding energy score of LAS_32135590, LAS_34036730 and LAS-51380924 is -12.63 kcal/mol, -12.22 kcal/mol and -12.10 kcal/mol, respectively. Further, the docked snapshot of the lead compounds and control were investigated for stability under time dependent dynamics environment. All the three leads complex and control system showed significant equilibrium (mean RMSD < 3 Å) both in term of intermolecular docked conformation and binding interactions network. Further validation on the complex's stability was acquired from the end-state MMPB/GBSA analysis that observed greater contribution from van der Waals forces and electrostatic energy while less contribution was noticed from solvation part. The compounds were also showed good drug-likeness and are non-toxic and non-mutagenic. In short, the compounds can be used in experimental testing's and might be subjected to structure modification to get better results.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Abdullah S Alawam
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Lina M Alneghery
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Maher S Alwethaynani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Al-Quwayiyah, Saudi Arabia
| | - Mubarak A Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| |
Collapse
|
4
|
Hameed AR, Ali SF, Alsallameh SMS, Muhseen ZT, Almansour NM, ALSuhaymi N, Alsugoor MH, Allemailem KS. Structural Dynamics of P-Rex1 Complexed with Natural Leads Establishes the Protein as an Attractive Target for Therapeutics to Suppress Cancer Metastasis. BIOMED RESEARCH INTERNATIONAL 2023; 2023:3882081. [PMID: 38098889 PMCID: PMC10721353 DOI: 10.1155/2023/3882081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 05/30/2022] [Accepted: 06/24/2022] [Indexed: 12/17/2023]
Abstract
Phosphatidylinositol 3,4,5-trisphosphate- (PIP3-) dependent Rac exchanger 1 (P-Rex1) functions as Rho guanine nucleotide exchange factor and is activated by synergistic activity of Gβγ and PIP3 of the heterotrimeric G protein. P-Rex1 activates Rac GTPases for regulating cell invasion and migration and promotes metastasis in several human cancers including breast, prostate, and skin cancer. The protein is a promising therapeutic target because of its multifunction roles in human cancers. Herein, the present study attempts to identify selective P-Rex1 natural inhibitors by targeting PIP3-binding pocket using large-size multiple natural molecule libraries. Each library was filtered subsequently in FAF-Drugs4 based on Lipinski's rule of five (RO5), toxicity, and filter pan assay interference compounds (PAINS). The output hits were virtually screened at the PIP3-binding pocket through PyRx AutoDock Vina and cross-checked by GOLD. The best binders at the PIP3-binding pocket were prioritized using a comparative analysis of the docking scores. Top-ranked two compounds with high GOLD fitness score (>80) and lowest AutoDock binding energy (< -12.7 kcal/mol) were complexed and deciphered for molecular dynamics along with control-P-Rex1 complex to validate compound binding conformation and disclosed binding interaction pattern. Both the systems were seen in good equilibrium, and along the simulation time, the compounds are in strong contact with the P-Rex1 PIP3-binding site. Hydrogen bonding analysis towards simulation end identified the formation of 16 and 22 short- and long-distance hydrogen bonds with different percent of occupancy to the PIP3 residues for compound I and compound 2, respectively. Radial distribution function (RDF) analysis of the key hydrogen bonds between the compound and the PIP3 residues demonstrated a strong affinity of the compounds to the mentioned PIP3 pocket. Additionally, MMGB/PBSA energies were performed that confirmed the dominance of Van der Waals energy in complex formation along with favorable contribution from hydrogen bonding. These findings were also cross-validated by a more robust WaterSwap binding energy predictor, and the results are in good agreement with a strong binding affinity of the compounds for the protein. Lastly, the key contribution of residues in interaction with the compounds was understood by binding free energy decomposition and alanine scanning methods. In short, the results of this study suggest that P-Rex1 is a good druggable target to suppress cancer metastasis; therefore, the screened druglike molecules of this study need in vitro and in vivo anti-P-Rex1 validation and may serve as potent leads to fight cancer.
Collapse
Affiliation(s)
- Alaa R. Hameed
- Department of Medical Laboratory Techniques, School of Life Sciences, Dijlah University College, Baghdad, Iraq
| | - Sama Fakhri Ali
- Department of Anesthesia Techniques, School of Life Sciences, Dijlah University College, Baghdad, Iraq
| | - Sarah M. S. Alsallameh
- Ministry of Higher Education and Scientific Research, Gilgamesh Ahliya University College, College of Health and Medical Techniques, Department of Medical Laboratories Techniques, Baghdad, Iraq
| | - Ziyad Tariq Muhseen
- Department of Pharmacy, Al-Mustaqbal University College, Hillah, Babylon 51001, Iraq
| | - Nahlah Makki Almansour
- Department of Biology, College of Science, University of Hafr Al Batin, Hafr Al Batin 31991, Saudi Arabia
| | - Naif ALSuhaymi
- Department of Emergency Medical Services, Faculty of Health Sciences, AlQunfudah, Umm Al-Qura University, Mecca 21912, Saudi Arabia
| | - Mahdi H. Alsugoor
- Department of Emergency Medical Services, Faculty of Health Sciences, AlQunfudah, Umm Al-Qura University, Mecca 21912, Saudi Arabia
| | - Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| |
Collapse
|
5
|
Sajjad W, Nadeem M, Alam T, Rehman AU, Abbasi SW, Ahmad S, Din G, Khan S, Badshah M, Gul S, Farman M, Shah AA. Biological Evaluation and Computational Studies of Methoxy-flavones from Newly Isolated Radioresistant Micromonospora aurantiaca Strain TMC-15. Appl Biochem Biotechnol 2023; 195:4915-4935. [PMID: 37115385 DOI: 10.1007/s12010-023-04517-7] [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: 04/11/2023] [Indexed: 04/29/2023]
Abstract
This study aims to determine UV-B resistance and to investigate computational analysis and antioxidant potential of methoxy-flavones of Micromonospora aurantiaca TMC-15 isolated from Thal Desert, Pakistan. The cellular extract was purified through solid-phase extraction and UV-Vis spectrum analysis indicated absorption peaks at λmax 250 nm, 343 nm, and 380 nm that revealed the presence of methoxy-flavones named eupatilin and 5-hydroxyauranetin. The flavones were evaluated for their antioxidant as well as protein and lipid peroxidation inhibition potential using di(phenyl)-(2,4,6-trinitrophenyl) iminoazanium (DPPH), 2,4-dinitrophenyl hydrazine (DNPH), and thiobarbituric acid reactive substances (TBARS) assays, respectively. The methoxy-flavones were further studied for their docking affinity and interaction dynamics to determine their structural and energetic properties at the atomic level. The antioxidant potential, protein, and lipid oxidation inhibition and DNA damage preventive abilities were correlated as predicted by computational analysis. The eupatilin and 5-hydroxyauranetin binding potential to their targeted proteins 1N8Q and 1OG5 is - 4.1 and - 7.5 kcal/mol, respectively. Moreover, the eupatiline and 5-hydroxyauranetin complexes illustrate van der Waals contacts and strong hydrogen bonds to their respective enzymes target. Both in vitro studies and computational analysis results revealed that methoxy-flavones of Micromonospora aurantiaca TMC-15 can be used against radiation-mediated oxidative damages due to its kosmotrophic nature. The demonstration of good antioxidant activities not only protect DNA but also protein and lipid oxidation and therefore could be a good candidate in radioprotective drugs and as sunscreen due to its kosmotropic nature.
Collapse
Affiliation(s)
- Wasim Sajjad
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Mahnoor Nadeem
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Tayyaba Alam
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Asim Ur Rehman
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 25000, Pakistan
| | - Ghufranud Din
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
- Department of Medical Laboratory Technology, University of Haripur, Haripur, 22620, Pakistan
| | - Samiullah Khan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Malik Badshah
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Sarah Gul
- Department of Biological Sciences, Faculty of Basic and Applied Sciences, International Islamic University, Islamabad, Pakistan
| | - Muhammad Farman
- Department of Chemistry, Faculty of Natural Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Aamer Ali Shah
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan.
| |
Collapse
|
6
|
Alrumaihi F. A cheminformatics-biophysics correlate to identify promising lead molecules against matrix metalloproteinase-2 (MMP-2) enzyme: A promising anti-cancer target. Saudi Pharm J 2023; 31:1244-1253. [PMID: 37284415 PMCID: PMC10239696 DOI: 10.1016/j.jsps.2023.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 05/10/2023] [Indexed: 06/08/2023] Open
Abstract
Matrix metalloproteinase-2 (MMP-2) is an endopeptidase enzyme that is devoted to extracellular matrix proteins degradation. The enzyme is warranted as promising drugs target for different light threating diseases such as arthritis, cancer and fibrosis. Herein, in this study, three drug molecules: CMNPD8322, CMNPD8320, and CMNPD8318 were filtered as high affinity binding compounds with binding energy score of -9.75 kcal/mol, -9.11 kcal/mol, -9.05 kcal/mol, respectively. The control binding energy score was -9.01 kcal/mol. The compounds docked deeply inside the pocket interacting with S1 pocket residues. The docked complexes dynamics in real time at cellular environment was then done to decipher the stable binding conformation and intermolecular interactions network. The compounds complexes achieved very stable dynamics with root mean square deviation (RMSD) with mean value of around 2-3 Å compared to control complex that showed higher fluctuations of 5 Å. The simulation trajectories frames based binding free energy demonstrated all the compounds-MMP-2 complexes reported highly stable energy, particularly the van der Waals energy dominate the overall net energy. Similarly, the complexes revalidation of WaterSwap based energies also disclosed the complexes highly stable in term docked conformation. Also, the compounds illustrated the compounds favorable pharmacokinetics and were non-toxic and non-mutagenic. Thus, the compounds might be used thorough experimental assays to confirm compounds selective biological potency against MMP-2 enzyme.
Collapse
|
7
|
Parvaiz N, Shahbaz M, Azam SS. Role of hinge motion and ATP dynamics in factors for inversion stimulation FIS protein deduced while targeting drug resistant Orientia tsutsugamushi. J Mol Graph Model 2023; 120:108425. [PMID: 36758328 DOI: 10.1016/j.jmgm.2023.108425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023]
Abstract
Orientia tsutsugamushi, the causative agent of scrub typhus has been found resistant to various classes of antibiotics such as penicillins, gentamycin and cephalosporins. Review of current literature suggests that the prevalence of scrub typhus has increased globally. Therefore, the current study has aimed at exploring the genome of O. tsutsugamushi to identify potential drug target proteins that can be used for developing novel antibiotics against the pathogen. Subtractive proteomics approach has revealed FIS as a potential drug target protein involved in two component system (TCS), a signaling pathway crucial for bacteria to survive and adjust in changing environmental conditions. Molecular docking studies have revealed compound-356 (CHEMBRIDGE-10040641-3710.356) as a potential inhibitor in both chains A and B of the FIS protein. Simulation results suggest that the docked complex has remained stable and compact throughout the 200 ns run. Significant conformational changes including the hinge motion was observed in the DNA binding domain. Furthermore, the presence of salt bridge between GLU910 and ARG417, rearrangement of interaction residues and displacement of ATP in the central AAA + domain upon binding to the inhibitor were also observed playing a role in stabilizing the protein structure.
Collapse
Affiliation(s)
- Nousheen Parvaiz
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Maham Shahbaz
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| |
Collapse
|
8
|
Naz A, Asif S, Alwutayd KM, Sarfaraz S, Abbasi SW, Abbasi A, Alenazi AM, Hasan ME. Repurposing FIASMAs against Acid Sphingomyelinase for COVID-19: A Computational Molecular Docking and Dynamic Simulation Approach. Molecules 2023; 28:molecules28072989. [PMID: 37049752 PMCID: PMC10096053 DOI: 10.3390/molecules28072989] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/16/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
Over the past few years, COVID-19 has caused widespread suffering worldwide. There is great research potential in this domain and it is also necessary. The main objective of this study was to identify potential inhibitors against acid sphingomyelinase (ASM) in order to prevent coronavirus infection. Experimental studies revealed that SARS-CoV-2 causes activation of the acid sphingomyelinase/ceramide pathway, which in turn facilitates the viral entry into the cells. The objective was to inhibit acid sphingomyelinase activity in order to prevent the cells from SARS-CoV-2 infection. Previous studies have reported functional inhibitors against ASM (FIASMAs). These inhibitors can be exploited to block the entry of SARS-CoV-2 into the cells. To achieve our objective, a drug library containing 257 functional inhibitors of ASM was constructed. Computational molecular docking was applied to dock the library against the target protein (PDB: 5I81). The potential binding site of the target protein was identified through structural alignment with the known binding pocket of a protein with a similar function. AutoDock Vina was used to carry out the docking steps. The docking results were analyzed and the inhibitors were screened based on their binding affinity scores and ADME properties. Among the 257 functional inhibitors, Dutasteride, Cepharanthine, and Zafirlukast presented the lowest binding affinity scores of −9.7, −9.6, and −9.5 kcal/mol, respectively. Furthermore, computational ADME analysis of these results revealed Cepharanthine and Zafirlukast to have non-toxic properties. To further validate these findings, the top two inhibitors in complex with the target protein were subjected to molecular dynamic simulations at 100 ns. The molecular interactions and stability of these compounds revealed that these inhibitors could be a promising tool for inhibiting SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Aliza Naz
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
- Department of Bioinformatics and Biotechnology, International Islamic University, Islamabad 44000, Pakistan
| | - Sumbul Asif
- Department of Bioinformatics and Biotechnology, International Islamic University, Islamabad 44000, Pakistan
- School of Interdisciplinary Engineering and Sciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Khairiah Mubarak Alwutayd
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Sara Sarfaraz
- Department of Bioinformatics, Kohsar University Murree, Murree 47150, Pakistan
- Correspondence:
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan
| | - Asim Abbasi
- Department of Environmental Sciences, Kohsar University Murree, Murree 47150, Pakistan
| | - Abdulkareem M. Alenazi
- Pediatric Senior Registrar, King Salman Armed Forces Hospital in Northwestern Region (KSAFH), Tabuk 47512, Saudi Arabia
| | - Mohamed E. Hasan
- Bioinformatic Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City 32897, Egypt
| |
Collapse
|
9
|
Abideen SA, Khan M, Irfan M, Ahmad S. Deciphering the dynamics of cathepsin D as a potential drug target to enhance anticancer drug-induced apoptosis. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
10
|
Qazi NG, Khan AU, Abbasi SW, Malik I, Naeem K. Effect of Rumex dentatus on Gastrointestinal Protection and Toxicology in Rodents via Investigating H+/K+-ATPase, Calcium Channels, and PDE Mediated Signaling. Front Pharmacol 2022; 13:936161. [PMID: 36052146 PMCID: PMC9424734 DOI: 10.3389/fphar.2022.936161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/01/2022] [Indexed: 01/01/2023] Open
Abstract
This present study aims to delineate Rumex dentatus crude extract (Rd.Cr), n-Hexane, ethyl acetate, aqueous fractions (Rd.n-Hex, Rd.ETAC, and Rd.Aq), and emodin for antidiarrheal, antisecretory effects, anti-spasmodic, gastrointestinal transient time, anti-H. pylori, antiulcer effects, and toxicology. Plant extracts attributed dose-dependent protection against castor oil-induced diarrhea and dose-dependently inhibited intestinal fluid secretions in mice. They decreased the distance transverse by charcoal in the gastrointestinal transit model in rats. In rabbit jejunum preparations, it causes a concentration-dependent relaxation of both spontaneous and K+ (80 mM)-induced contraction, Rd.n-Hex and verapamil were relatively potent against K+-induced contractions and shifted the Ca2+ concentration-response curves (CRCs) to the right, Rd.Cr and Rd.ETAC shifted the isoprenaline-induced inhibitory CRCs to the left, showing potentiating effect similar to papaverine. Rd.n-Hex showed anti-H. pylori effect. Extracts and emodin also show an inhibitory effect against H+/K+-ATPase. Rumex dentatus showed a gastroprotective and antioxidant effect. Histopathological evaluation showed improvement in cellular architecture and decrease in the expression of inflammatory markers such as cyclooxygenase (COX2), tumor necrosis factor (TNF-α), and phosphorylated nuclear factor kappa B (p-NFƙB), validated through immunohistochemistry, ELISA, and western blot techniques. In RT-PCR, it decreases H+/K+-ATPase mRNA levels. Rumex dentatus was analyzed for certain safety aspects and exhibited a relative safety profile as no impairment was observed in kidneys, heart, liver, and brain further assisted by biochemical and hematological analysis. Docking studies revealed that emodin against H+/K+-ATPase pump and voltage gated L-type calcium channel showed E-value of −7.9 and −7.4 kcal/mol, respectively. MD simulations and molecular mechanics Poisson Boltzmann surface area and molecular mechanics Generalized Born surface area MMPBSA/GBSA findings are consistent with the in-vitro, in-vivo, and docking results. In conclusion, Rumex dentatus extracts and its phytoconstituent could be considered a potent antioxidant and anti-inflammatory drug candidates that possess anti-diarrheal, anti-secretary, antispasmodic, anti-H. pylori, and anti-ulcer potential. Toxicity studies were done according to OECD standards 425. It belongs to group 5 (LD50 > 2000 mg/kg), which suggests that it is in the lower toxicity class.
Collapse
Affiliation(s)
- Neelam Gul Qazi
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Arif-ullah Khan
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
- *Correspondence: Arif-ullah Khan,
| | - Sumra Wajid Abbasi
- Nums Department of Biological Sciences, National University of Medical Sciences Rawalpindi, Rawalpindi, Pakistan
| | - Imran Malik
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Komal Naeem
- University of Northern British Columbia, Prince George, BC, Canada
| |
Collapse
|
11
|
El Bakri Y, Saravanan K, Ahmad S, Mague JT. Synthesis, virtual screening and computational approach of a quinoxaline derivative as potent anti-HIV agent targeting the reverse transcriptase enzyme. J Biomol Struct Dyn 2022:1-14. [PMID: 35665631 DOI: 10.1080/07391102.2022.2084456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Infection by the human immunodeficiency virus still represents a continuous serious concern and a global threat to human health. Due to the appearance of multi-resistant virus strains and the serious adverse side effects of the antiretroviral therapy administered, there is an urgent need for the development of new treatment agents that are more active, less toxic, and with increased tolerability to mutations. Quinoxaline derivatives are a class of heterocyclic compounds with a wide range of organic and remedial applications. In addition, they are known to significantly inhibit HIV reverse transcriptase (RT) and HIV replication in cell cultures. For these reasons, we are investigating the synthesis and computational studies of quinoxaline derivatives with a focus on their effects on the HIV RT enzyme, and we present here the structure of one such molecule, methyl 2-[(2E)-3-oxo-1,2,3,4-tetrahydroquinoalin-2-ylidene] acetate, which was confirmed by X-ray diffraction studies. In the crystal, N-H···O and C-H···O hydrogen bonds form ribbons whose mean planes are inclined to (111) by 25.69(8)°. The ribbons are formed into stacks by C-H···π(ring) interactions and π-stacking interactions between carbonyl groups. The Hirshfeld surface map allows us to understand the nature of interactions in the contribution to crystal packing. A density functional theory (DFT) calculation was performed to optimize the geometrical parameters and then they were compared with the solid-state phase. The molecular electrostatic potential map displays reactive sites on the surface, which are responsible for intermolecular interaction in the chemical species. Computational molecular docking, in addition to molecular dynamics simulations and MMGB/PBSA binding energy techniques, was used to assess the affinity of the molecule for the HIV reverse transcriptase enzyme. The new quinoxaline derivative is more powerful in terms of binding affinity and binding conformation stability with the HIV reverse transcriptase enzyme, which suggests the molecule is a good candidate for further biological optimization.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russian Federation
| | | | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Joel T Mague
- Department of Chemistry, Tulane University, New Orleans, Los Angeles, USA
| |
Collapse
|
12
|
Atanasova M, Dimitrov I, Ivanov S, Georgiev B, Berkov S, Zheleva-Dimitrova D, Doytchinova I. Virtual Screening and Hit Selection of Natural Compounds as Acetylcholinesterase Inhibitors. Molecules 2022; 27:3139. [PMID: 35630613 PMCID: PMC9145144 DOI: 10.3390/molecules27103139] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 12/10/2022] Open
Abstract
Acetylcholinesterase (AChE) is one of the classical targets in the treatment of Alzheimer's disease (AD). Inhibition of AChE slows down the hydrolysis of acetycholine and increases choline levels, improving the cognitive function. The achieved success of plant-based natural drugs acting as AChE inhibitors, such as galantamine (GAL) from Galanthus genus and huperzine A from Huperzia serrate (approved drug in China), in the treatment of AD, and the fact that natural compounds (NCs) are considered as safer and less toxic compared to synthetic drugs, led us to screen the available NCs (almost 150,000) in the ZINC12 database for AChE inhibitory activity. The compounds were screened virtually by molecular docking, filtered for suitable ADME properties, and 32 ligands from 23 structural groups were selected. The stability of the complexes was estimated via 1 μs molecular dynamics simulation. Ten compounds formed stable complexes with the enzyme and had a vendor and a reasonable price per mg. They were tested for AChE inhibitory and antioxidant activity. Five compounds showed weak AChE inhibition and three of them exhibited high antioxidant activity.
Collapse
Affiliation(s)
- Mariyana Atanasova
- Chemistry Department, Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria; (I.D.); (S.I.); (D.Z.-D.); (I.D.)
| | - Ivan Dimitrov
- Chemistry Department, Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria; (I.D.); (S.I.); (D.Z.-D.); (I.D.)
| | - Stefan Ivanov
- Chemistry Department, Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria; (I.D.); (S.I.); (D.Z.-D.); (I.D.)
- Redesign Science, 180 Varick St, New York, NY 10014, USA
| | - Borislav Georgiev
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (B.G.); (S.B.)
| | - Strahil Berkov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (B.G.); (S.B.)
| | - Dimitrina Zheleva-Dimitrova
- Chemistry Department, Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria; (I.D.); (S.I.); (D.Z.-D.); (I.D.)
| | - Irini Doytchinova
- Chemistry Department, Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria; (I.D.); (S.I.); (D.Z.-D.); (I.D.)
| |
Collapse
|
13
|
Almihyawi RAH, Naman ZT, Al-Hasani HMH, Muhseen ZT, Zhang S, Chen G. Integrated computer-aided drug design and biophysical simulation approaches to determine natural anti-bacterial compounds for Acinetobacter baumannii. Sci Rep 2022; 12:6590. [PMID: 35449379 PMCID: PMC9023527 DOI: 10.1038/s41598-022-10364-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 04/04/2022] [Indexed: 11/23/2022] Open
Abstract
Acinetobacter baumannii is a nosocomial bacterial pathogen and is responsible for a wide range of diseases including pneumonia, necrotizing fasciitis, meningitis, and sepsis. The enzyme 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase (encoded by aroA gene) in ESKAPE pathogens catalyzes the sixth step of shikimate pathway. The shikimate pathway is an attractive drug targets pathway as it is present in bacteria but absent in humans. As EPSP is essential for the A. baumannii growth and needed during the infection process, therefore it was used as a drug target herein for high-throughput screening of a comprehensive marine natural products database (CMNPD). The objective was to identify natural molecules that fit best at the substrate binding pocket of the enzyme and interact with functionally critical residues. Comparative assessment of the docking scores allowed selection of three compounds namely CMNPD31561, CMNPD28986, and CMNPD28985 as best binding molecules. The molecules established a balanced network of hydrophobic and hydrophilic interactions, and the binding pose remained in equilibrium throughout the length of molecular simulation time. Radial distribution function (RDF) analysis projected key residues from enzyme active pocket which actively engaged the inhibitors. Further validation is performed through binding free energies estimation that affirms very low delta energy of <-22 kcal/mol in MM-GBSA method and <-12 kcal/mol in MM-PBSA method. Lastly, the most important active site residues were mutated and their ligand binding potential was re-investigated. The molecules also possess good druglike properties and better pharmacokinetics. Together, these findings suggest the potential biological potency of the leads and thus can be used by experimentalists in vivo and in vitro studies.
Collapse
Affiliation(s)
- Raed A H Almihyawi
- College of Life Sciences, Jilin Agricultural University, Jilin, China
- Department of Quality Control, Baghdad Water Authority, Mayoralty of Baghdad, Baghdad, Iraq
| | - Ziad Tareq Naman
- Department of Medical Laboratory Techniques, Al Mamoon University College, Baghdad, Iraq
| | - Halah M H Al-Hasani
- Department of Biotechnology, College of Science, University of Diyala, Baqubah, Iraq
| | - Ziyad Tariq Muhseen
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210093, China
| | - Sitong Zhang
- College of Life Sciences, Jilin Agricultural University, Jilin, China.
- Key Laboratory of Straw Biology and Utilization, Ministry of Education, Jilin, China.
| | - Guang Chen
- College of Life Sciences, Jilin Agricultural University, Jilin, China.
- Key Laboratory of Straw Biology and Utilization, Ministry of Education, Jilin, China.
| |
Collapse
|
14
|
Ahmad F, Albutti A, Tariq MH, Din G, Tahir ul Qamar M, Ahmad S. Discovery of Potential Antiviral Compounds against Hendra Virus by Targeting Its Receptor-Binding Protein (G) Using Computational Approaches. Molecules 2022; 27:554. [PMID: 35056869 PMCID: PMC8779602 DOI: 10.3390/molecules27020554] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/07/2022] [Accepted: 01/12/2022] [Indexed: 01/10/2023] Open
Abstract
Hendra virus (HeV) belongs to the paramyxoviridae family of viruses which is associated with the respiratory distress, neurological illness, and potential fatality of the affected individuals. So far, no competitive approved therapeutic substance is available for HeV. For that reason, the current research work was conducted to propose some novel compounds, by adopting a Computer Aided Drug Discovery approach, which could be used to combat HeV. The G attachment Glycoprotein (Ggp) of HeV was selected to achieve the primary objective of this study, as this protein makes the entry of HeV possible in the host cells. Briefly, a library of 6000 antiviral compounds was screened for potential drug-like properties, followed by the molecular docking of short-listed compounds with the Protein Data Bank (PDB) structure of Ggp. Docked complexes of top two hits, having maximum binding affinities with the active sites of Ggp, were further considered for molecular dynamic simulations of 200 ns to elucidate the results of molecular docking analysis. MD simulations and Molecular Mechanics Energies combined with the Generalized Born and Surface Area (MMGBSA) or Poisson-Boltzmann and Surface Area (MMPBSA) revealed that both docked complexes are stable in nature. Furthermore, the same methodology was used between lead compounds and HeV Ggp in complex with its functional receptor in human, Ephrin-B2. Surprisingly, no major differences were found in the results, which demonstrates that our identified compounds can also perform their action even when the Ggp is attached to the Ephrin-B2 ligand. Therefore, in light of all of these results, we strongly suggest that compounds (S)-5-(benzylcarbamoyl)-1-(2-(4-methyl-2-phenylpiperazin-1-yl)-2-oxoethyl)-6-oxo-3,6-dihydropyridin-1-ium-3-ide and 5-(cyclohexylcarbamoyl)-1-(2-((2-(3-fluorophenyl)-2-methylpropyl)amino)-2-oxoethyl)-6-oxo-3,6-dihydropyridin-1-ium-3-ide could be considered as potential therapeutic agents against HeV; however, further in vitro and in vivo experiments are required to validate this study.
Collapse
Affiliation(s)
- Faisal Ahmad
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Aqel Albutti
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Muhammad Hamza Tariq
- Department of Biotechnology, Virtual University of Pakistan, Lahore 54000, Pakistan;
| | - Ghufranud Din
- Department of Medical Lab Technology, The University of Haripur, Haripur 22660, Pakistan;
| | | | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
| |
Collapse
|
15
|
Muhseen ZT, Ali MH, Jaber NR, Mashrea DS, Alfalki AM, Li G. Determination of Novel Anti-Cancer Agents by Targeting OGG1 Enzyme Using Integrated Bioinformatics Methods. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:13290. [PMID: 34948899 PMCID: PMC8706639 DOI: 10.3390/ijerph182413290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 12/18/2022]
Abstract
The 8-oxoguanine DNA glycosylase (OGG1) enzyme is a key DNA glycosylase mediating the excision of 7,8-dihydro-8-oxoguanine (8-oxoG) from DNA molecule to the start base excision repair pathway. The OGG1 glycosylase function depletion has been seen to obstruct pathological conditions such as inflammation, A3 T-cell lymphoblastic acute leukemia growth, and neurodegenerative diseases, thus warranting OGG1 as an attractive anti-cancer enzyme. Herein, we employed several drug libraries intending to screen non-toxic inhibitory molecules against the active pocket of the enzyme that achieved stable binding mode in dynamics. Two anti-cancer compounds ([O-]C1=C(CC2=CC=CC=C2)SC(=[N+]1CC(=O)NC3=NC=C(CC4=CC=CC=C4)S3)S and CCCN(CCC)[S]-(=O)(=O)C1=CC=C(C=C1)C(=O)NNC2=NC3=CC=C(Br)C=C3C(=N2)C4=CC=CC=C4) from Selleckchem.com were identified to occupy the active pocket of OGG1 and bind with greater affinity than Control TH5487. The binding affinity of Top-1 is -11.6 kcal/mol while that of Top-2 is -10.7 kcal/mol in contrast to TH5487 Control (-9 kcal/mol). During molecular dynamic simulations versus time, the said compounds are tightly held by the enzyme with no minor structural deviations reported except flexible loops in particular those present at the N and C-terminal. Both the compounds produced extensive hydrophobic interactions with the enzyme along with stable hydrogen bonding. The docking and molecular dynamics simulations predictions were further validated by molecular mechanics with generalized Born and surface area solvation (MM/GBSA) and Poisson Boltzmann surface area (MM/PBSA), and WaterSwap binding energies that validated strong binding of the compounds to the enzyme. The MM/GBSA binding free energy for Top-1 complex is -28.10 kcal/mol, Top-2 complex is -50.14 kcal/mol) and Control is -46.91 kcal/mol while MM/PBSA value for Top-1, Top-2 and Control is -23.38 kcal/mol, -35.29 kcal/mol and -38.20 kcal/mol, respectively. Computational pharmacokinetics support good druglike candidacy of the compounds with acceptable profile of pharmacokinetics and very little toxicity. All these findings support the notion that the compounds can be used in experiments to test their anti-cancer activities.
Collapse
Affiliation(s)
- Ziyad Tariq Muhseen
- School of Life Sciences, Shaanxi Normal University, Xi’an 710062, China;
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi’an 710062, China
| | - Mustafa Hussein Ali
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China;
| | - Nawar Rushdi Jaber
- Department of Medical Laboratory Techniques, School of Life Sciences, Dijlah University College, Baghdad 00964, Iraq;
| | - Dheyaa Shakir Mashrea
- Educational Directorate of Babylon Province, Ministry of Education, Babylon 51002, Iraq;
| | - Ali Mamoon Alfalki
- Department of Health Professional Graduate, University of New England, Biddeford, Portland, ME 04005, USA;
| | - Guanglin Li
- School of Life Sciences, Shaanxi Normal University, Xi’an 710062, China;
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi’an 710062, China
| |
Collapse
|
16
|
Almihyawi RAH, Al-Hasani HMH, Jassim TS, Muhseen ZT, Zhang S, Chen G. Molecular Insights into Binding Mode and Interactions of Structure-Based Virtually Screened Inhibitors for Pseudomonas aeruginosa Multiple Virulence Factor Regulator (MvfR). Molecules 2021; 26:6811. [PMID: 34833903 PMCID: PMC8619476 DOI: 10.3390/molecules26226811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 11/16/2022] Open
Abstract
Multi-drug resistance (MDR) bacterial pathogens pose a threat to global health and warrant the discovery of new therapeutic molecules, particularly those that can neutralize their virulence and stop the evolution of new resistant mechanisms. The superbug nosocomial pathogen, Pseudomonas aeruginosa, uses a multiple virulence factor regulator (MvfR) to regulate the expression of multiple virulence proteins during acute and persistent infections. The present study targeted MvfR with the intention of designing novel anti-virulent compounds, which will function in two ways: first, they will block the virulence and pathogenesis P. aeruginosa by disrupting the quorum-sensing network of the bacteria, and second, they will stop the evolution of new resistant mechanisms. A structure-based virtual screening (SBVS) method was used to screen druglike compounds from the Asinex antibacterial library (~5968 molecules) and the comprehensive marine natural products database (CMNPD) (~32 thousand compounds), against the ligand-binding domain (LBD) of MvfR, to identify molecules that show high binding potential for the relevant pocket. In this way, two compounds were identified: Top-1 (4-((carbamoyloxy)methyl)-10,10-dihydroxy-2,6-diiminiodecahydropyrrolo[1,2-c]purin-9-yl sulfate) and Top-2 (10,10-dihydroxy-2,6-diiminio-4-(((sulfonatocarbamoyl)oxy)methyl)decahydropyrrolo[1,2-c]purin-9-yl sulfate), in contrast to the co-crystallized M64 control. Both of the screened leads were found to show deep pocket binding and interactions with several key residues through a network of hydrophobic and hydrophilic interactions. The docking results were validated by a long run of 200 ns of molecular dynamics simulation and MM-PB/GBSA binding free energies. All of these analyses confirmed the presence of strong complex formation and rigorous intermolecular interactions. An additional analysis of normal mode entropy and a WaterSwap assay were also performed to complement the aforementioned studies. Lastly, the compounds were found to show an acceptable range of pharmacokinetic properties, making both compounds potential candidates for further experimental studies to decipher their real biological potency.
Collapse
Affiliation(s)
- Raed A. H. Almihyawi
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China;
- Department of Quality Control, Baghdad Water Authority, Baghdad 10011, Iraq
| | - Halah M. H. Al-Hasani
- Department of Biotechnology, College of Science, University of Diyala, Baqubah 32001, Iraq;
| | - Tabarak Sabah Jassim
- Department of Prosthodontic Technologies, Dijlah University College, Baghdad 00964, Iraq;
| | - Ziyad Tariq Muhseen
- School of Life Sciences, Shaanxi Normal University, Xi’an 710119, China;
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi’an 710119, China
| | - Sitong Zhang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China;
- Key Laboratory of Straw Biology and Utilization, Ministry of Education, Jilin 130118, China
| | - Guang Chen
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China;
- Key Laboratory of Straw Biology and Utilization, Ministry of Education, Jilin 130118, China
| |
Collapse
|
17
|
Khan J, Ali G, Rashid U, Khan R, Jan MS, Ullah R, Ahmad S, Abbasi SW, Khan Khalil AA, Sewell RE. Mechanistic evaluation of a novel cyclohexenone derivative's functionality against nociception and inflammation: An in-vitro, in-vivo and in-silico approach. Eur J Pharmacol 2021; 902:174091. [PMID: 33865830 DOI: 10.1016/j.ejphar.2021.174091] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 12/18/2022]
Abstract
The synthesis of a novel cyclohexanone derivative (CHD; Ethyl 6-(4-metohxyphenyl)-2-oxo-4-phenylcyclohexe-3-enecarboxylate) was described and the subsequent aim was to perform an in vitro, in vivo and in silico pharmacological evaluation as a putative anti-nociceptive and anti-inflammatory agent in mice. Initial in vitro studies revealed that CHD inhibited both cyclooxygenase-2 (COX-2) and 5-lipoxygenase (5-LOX) enzymes and it also reduced mRNA expression of COX-2 and the pro-inflammatory cytokines TNF-α and IL-1β. It was then shown that CHD dose dependently inhibited chemically induced tonic nociception in the abdominal constriction assay and also phasic thermal nociception (i.e. anti-nociception) in the hot plate and tail immersion tests in comparison with aspirin and tramadol respectively. The thermal test outcomes indicated a possible moderate centrally mediated anti-nociception which, in the case of the hot plate test, was pentylenetetrazole (PTZ) and naloxone reversible, implicating GABAergic and opioidergic mechanisms. CHD was also effective against both the neurogenic and inflammatory mediator phases induced in the formalin test and it also disclosed anti-inflammatory activity against the phlogistic agents, carrageenan, serotonin, histamine and xylene compared with standard drugs in edema volume tests. In silico studies indicated that CHD possessed preferential affinity for GABAA, opioid and COX-2 target sites and this was supported by molecular dynamic simulations where computation of free energy of binding also favored the formation of stable complexes with these sites. These findings suggest that CHD has prospective anti-nociceptive and anti-inflammatory properties, probably mediated through GABAergic and opioidergic interactions supplemented by COX-2 and 5-LOX enzyme inhibition in addition to reducing pro-inflammatory cytokine expression. CHD may therefore possess potentially beneficial therapeutic effectiveness in the management of inflammation and pain.
Collapse
Affiliation(s)
- Jawad Khan
- Department of Pharmacy, University of Peshawar, Peshawar, 25120, Pakistan
| | - Gowhar Ali
- Department of Pharmacy, University of Peshawar, Peshawar, 25120, Pakistan.
| | - Umer Rashid
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Pakistan
| | - Rasool Khan
- Institute of Chemical Sciences, University of Peshawar, 25120, Pakistan
| | - Muhammad Saeed Jan
- Department of Pharmacy, Faculty of Biological Sciences, University of Malakand, Chakdara, 18000 Dir (L), Pakistan
| | - Rahim Ullah
- Department of Pharmacy, University of Peshawar, Peshawar, 25120, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 25000, Pakistan
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Atif Ali Khan Khalil
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - RobertD E Sewell
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, CF10 3NB, UK. UK
| |
Collapse
|
18
|
Akhtar N, Abbasi SW, Rubnawaz S, Jafri L, Rani R. Proteomic profiling the molecular signatures of plectranthoic acid in prostate cancer cells. J Proteomics 2021; 246:104311. [PMID: 34214676 DOI: 10.1016/j.jprot.2021.104311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/09/2021] [Accepted: 06/25/2021] [Indexed: 11/26/2022]
Abstract
Among cancers, prostate cancer (PCa) is frequently detected solid tumor and a growing problem for the male population, globally. Newer treatment modalities with specific targets are required for management. Plant-derived agents/drugs have historically been useful in cancer therapeutics. Natural metabolite i.e. plectranthoic acid (PA), inhibits the proliferation of PCa cells and has potent anti-cancer potential. Herein, we aim to identify the molecular signatures of PA. Proteins from control and PA-treated PCa cells were analysed using high-throughput labeled free proteomics approach. Data was processed with the SIEVE software and thoroughly analysed by using Ingenuity pathway analysis (IPA) and PANTHER. A total of 98 unique peptides, showing >2 fold change, were identified. Results indicated that PA modulates oncogenic pro-survival and pro-apoptotic signaling pathways in PCa cells. mTOR was the major canonical pathway targeted by PA, the inhibition of which was likely to induce PA mediated apoptosis. Moreover, PA interacts with the rapamycin binding domain of mTOR, demonstrated by the molecular dynamic (MD) simulation and binding free energy calculations. Furthermore, the biological process moderated by PA with a high percentage was a metabolic process. Taken together, PA appears to have pleiotropic effects, as it modulates multiple key signaling pathways, supporting the potential usefulness. SIGNIFICANCE: Studies on the mechanism of action of therapeutic agents are crucial for drug development. These studies support the selection of a therapeutic agent, appropriate models of its efficacy, and designing of further experiments. Furthermore, information on mechanism of action may suggest strategies for combination therapies. In this regard Proteomics provide the platform for comprehensive understanding of the molecular action mechanisms of newly discovered therapeutic agents. Current research highlights the new insights into mode of action of novel therapeutic metabolite i.e. Plectranthoic acid (PA). Using labeled free proteomics approach we extracted the underlying mechanisms for the anticancer activity of PA using prostate cancer model. The result of the study will pay the way for further investigations on this potent natural compound in different cancers and will provide a root for its development as a lead.
Collapse
Affiliation(s)
- Nosheen Akhtar
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan.
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Samina Rubnawaz
- Department of Biochemistry, Quaid-e-Azam University, Islamabad, Pakistan
| | - Laila Jafri
- Department of Life Sciences, Abasyn University, Islamabad, Pakistan
| | - Rehana Rani
- Department of Life Sciences, Abasyn University, Islamabad, Pakistan
| |
Collapse
|
19
|
Alam S, Sadiqi S, Sabir M, Nisa S, Ahmad S, Abbasi SW. Bacillus species; a potential source of anti-SARS-CoV-2 main protease inhibitors. J Biomol Struct Dyn 2021; 40:5748-5758. [PMID: 33446058 PMCID: PMC7814571 DOI: 10.1080/07391102.2021.1873188] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The COVID-19 being a preconized global pandemic by the World Health Organization needs persuasive immediate research for possible medications. The present study was carried out with a specific aim to computationally evaluate and identify compounds derived from Bacillus species as the plausible inhibitors against 3-chymotrypsin-like main protease (3CLpro) or main protease (MPro), which is a key enzyme in the life-cycle of coronavirus. The compounds were isolated from the crude extracts of Bacillus species. Among the isolated compounds, novel inhibitory leads were identified using in silico techniques. Molecular docking revealed that stigmasterol (-8.3 kcal/mol), chondrillasterol (-7.9 kcal/mol) and hexadecnoic acid (-6.9 kcal/mol)) among others bind in the substrate-binding pocket and also interacted with the catalytic dyad of the 3-CLpro. Further evaluation using 50 ns molecular dynamic simulation and MMPB-GBSA indicated that among the top three docking hits, hexadecanoic acid was found to be the most promising anti-COVID-19 lead against the main protease. Hexadecanoic acid might serve as a potent anti-SARS-CoV-2 compound to combat COVID-19, however, in vitro and in vivo validation and optimization is needed. Communicated by Ramaswamy H. Sarma
Collapse
Affiliation(s)
- Sadia Alam
- Department of Microbiology, The University of Haripur, Haripur, Pakistan
| | - Shahida Sadiqi
- Department of Microbiology, Hazara University, Mansehra, Pakistan
| | - Maimoona Sabir
- Department of Microbiology, The University of Haripur, Haripur, Pakistan
| | - Sobia Nisa
- Department of Microbiology, The University of Haripur, Haripur, Pakistan
| | - Sajjad Ahmad
- National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, Pakistan
| | - Sumra Wajid Abbasi
- NUMS Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| |
Collapse
|
20
|
Deciphering the role of sulfonamides and molecular basis of thioredoxin domain dynamics through comparative simulations. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
21
|
Noreen, Ali R, Badshah SL, Faheem M, Abbasi SW, Ullah R, Bari A, Jamal SB, Mahmood HM, Haider A, Haider S. Identification of potential inhibitors of Zika virus NS5 RNA-dependent RNA polymerase through virtual screening and molecular dynamic simulations. Saudi Pharm J 2020; 28:1580-1591. [PMID: 33424251 PMCID: PMC7783101 DOI: 10.1016/j.jsps.2020.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/15/2020] [Indexed: 01/11/2023] Open
Abstract
Zika virus (ZIKV) is one of the mosquito borne flavivirus with several outbreaks in past few years in tropical and subtropical regions. The non-structural proteins of flaviviruses are suitable active targets for inhibitory drugs due to their role in pathogenicity. In ZIKV, the non-structural protein 5 (NS5) RNA-Dependent RNA polymerase replicates its genome. Here we have performed virtual screening to identify suitable ligands that can potentially halt the ZIKV NS5 RNA dependent RNA polymerase (RdRp). During this process, we searched and screened a library of ligands against ZIKV NS5 RdRp. The selected ligands with significant binding energy and ligand-receptor interactions were further processed. Among the selected docked conformations, top five was further optimized at atomic level using molecular dynamic simulations followed by binding free energy calculations. The interactions of ligands with the target structure of ZIKV RdRp revealed that they form strong bonds within the active sites of the receptor molecule. The efficacy of these drugs against ZIKV can be further analyzed through in-vitro and in-vivo studies.
Collapse
Affiliation(s)
- Noreen
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
- Department of Chemistry, Islamia College University, Peshawar, Pakistan
| | - Roshan Ali
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Syed Lal Badshah
- Department of Chemistry, Islamia College University, Peshawar, Pakistan
| | - Muhammad Faheem
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Riaz Ullah
- Department of Pharmacognosy (MAPPRC), College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed Bari
- Department of Pharmacuitcal Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Syed Babar Jamal
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Hafiz Majid Mahmood
- Department of Pharmacology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Adnan Haider
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Sajjad Haider
- Department of Chemical Engineering, College of Engineering, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
22
|
From pan-genome to protein dynamics: A computational hierarchical quest to identify drug target in multi-drug resistant Burkholderia cepacia. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
23
|
Ismail S, Ahmad S, Azam SS. Immunoinformatics characterization of SARS-CoV-2 spike glycoprotein for prioritization of epitope based multivalent peptide vaccine. J Mol Liq 2020; 314:113612. [PMID: 32834259 PMCID: PMC7297697 DOI: 10.1016/j.molliq.2020.113612] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/14/2020] [Accepted: 06/14/2020] [Indexed: 12/20/2022]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 is a public health emergency of international concern and thus calling for the development of effective and safe therapeutics and prophylactics particularly a vaccine to protect against the infection. SARS-CoV-2 spike glycoprotein is an attractive candidate for a vaccine, antibodies, and inhibitors development because of the many roles it plays in attachment, fusion and entry into the host cell. In the present investigation, we characterized the SARS-CoV-2 spike glycoprotein by immunoinformatics techniques to put forward potential B and T cell epitopes, followed by the use of epitopes in construction of a multi-epitope peptide vaccine construct (MEPVC). The MEPVC revealed robust host immune system simulation with high production of immunoglobulins, cytokines and interleukins. Stable conformation of the MEPVC with a representative innate immune TLR3 receptor was observed involving strong hydrophobic and hydrophilic chemical interactions, along with enhanced contribution from salt-bridges towards inter-molecular stability. Molecular dynamics simulation in aqueous milieu aided further in interpreting strong affinity of the MEPVC for TLR3. This stability is the attribute of several vital residues from both TLR3 and MEPVC as shown by radial distribution function (RDF) and a novel axial frequency distribution (AFD) analytical tool. Comprehensive binding free energies estimation was provided at the end that concluded major domination by electrostatic and minor from van der Waals. Summing all, the designed MEPVC has tremendous potential of providing protective immunity against COVID-19 and thus could be considered in experimental studies.
Collapse
Affiliation(s)
- Saba Ismail
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Sajjad Ahmad
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad 45320, Pakistan
| |
Collapse
|
24
|
Nazar A, Abbas G, Azam SS. Deciphering the Inhibition Mechanism of under Trial Hsp90 Inhibitors and Their Analogues: A Comparative Molecular Dynamics Simulation. J Chem Inf Model 2020; 60:3812-3830. [PMID: 32659088 DOI: 10.1021/acs.jcim.9b01134] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Heat shock protein 90 (Hsp90) performs functions in cellular activities together with other signaling pathways. Hsp90 is evolutionarily conserved and universally articulated as a human cancer-causing agent involved in lung cancer and breast cancer followed by colon and rectum cancers. It has emerged as an effective drug candidate, and inhibition may affect several signaling pathways associated with cancer spread. Therefore, in-silico approaches, molecular docking, molecular dynamics simulation, and binding free energy calculations were applied to create insights into the inhibition mechanism against Hsp90 to identify new cancer therapeutic drugs. Top-docked Hsp90-inhibitor complexes with their analogues were selected as the best complexes based on the GOLD fitness score and orientation. The significant interaction of Hsp90 inhibitors and their analogues were observed to be bound with active site residues as well as residing within the same cavity region. System stability factors RMSD, RMSF, beta-factor, and radius of gyration were analyzed for top-docked complexes and ensure strong binding interaction between inhibitors and the Hsp90 cavity. Cavity bound inhibitors were found to retain consistent hydrogen bonding during the simulation. The radial distribution function (RDF) illustrated that interacting active site residues drive the binding and stability of the inhibitors. Similarly, the axial frequency distribution, which is an indigenously developed analytical tool, produced noteworthy knowledge of the hydrogen-bonding pattern. Results yielded new insights into the design of cancer therapeutic drugs against Hsp90. This finding suggests that under trial Hsp90 inhibitors MPC-3100 could be a potential starting point into the development of potential anticancer agents with the possibility of future directions for the improvement of early existing Hsp90 inhibitors CNF-2024 and SNX-5422 as an anticancer agent.
Collapse
Affiliation(s)
- Asma Nazar
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Ghulam Abbas
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad 45320, Pakistan
| |
Collapse
|
25
|
Ahmad F, Shabaz Z, Azam SS. Insight into natural inhibitors and bridging docking to dynamic simulation against sugar Isomerase (SIS) domain protein. J Mol Model 2020; 26:221. [PMID: 32748070 DOI: 10.1007/s00894-020-04475-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/14/2020] [Indexed: 11/28/2022]
Abstract
The pathogen Legionella longbeachae is a causative agent of legionellosis. The antibiotic resistance is the major problem of this modern world. Thus, selective pressure warrants the need for identification of newer drug target. In current study, subtractive proteomics approach screen out SIS (sugar isomerase) domain protein as an attractive receptor molecule for rational drug design. This protein is involved in lipopolysaccharide biosynthesis and catalyzes the isomerization of sedoheptulose 7-phosphate in D-glycero-D-manno-heptose 7-phosphate. Molecular docking revealed compound 1 (2-(6-(N,N-dimethyl sulfamoyl)pipridin-4-yl)pyrazin-2-yl)imidazol-3-ium-1-ide) as the potent inhibitor having GOLD fitness score of 69. The complex is affirmed by half-site effect via simulation analysis. Complex stability was investigated via several approaches that follows dynamic simulation and binding energies. Trajectory analysis revealed slight change in ring positioning of inhibitor inside the active pocket during 130 ns (nanosecond). Interestingly, it was affirmed via binding interactions' density distribution. Hence, radial distribution function (RDF) inferred that SER55 and SER83 are the major residues that take part in hydrogen bonding and complex stability. Furthermore, an indigenously developed method axial frequency distribution (AFD) has revealed that ligand moved closer to the active site with both the residues SER55 and SER83 binding to the ligand. The phenomena was observed via rotating motion with respect to receptor center cavity. Thus, inhibitor movement towards allosteric site was observed at the end of simulations. Finally, binding free energy calculations by MMPB/GBSA predicts high compound affinity for the complex. Hence, findings from the current study will aid in the novel drug discovery and future experimental studies. Graphical abstract.
Collapse
Affiliation(s)
- Faisal Ahmad
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Zartasha Shabaz
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan.
| |
Collapse
|
26
|
Ahmad S, Abbasi HW, Shahid S, Gul S, Abbasi SW. Molecular docking, simulation and MM-PBSA studies of nigella sativa compounds: a computational quest to identify potential natural antiviral for COVID-19 treatment. J Biomol Struct Dyn 2020; 39:4225-4233. [PMID: 32462996 PMCID: PMC7298883 DOI: 10.1080/07391102.2020.1775129] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nigella sativa or black seed is used as a medicinal plant around the globe. Oil and seeds have a long tradition of folklore use in various medicinal and food systems. The conventional therapeutic use of Nigella sativa, in different ways, has been reported in several studies to treat different diseases including influenza, headache, hypertension, diabetes, inflammation, eczema, fever, cough, asthma, bronchitis, and fever. Based on previously reported potential therapeutic uses of N. sativa compounds, and keeping in mind the dire need of time for the development of potent antiviral, a combined docking, ADMET properties calculation, molecular dynamics, and MM-PBSA approaches were applied in the current study to check the therapeutic potentials of N. sativa chief constituents against COVID-19. Among the studied compounds, we found that dithymoquinone (DTQ), with binding affinity of −8.6 kcal/mol compared to a positive control (chloroquine, −7.2 kcal/mol) , has the high potential of binding at SARS-CoV-2:ACE2 interface and thus could be predicted as a plausible inhibitor to disrupt viral-host interactions. Molecular dynamics simulation of 100 ns well complemented binding affinity of the compound and revealed strong stability of DTQ at the docked site. Additionally, MM-PBSA also affirms the docking results. Compound DTQ of the present study, if validated in wet lab experiments, could be used to treat COVID-19 and could serve as a lead in the future for development of more effective natural antivirals against COVID-19. Communicated by Ramaswamy H. Sarma
Collapse
Affiliation(s)
- Sajjad Ahmad
- National Center of Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Hyder Wajid Abbasi
- Pakistan Institute of Medical Sciences, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Sara Shahid
- Pakistan Institute of Medical Sciences, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Sana Gul
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| |
Collapse
|
27
|
Shahzadi Z, Abbas G, Azam SS. Relational dynamics obtained through simulation studies of thioredoxin reductase: From a multi-drug resistant Entamoeba histolytica. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
28
|
Gulistan T, Ahmad S, Azam SS. Conformational transition of Acinetobacter baumannii KdsC enzyme and the role of magnesium in binding: An insight from comparative molecular dynamics simulation and its implications in novel antibiotics design. J Mol Graph Model 2020; 99:107625. [PMID: 32417725 DOI: 10.1016/j.jmgm.2020.107625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 04/17/2020] [Accepted: 04/17/2020] [Indexed: 11/08/2022]
Abstract
The 3-deoxy-d-manno-octulosonate 8-phosphate phosphatase (KdsC) catalyzes the hydrolysis of 3-deoxy-d-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-d-manno-octulosonate (KDO) and inorganic phosphate in KDO biosynthesis pathway of Gram-negative bacteria lipopolysaccharide (LPS) hydrophobic lipid-A core. The essentiality of KDO for bacterial cell viability presents the possibility of its targeting to develop broad-spectrum antibacterial agents. In this study, a receptor based virtually screening method was put forward to identify novel lead inhibitory molecules for KdsC enzyme. Dynamics evaluation in solution revealed three complexes: Asinex-1197, Asinex-1705, and Asinex-1710 from Asinex antibacterial library as highly stable, involving conformational transition from open to close upon lead molecules binding and eloquent role of active pocket magnesium towards inhibitors binding and movements. Interconversion of local secondary structure elements in sequence region of Asp192-Asp208 covering motif β-turn, β-hairpin, and β-sheets is seen recurrently that could be in all likelihood of the pressure excreted on this region during closing conformation event or magnesium driven inhibitor adjustments. The binding free energy estimation predicted gas phase energy for all the three complexes dominating with major contribution from van der Waals energy (in case of Asinex-1705 and Asinex-1710) and balanced contributions of both electrostatic and van der Waals (in case of Asinex-1197). Key residues-scanning shortlisted Leu45, Asp185, Gy188, Arg231, and Lys255 as vital in the interaction network of magnesium and inhibitors at the binding site. Their crucial roles in net binding energy were reaffirmed via in silico site directed alanine scanning method. The filtered hits might be useful to further scaffolds addition and structural optimization to yield high affinity binders of KdsC enzyme, whose inhibition, in turn, will disrupt the outer membrane synthesis.
Collapse
Affiliation(s)
- Tayyaba Gulistan
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Sajjad Ahmad
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| |
Collapse
|
29
|
Ahmad S, Murtaza UA, Raza S, Azam SS. Blocking the catalytic mechanism of MurC ligase enzyme from Acinetobacter baumannii: An in Silico guided study towards the discovery of natural antibiotics. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.02.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
30
|
Combating tigecycline resistant Acinetobacter baumannii: A leap forward towards multi-epitope based vaccine discovery. Eur J Pharm Sci 2019; 132:1-17. [DOI: 10.1016/j.ejps.2019.02.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/31/2019] [Accepted: 02/16/2019] [Indexed: 01/27/2023]
|
31
|
Ahmad S, Shaker B, Ahmad F, Raza S, Azam SS. Moleculer dynamics simulaiton revealed reciever domain of Acinetobacter baumannii BfmR enzyme as the hot spot for future antibiotics designing. J Biomol Struct Dyn 2018; 37:2897-2912. [DOI: 10.1080/07391102.2018.1498805] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Sajjad Ahmad
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Bilal Shaker
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Faisal Ahmad
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Saad Raza
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| |
Collapse
|
32
|
Ahmad S, Raza S, Qurat-ul-Ain, Uddin R, Rungrotmongkol T, Azam SS. From phylogeny to protein dynamics: A computational hierarchical quest for potent drug identification against an emerging enteropathogen “Yersinia enterocolitica”. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.06.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
33
|
Ahmad S, Raza S, Uddin R, Azam SS. Comparative subtractive proteomics based ranking for antibiotic targets against the dirtiest superbug: Acinetobacter baumannii. J Mol Graph Model 2018; 82:74-92. [PMID: 29705560 DOI: 10.1016/j.jmgm.2018.04.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 04/06/2018] [Accepted: 04/09/2018] [Indexed: 11/27/2022]
Abstract
Multidrug-resistant Acinetobacter baumannii is indeed to be the most successful nosocomial pathogen responsible for myriad infections in modern health care system. Computational methodologies based on genomics and proteomics proved to be powerful tools for providing substantial information about different aspects of A. baumannii biology that made it possible to design new approaches for treating multi, extensive and total drug resistant isolates of A. baumannii. In this current approach, 35 completely annotated proteomes of A. bauamnnii were filtered through a comprehensive subtractive proteomics pipeline for broad-spectrum drug candidates. In total, 10 proteins (KdsA, KdsB, LpxA, LpxC, LpxD, GpsE, PhoB, UvrY, KdpE and OmpR) could serve as ideal candidates for designing novel antibiotics. The work was extended with KdsA enzyme for structure information, prediction of intrinsic disorders, active site details, and structure based virtual screening of library containing natural product-like scaffolds. Most of the enzyme structure has fixed three-dimensional conformation. The selection of inhibitor for KdsA enzyme was based on druglikeness, pharmacokinetics and docking scores. Compound-4636 (5-((3-chloro-5-methyl-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)methoxy)-2-(((1-hydroxy-4-methylpentan-2-yl)amino)methyl)phenol) was revealed as the most potent inhibitor against A. baumannii KdsA enzyme having Gold fitness score of 77.68 and Autodock binding energy of -6.2 kcal/mol. The inhibitor completely follows Lipinski rule of five, Ghose rule, and Egan rule. Molecular dynamics simulation for KdsA and KdsA-4636 complex was performed for 100 ns to unveil what conformational changes the enzyme underwent in the absence and presence of the inhibitor, respectively. The average root means square deviation (RMSD) for both systems was found 3.5 Å, which signifies stable structure of the enzyme in both bounded and unbounded states. Absolute binding energy using Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) reflected high affinity and vigorous interactions of the inhibitor with enzyme active residues. Findings of the current study could open up new avenues for experimentalists to design new potent antibiotics by targeting the targets screened in this study.
Collapse
Affiliation(s)
- Sajjad Ahmad
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Saad Raza
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| |
Collapse
|
34
|
Ahmad S, Raza S, Abro A, Liedl KR, Azam SS. Toward novel inhibitors against KdsB: a highly specific and selective broad-spectrum bacterial enzyme. J Biomol Struct Dyn 2018; 37:1326-1345. [DOI: 10.1080/07391102.2018.1459318] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Sajjad Ahmad
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Saad Raza
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Asma Abro
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
- Faculty of Life Sciences and Informatics, Department of Biotechnology, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan
| | - Klaus R. Liedl
- Institute for General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, Innsbruck 6020, Austria
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
| |
Collapse
|
35
|
Raza S, Azam SS. AFD: an application for bi-molecular interaction using axial frequency distribution. J Mol Model 2018; 24:84. [DOI: 10.1007/s00894-018-3601-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/29/2018] [Indexed: 11/29/2022]
|
36
|
Ahmad S, Raza S, Uddin R, Azam SS. Binding mode analysis, dynamic simulation and binding free energy calculations of the MurF ligase from Acinetobacter baumannii. J Mol Graph Model 2017; 77:72-85. [DOI: 10.1016/j.jmgm.2017.07.024] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 01/16/2023]
|
37
|
Ul Haq F, Abro A, Raza S, Liedl KR, Azam SS. Molecular dynamics simulation studies of novel β-lactamase inhibitor. J Mol Graph Model 2017; 74:143-152. [PMID: 28432959 DOI: 10.1016/j.jmgm.2017.03.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 03/03/2017] [Accepted: 03/06/2017] [Indexed: 01/31/2023]
Abstract
New Delhi Metallo-β-Lactamase-1 (NDM-1) has drawn great attention due to its diverse antibiotic resistant activity. It can hydrolyze almost all clinically available β-lactam antibiotics. To inhibit the activity of NDM-1 a new strategy is proposed using computational methods. Molecular dynamics (MD) simulations are used to analyze the molecular interactions between selected inhibitor candidates and NDM-1 structure. The enzyme-ligand complex is subject to binding free energy calculations using MM(PB/GB)SA methods. The role of each residue of the active site contributing in ligand binding affinity is explored using energy decomposition analysis. Furthermore, a hydrogen bonding network between ligand and enzyme active site is observed and key residues are identified ensuring that the ligand stays inside the active site and maintains its movement towards the active site pocket. A production run of 150ns is carried out and results are analyzed using root mean square deviation (RMSD), root mean square fluctuation (RMSF), and radius of gyration (Rg) to explain the stability of enzyme ligand complex. Important active site residue e.g. PHE70, VAL73, TRP93, HIS122, GLN123, ASP124, HIS189, LYS216, CYS208, LYS211, ALA215, HIS250, and SER251 were observed to be involved in ligand attachemet inside the active site pocket, hence depicting its inhibitor potential. Hydrogen bonds involved in structural stability are analyzed through radial distribution function (RDF) and contribution of important residues involved in ligand movement is explained using a novel analytical tool, axial frequency distribution (AFD) to observe the role of important hydrogen bonding partners between ligand atoms and active site residues.
Collapse
Affiliation(s)
- Farhan Ul Haq
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Asma Abro
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Saad Raza
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Klaus R Liedl
- University of Innsbruck, Institute for General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), Innrain 80/82, 6020 Innsbruck, Austria
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| |
Collapse
|