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Hayat C, Subramaniyan V, Alamri MA, Wong LS, Khalid A, Abdalla AN, Afridi SG, Kumarasamy V, Wadood A. Identification of new potent NLRP3 inhibitors by multi-level in-silico approaches. BMC Chem 2024; 18:76. [PMID: 38637900 PMCID: PMC11027297 DOI: 10.1186/s13065-024-01178-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/02/2024] [Indexed: 04/20/2024] Open
Abstract
Nod-like receptor protein 3 (NLRP-3), is an intracellular sensor that is involved in inflammasome activation, and the aberrant expression of NLRP3 is responsible for diabetes mellitus, its complications, and many other inflammatory diseases. NLRP3 is considered a promising drug target for novel drug design. Here, a pharmacophore model was generated from the most potent inhibitor, and its validation was performed by the Gunner-Henry scoring method. The validated pharmacophore was used to screen selected compounds databases. As a result, 646 compounds were mapped on the pharmacophore model. After applying Lipinski's rule of five, 391 hits were obtained. All the hits were docked into the binding pocket of target protein. Based on docking scores and interactions with binding site residues, six compounds were selected potential hits. To check the stability of these compounds, 100 ns molecular dynamic (MD) simulations were performed. The RMSD, RMSF, DCCM and hydrogen bond analysis showed that all the six compounds formed stable complex with NLRP3. The binding free energy with the MM-PBSA approach suggested that electrostatic force, and van der Waals interactions, played a significant role in the binding pattern of these compounds. Thus, the outcomes of the current study could provide insights into the identification of new potential NLRP3 inflammasome inhibitors against diabetes and its related disorders.
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Affiliation(s)
- Chandni Hayat
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Mardan, 23200, Pakistan
| | - Vetriselvan Subramaniyan
- Pharmacology Unit, Jeffrey Cheah School of Medicine and Health Sciences, Monash University, Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Subang Jaya, Selangor Darul Ehsan, Malaysia.
- Center for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Chennai, 602105, India.
| | - Mubarak A Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, 11942, Al-Kharj, Saudi Arabia
| | - Ling Shing Wong
- Faculty of Health and Life Sciences, INTI International University, 71800, Nilai, Malaysia
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box: 114, 45142, Jazan, Saudi Arabia.
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, 21955, Makkah, Saudi Arabia
| | - Sahib Gul Afridi
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Mardan, 23200, Pakistan
| | - Vinoth Kumarasamy
- Department of Parasitology and Medical Entomology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, 56000, Cheras, Kuala Lumpur, Malaysia.
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Mardan, 23200, Pakistan.
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Taha M, Rahim F, Uddin I, Amir M, Iqbal N, Wadood A, Khan KM, Uddin N, Rehman AU, Farooq RK. Discovering phenoxy acetohydrazide derivatives as urease inhibitors and molecular docking studies. J Biomol Struct Dyn 2024; 42:3118-3127. [PMID: 37211867 DOI: 10.1080/07391102.2023.2212794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/01/2023] [Indexed: 05/23/2023]
Abstract
Helicobacter pylori causes severe stomach disorders and the use of enzyme inhibitors for treatment is one of the possible therapies. The great biological potential of imine analogs as urease inhibitors has been the focus of researchers in past years. In this regard, we have synthesized twenty-one derivatives of dichlorophenyl hydrazide. These compounds were characterized by different spectroscopic techniques i.e. NMR and HREI-MS. Compounds 2 and 10 were found to be the most active in the series. Structure-activity relationship has been established for all compounds based on different substituents attached to the phenyl ring that play a vital role in enzyme inhibition. From the structure-activity relationship, it has been observed that these analogs showed excellent potential for urease and can be an alternate therapy in the future. The molecular docking study was performed to further explore the binding interactions of synthesized analogs with enzyme active sites.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muhammad Taha
- Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Fazal Rahim
- Department of Chemistry, Hazara University, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - Imad Uddin
- Department of Chemistry, University of Haripur, Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Mohd Amir
- Department of Natural Products & Alternative Medicine College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Naveed Iqbal
- Department of Chemistry, University of Poonch, Rawalakot, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Khalid Mohammed Khan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Nizam Uddin
- Department of Chemistry, University of Karachi, Karachi, Pakistan
| | - Ashfaq Ur Rehman
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Rai Khalid Farooq
- Department of Neuroscience Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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Mu J, Li Z, Zhang B, Zhang Q, Iqbal J, Wadood A, Wei T, Feng Y, Chen HF. Graphormer supervised de novo protein design method and function validation. Brief Bioinform 2024; 25:bbae135. [PMID: 38557677 PMCID: PMC10982952 DOI: 10.1093/bib/bbae135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 01/31/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
Protein design is central to nearly all protein engineering problems, as it can enable the creation of proteins with new biological functions, such as improving the catalytic efficiency of enzymes. One key facet of protein design, fixed-backbone protein sequence design, seeks to design new sequences that will conform to a prescribed protein backbone structure. Nonetheless, existing sequence design methods present limitations, such as low sequence diversity and shortcomings in experimental validation of the designed functional proteins. These inadequacies obstruct the goal of functional protein design. To improve these limitations, we initially developed the Graphormer-based Protein Design (GPD) model. This model utilizes the Transformer on a graph-based representation of three-dimensional protein structures and incorporates Gaussian noise and a sequence random masks to node features, thereby enhancing sequence recovery and diversity. The performance of the GPD model was significantly better than that of the state-of-the-art ProteinMPNN model on multiple independent tests, especially for sequence diversity. We employed GPD to design CalB hydrolase and generated nine artificially designed CalB proteins. The results show a 1.7-fold increase in catalytic activity compared to that of the wild-type CalB and strong substrate selectivity on p-nitrophenyl acetate with different carbon chain lengths (C2-C16). Thus, the GPD method could be used for the de novo design of industrial enzymes and protein drugs. The code was released at https://github.com/decodermu/GPD.
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Affiliation(s)
- Junxi Mu
- State Key Laboratory of Microbial metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
- Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, No.5 Yiheyuan Road, Beijing, 100871, China
| | - Zhengxin Li
- State Key Laboratory of Microbial metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Bo Zhang
- State Key Laboratory of Microbial metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Qi Zhang
- State Key Laboratory of Microbial metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jamshed Iqbal
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Ting Wei
- State Key Laboratory of Microbial metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yan Feng
- State Key Laboratory of Microbial metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
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Ajmal A, Alkhatabi HA, Alreemi RM, Alamri MA, Khalid A, Abdalla AN, Alotaibi BS, Wadood A. Prospective virtual screening combined with bio-molecular simulation enabled identification of new inhibitors for the KRAS drug target. BMC Chem 2024; 18:57. [PMID: 38528576 DOI: 10.1186/s13065-024-01152-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/26/2024] [Indexed: 03/27/2024] Open
Abstract
Lung cancer is a disease with a high mortality rate and it is the number one cause of cancer death globally. Approximately 12-14% of non-small cell lung cancers are caused by mutations in KRASG12C. The KRASG12C is one of the most prevalent mutants in lung cancer patients. KRAS was first considered undruggable. The sotorasib and adagrasib are the recently approved drugs that selectively target KRASG12C, and offer new treatment approaches to enhance patient outcomes however drug resistance frequently arises. Drug development is a challenging, expensive, and time-consuming process. Recently, machine-learning-based virtual screening are used for the development of new drugs. In this study, we performed machine-learning-based virtual screening followed by molecular docking, all atoms molecular dynamics simulation, and binding energy calculations for the identifications of new inhibitors against the KRASG12C mutant. In this study, four machine learning models including, random forest, k-nearest neighbors, Gaussian naïve Bayes, and support vector machine were used. By using an external dataset and 5-fold cross-validation, the developed models were validated. Among all the models the performance of the random forest (RF) model was best on the train/test dataset and external dataset. The random forest model was further used for the virtual screening of the ZINC15 database, in-house database, Pakistani phytochemicals, and South African Natural Products database. A total of 100 ns MD simulation was performed for the four best docking score complexes as well as the standard compound in complex with KRASG12C. Furthermore, the top four hits revealed greater stability and greater binding affinities for KRASG12C compared to the standard drug. These new hits have the potential to inhibit KRASG12C and may help to prevent KRAS-associated lung cancer. All the datasets used in this study can be freely available at ( https://github.com/Amar-Ajmal/Datasets-for-KRAS ).
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Affiliation(s)
- Amar Ajmal
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Hind A Alkhatabi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, 21959, Saudi Arabia
| | - Roaa M Alreemi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, 21959, Saudi Arabia
| | - Mubarak A Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box: 114, Jazan, 45142, Saudi Arabia.
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Bader S Alotaibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra Univesity, Al- Quwayiyah, Riyadh, Saudi Arabia
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan.
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Abu-Izneid T, Rauf A, Akram Z, Naz S, Wadood A, Muhammad N, Hayat C, Al-Awthan YS, Bahattab OS. Discovery of new α-glucosides, antiglycation agent, and in silico study of 2-(3,4-dihydroxyphenyl)-7,8-dihydroxy-3-methoxy-4H-chromen-4-one isolated from Pistacia chinensis. Heliyon 2024; 10:e27298. [PMID: 38495136 PMCID: PMC10943337 DOI: 10.1016/j.heliyon.2024.e27298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/19/2024] Open
Abstract
Pistacia chinensis is locally practiced for treating diabetes, pain, inflammation, and erectile dysfunction. Therefore, the current studies subjected the crude extract/fractions and the isolated compound (2-(3,4-dihydroxyphenyl)-7,8-dihydroxy-3-methoxy-4H-chromen-4-one) to α-glucosidase inhibitor and anti-glycation activities. The development of long-term complications associated with diabetes is primarily caused by chronic hyperglycemia. Regarding α-glucosidase, the most significant inhibitory effect was observed with compound 1 (93.09%), followed by the methanolic extract (80.87%) with IC50 values of 45.86 and 86.32 μM. The maximum anti-glycation potential was shown by an isolated compound 1 followed by methanolic extract with effect inhibition of 90.12 and 72.09, respectively. Compound 1 is expected to have the highest gastrointestinal absorption rate, with a predicted absorption rate of 86.156%. This indicates oral suitability. The compound 1 is expected to have no harmful effects on the liver. In addition, our docking results suggest that alpha-glucosidase and isolated compounds showed strong interaction with ILE821, GLN900, and ALA901 residues, along with a -11.95 docking score.
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Affiliation(s)
- Tareq Abu-Izneid
- Pharmaceutical Sciences Program, College of Pharmacy, Al Ain University, Al Ain, 64141, United Arab Emirates
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Swabi, Anbar, Khyber Pakhtunkhwa, Pakistan
| | - Zuneera Akram
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Baqai Medical University, Karachi, Pakistan
| | - Saima Naz
- Institute of Biotechnology & Microbiology, Bacha Khan University Charsadda, Charsadda, Khyber Pakhtunkhwa, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan KPK, Pakistan
| | - Naveed Muhammad
- Department of Pharmacy, Abdul Wali Khan, University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Chandni Hayat
- Department of Biochemistry, Abdul Wali Khan University Mardan KPK, Pakistan
| | - Yahya S. Al-Awthan
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk, 71491, Saudi Arabia
| | - Omar S. Bahattab
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk, 71491, Saudi Arabia
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Bano B, Kanwal, Hameed S, Lateef M, Wadood A, Shams S, Hussain S, Ain NU, Perveen S, Taha M, Khan KM. Unsymmetrical thiourea derivatives: synthesis and evaluation as promising antioxidant and enzyme inhibitors. Future Med Chem 2024; 16:497-511. [PMID: 38372209 DOI: 10.4155/fmc-2023-0213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024] Open
Abstract
Background: Unsymmetrical thioureas 1-20 were synthesized and then characterized by various spectroscopy techniques such as UV, IR, fast atom bombardment (FAB)-MS, high-resolution FAB-MS, 1H-NMR and 13C-NMR. Methods: Synthetic compounds 1-20 were tested for their ability for antioxidant, lipoxygenase and xanthine oxidase activities. Results: Compounds 1, 2, 9, 12 and 15 exhibited strong antioxidant potential, whereas compounds 1-3, 9, 12, 15 and 19 showed good to moderate lipoxygenase activity. Ten compounds demonstrated moderate xanthine oxidase inhibition. Conclusion: Compound 15 displayed the highest potency among the series, exhibiting good antioxidant, lipoxygenase and xanthine oxidase activities. Theoretical calculations using density functional theory and molecular docking studies supported the experimental findings, indicating the potential of the synthesized compounds as potent antioxidants, lipoxygenases and xanthine oxidase agents.
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Affiliation(s)
- Bilquees Bano
- H. E. J. Research Institute of Chemistry, International Center for Chemical & Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Kanwal
- H. E. J. Research Institute of Chemistry, International Center for Chemical & Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Shehryar Hameed
- H. E. J. Research Institute of Chemistry, International Center for Chemical & Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Mehreen Lateef
- Department of Biochemistry, Multi-Disciplinary Research Laboratory, Bahria University Medical & Dental College, Karachi - 74400, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Shankar Campus, Abdul Wali Khan University, Mardan, 23200, Khyber Pakhtunkhwa, Pakistan
| | - Sulaiman Shams
- Department of Biochemistry, Shankar Campus, Abdul Wali Khan University, Mardan, 23200, Khyber Pakhtunkhwa, Pakistan
| | - Shafqat Hussain
- Department of Chemistry, University of Baltistan, Skardu, Gilgit-Baltistan, 1600, Pakistan
| | - Noor Ui Ain
- Pharmacy Department City University of Science & Information Technology, Peshawar, Pakistan
| | - Shahnaz Perveen
- PCSIR Laboratories Complex, Karachi, Shahrah-e-Dr. Salimuzzaman Siddiqui, Karachi - 75280, Pakistan
| | - Muhammad Taha
- Department of Clinical Pharmacy, Institute for Research & Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam - 31441, Saudi Arabia
| | - Khalid Mohammed Khan
- H. E. J. Research Institute of Chemistry, International Center for Chemical & Biological Sciences, University of Karachi, Karachi-75270, Pakistan
- Department of Clinical Pharmacy, Institute for Research & Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam - 31441, Saudi Arabia
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Hanifa B, Bibi N, Sirajuddin M, Tiekink ERT, Kubicki M, Khan I, Bari A, Wadood A, Shams S. Synthesis, spectral characterisation, biocidal investigation, in-silico and molecular docking studies of 4-[(2-chloro-4-methylphenyl)carbamoyl]butanoic acid derived triorganotin(IV) compounds. J Biomol Struct Dyn 2024; 42:1826-1845. [PMID: 37114651 DOI: 10.1080/07391102.2023.2204160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/08/2023] [Indexed: 04/29/2023]
Abstract
Three triorganotin(IV) compounds, R3Sn(L), with R = CH3 (1), n-C4H9 (2) and C6H5 (3), and LH = 4-[(2-chloro-4-methylphenyl)carbamoyl]butanoic acid, were prepared and confirmed by various techniques. A five-coordinate, distorted trigonal-bipyramidal geometry was elucidated for tin(IV) centres both in solution and solid states. An intercalation mode was confirmed for the compound SS-DNA interaction by UV-visible, viscometric techniques and molecular docking. MD simulation revealed stable binding of LH with SS-DNA. Anti-bacterial investigation revealed 2 to be generally the most potent, especially against Sa and Ab, i.e. having the lowest MIC values (≤0.25 μg/mL) compared to the standard anti-biotics vancomycin-HCl (MIC = 1 μg/mL) and colistin-sulphate (MIC = 0.25 μg/mL). Similarly, the anti-fungal profile shows 2 exhibits 100% inhibition against Ca and Cn fungal strains and has MIC values (≤0.25 μg/mL) comparatively lower than standard drug fluconazole (0.125 and 8 μg/mL for Ca and Cn, respectively). Compound 2 has the greatest activity with CC50 ≤ 25 μg/mL and HC50 > 32 μg/mL performed against HEC239 and RBC cell lines. The anti-cancer potential was assessed against the MG-U87 cell line, using cisplatin as the standard (133 µM), indicates 2 displays the greatest activity (IC50: 5.521 µM) at a 5 µM dose. The greatest anti-leishmanial potential was observed for 2 (87.75 at 1000 μg/mL) in comparison to amphotericin B (90.67). The biological assay correlates with the observed maximum of 89% scavenging activity exhibited by 2. The Swiss-ADME data publicised the screened compounds generally follow the rule of 5 of drug-likeness and have good bioavailability potential.
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Affiliation(s)
- Bibi Hanifa
- Department of Chemistry, University of Science & Technology, Bannu, Pakistan
| | - Naila Bibi
- Department of Chemistry, University of Science & Technology, Bannu, Pakistan
| | - Muhammad Sirajuddin
- Department of Chemistry, University of Science & Technology, Bannu, Pakistan
| | - Edward R T Tiekink
- Research Centre for Crystalline Materials, School of Medical and Life Sciences, Sunway University, Selangor Darul Ehsan, Malaysia
| | - Maciej Kubicki
- Department of Chemistry, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - Ishaq Khan
- Cancer Cell Culture & Precision Oncomedicine Lab, Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Ahmed Bari
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Sulaiman Shams
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
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Abu-Izneid T, Rauf A, Ahmad Z, Wadood A, Ayub K, Muhammad N, Al-Awthan YS, Maqbool M, Bahattab OS, Hemeg HA, Naz S, Formanowicz D. Density functional theory (DFT), molecular docking, and xanthine oxidase inhibitory studies of dinaphthodiospyrol S from Diospyros kaki L. Saudi Pharm J 2024; 32:101936. [PMID: 38261938 PMCID: PMC10797153 DOI: 10.1016/j.jsps.2023.101936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 12/25/2023] [Indexed: 01/25/2024] Open
Abstract
In this work, we investigated Diospyros kaki extract and an isolated compound for their potential as xanthine oxidase (XO) inhibitors, a target enzyme involved in inflammatory disorders. The prepared extract was subjected to column chromatography, and dinaphthodiospyrol S was isolated. Then XO inhibitory properties were assessed using a spectrophotometry microplate reader. DMSO was taken as a negative control, and allopurinol was used as a standard drug. The molecular docking study of the isolated compound to the XO active site was performed, followed by visualization and protein-ligand interaction. The defatted chloroform extract showed the highest inhibitory effect, followed by the chloroform extract and the isolated compound. The isolated compound exhibited significant inhibitory activity against XO with an IC50 value of 1.09 µM. Molecular docking studies showed that the compound strongly interacts with XO, forming hydrogen bond interactions with Arg149 and Cys113 and H-pi interactions with Cys116 and Leu147. The binding score of -7.678 kcal/mol further supported the potential of the isolated compound as an XO inhibitor. The quantum chemical procedures were used to study the electronic behavior of dinaphthodiospyrol S isolated from D. kaki. Frontier molecular orbital (FMO) analysis was performed to understand the distribution of electronic density, highest occupied molecular orbital HOMO, lowest unoccupied molecular orbital LUMO, and energy gaps. The values of HOMO, LUMO, and energy gap were found to be -6.39, -3.51 and 2.88 eV respectively. The FMO results indicated the intramolecular charge transfer. Moreover, reactivity descriptors were also determined to confirm the stability of the compound. The molecular electrostatic potential (MEP) investigation was done to analyze the electrophilic and nucleophilic sites within a molecule. The oxygen atoms in the compound exhibited negative potential, indicating that they are favorable sites for electrophilic attacks. The results indicate its potential as a therapeutic agent for related disorders. Further studies are needed to investigate this compound's in vivo efficacy and safety as a potential drug candidate.
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Affiliation(s)
- Tareq Abu-Izneid
- Pharmaceutical Sciences Department, College of Pharmacy, Al Ain University, Al Ain 64141, United Arab Emirates
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Ambar 23561, Khyber Pakhtunkhwa, Pakistan
| | - Zubair Ahmad
- Department of Chemistry, University of Swabi, Ambar 23561, Khyber Pakhtunkhwa, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan, University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Khurshid Ayub
- Department of Chemistry, COMSATS University Islamabad, Islamabad, Pakistan
| | - Naveed Muhammad
- Department of Pharmacy, Abdul Wali Khan, University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Yahya S. Al-Awthan
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71421, Saudi Arabia
- Department of Biology, Faculty of Science, Ibb University, Ibb 70270, Yemen
| | - Maria Maqbool
- Department of Chemistry, COMSATS University Islamabad, Islamabad, Pakistan
| | - Omar S. Bahattab
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71421, Saudi Arabia
| | - Hassan A. Hemeg
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Taibah University, P.O. Box 344, Al-Madinah Al-Monawra 41411, Saudi Arabia
| | - Saima Naz
- Institute of Biotechnology & Microbiology, Bacha Khan University Charsadda, Khyber Pakhtunkhwa (K.P.), Pakistan
| | - Dorota Formanowicz
- Chair and Department of Medical Chemistry and Laboratory Medicine, Poznan University of Medical Sciences, Rokietnicka 8, 60-806 Poznan, Poland
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Rauf A, Anyanwu M, Aliiri AA, Alanazi HAH, Alharbi AMA, Wadood A, Aljohani ASM, Muhammad N, Samad A, Shah SUA, Gianoncelli A, Ribaudo G. Antifungal and Antiproliferative Activity of Pistagremic Acid and Flavonoids Extracted from the Galls of Pistacia chinensis subsp. integerrima. Chem Biodivers 2024; 21:e202301815. [PMID: 38152840 DOI: 10.1002/cbdv.202301815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/19/2023] [Accepted: 12/27/2023] [Indexed: 12/29/2023]
Abstract
Pistacia chinensis subsp. integerrima (J.L. Stewart) Rech. f. is a plant known for its therapeutic applications in traditional medicine, which are related to its antimicrobial, anticancer, antioxidant, anti-inflammatory, analgesic, antidiarrheal, and muscle relaxant properties. The galls of P. chinensis are rich in triterpenes and flavonoids, and we here report the extraction of pistagremic acid (1), apigenin (2) and sakuranetin (3) from this source. The isolated compounds were tested against Aspergillus flavus, Candida albicans, Candida glabrata, Fusarium solani, Microsporum canis and Trichoderma longibrachiatum. The results highlighted the antimicrobial activity of flavonoids 2 and 3, suggesting that this class of molecules may be responsible for the effect related to the traditional use. On the other hand, when the compounds and the extract were tested for their antiproliferative activity on a panel of 4 human cancer cell lines, the triterpene pistagremic acid (1) showed a higher potential, thus demonstrating a different bioactivity profile. Structure-based docking and molecular dynamics simulations were used to help the interpretation of experimental results. Taken together, the here reported findings pave the way for the rationalization of the use of P. chinensis extracts, highlighting the contributions of the different components of galls to the observed bioactivity.
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Affiliation(s)
- Abdur Rauf
- Department of Chemistry, University of Swabi, Anbar, Khyber Pakhtunkhwa, Pakistan
| | - Margrate Anyanwu
- Department of Molecular and Translational Medicine, University of Brescia, Italy
| | - Ahmad A Aliiri
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, Saudi Arabia
- Department of Animal Resource, Ministry of Environment, Water and Agriculture, Saudi Arabia
| | - Hamdan A H Alanazi
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, Saudi Arabia
- Directorie of Markets and Slaughterhouses, Ministry of Environment, Water and Agriculture, Saudi Arabia
| | - Abdulrahman M A Alharbi
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, Saudi Arabia
- Environmental Health Department, Al-Dhahria Municipality, Ministry of Municipal Rural Affaires & Housing, Saudi Arabia
| | - Abdul Wadood
- Department of Pharmacy, Abdul Wali Khan University Mardan KPK, Pakistan
| | - Abdullah S M Aljohani
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, Saudi Arabia
| | - Naveed Muhammad
- Department of Pharmacy, Abdul Wali Khan University Mardan KPK, Pakistan
| | - Abdus Samad
- Department of Pharmacy, Abdul Wali Khan University Mardan KPK, Pakistan
| | - Syed Uzair Ali Shah
- Department of Pharmacy, University of Swabi, Anbar, Khyber Pakhtunkhwa, Pakistan
| | | | - Giovanni Ribaudo
- Department of Molecular and Translational Medicine, University of Brescia, Italy
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10
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Awan ZA, Khan HA, Jamal A, Shams S, Zheng G, Wadood A, Shahab M, Khan MI, Kalantan AA. In silico exploration of the potential inhibitory activities of in-house and ZINC database lead compounds against alpha-glucosidase using structure-based virtual screening and molecular dynamics simulation approach. J Biomol Struct Dyn 2024:1-11. [PMID: 38294714 DOI: 10.1080/07391102.2023.2298391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/14/2023] [Indexed: 02/01/2024]
Abstract
Inhibitors of α-glucosidase have been used to treat type-2 diabetes (T2DM) by preventing the breakdown of carbohydrates into glucose and prevent enhancing glucose conversion. Structure-based virtual screening (SBVS) was used to generate novel chemical scaffold-ligand α-glucosidase inhibitors. The databases were screened against the receptor α-glucosidase using SBVS and molecular dynamics simulation (MDS) techniques in this study. Based on molecular docking studies, three and two compounds of α-glucosidase inhibitors were chosen from a commercial database (ZINC) and an In-house database for this study respectively. The mode of binding interactions of the selected compounds later predicted their α-glucosidase inhibitory potential. Finally, one out of three lead compound from ZINC and one out of two lead compound from In-house database were shortlisted based on interactions. Furthermore, MDS and post-MDS strategies were used to refine and validate the shortlisted leads along with the reference acarbose/α-glucosidase. The Hits' ability to inhibit α-glucosidase was predicted by SBVS, indicating that these compounds have good inhibitory activities. The lead inhibitor's structure may serve as templates for the design of novel inhibitors, and in vitro testing to confirm their anti-diabetic potential is necessary. These insights can help rationally design new effective anti-diabetic drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zuhier A Awan
- Department of Clinical Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Mohamed Saeed Tamer Chair for Pharmaceutical Industries, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Excellence for Drug Research and Pharmaceutical Industries, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Haider Ali Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Alam Jamal
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sulaiman Shams
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Guojun Zheng
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Shahab
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Mohammad Imran Khan
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre of Artificial Intelligence for Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulaziz A Kalantan
- Department of Biochemistry, Faculty of Science, Cancer and Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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11
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Muhammad N, Khan R, Seraj F, Khan A, Ullah U, Wadood A, Ajmal A, Uzma, Ali B, Khan KM, Ain Nawaz NU, AlMasoud N, Alomar TS, Rauf A. In vivo analgesic, anti-inflammatory and molecular docking studies of S-naproxen derivatives. Heliyon 2024; 10:e24267. [PMID: 38304837 PMCID: PMC10831619 DOI: 10.1016/j.heliyon.2024.e24267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/27/2023] [Accepted: 01/05/2024] [Indexed: 02/03/2024] Open
Abstract
In the current studies two naproxen derivatives (NPD) were evaluated for analgesic and anti-inflammatory properties. The acetic acid and hot plate animal models were used to screen the compounds for analgesic potential. While the anti-inflammatory potential was evaluated through animal paw edema, induced by several inflammatory mediators (carrageenan, bradykinin, and prostaglandin E2), the xylene-induced ear edema was also used as an inflammatory model. Both NPDs showed significant (p < 0.001) antinociceptive effects in the acetic acid-induced writhing paradigm. In the case of the hot plate, the NPD 1 at the tested dose of 5 mg/kg enhanced the latency time after 60 min of injection, which remained significant (p < 0.001) up to the end of the experiment duration. The maximum percent inhibition of NPD 1 was 87.53. The naloxone injection significantly lowered the latency time of NPD 1 as compared to NPD 2. Regarding the anti-inflammatory effect, both of the tested NPDs demonstrated a significant reduction in paw edema against various inflammatory mediators, as mentioned above; however, the anti-inflammatory effect of NPD 1 was better. The maximal percent inhibition by NPD 1 and 2 was 43.24 (after 60 min) and 45.93 (after 90 min). A considerable effect also resulted from xylene-induced ere edema. Further, a molecular docking study was carried out to investigate the binding modes of the NPD. The docking analysis revealed that the NPD significantly interacted with the COX2 enzyme. Furthermore, molecular dynamics simulation was carried out for the docked complexes. The MD simulation analysis revealed the high stability of the two naproxen derivatives.
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Affiliation(s)
- Naveed Muhammad
- Department of Pharmacy, Abdul Wali Khan University, Mardan, Pakhtunkhwa, Pakistan
| | - Rashid Khan
- Department of Pharmacy, University of Swabi, Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Faiza Seraj
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Abad Khan
- Department of Pharmacy, University of Swabi, Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Ubaid Ullah
- Department of Pharmacy, University of Swabi, Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakhtunkhwa, Pakistan
| | - Amar Ajmal
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakhtunkhwa, Pakistan
| | - Uzma
- Department of Pharmacy, Abdul Wali Khan University, Mardan, Pakhtunkhwa, Pakistan
| | - Basharat Ali
- Sulaiman Bin Abdullah Aba Al-Khail (SA)- Center for Interdisciplinary Research in Basic Science, International Islamic University, Islamabad, Pakistan
| | - Khalid Mohammed Khan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
- Pakistan Academy of Science, 3-Constitution Avenue, G-5/2, Islamabad, 44000, Pakistan
| | - Noor Ul Ain Nawaz
- Department of Pharmacy, City University of Science and Information Technology Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Najla AlMasoud
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84427, Riyadh, 11671, Saudi Arabia
| | - Taghrid S. Alomar
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84427, Riyadh, 11671, Saudi Arabia
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Swabi, 23430, Pakistan
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12
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Khan M, Ahad G, Alam A, Ullah S, Khan A, Kanwal, Salar U, Wadood A, Ajmal A, Khan KM, Perveen S, Uddin J, Al-Harrasi A. Synthesis of new bis(dimethylamino)benzophenone hydrazone for diabetic management: In-vitro and in-silico approach. Heliyon 2024; 10:e23323. [PMID: 38163112 PMCID: PMC10757017 DOI: 10.1016/j.heliyon.2023.e23323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024] Open
Abstract
Inhibiting α-glucosidase is a reliable method for reducing blood sugar levels in diabetic individuals. Bis(dimethylamino)benzophenone derivatives 1-27 were synthesized from bis(dimethylamino)benzophenone via two-step reaction. Different spectroscopic techniques, including EI-MS and 1H NMR, were employed to characterize all synthetic derivatives. The elemental composition of synthetic compounds was confirmed by elemental analysis and results were found in agreement with the calculated values. The synthetic compounds 1-27 were evaluated for α-glucosidase inhibitory activity, except five compounds all derivatives showed good to moderate inhibitory potential in the range of IC50 = 0.28 ± 2.65 - 0.94 ± 2.20 μM. Among them, the most active compounds were 5, 8, 9, and 12 with IC50 values of 0.29 ± 4.63, 0.29 ± 0.93, 0.28 ± 3.65, and 0.28 ± 2.65, respectively. Furthermore, all these compounds were found to be non-toxic on human fibroblast cell lines (BJ cell lines). Kinetics study of compounds 8 and 9 revealed competitive type of inhibition with Ki values 2.79 ± 0.011 and 3.64 ± 0.012 μM, respectively. The binding interactions of synthetic compounds were also confirmed through molecular docking studies that indicated that compounds fit well in the active site of enzyme. Furthermore, a total of 30ns MD simulation was carried out for the most potent complexes of the series. The molecular dynamics study revealed that compound-8 and compound-12 were stable during the MD simulation.
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Affiliation(s)
- Momin Khan
- Department of Chemistry, Abdul Wali Khan University, Mardan, 23200, Pakistan
| | - Ghulam Ahad
- Department of Chemistry, Abdul Wali Khan University, Mardan, 23200, Pakistan
| | - Aftab Alam
- Department of Chemistry, University of Malakand, Chakdara, Lower Dir, 18800, Pakistan
| | - Saeed Ullah
- Natural & Medical Sciences Research Center, University of Nizwa, P.O Box 33, Postal Code 616, Birkat Al Mauz, Nizwa, Oman
| | - Ajmal Khan
- Natural & Medical Sciences Research Center, University of Nizwa, P.O Box 33, Postal Code 616, Birkat Al Mauz, Nizwa, Oman
| | - Kanwal
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Uzma Salar
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan, 23200, Pakistan
| | - Amar Ajmal
- Department of Biochemistry, Abdul Wali Khan University, Mardan, 23200, Pakistan
| | - Khalid Mohammed Khan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
- Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 31441, Dammam, Saudi Arabia
| | - Shahnaz Perveen
- PCSIR Laboratories Complex, Karachi, Shahrah-e-Dr. Salimuzzaman Siddiqui, Karachi, 75280, Pakistan
| | - Jalal Uddin
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, 62529, Kingdom of Saudi Arabia
| | - Ahmed Al-Harrasi
- Natural & Medical Sciences Research Center, University of Nizwa, P.O Box 33, Postal Code 616, Birkat Al Mauz, Nizwa, Oman
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13
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Ahmad K, Batool SA, Farooq MT, Minhas B, Manzur J, Yasir M, Wadood A, Avcu E, Ur Rehman MA. Corrosion, surface, and tribological behavior of electrophoretically deposited polyether ether ketone coatings on 316L stainless steel for orthopedic applications. J Mech Behav Biomed Mater 2023; 148:106188. [PMID: 37856992 DOI: 10.1016/j.jmbbm.2023.106188] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/21/2023]
Abstract
Electrophoretic deposition (EPD) of polyether ether ketone (PEEK) coatings on metallic implants has recently attracted a great deal of interest; however, further investigation into their corrosion, surface, and tribological properties is required for their clinical application. Using Potentiodynamic polarization and Mott-Schottky analysis of PEEK coatings, we analyzed the electrochemical corrosion behavior of electrophoretically deposited PEEK coatings on 316L stainless steel (SS) substrates. In addition, the tribological behavior of the coatings was determined through pin-on-disc and scratch testing. Initially, the EPD parameters were optimized using a Taguchi Design of Experiment (DoE) approach. The coatings exhibited irregular shaped grains along with ∼66 μm of thickness. Fourier transform infrared spectroscopy confirmed the presence of functional groups ascribed with PEEK. The coatings were moderately hydrophobic and had an average roughness of ∼2 μm. The corrosion studies demonstrated promising features of current density and corrosion potential, indicating that corrosion resistance significantly improves with PEEK coating. Electrochemical impedance spectroscopy also confirmed the corrosion resistance of PEEK coating. The coatings exhibited a slightly lower wear resistance than SS samples, but still possessed adequate wear and scratch resistance for biomedical applications. The current study confirmed that the PEEK coatings on metallic implants is effective for orthopedic applications where corrosion and tribology are major concerns.
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Affiliation(s)
- Khalil Ahmad
- Department of Materials Science & Engineering, Institute of Space Technology Islamabad, Islamabad Highway, Islamabad, 44000, Pakistan
| | - Syeda Ammara Batool
- Department of Materials Science & Engineering, Institute of Space Technology Islamabad, Islamabad Highway, Islamabad, 44000, Pakistan
| | - Muhammad Tahir Farooq
- Department of Materials Science & Engineering, Institute of Space Technology Islamabad, Islamabad Highway, Islamabad, 44000, Pakistan
| | - Badar Minhas
- Department of Materials Science & Engineering, Institute of Space Technology Islamabad, Islamabad Highway, Islamabad, 44000, Pakistan
| | - Jawad Manzur
- Department of Materials Science & Engineering, Institute of Space Technology Islamabad, Islamabad Highway, Islamabad, 44000, Pakistan
| | - Muhammad Yasir
- Department of Materials Science & Engineering, Institute of Space Technology Islamabad, Islamabad Highway, Islamabad, 44000, Pakistan.
| | - Abdul Wadood
- Department of Materials Science & Engineering, Institute of Space Technology Islamabad, Islamabad Highway, Islamabad, 44000, Pakistan
| | - Egemen Avcu
- Department of Mechanical Engineering, Kocaeli University, Kocaeli, 41001, Turkey; Ford Otosan Ihsaniye Automotive Vocational School, Kocaeli University, Kocaeli, 41650, Turkey
| | - Muhammad Atiq Ur Rehman
- Department of Materials Science & Engineering, Institute of Space Technology Islamabad, Islamabad Highway, Islamabad, 44000, Pakistan.
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14
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Ahmed S, Hussain R, Khan A, Batool SA, Mughal A, Nawaz MH, Irfan M, Wadood A, Avcu E, Rehman MAU. 3D Printing Assisted Fabrication of Copper-Silver Mesoporous Bioactive Glass Nanoparticles Reinforced Sodium Alginate/Poly(vinyl alcohol) Based Composite Scaffolds: Designed for Skin Tissue Engineering. ACS Appl Bio Mater 2023; 6:5052-5066. [PMID: 37857344 DOI: 10.1021/acsabm.3c00726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Additive manufacturing (also known as 3D printing) is a promising method for producing patient-specific implants. In the present study, sodium alginate (Na-ALG)/poly(vinyl alcohol) (PVA) polymer blends of varying ratios (1:0, 3:1, 1:1, and 1:3) were used to produce tailored-designed skin scaffolds using a 3D bioprinter. Samples of skin scaffolds were printed at 20 layers with a layer height of 0.15 mm using a needle with an inner diameter of 330 μm while maintaining the extrusion speed, extrusion width, and fill density at 10 mm/s, 0.2 mm, and 85%, respectively. The Na-ALG/PVA blend with a 3:1 ratio showed the best printability due to its good viscosity and minimal nozzle leakage, allowing for the fabrication of skin scaffolds with high fidelity and the desired morphological characteristics. Then, copper-silver doped mesoporous bioactive glass nanoparticles (Cu-Ag MBGNs) were incorporated into the Na-ALG/PVA blend (which had already been prepared by using a Na-ALG:PVA ratio of 3:1) in order to obtain therapeutic (angiogenic and antibacterial) effects. The fabricated Na-ALG/PVA/Cu-Ag MBGNs biocomposite scaffolds with dimensions of 20 mm× 20 × 3 mm3 and pore size of 400 ± 60 μm exhibited a promising fidelity. The presence of chemical bonds attributed to Na-ALG, PVA, and Cu-Ag MBGNs and the uniform distribution of Na, C, and O elements within the microstructure of the scaffolds were confirmed by EDX, SEM, and FTIR analyses. The scaffolds were hydrophilic and exhibited proper swelling and degradation behavior for skin tissue engineering. According to the inhibition halo test, the scaffolds exhibited strong antibacterial activity against Staphylococcus aureus and Escherichia coli. The cytocompatibility to human-derived fibroblast cells was confirmed by the WST-8 assay and in vivo Chorioallantoic Membrane Assay. In addition, Na-ALG/PVA/Cu-Ag MBGNs showed angiogenic potential, exhibiting favorable wound healing properties.
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Affiliation(s)
- Sheraz Ahmed
- Department of Materials Science & Engineering, Institute of Space Technology, Islamabad 44000, Pakistan
| | - Rabia Hussain
- Department of Materials Science & Engineering, Institute of Space Technology, Islamabad 44000, Pakistan
| | - Ahmad Khan
- Department of Materials Science & Engineering, Institute of Space Technology, Islamabad 44000, Pakistan
| | - Syeda Ammara Batool
- Department of Materials Science & Engineering, Institute of Space Technology, Islamabad 44000, Pakistan
| | - Awab Mughal
- Department of Materials Science & Engineering, Institute of Space Technology, Islamabad 44000, Pakistan
| | - Muhammad Haseeb Nawaz
- Department of Materials Science & Engineering, Institute of Space Technology, Islamabad 44000, Pakistan
| | - Muhammad Irfan
- School of Chemical and Materials Engineering, National University of Science & Technology, Islamabad 44000, Pakistan
| | - Abdul Wadood
- Department of Materials Science & Engineering, Institute of Space Technology, Islamabad 44000, Pakistan
| | - Egemen Avcu
- Department of Mechanical Engineering, Institute of Natural and Applied Sciences, Kocaeli University, Kocaeli 41001, Turkey
- Department of Machine and Metal Technologies, Ford Otosan Ihsaniye Automotive Vocational School, Kocaeli University, Kocaeli 41650, Turkey
| | - Muhammad Atiq Ur Rehman
- Department of Materials Science & Engineering, Institute of Space Technology, Islamabad 44000, Pakistan
- Centre of Excellence in Biomaterials and Tissue Engineering, Government College University, Lahore, 54000, Pakistan
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15
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Rafiq H, Hu J, Hakami MA, Hazazi A, Alamri MA, Alkhatabi HA, Mahmood A, Alotaibi BS, Wadood A, Huang X. Identification of novel STAT3 inhibitors for liver fibrosis, using pharmacophore-based virtual screening, molecular docking, and biomolecular dynamics simulations. Sci Rep 2023; 13:20147. [PMID: 37978263 PMCID: PMC10656421 DOI: 10.1038/s41598-023-46193-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/29/2023] [Indexed: 11/19/2023] Open
Abstract
The signal transducer and activator of transcription 3 (STAT3) plays a fundamental role in the growth and regulation of cellular life. Activation and over-expression of STAT3 have been implicated in many cancers including solid blood tumors and other diseases such as liver fibrosis and rheumatoid arthritis. Therefore, STAT3 inhibitors are be coming a growing and interesting area of pharmacological research. Consequently, the aim of this study is to design novel inhibitors of STAT3-SH3 computationally for the reduction of liver fibrosis. Herein, we performed Pharmacophore-based virtual screening of databases including more than 19,481 commercially available compounds and in-house compounds. The hits obtained from virtual screening were further docked with the STAT3 receptor. The hits were further ranked on the basis of docking score and binding interaction with the active site of STAT3. ADMET properties of the screened compounds were calculated and filtered based on drug-likeness criteria. Finally, the top five drug-like hit compounds were selected and subjected to molecular dynamic simulation. The stability of each drug-like hit in complex with STAT3 was determined by computing their RMSD, RMSF, Rg, and DCCM analyses. Among all the compounds Sa32 revealed a good docking score, interactions, and stability during the entire simulation procedure. As compared to the Reference compound, the drug-like hit compound Sa32 showed good docking scores, interaction, stability, and binding energy. Therefore, we identified Sa32 as the best small molecule potent inhibitor for STAT3 that will be helpful in the future for the treatment of liver fibrosis.
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Affiliation(s)
- Huma Rafiq
- Department of Biochemistry, Computational Medicinal Chemistry Laboratory, Abdul Wali Khan University, Mardan, Pakistan
| | - Junjian Hu
- Department of Central Laboratory, Dongguan Songshan Lake Central Hospital, Dongguan, China
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Ali Hazazi
- Department of Pathology and Laboratory Medicine, Security Forces Hospital Program, Riyadh, Saudi Arabia
| | - Mubarak A Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, 11942, Al-Kharj, Saudi Arabia
| | - Hind A Alkhatabi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Arif Mahmood
- Center for Medical Genetics and Human Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Bader S Alotaibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Abdul Wadood
- Department of Biochemistry, Computational Medicinal Chemistry Laboratory, Abdul Wali Khan University, Mardan, Pakistan.
| | - Xiaoyun Huang
- Department of Neurology, Dongguan Songshan Lake Central Hospital, Dongguan, China.
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16
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Islam MS, Al-Majid AM, Haukka M, Parveen Z, Ravaiz N, Wadood A, Rehman AU, Ríos-Gutiérrez M, Domingo LR, Barakat A. A novel alpha-amylase inhibitor-based spirooxindole-pyrrolidine-clubbed thiochromene-pyrzaole pharmacophores: Unveiling the [3+2] cycloaddition reaction by molecular electron density theory. Chem Biol Drug Des 2023; 102:972-995. [PMID: 37563748 DOI: 10.1111/cbdd.14299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/29/2023] [Accepted: 07/14/2023] [Indexed: 08/12/2023]
Abstract
A novel spirooxindole-pyrrolidine clubbed thiochromene and pyrazole motifs were synthesized by [3+2] cycloaddition (32CA) reactions in one step process starting from the ethylene-based thiochromene and pyrazole scaffolds with the secondary amino-acids and substituted isatins in high yield. The 32CA reaction of AY 10 with ethylene derivative 6 has also been studied with Molecular Electron Density Theory. The high nucleophilic character of AY 10, N = 4.39 eV, allows explaining that the most favorable TS-on is 13.9 kcal mol-1 below the separated reagent. This 32CA, which takes place through a non-concerted one-step mechanism, presents a total ortho regio- and endo stereoselectivity, which is controlled by the formation of two intramolecular H… O hydrogen bonds. The design of spirooxindole-pyrrolidines engrafted thiochromene and pyrazole was tested for alpha-amylase inhibition and show a high efficacy in nanoscale range of reactivity. The key interaction between the most active hybrids and the receptor was studied by molecular docking. The physiochemical properties of the designed spirooxindole-pyrrolidines were carried out by in silico ADMET prediction. The newly synthesized most potent hybrid could be considered as a lead compound for drug discovery development for type 2 diabetes mellitus (T2DM).
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Affiliation(s)
| | | | - Matti Haukka
- Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland
| | - Zahida Parveen
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Nabeela Ravaiz
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Ashfaq Ur Rehman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Mar Ríos-Gutiérrez
- Department of Organic Chemistry, University of Valencia, Valencia, Spain
| | - Luis R Domingo
- Department of Organic Chemistry, University of Valencia, Valencia, Spain
| | - Assem Barakat
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
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17
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Homoud ZA, Taha M, Rahim F, Iqbal N, Nawaz M, Farooq RK, Wadood A, Alomari M, Islam I, Algheribe S, Rehman AU, Khan KM, Uddin N. Synthesis of indole derivatives as Alzheimer inhibitors and their molecular docking study. J Biomol Struct Dyn 2023; 41:9865-9878. [PMID: 36404604 DOI: 10.1080/07391102.2022.2148126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022]
Abstract
Acetylcholinesterase prevails in the healthy brain, with butyrylcholinesterase reflected to play a minor role in regulating brain acetylcholine (ACh) levels. However, BuChE activity gradually increases in patients with (AD), while AChE activity remains unaffected or decays. Both enzymes therefore represent legitimate therapeutic targets for ameliorating the cholinergic deficit considered to be responsible for the declines in cognitive, behavioural, and global functioning characteristic of AD. Current study described the synthesis of indole-based sulfonamide derivatives (1-23) and their biological activity. Synthesis of these scaffolds were achieved by mixing chloro-substituted indole bearing amine group with various substituted benzene sulfonyl chloride in pyridine, under refluxed condition to obtained desired products. All products were then evaluated for AchE and BuchE inhibitory potential compare with positive Donepezil as standard drug for both AchE and BchE having IC50 = 0.016 ± 0.12 and 0.30 ± 0.010 μM respectively. In this regard analog 9 was found potent having IC50 value 0.15 ± 0.050 μM and 0.20 ± 0.10 for both AchE and BuChE respectively. All other derivatives also found with better potential. All compounds were characterized by various techniques such as 1H, 13C-NMR and HREI-MS. In addition, biological activity was maintained to explore the bioactive nature of scaffolds and their protein-ligand interaction (PLI) was checked through molecular docking study.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zahra Abdulkarim Homoud
- Mawhiba Research Enrichment Program-2021, King Abdulaziz and His Companions Foundation for Giftedness and Creativity, Riyadh, Saudi Arabia
- Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Muhammad Taha
- Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Fazal Rahim
- Department of Chemistry, Hazara University, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - Naveed Iqbal
- Department of Chemistry, University of Poonch, Rawalakot, AJK, Pakistan
| | - Muhammad Nawaz
- Department of Nano-Medicine Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Rai Khalid Farooq
- Department of Neuroscience Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Munther Alomari
- Medical Laboratory Science, Faculty of Health Science, Abu Dhabi Women's College, Higher Colleges of Technology, Abu Dhabi, UAE
| | - Imadul Islam
- Medical Research Core Facility and Platforms, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs, Riyadh, Kingdom of Saudi Arabia
| | - Shatha Algheribe
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Ashfaq Ur Rehman
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Khalid Mohammed Khan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Nizam Uddin
- Department of Chemistry, University of Karachi, Karachi, Pakistan
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18
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Habib Ullah S, Khan A, Ahsan Halim S, Khan R, Pan XD, Ullah R, Wadood A, Khalid A, Abdalla AN, Khogeer S, Al-Harrasi A. Blocking the major inflammatory pathways by newly synthesized thiadiazine derivatives via in-vivo, in-vitro and in-silico mechanism. Bioorg Chem 2023; 140:106760. [PMID: 37647806 DOI: 10.1016/j.bioorg.2023.106760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/18/2023] [Accepted: 07/30/2023] [Indexed: 09/01/2023]
Abstract
A series of new thiadiazine derivatives including 2-(5-alkyl/aryl-6-thioxo-1,3,5-thiadiazinan-3-yl) propanoic acids (a) and 4-methyl-2-(5-alkyl/aryl-6-thioxo-1,3,5-thiadiazinan-3-yl) pentanoic acids (b) were synthesized by reacting primary alkyl/aryl amines with CS2, followed by reaction with formaldehyde and amino acids. The chemical structures of synthesized compounds were confirmed by 13C- NMR and 1H- NMR techniques. The inhibitory potential of major inflammatory enzymes, COX-2 and 5-LOX was examined. Moreover, anti-nociceptive and anti-inflammatory activities were evaluated in the in vivo thermally induced nociceptive, and carrageenan induced paw edema models in mice. The in-vitro results reflect that these compounds exhibited concentration dependent inhibition of COX-2 and 5-LOX. The tested compounds at 50 mg/kg showed significant effect on thermally induced pain, and reduced latency time (seconds) as compared to the vehicle treated animals. Moreover, tested compounds exhibited percent inhibition of paw edema in the carrageenan induced paw edema model in mice. Furthermore, the binding modes of the most active COX-2 and 5-LOX inhibitors were determined through computational methods. The computational study reflects that the docked compounds have high binding affinities for COX-2 and 5-LOX enzymes, which leads to inhibition of these enzymes.
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Affiliation(s)
- Syed Habib Ullah
- Institute of Chemical Sciences, University of Peshawar, Peshawar-25120, Pakistan
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Rasool Khan
- Institute of Chemical Sciences, University of Peshawar, Peshawar-25120, Pakistan.
| | - Xian-Dao Pan
- Institute of Material Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
| | - Rahim Ullah
- Department of Pharmacy, Faculty of Life Sciences,Sarhad University of Science and Information Technology, Peshawar, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Pakistan
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box: 114, Jazan 45142, Saudi Arabia
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Soud Khogeer
- Department of Biochemistry, Faculty of Medicine, Umm Alqura University, Makka 21955, Saudi Arabia
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman.
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Viola, Muhammad N, Noor A, Sirajuddin M, Kubicki M, Rahim S, Samad A, Shujah S, Wadood A, Ali S. Designing and Exploration of the Biological Potentials of Novel Centrosymmetric Heteroleptic Copper(II) Carboxylates. Pharmaceuticals (Basel) 2023; 16:1462. [PMID: 37895933 PMCID: PMC10610105 DOI: 10.3390/ph16101462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Copper(II) complexes with a general formula [Cu2(3,4-F2C6H3CH2COO)4(L)2], where L = 2-methylpyridine (1) and 3-methylpyridine (2), are reported here. The FTIR spectra of the complexes confirmed the bridging bidentate coordination mode of the carboxylate ligand. The low (475 and 449 cm-1) and strong (727 & 725 cm-1) intensity bands in the FTIR spectra, due to Cu-N stretches and pyridyl ring vibrations, confirmed coordination of the 2-/3-methyl pyridine co-ligands in complexes 1 and 2, respectively. A binuclear paddlewheel structural arrangement with a square pyramidal geometry was confirmed for copper atoms in the complexes via single-crystal X-ray analysis. The DPPH, •OH radical, and α-amylase enzyme inhibition assays showed higher activities for the complexes than for the free ligand acid. The binding constant (Kb = 1.32 × 105 for 1 and 5.33 × 105 for 2) calculated via UV-VIS absorption measurements and docking scores (-6.59 for 1 and -7.43 for 2) calculated via molecular docking showed higher SS-DNA binding potential for 2 compared to 1. Viscosity measurement also reflected higher DNA binding ability for 2 than 1. Both complexes 1 and 2 (docking scores of -7.43 and -6.95, respectively) were found to be more active inhibitors than the free ligand acid (docking score of -5.5159) against the target α-amylase protein. This in silico study has shown that the herein reported compounds follow the rules of drug-likeness and exhibit good potential for bioavailability.
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Affiliation(s)
- Viola
- Department of Chemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan; (V.); (S.R.)
| | - Niaz Muhammad
- Department of Chemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan; (V.); (S.R.)
| | - Awal Noor
- Department of Basic Sciences, Preparatory Year Deanship, King Faisal University, Al-Hassa 31982, Saudi Arabia
| | - Muhammad Sirajuddin
- Department of Chemistry, University of Science and Technology Bannu, Bannu 28100, Pakistan;
| | - Maciej Kubicki
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61-614 Poznań, Poland;
| | - Shahnaz Rahim
- Department of Chemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan; (V.); (S.R.)
| | - Abdus Samad
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan; (A.S.); (A.W.)
| | - Shaukat Shujah
- Department of Chemistry, Kohat University of Science & Technology, Kohat 26000, Pakistan;
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan; (A.S.); (A.W.)
| | - Saqib Ali
- Department of Chemistry, Quaid-I-Azam University Islamabad, Islamabad 45320, Pakistan;
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Ajmal A, Ali Y, Khan A, Wadood A, Rehman AU. Identification of novel peptide inhibitors for the KRas-G12C variant to prevent oncogenic signaling. J Biomol Struct Dyn 2023; 41:8866-8875. [PMID: 36300526 DOI: 10.1080/07391102.2022.2138550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/15/2022] [Indexed: 10/31/2022]
Abstract
Kirsten rat sarcoma viral oncogene homolog (KRas) activating mutations are common in solid tumors, accounting for 90%, 45%, and 35% of pancreatic, colorectal, and lung cancers (LC), respectively. Each year, nearly 150k new cases (both men and women) of KRas-mutated malignancies are reported in the United States. NSCLC (non-small cell lung cancer) accounts for 80% of all LC cases. KRas mutations are found in 15% to 25% of NSCLC patients. The main cause of NSCLC is the KRas-G12C mutation. The drugs Sotorasib and Adagrasib were recently developed to treat advanced NSCLC caused by the KRas-G12C mutation. Most patients do not respond to KRas-G12C inhibitors due to cellular, molecular, and genetic resistance. Because of their safety, efficacy, and selectivity, peptide inhibitors have the potential to treat newly developing KRas mutations. Based on the KRas mutations, peptide inhibitors that are highly selective and specific to individual lung cancers can be rationally designed. The current study uses an alanine and residue scanning approach to design peptide inhibitors for KRas-G12C based on the known peptide. Our findings show that substitution of F3K, G11T, L8C, T14C, K13D, G11S, and G11P considerably enhances the binding affinity of the novel peptides, whereas F3K, G11T, L8C, and T14C peptides have higher stability and favorable binding to the altered peptides. Overall, our study paves the road for the development of potential therapeutic peptidomimetics that target the KRas-G12C complex and may inhibit the KRas and SOS complex from interacting.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amar Ajmal
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Yasir Ali
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Sultanate of Oman
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Ashfaq Ur Rehman
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
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21
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Khan H, Waqas M, Khurshid B, Ullah N, Khalid A, Abdalla AN, Alamri MA, Wadood A. Investigating the role of Sterol C24-Methyl transferase mutation on drug resistance in leishmaniasis and identifying potential inhibitors. J Biomol Struct Dyn 2023:1-14. [PMID: 37723868 DOI: 10.1080/07391102.2023.2256879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 09/02/2023] [Indexed: 09/20/2023]
Abstract
Leishmaniasis is a fatal disease caused by the leishmania parasite. For the survival of the leishmania parasite, Sterol C24-Methyl Transferase (SMT) is essential which is an enzyme of the ergosterol pathway. SMT protein mutation is responsible for Amphotericin-B drug resistance in Leishmania, which is the main treatment for visceral leishmaniasis. Amphotericin-B resistance is caused by three mutated residues V131I, V321I and F72C. The underlying mechanisms and structural changes in SMT enzymes responsible for resistance due to mutation are still not well understood. In the current study, the potential mechanism of resistance due to these mutations and the structure variation of wild and mutant SMT proteins were investigated through molecular dynamics simulations and molecular docking analysis. The results showed that AmB established strong bonding interaction with wild SMT as compare to mutants SMT. The binding energy calculation showed that binding energy of AmB with mutants SMT increases as compare to the wild SMT. Further structural based virtual screening was carried out to design potential inhibitors for the mutant SMT. On the basis of structural-based virtual screening four inhibitors (SANC01057, SANC00882, SANC00414, SANC01047) were computationally identified as potential mutant SMT (F72C) inhibitors. This work provides valuable information for improved management of drug resistant Leishmaniasis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Huma Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Muhammad Waqas
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat Al-Mouz Nizwa, Oman
| | - Beenish Khurshid
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Nazif Ullah
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, Jazan, Saudi Arabia
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mubarak A Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
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22
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Shahab M, Al-Madhagi H, Zheng G, Zeb A, Alasmari AF, Alharbi M, Alasmari F, Khan MQ, Khan M, Wadood A. Structure based virtual screening and molecular simulation study of FDA-approved drugs to inhibit human HDAC6 and VISTA as dual cancer immunotherapy. Sci Rep 2023; 13:14466. [PMID: 37660065 PMCID: PMC10475047 DOI: 10.1038/s41598-023-41325-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/24/2023] [Indexed: 09/04/2023] Open
Abstract
Cancer immunotherapy has significantly contributed to the treatment of various types of cancers mainly by targeting immune checkpoint inhibitors (ICI). Among them, V-domain immunoglobulin suppressor of T cell activation (VISTA) has been explored as a promising therapeutic target. Besides, histone deacetylase 6 (HDAC6) has been demonstrated to be efficacious target for several cancers. The current theoretical work was performed to explore the virtual repurposing of the FDA-approved drugs as inhibitors against these two (VISTA and HDAC6) cancers therapeutic targets. The crystal structure of the two proteins were downloaded from PDB and subjected to virtual screening by DrugRep webserver while using FDA-approved drugs library as ligands database. Our study revealed that Oxymorphone and Bexarotene are the top-ranked inhibitors of VISTA and HDAC6, respectively. The docking score of Bexarotene was predicted as - 10 kcal/mol while the docking score of Oxymorphone was predicted as - 6.2 kcal/mol. Furthermore, a total of 100 ns MD simulation revealed that the two drugs Oxymorphone and Bexarotene formed stable complexes with VISTA and HDAC6 drug targets. As compared to the standard drug the two drugs Oxymorphone and Bexarotene revealed great stability during the whole 100 ns MD simulation. The binding free energy calculation further supported the Root Mean Square Deviation (RMSD) result which stated that as compared to the ref/HDAC6 (- 18.0253 ± 2.6218) the binding free energy score of the Bexarotene/HDAC6 was good (- 51.9698 ± 3.1572 kcal/mol). The binding free energy score of Oxymorphone/VISTA and Ref/VISTA were calculated as - 36.8323 ± 3.4565, and - 21.5611 ± 4.8581 respectively. In conclusion, the two drugs deserve further consideration as cancer treatment option.
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Affiliation(s)
- Muhammad Shahab
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | | | - Guojun Zheng
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Amir Zeb
- Department of Natural and Basic Science, Faculty of Science and Engineering, University of Turbat, Turbat, 92600, Pakistan
| | - Abdullah Fayez Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Fawaz Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Muhammad Qayash Khan
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Momin Khan
- Department of Chemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan.
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23
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Ghufran M, Rehman AU, Ayaz M, Ul-Haq Z, Uddin R, Azam SS, Wadood A. New lead compounds identification against KRas mediated cancers through pharmacophore-based virtual screening and in vitro assays. J Biomol Struct Dyn 2023; 41:8053-8067. [PMID: 36184737 DOI: 10.1080/07391102.2022.2128878] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/20/2022] [Indexed: 10/07/2022]
Abstract
Cancer remains the leading cause of mortality and morbidity in the world, with 19.3 million new diagnoses and 10.1 million deaths in 2020. Cancer is caused due to mutations in proto-oncogenes and tumor-suppressor genes. Genetic analyses found that Ras (Rat sarcoma) is one of the most deregulated oncogenes in human cancers. The Ras oncogene family members including NRas (Neuroblastoma ras viral oncogene homolog), HRas (Harvey rat sarcoma) and KRas are involved in different types of human cancers. The mutant KRas is considered as the most frequent oncogene implicated in the development of lung, pancreatic and colon cancers. However, there is no efficient clinical drug even though it has been identified as an oncogene for 30 years. Therefore there is an emerging need to develop potent, new anticancer drugs. In this study, computer-aided drug designing approaches as well as experimental methods were employed to find new and potential anti-cancer drugs. The pharmacophore model was developed from an already known FDA approved anti-cancer drug Bortezomib using the software MOE. The validated pharmacophore model was then used to screen the in-house and commercially available databases. The pharmacophore-based virtual screening resulted in 26 and 86 hits from in-house and commercial databases respectively. Finally, 6/13 (in-house database) and 24/64 hits (commercial databases) were selected with different scaffolds having good interactions with the significant active residues of KRasG12D protein that were predicted as potent lead compounds. Finally, the results of pharmacophore-based virtual screening were further validated by molecular dynamics simulation analysis. The 6 hits of the in-house database were further evaluated experimentally. The experimental results showed that these compounds have good anti-cancer activity which validate the protocol of our in silico studies. KRasG12D protein is a very important anti-cancer target and potent inhibitors for this target are still not available, so small lead compound inhibitors were identified to inhibit the activity of this protein by blocking the GTP-binding pocket.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mehreen Ghufran
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
- Department of Pathology, Medical Teaching Institution Bacha Khan Medical College (BKMC) Mardan, Mardan, Pakistan
| | - Ashfaq Ur Rehman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Muhammad Ayaz
- Department of Pharmacy, University of Malakand, Chakdara, Pakistan
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, University of Karachi, Karachi, Pakistan
| | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, University of Karachi, Karachi, Pakistan
| | - Syed Sikander Azam
- Department of Bioinformatics, Quaid-e-Azam University, Islamabad, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
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24
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Ahmad S, Khan M, Alam A, Ajmal A, Wadood A, Khan A, AlAsmari AF, Alharbi M, Alshammari A, Shakoor A. Novel flurbiprofen clubbed oxadiazole derivatives as potential urease inhibitors and their molecular docking study. RSC Adv 2023; 13:25717-25728. [PMID: 37649663 PMCID: PMC10464598 DOI: 10.1039/d3ra03841f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023] Open
Abstract
In this study, twenty eight novel oxadiazole derivatives (5-32) of the marketed available non-steroidal anti-inflammatory drug (NSAID), (S)-flurbiprofen (1), were synthesized via I2 mediated cyclo-addition reaction in better yields. The synthesized hydrazone-Schiff bases were cyclized with iodine by using potassium hydroxide as a base in DMSO solvent to obtain oxadiazole derivatives (5-32). Structures of the synthesized products were confirmed with HR-ESI-MS, 1H-NMR spectroscopy and CHN analysis. After structure confirmations all analogs were evaluated for urease (in vitro) inhibitory activity. Amongst the series, fourteen compounds 20, 26, 30, 24, 21, 16, 28, 31, 32, 7, 19, 13, 10, and 6 were found to be excellent inhibitors of urease enzyme, having IC50 values of 12 ± 0.9 to 20 ± 0.5 μM, better than the standard thiourea (IC50 = 22 ± 2.2 μM), whereas the remaining fourteen derivatives displayed good to moderate activity. The in silico study was executed to analyse the interaction between the active site of the enzyme (urease) and the produced compounds. The docking study revealed that compounds 20, 26, 30, 24, 21, 16, 28, 31, 32, 7, 19, 13, 10, and 6 had lower docking scores than the standard compound thiourea and revealed better interactions with the urease enzyme.
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Affiliation(s)
- Sajjad Ahmad
- Department of Chemistry, Abdul Wali Khan University Mardan-23200 Pakistan
| | - Momin Khan
- Department of Chemistry, Abdul Wali Khan University Mardan-23200 Pakistan
| | - Aftab Alam
- Department of Chemistry, University of Malakand Chakdara Lower Dir 18800 Pakistan
| | - Amar Ajmal
- Department of Biochemistry, Abdul Wali Khan University Mardan-23200 Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan-23200 Pakistan
| | - Azim Khan
- Laboratory for Corrosion and Protection, Institute of Metal Research, Chinese Academy of Sciences Shenyang 62 Wencui Road 110016 China
| | - Abdullah F AlAsmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University Riyadh 11451 Saudi Arabia
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University Riyadh 11451 Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University Riyadh 11451 Saudi Arabia
| | - Abdul Shakoor
- Department of Chemistry, Abdul Wali Khan University Mardan-23200 Pakistan
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25
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Muhammad N, Haq IU, Jan MS, AlOmar TS, Rauf A, Wadood A, Almasoud N, Shams S. In-vitro and in-vivo assessment of the anti-diabetic, analgesic, and anti-inflammatory potenstials of metal-based carboxylates derivative. Heliyon 2023; 9:e19160. [PMID: 37636438 PMCID: PMC10458700 DOI: 10.1016/j.heliyon.2023.e19160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 07/28/2023] [Accepted: 08/14/2023] [Indexed: 08/29/2023] Open
Abstract
In the current research work, an amide based metal carboxylate chemical ([((5-((5-(2-hydroxyethyl)-4-methylthiazol-3-ium-3-yl)methyl)-2-methylpyrimidin-4-yl)amino)bis((4-((4-methoxy-2-nitrophenyl)amino)-4-oxobutanoyl)oxy)zinc]) was identified as anti-diabetic analgesic and anti-inflammatory. The identified chemical(MT-1) was tested for acute toxicity (the MT-1 was fund safe), antidiabetic analgesic, and anti-inflammatory potentials. The in-vitro study was conducted for antidiabetic enzyme inhibition (α-amylase and α-glucosidase) and the in-vivo studies included analgesic (acetic acid-induced writing and hot plate model) and anti-inflammatory (carrageenan etc induced edema) effects. The tested compound showed 88.63% (IC50 = 3.23 μg/ml) and 89.10%(IC50 = 5.10 μg/ml) againstα-amylase and α-glucosidase respectively. A significant (p < 0.001) analgesic effect was noted by MT-1 in acetic acid-induced animal models with a percent effect of 86.00, 60.,06, and 55.29 at the tested doses of 20, 1,0, and 5 mg/kg respectively. In the case of the hot plate model, the MT-1 showed a significant (p < 0.001) effect with maximum percent prolongation in latency observed after 60 min.08, 22.2,9, and 11.61) against 20, 1,0, and 5 mg/kg. The analgesic effect in the hot plate model was significantly (p < 0.01) reversed by the injection of naloxone (0.125 mg/kg). The paw edema induced by carrageenan, histamine, bradykinin, arachidonic acid, and PGE2 was significantly antagonized with percent attenuation of 34.09, 33.57, 34.60, 34.14, and 48.04 respectively. Furthermore, to predict the interactions between the MT-1 compound and COX-2 molecular docking was carried out and the result was compared with the standard compound. The docking score of MT-1 was predicted as -6.30 while that of Diclofenac was predicted as -6.82. Both compounds made several hydrogen bond interactions with the active site of the COX-2 enzyme. The docking study revealed the potent inhibitory potential of the compound MT-1 against the COX-2 receptor.
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Affiliation(s)
- Naveed Muhammad
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Ihtesham Ul Haq
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Saeed Jan
- Department of Pharmacy, Bacha Khan University, Charsadda, Khyber Pakhtunkhwa, Pakistan, 24420, Pakistan
| | - Taghrid S. AlOmar
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84427, Riyadh 11671, Saudi Arabia
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Swabi, Anbar, Khyber Pakhtunkhwa, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Najla Almasoud
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84427, Riyadh 11671, Saudi Arabia
| | - Sulaiman Shams
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
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Farooq QUA, Aiman S, Ali Y, Shaukat Z, Ali Y, Khan A, Samad A, Wadood A, Li C. A comprehensive protein interaction map and druggability investigation prioritized dengue virus NS1 protein as promising therapeutic candidate. PLoS One 2023; 18:e0287905. [PMID: 37498862 PMCID: PMC10374080 DOI: 10.1371/journal.pone.0287905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/15/2023] [Indexed: 07/29/2023] Open
Abstract
Dengue Virus (DENV) is a serious threat to human life worldwide and is one of the most dangerous vector-borne diseases, causing thousands of deaths annually. We constructed a comprehensive PPI map of DENV with its host Homo sapiens and performed various bioinformatics analyses. We found 1195 interactions between 858 human and 10 DENV proteins. Pathway enrichment analysis was performed on the two sets of gene products, and the top 5 human proteins with the maximum number of interactions with dengue viral proteins revealed noticeable results. The non-structural protein NS1 in DENV had the maximum number of interactions with the host protein, followed by NS5 and NS3. Among the human proteins, HBA1 and UBE2I were associated with 7 viral proteins, and 3 human proteins (CSNK2A1, RRP12, and HSP90AB1) were found to interact with 6 viral proteins. Pharmacophore-based virtual screening of millions of compounds in the public databases was performed to identify potential DENV-NS1 inhibitors. The lead compounds were selected based on RMSD values, docking scores, and strong binding affinities. The top ten hit compounds were subjected to ADME profiling which identified compounds C2 (MolPort-044-180-163) and C6 (MolPort-001-742-737) as lead inhibitors against DENV-NS1. Molecular dynamics trajectory analysis and intermolecular interactions between NS1 and the ligands displayed the molecular stability of the complexes in the cellular environment. The in-silico approaches used in this study could pave the way for the development of potential specie-specific drugs and help in eliminating deadly viral infections. Therefore, experimental and clinical assays are required to validate the results of this study.
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Affiliation(s)
- Qurrat Ul Ain Farooq
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Sara Aiman
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Yasir Ali
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Zeeshan Shaukat
- Faculty of Information Technology, Beijing University of Technology, Beijing, China
| | - Yasir Ali
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Abdus Samad
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
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Alotaibi BS, Ajmal A, Hakami MA, Mahmood A, Wadood A, Hu J. New drug target identification in Vibrio vulnificus by subtractive genome analysis and their inhibitors through molecular docking and molecular dynamics simulations. Heliyon 2023; 9:e17650. [PMID: 37449110 PMCID: PMC10336522 DOI: 10.1016/j.heliyon.2023.e17650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/29/2023] [Accepted: 06/24/2023] [Indexed: 07/18/2023] Open
Abstract
Vibrio vulnificus is a rod shape, Gram-negative bacterium that causes sepsis (with a greater than 50% mortality rate), necrotizing fasciitis, gastroenteritis, skin, and soft tissue infection, wound infection, peritonitis, meningitis, pneumonia, keratitis, and arthritis. Based on pathogenicity V. vulnificus is categorized into three biotypes. Type 1 and type 3 cause diseases in humans while biotype 2 causes diseases in eel and fish. Due to indiscriminate use of antibiotics V. vulnificus has developed resistance to many antibiotics so curing is dramatically a challenge. V. vulnificus is resistant to cefazolin, streptomycin, tetracycline, aztreonam, tobramycin, cefepime, and gentamycin. Subtractive genome analysis is the most effective method for drug target identification. The method is based on the subtraction of homologous proteins from both pathogen and host. By this process set of proteins present only in the pathogen and perform essential functions in the pathogen can be identified. The entire proteome of Vibrio vulnificus strain ATCC 27562 was reduced step by step to a single protein predicted as the drug target. AlphaFold2 is one of the applications of deep learning algorithms in biomedicine and is correctly considered the game changer in the field of structural biology. Accuracy and speed are the major strength of AlphaFold2. In the PDB database, the crystal structure of the predicted drug target was not present, therefore the Colab notebook was used to predict the 3D structure by the AlphaFold2, and subsequently, the predicted model was validated. Potent inhibitors against the new target were predicted by virtual screening and molecular docking study. The most stable compound ZINC01318774 tightly attaches to the binding pocket of bisphosphoglycerate-independent phosphoglycerate mutase. The time-dependent molecular dynamics simulation revealed compound ZINC01318774 was superior as compared to the standard drug tetracycline in terms of stability. The availability of V. vulnificus strain ATCC 27562 has allowed in silico identification of drug target which will provide a base for the discovery of specific therapeutic targets against Vibrio vulnificus.
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Affiliation(s)
- Bader S. Alotaibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra Univesity, Riyadh, Saudi Arabia
| | - Amar Ajmal
- Department of Biochemistry, Computational Medicinal Chemistry Laboratory, UCSS, Abdul Wali Khan University, Mardan, Pakistan
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra Univesity, Riyadh, Saudi Arabia
| | - Arif Mahmood
- Center for Medical Genetics and Human Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Abdul Wadood
- Department of Biochemistry, Computational Medicinal Chemistry Laboratory, UCSS, Abdul Wali Khan University, Mardan, Pakistan
| | - Junjian Hu
- Department of Central Laboratory, SSL, Central Hospital of Gongguan City, Affiliated Dongguan Shilong People's Hospital of Southern Medical University, Dongguan, China
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Ahmad SU, Ali Y, Jan Z, Rasheed S, Nazir NUA, Khan A, Rukh Abbas S, Wadood A, Rehman AU. Computational screening and analysis of deleterious nsSNPs in human p14ARF ( CDKN2A gene) protein using molecular dynamic simulation approach. J Biomol Struct Dyn 2023; 41:3964-3975. [PMID: 35446184 DOI: 10.1080/07391102.2022.2059570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/24/2022] [Indexed: 10/18/2022]
Abstract
Cyclin-dependent kinase inhibitor 2 A (CDKN2A) gene belongs to the cyclin-dependent kinase family that code for two transcripts (p16INK4A and p14ARF), both work as tumor suppressors proteins. The mutation that occurs in the p14ARF protein can lead to different types of cancers. Single nucleotide polymorphisms (SNPs) are an important type of genetic alteration that can lead to different types of diseases. In this study, we applied the computational strategy on human p14ARF protein to identify the potential deleterious nsSNPs and check their impact on the structure, function, and protein stability. We applied more than ten prediction tools to screen the retrieved 288 nsSNPs, consequently extracting four deleterious nsSNPs i.e., rs139725688 (R10G), rs139725688 (R21W), rs374360796 (F23L) and rs747717236 (L124R). Homology modeling, conservation and conformational analysis of mutant models were performed to examine the divergence of these variants from the native p14ARF structure. All-atom molecular dynamics simulation revealed a significant impact of these mutations on protein stability, compactness, globularity, solvent accessibility and secondary structure elements. Protein-protein interactions indicated that p14ARF operates as a hub linking clusters of different proteins and that changes in p14ARF may result in the disassociation of numerous signal cascades. Our current study is the first survey of computational analysis on p14ARF protein that determines the association of these nsSNPs with the altered function of p14ARF protein and leads to the development of various types of cancers. This research proposes the described functional SNPs as possible targets for proteomic investigations, diagnostic procedures, and treatments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Syed Umair Ahmad
- Department of Bioinformatics, Hazara University, Mansehra, Pakistan
| | - Yasir Ali
- National Center for Bioinformatics, Quaid-i- Azam University, Islamabad, Pakistan
| | - Zainab Jan
- Department of Bioinformatics, Hazara University, Mansehra, Pakistan
| | - Salman Rasheed
- National Center for Bioinformatics, Quaid-i- Azam University, Islamabad, Pakistan
| | - Noor Ul Ain Nazir
- Atta Ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Asif Khan
- Department of Botany, Abdul Wali Khan University, Mardan, KPK, Pakistan
| | - Shah Rukh Abbas
- Atta Ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan, KPK, Pakistan
| | - Ashfaq Ur Rehman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
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Akbar S, Subhan F, Akbar A, Habib F, Shahbaz N, Ahmad A, Wadood A, Salman S. Targeting Anti-Inflammatory Pathways to Treat Diabetes-Induced Neuropathy by 6-Hydroxyflavanone. Nutrients 2023; 15:nu15112552. [PMID: 37299516 DOI: 10.3390/nu15112552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/12/2023] [Accepted: 05/14/2023] [Indexed: 06/12/2023] Open
Abstract
It is evident that inflammation and metabolic syndrome instigated by diabetes mellitus can precipitate diabetes-induced neuropathy (DIN) and pain. In order to find an effective therapeutic method for diabetes-related problems, a multi-target-directed ligand model was used. 6-Hydroxyflavanone (6-HF) carrying anti-inflammatory and anti-neuropathic pain potential due to its quadruplicate mechanisms, targeting cyclooxygenase-2 (COX-2), 5-lipoxygenase (5-LOX), and opioid and GABA-A receptors was investigated. The anti-inflammatory potential of the test drug was confirmed utilizing in silico, in vitro, and in vivo tests. A molecular simulation approach was utilized to observe the interaction of 6-HF with the inflammatory enzyme COX-2 as well as opioid and GABA-A receptors. The same was confirmed via in vitro COX-2 and 5-LOX inhibitory assays. In vivo tests were performed to analyze the thermal anti-nociception in the hot-plate analgesiometer and anti-inflammatory action in the carrageenan-induced paw edema model in rodents. The potential anti-nociceptive effect of 6-HF was evaluated in the DIN model in rats. The Naloxone and Pentylenetetrazole (PTZ) antagonists were used to confirm the underlying mechanism of 6-HF. The molecular modeling studies revealed a favorable interaction of 6-HF with the identified protein molecules. In vitro inhibitory studies revealed that 6-HF inhibited the COX-2 and 5-LOX enzymes significantly. The 6-HF at dosages of 15, 30, and 60 mg/kg substantially reduced heat nociception in a hot plate analgesiometer as well as carrageenan-induced paw edema in rodent models. The authors discovered that 6-HF had anti-nociception properties in a streptozotocin-induced diabetic neuropathy model. According to the findings of this study, 6-HF was demonstrated to diminish inflammation caused by diabetes as well as its anti-nociception effect in DIN.
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Affiliation(s)
- Shehla Akbar
- Department of Pharmacy, CECOS University of IT and Emerging Sciences, Peshawar 25000, Pakistan
| | - Fazal Subhan
- Department of Pharmacy, CECOS University of IT and Emerging Sciences, Peshawar 25000, Pakistan
| | - Aroosha Akbar
- North West Institute of Health Sciences, Peshawar 25000, Pakistan
| | - Faiza Habib
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar 25000, Pakistan
| | - Naila Shahbaz
- Department of Pharmacy, Sarhad University of Science and Technology, Peshawar 25000, Pakistan
| | - Ashfaq Ahmad
- Department of Pharmacy, Sarhad University of Science and Technology, Peshawar 25000, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Shankar Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Saad Salman
- Department of Pharmacy, CECOS University of IT and Emerging Sciences, Peshawar 25000, Pakistan
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Ajmal A, Mahmood A, Hayat C, Hakami MA, Alotaibi BS, Umair M, Abdalla AN, Li P, He P, Wadood A, Hu J. Computer-assisted drug repurposing for thymidylate kinase drug target in monkeypox virus. Front Cell Infect Microbiol 2023; 13:1159389. [PMID: 37313340 PMCID: PMC10258308 DOI: 10.3389/fcimb.2023.1159389] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 05/10/2023] [Indexed: 06/15/2023] Open
Abstract
Introduction Monkeypox is a zoonotic disease caused by brick-shaped enveloped monkeypox (Mpox) virus that belongs to the family of ancient viruses known as Poxviridae. Subsequently, the viruses have been reported in various countries. The virus is transmitted by respiratory droplets, skin lesions, and infected body fluids. The infected patients experience fluid-filled blisters, maculopapular rash, myalgia, and fever. Due to the lack of effective drugs or vaccines, there is a need to identify the most potent and effective drugs to reduce the spread of monkeypox. The current study aimed to use computational methods to quickly identify potentially effective drugs against the Mpox virus. Methods In our study, the Mpox protein thymidylate kinase (A48R) was targeted because it is a unique drug target. We screened a library of 9000 FDA-approved compounds of the DrugBank database by using various in silico approaches, such as molecular docking and molecular dynamic (MD) simulation. Results Based on docking score and interaction analysis, compounds DB12380, DB13276, DB13276, DB11740, DB14675, DB11978, DB08526, DB06573, DB15796, DB08223, DB11736, DB16250, and DB16335 were predicted as the most potent. To examine the dynamic behavior and stability of the docked complexes, three compounds-DB16335, DB15796, and DB16250 -along with the Apo state were simulated for 300ns. The results revealed that compound DB16335 revealed the best docking score (-9.57 kcal/mol) against the Mpox protein thymidylate kinase. Discussion Additionally, during the 300 ns MD simulation period, thymidylate kinase DB16335 showed great stability. Further, in vitro and in vivo study is recommended for the final predicted compounds.
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Affiliation(s)
- Amar Ajmal
- Department of Biochemistry, Computational Medicinal Chemistry Laboratory, Abdul Wali Khan University, Mardan, Pakistan
| | - Arif Mahmood
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Chandni Hayat
- Department of Biochemistry, Computational Medicinal Chemistry Laboratory, Abdul Wali Khan University, Mardan, Pakistan
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Bader S. Alotaibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Muhammad Umair
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
| | - Ashraf N. Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ping Li
- Institute of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Pei He
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Abdul Wadood
- Department of Biochemistry, Computational Medicinal Chemistry Laboratory, Abdul Wali Khan University, Mardan, Pakistan
| | - Junjian Hu
- Department of Central Laboratory, SSL Central Hospital of Dongguan City, Affiliated Dongguan Shilong People’s Hospital of Southern Medical University, Dongguan, China
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Ali A, Masood A, Khan AA, Zhu FY, Cheema MAR, Samad A, Wadood A, Khan A, Yu Q, Heng W, Li D, Wei DQ. Comparative binding analysis of WGX50 and Alpha-M with APP family proteins APLP1 and APLP2 using structural-dynamics and free energy calculation approaches. Phys Chem Chem Phys 2023; 25:14887-14897. [PMID: 37199163 DOI: 10.1039/d2cp06083c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
A.D. is a common disease among other neurodegenerative disorders primarily developing due to amyloid-β (Aβ) neurotoxicity derived from the amyloid-β protein precursor (AβPP). The amyloid precursor-like proteins 1 and 2 (APP1 and APLP2) biochemically behave similarly in many aspects to AβPP. We, therefore, proposed to test WGX-50 and Alpha-M for their interaction mechanism with APLP1 and APLP2 because both these drug candidate compounds previously showed inhibition of Aβ aggregation. We employed a comparative atomic investigation on Alpha-M and WGX-50 in complex with novel targets, i.e., APLP1 and APLP2, using biophysical and molecular simulation methods. The docking score was -6.83 kcal mol-1 for Alpha-M-APLP1, -8.41 kcal mol-1 for WGX-50-APLP1, -7.02 kcal mol-1 for Alpha-M-APLP2 and -8.25 kcal mol-1 for the WGX-50-APLP2 complex. Our results also elaborate that in the case of their interaction with both APLP1 and APLP2, the WGX-50 complex exhibits better stability than the APLP1/2-Alpha-M complexes during simulation. Furthermore, WGX50 in both APLP1 and APLP2 stabilized the internal flexibility upon binding in contrast to the Alpha-M complexes. The data showed that the BFE for Alpha-M-APLP1 was calculated to be -27.38 ± 0.93 kcal mol-1, for WGX-50-APLP1 -39.65 ± 0.95 kcal mol-1, for Alpha-M-APLP2 -24.80 ± 0.63 kcal mol-1 while for WGX-50-APLP2 the BFE was -57.16 ± 1.03 kcal mol-1 respectively. These results highlight that APLP2-WGX50 has greater binding energies in all four systems. PCA and FEL analysis further revealed variations in the dynamic behavior of these complexes. Overall, our findings demonstrate that WGX50 potentially acts as a more potent inhibitor for APLP1 and APLP2 than Alpha-M and thus shows the diverse pharmacological potential of WGX50. Due to its stable binding interaction, WGX50 might be a suitable candidate drug compound for targeting these precursors under pathological conditions.
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Affiliation(s)
- Arif Ali
- Department of Bioinformatics and Biological Statistics, Shanghai Jiao Tong University, Shanghai, P. R. China.
| | - Adan Masood
- University Medical and Dental College, Faisalabad, Punjab, Pakistan.
| | - Abdul Aziz Khan
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Institute of Psychology and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai, China.
| | - Feng-Yun Zhu
- College of Biology and Food Engineering, Huanghuai University, Zhumadian, 463000, Henan, China.
| | | | - Abdus Samad
- Department of Biochemistry, Abdul Wali khan University Mardan, 23200 Khyber Pakhtunkhwa, Pakistan.
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali khan University Mardan, 23200 Khyber Pakhtunkhwa, Pakistan.
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, Shanghai Jiao Tong University, Shanghai, P. R. China.
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, P. R. China
| | - Qiu Yu
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Wang Heng
- International School of Cosmetics, School of Perfume and Aroma Technology, Shanghai Institute of Technology, China.
| | - Daixi Li
- Institute of Biothermal Science and Technology, University of Shanghai for Science and Technology, Shanghai, 20093, China.
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, P. R. China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, Shanghai Jiao Tong University, Shanghai, P. R. China.
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, P. R. China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nayang, Henan, 473006, P. R. China
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Abbasi Z, Mateen A, Niaz A, Ur Rehman MA, Wadood A. Development and Characterization of Natural Chromite Coating on Metal Substrate Using the Plasma Spray Process. ACS Omega 2023; 8:15193-15202. [PMID: 37151503 PMCID: PMC10157692 DOI: 10.1021/acsomega.3c00194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/04/2023] [Indexed: 05/09/2023]
Abstract
Natural materials are gaining interest as coating feedstock because their "quality to cost" ratio is better and they are more environmentally friendly than most of the synthetic ceramics. They give sufficient protection to metal surfaces against harsh conditions such as corrosion, wear, and high temperature. In the current study, chromite mineral was beneficiated and reduced to two different sizes to be used as feedstock material for thermal spray coating. Powders were upgraded by gravity and magnetic separation, respectively, and thermally sprayed onto mild steel samples by using atmospheric plasma spray (APS) equipment. Morphology, structure, phases, elemental distribution of chromite powder, and coatings were studied using field emission scanning electron microscopy, X-ray diffraction, X-ray fluorescence spectroscopy, and energy-dispersive X-ray spectroscopy. Tribological properties of APS chromite coatings were investigated by using a ball-on-disk tribometer, and corrosion resistance properties were evaluated by carrying out potentiodynamic polarization testing in 3.5% NaCl solution. It is observed that the coating has better wear and corrosion resistance and is worn by abrasive wear that includes scratching and particles pull out. Coating efficiency, surface morphology, and microhardness of the coating developed by fine powder were better than those of coarse powder coating.
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Affiliation(s)
- Zeeshan
Ahmad Abbasi
- Materials
Science and Engineering Department, Institute
of Space Technology, 44000 Islamabad, Pakistan
| | - Abdul Mateen
- Materials
Science and Engineering Department, Institute
of Space Technology, 44000 Islamabad, Pakistan
| | - Akbar Niaz
- Department
of Mechanical Engineering, King Faisal University, Al Hufu̅f 31982, Saudi Arabia
| | - Muhammad Atiq Ur Rehman
- Materials
Science and Engineering Department, Institute
of Space Technology, 44000 Islamabad, Pakistan
| | - Abdul Wadood
- Materials
Science and Engineering Department, Institute
of Space Technology, 44000 Islamabad, Pakistan
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Nadeem I, Khan WJ, Nadeem A, Wadood A, Thapa S. Panhypopituitarism and Central Hypothyroidism Presenting as Myoclonus and Hyperreflexia. Cureus 2023; 15:e39140. [PMID: 37332415 PMCID: PMC10275397 DOI: 10.7759/cureus.39140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2023] [Indexed: 06/20/2023] Open
Abstract
Panhypopituitarism may present with symptoms of predominantly one or more hormonal deficiencies. Central hypothyroidism usually presents with typical symptoms of hypothyroidism, such as fatigue, weight gain, menstrual abnormalities, bradycardia, thick, coarse skin, muscle fasciculations, and hyporeflexia, among others. Herein we present a case of central hypothyroidism along with panhypopituitarism presenting with unusual symptoms of tongue fasciculation, hyperreflexia, and myoclonic jerks.
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Affiliation(s)
- Ifrah Nadeem
- Internal Medicine, University of South Dakota Sanford School of Medicine, Sioux Falls, USA
| | - Wahab J Khan
- Internal Medicine, University of South Dakota Sanford School of Medicine, Sioux Falls, USA
| | - Anum Nadeem
- Physiology, Rashid Latif Medical College, Lahore, PAK
| | - Abdul Wadood
- Internal Medicine, National Hospital and Medical Center, Lahore, PAK
| | - Sudan Thapa
- Endocrinology, Diabetes and Metabolism, University of South Dakota Sanford School of Medicine, Sioux Falls, USA
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Jan SM, Fahira A, Shi Y, Khan MI, Jamal A, Mahmood A, Shams S, Parveen Z, Hu J, Umair M, Wadood A. Integrative Genomic Analysis of m6a-SNPs Identifies Potential Functional Variants Associated with Alzheimer's Disease. ACS Omega 2023; 8:13332-13341. [PMID: 37065064 PMCID: PMC10099436 DOI: 10.1021/acsomega.3c00696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/24/2023] [Indexed: 06/19/2023]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder that affects 35 million people worldwide. However, no potential therapeutics currently are available for AD because of the multiple factors involved in it, such as regulatory factors with their candidate genes, factors associated with the expression levels of its corresponding genes, and many others. To date, 29 novel loci from GWAS have been reported for AD by the Psychiatric Genomics Consortium (PGC2). Nevertheless, the main challenge of the post-GWAS era, namely to detect significant variants of the target disease, has not been conducted for AD. N6-methyladenosine (m6a) is reported as the most prevalent mRNA modification that exists in eukaryotes and that influences mRNA nuclear export, translation, splicing, and the stability of mRNA. Furthermore, studies have also reported m6a's association with neurogenesis and brain development. We carried out an integrative genomic analysis of AD variants from GWAS and m6a-SNPs from m6AVAR to identify the effects of m6a-SNPs on AD and identified the significant variants using the statistically significance value (p-value <0.05). The cis-regularity variants with their corresponding genes and their influence on gene expression in the gene expression profiles of AD patients were determined, and showed 1458 potential m6a-SNPs (based on p-value <0.05) associated with AD. eQTL analysis showed that 258 m6a-SNPs had cis-eQTL signals that overlapped with six significant differentially expressed genes based on p-value <0.05 in two datasets of AD gene expression profiles. A follow-up study to elucidate the impact of our identified m6a-SNPs in the experimental study would validate our findings for AD, which would contribute to the etiology of AD.
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Affiliation(s)
- Syed Mansoor Jan
- Department
of Biochemistry, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Aamir Fahira
- Bio-X
Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric
Disorders (Ministry of Education), Collaborative Innovation Center
for Brain Science, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yongyong Shi
- Bio-X
Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric
Disorders (Ministry of Education), Collaborative Innovation Center
for Brain Science, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mohammad Imran Khan
- Department
of Biochemistry, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Centre for
Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Alam Jamal
- Department
of Biochemistry, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Arif Mahmood
- Center
for
Medical Genetics and Hunan Key Laboratory of Medical Genetics, School
of Life Sciences, Central South University, Changsha 410078, Hunan, China
| | - Sulaiman Shams
- Department
of Biochemistry, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Zahida Parveen
- Department
of Biochemistry, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Junjian Hu
- Department
of Central Laboratory, SSL, Central Hospital of Gongguan City, Affiliated Dongguan Shilong People’s Hospital
of Southern Medical University, Dongguan 523000, China
| | - Muhammad Umair
- Department
of Life Sciences, School of Science, University
of Management and Technology (UMT), Lahore 54770, Pakistan
| | - Abdul Wadood
- Department
of Biochemistry, Abdul Wali Khan University, Mardan 23200, Pakistan
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Khan WJ, Khan D, Nadeem A, Wadood A, Nadeem I, Asif M. ST-Elevation Myocardial Infarction Precipitated by Disseminated Intravascular Coagulation: A Therapeutic Challenge. Cureus 2023; 15:e37119. [PMID: 37153300 PMCID: PMC10159217 DOI: 10.7759/cureus.37119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2023] [Indexed: 04/07/2023] Open
Abstract
Acute coronary syndrome (ACS) can manifest as ST-elevation myocardial infarction (STEMI), non-ST-elevation myocardial infarction (NSTEMI), and unstable angina (UA). Common etiologies for STEMI include atherosclerotic plaque disruption or erosion manifesting as type 1 myocardial ischemia (MI). Causes of type 2 MI presenting as STEMI may include spontaneous coronary artery dissection, coronary artery spasm, and coronary embolism. STEMI is an emergency mandating immediate coronary intervention. We present a case of STEMI as a complication of disseminated intravascular coagulation (DIC). This case highlights the unique challenge of managing STEMI with active DIC.
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Samad A, Khurshid B, Mahmood A, Rehman AU, Khalid A, Abdalla AN, Algarni AS, Wadood A. Identification of novel peptide inhibitors for oncogenic KRAS G12D as therapeutic options using mutagenesis-based remodeling and MD simulations. J Biomol Struct Dyn 2023; 41:13425-13437. [PMID: 37010994 DOI: 10.1080/07391102.2023.2192298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/22/2023] [Indexed: 04/04/2023]
Abstract
The Kirsten rat sarcoma 2 viral oncogene homolog (KRAS) serves as a molecular switch, cycling between guanosine triphosphate (GTP)-bound and inactive guanosine diphosphate (GDP)-bound states. KRAS modulates numerous signal transduction pathways including the conventional RAF-MEK-ERK pathway. Mutations in the RAS genes have been linked to the formation of malignant tumors. Human malignancies typically show mutations in the Ras gene including HRAS, KRAS, and NRAS. Among all the mutations in exon 12 and exon 13 of the KRAS gene, the G12D mutation is more prevalent in pancreatic and lung cancer and accounts for around 41% of all G12 mutations, making them potential anticancer therapeutic targets. The present study is aimed at repurposing the peptide inhibitor KD2 of the KRAS G12D mutant. We employed an in-silico mutagenesis approach to design novel peptide inhibitors from the experimentally reported peptide inhibitor, and it was found that substitutions (N8W, N8I, and N8Y) might enhance the peptide's binding affinity toward the KRAS. Molecular dynamics simulations and binding energy calculations confirmed that the newly designed peptide inhibitors are stable and that their binding affinities are stronger as compared to the wild-type peptide. The detailed analysis revealed that newly designed peptides have the potential to inhibit KRAS/Raf interaction and the oncogenic signal of the KRAS G12D mutant. Our findings strongly suggest that these peptides should be tested and clinically validated to combat the oncogenic activity of KRAS.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdus Samad
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Beenish Khurshid
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Arif Mahmood
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Ashfaq Ur Rehman
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California, Irvine, California, USA
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, Jazan, Saudi Arabia
- Medicinal and Aromatic Plants and Traditional Medicine Research Institute, National Center for Research, Khartoum, Sudan
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Alanood S Algarni
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
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Mujawah A, Rauf A, Bawazeer S, Wadood A, Hemeg HA, Bawazeer S. Erratum to “In-vitro antioxidant, lipoxygenase inhibitory, and in-vivo muscle relaxant potential of the extract and constituent isolated from Diospyros kaki (Japanese Persimmon)”[Heliyon Volume 9, Issue 3, MARCH 2023, Article e13816]. Heliyon 2023. [DOI: 10.1016/j.heliyon.2023.e15141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
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Shahab M, Liang C, Duan X, Zheng G, Wadood A. In silico Mutagenesis and Modeling of Decoy Peptides Targeting CIB1 to Obscure its Role in Triple-negative Breast Cancer Progression. Curr Pharm Des 2023; 29:630-638. [PMID: 36998135 DOI: 10.2174/1381612829666230327162852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/29/2023] [Accepted: 02/17/2023] [Indexed: 04/01/2023]
Abstract
BACKGROUND Cancer is recognized globally as the second-most dominating and leading cause of morbidities. Breast cancer is the most often diagnosed disease in women and one of the leading causes of cancer mortality. In women, 287,850, and in males, 2710 cases were reported in 2022. Approximately 10-20% of all new cases of breast cancer diagnosed in the United States in 2017 were triple-negative breast cancers (TNBCs), which lack the expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). OBJECTIVE This study aims to adopt different strategies for targeting calcium integrin-binding protein 1 by computer- aided drug design methods. Our results showed that the top four selected peptides interact with CIB1 more strongly than the reference peptide and restore normal cell function by engaging CIB1. Our binding affinity analyses explore an innovative approach to planning a new peptide to inhibit triple-negative breast cancer. METHODS Molecular dynamic simulation of the CIB1-UNC10245092 interaction highlights the potential peptide inhibitors through in-silico mutagenesis and designs novel peptide inhibitors from the reference peptide (UNC10245092) through residue scan methodology. RESULTS The top four designed peptides (based on binding free energy) were subjected to molecular dynamics simulations using AMBER to evaluate stability. CONCLUSION Our results indicate that among the top five selected peptides, the mutant 2nd mutants have more potential to inhibit CIB1 than the reference peptide (UNC10245092) and have the potency to prevent or restore the tumor suppressor function of UNC10245092.
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Affiliation(s)
- Muhammad Shahab
- State key laboratories of chemical Resources Engineering Beijing University of chemical technology, Beijing 100029, china
| | - Chaoqun Liang
- State key laboratories of chemical Resources Engineering Beijing University of chemical technology, Beijing 100029, china
| | - Xiuyuan Duan
- State key laboratories of chemical Resources Engineering Beijing University of chemical technology, Beijing 100029, china
| | - Guojun Zheng
- State key laboratories of chemical Resources Engineering Beijing University of chemical technology, Beijing 100029, china
| | - Abdul Wadood
- Department of Biochemistry, Computational Medicinal Chemistry Laboratory, UCSS, Abdul Wali Khan University, Mardan, Pakistan
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Rehman AU, Khurshid B, Ali Y, Rasheed S, Wadood A, Ng HL, Chen HF, Wei Z, Luo R, Zhang J. Computational approaches for the design of modulators targeting protein-protein interactions. Expert Opin Drug Discov 2023; 18:315-333. [PMID: 36715303 PMCID: PMC10149343 DOI: 10.1080/17460441.2023.2171396] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/18/2023] [Indexed: 01/31/2023]
Abstract
BACKGROUND Protein-protein interactions (PPIs) are intriguing targets for designing novel small-molecule inhibitors. The role of PPIs in various infectious and neurodegenerative disorders makes them potential therapeutic targets . Despite being portrayed as undruggable targets, due to their flat surfaces, disorderedness, and lack of grooves. Recent progresses in computational biology have led researchers to reconsider PPIs in drug discovery. AREAS COVERED In this review, we introduce in-silico methods used to identify PPI interfaces and present an in-depth overview of various computational methodologies that are successfully applied to annotate the PPIs. We also discuss several successful case studies that use computational tools to understand PPIs modulation and their key roles in various physiological processes. EXPERT OPINION Computational methods face challenges due to the inherent flexibility of proteins, which makes them expensive, and result in the use of rigid models. This problem becomes more significant in PPIs due to their flexible and flat interfaces. Computational methods like molecular dynamics (MD) simulation and machine learning can integrate the chemical structure data into biochemical and can be used for target identification and modulation. These computational methodologies have been crucial in understanding the structure of PPIs, designing PPI modulators, discovering new drug targets, and predicting treatment outcomes.
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Affiliation(s)
- Ashfaq Ur Rehman
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California Irvine, Irvine, California, USA
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, Zhejiang, China
| | - Beenish Khurshid
- Department of Biochemistry, Abdul Wali Khan University Mardan, Pakistan
| | - Yasir Ali
- National Center for Bioinformatics, Quaid-e-Azam University, Islamabad, Pakistan
| | - Salman Rasheed
- National Center for Bioinformatics, Quaid-e-Azam University, Islamabad, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Pakistan
| | - Ho-Leung Ng
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, Zhejiang, China
| | - Zhiqiang Wei
- Medicinal Chemistry and Bioinformatics Center, Ocean University of China, Qingdao, Shandong, China
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California Irvine, Irvine, California, USA
| | - Jian Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, Zhejiang, China
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
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Taha M, Rahim F, Zaman K, Anouar EH, Uddin N, Nawaz F, Sajid M, Khan KM, Shah AA, Wadood A, Rehman AU, Alhibshi AH. Synthesis, in vitro biological screening and docking study of benzo[ d]oxazole bis Schiff base derivatives as a potent anti-Alzheimer agent. J Biomol Struct Dyn 2023; 41:1649-1664. [PMID: 34989316 DOI: 10.1080/07391102.2021.2023640] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We have synthesized benzo[d]oxazole derivatives (1-21) through a multistep reaction. Alteration in the structure of derivatives was brought in the last step via using various substituted aromatic aldehydes. In search of an anti-Alzheimer agent, all derivatives were evaluated against acetylcholinesterase and butyrylcholinesterase enzyme under positive control of standard drug donepezil (IC50 = 0.016 ± 0.12 and 4.5 ± 0.11 µM) respectively. In case of acetylcholinesterase enzyme inhibition, derivatives 8, 9 and 18 (IC50 = 0.50 ± 0.01, 0.90 ± 0.05 and 0.3 ± 0.05 µM) showed very promising inhibitory potentials. While in case of butyrylcholinesterase enzyme inhibition, most of the derivatives like 6, 8, 9, 13, 15, 18 and 19 (IC50 = 2.70 ± 0.10, 2.60 ± 0.10, 2.20 ± 0.10, 4.25 ± 0.10, 3.30 ± 0.10, 0.96 ± 0.05 and 3.20 ± 0.10 µM) displayed better inhibitory potential than donepezil. Moreover, derivative 18 is the most potent one among the series in both inhibitions. The binding interaction of derivatives with the active gorge of the enzyme was confirmed via a docking study. Furthermore, the binding interaction between derivatives and the active site of enzymes was correlated through the SAR study. Structures of all derivatives were confirmed through spectroscopic techniques such as 1H-NMR, 13C-NMR and HREI-MS, respectively.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muhammad Taha
- Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Fazal Rahim
- Department of Chemistry, Hazara University, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - Khalid Zaman
- Department of Chemistry, Hazara University, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - El Hassane Anouar
- Department of Chemistry, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Nizam Uddin
- Department of Chemistry, University of Karachi, Karachi, Pakistan
| | - Faisal Nawaz
- Department of Chemistry, University of Wah, Wah Cantt, Pakistan
| | - Muhammad Sajid
- Department of Biochemistry, Hazara University, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - Khalid Mohammed Khan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Adnan Ali Shah
- Atta-ur-Rahman Institute for Natural Product Discovery (AuRIns), Universiti Teknologi MARA Cawangan Selangor Kampus Puncak Alam, Bandar Puncak Alam, Selangor 42300, Malaysia.,Faculty of Pharmacy, Universiti Teknologi MARA Cawangan Selangor Kampus Puncak Alam, Bandar Puncak Alam, Selangor 42300, Malaysia
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Ashfaq Ur Rehman
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Amani H Alhibshi
- Department of Neuroscience Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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Khan M, Gohar H, Alam A, Wadood A, Shareef A, Ali M, Khalid A, Abdalla AN, Ullah F. Para-Substituted Thiosemicarbazones as Cholinesterase Inhibitors: Synthesis, In Vitro Biological Evaluation, and In Silico Study. ACS Omega 2023; 8:5116-5123. [PMID: 36777613 PMCID: PMC9910069 DOI: 10.1021/acsomega.2c08108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
The current research reports the synthesis of 14 para-substituted thiosemicarbazone derivatives in good to excellent yields using standard procedures. Initially, 4-ethoxybenzaldehyde (1) and 4-nitrobenzaldehyde (2) were refluxed with thiosemicarbazide in the presence of acetic acid in ethanol for 4-5 h. Then, various substituted phenacyl bromides were treated with the desired thiosemicarbazones (3 and 4) in the presence of triethylamine in ethanol with constant stirring for 5-6 h. The resulting derivatives were confirmed through electron impact mass spectrometry and 1H NMR spectroscopy and evaluated for anticholinesterase inhibitory activity. Among the series, four compounds, 19, 17, 7, and 6, showed potent inhibitory activity against the acetylcholinesterase (AChE) enzyme, having IC50 values of 110.19 ± 2.32, 114.57 ± 0.15, 140.52 ± 0.11, and 160.04 ± 0.02 μM, respectively, compared with standard galantamine (IC50 = 104.5 ± 1.20 μM). Similarly, compounds 19 (IC50 = 145.11 ± 1.03 μM), 9 (IC50 = 147.20 ± 0.09 μM), 17 (IC50 = 150.36 ± 0.18 μM), and 6 (IC50 = 190.21 ± 0.13 μM) were the most excellent inhibitors of butyrylcholinesterase (BChE) when compared with the standard drug galantamine (IC50 = 156.8 ± 1.50 μM). In silico studies were accomplished on the produced derivatives in order to explain the binding interface of compounds with the active sites of AChE and BChE enzymes.
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Affiliation(s)
- Momin Khan
- Department
of Chemistry, Abdul Wali Khan University, Mardan23200, Pakistan
| | - Hina Gohar
- Department
of Chemistry, Abdul Wali Khan University, Mardan23200, Pakistan
| | - Aftab Alam
- Department
of Chemistry, University of Malakand, Lower Dir, Chakdara18800, Pakistan
| | - Abdul Wadood
- Department
of Biochemistry, Abdul Wali Khan University, Mardan23200, Pakistan
| | - Azam Shareef
- Department
of Biochemistry, Abdul Wali Khan University, Mardan23200, Pakistan
| | - Mahboob Ali
- Department
of Chemistry, Abdul Wali Khan University, Mardan23200, Pakistan
| | - Asaad Khalid
- Substance
Abuse and Toxicology Research Center, Jazan
University, P.O. Box: 114, Jazan45142, Saudi Arabia
- National
Center for Research, Medicinal and Aromatic
Plants and Traditional Medicine Research Institute, P.O. Box 2404, Khartoum11111, Sudan
| | - Ashraf N. Abdalla
- Department
of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah21955, Saudi Arabia
| | - Farhat Ullah
- Department
of Pharmacy, University of Malakand, Dir Lower, Chakdara, Khyber
Pakhtunkhwa18800, Pakistan
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Azmi MB, Khan F, Asif U, Khurshid B, Wadood A, Qureshi SA, Ahmed SDH, Mudassir HA, Sheikh SI, Feroz N. In Silico Characterization of Withania coagulans Bioactive Compounds as Potential Inhibitors of Hydroxymethylglutaryl (HMG-CoA) Reductase of Mus musculus. ACS Omega 2023; 8:5057-5071. [PMID: 36777558 PMCID: PMC9909811 DOI: 10.1021/acsomega.2c07893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Hypercholesterolemia is a mediator for the etiology of cardiovascular diseases, which are characterized as the global leading cause of mortality. We aimed to investigate the inhibitory activity of Withania coagulans compounds against 3-hydroxy-3-methylglutaryl-coenzyme A reductase (Hmgcr) of Mus musculus using an extensive in silico approach. The 3D structure of the Hmgcr protein is not yet known, so we performed the homology modeling using MODELLER and SWISS-MODEL tools, followed with structural validation and assessment. The PROCHECK web server showed that the top-ranked homology model from SWISS-MODEL has 93.4% of residues in the most-favorable region, the quality factor was 98%, and the Verify3D score was 91.43%, compared to the other generated models. The druggable protein-binding cavities in a 3D model of Hmgcr were investigated with the aid of commonly prescribed statin compounds using the CB-dock approach. We compiled a 3D compound library of W. coagulans, followed by drug-likeness evaluation, and found 20 eligible compounds. The pattern of consensus residues obtained from the CB-dock procedure was then used for grid-box docking of W. coagulans compounds and statin drugs using AutoDock 4.2, respectively. The results showed that withanolide R (-10.77 kcal/mol), withanolide Q (-10.56 kcal/mol), withanolide J (-10.52 kcal/mol), atorvastatin (-8.99 kcal/mol), simvastatin (-8.66 kcal/mol), and rosuvastatin (-8.58 kcal/mol) were promising candidates that bind Hmgcr protein. The key residues involved in protein-ligand (withanolide R) interactions were Y516, C526, V529, I530, M533, I535, and V537, and the formation of a H-bond was at C526, M533, and I535 residues. M533 was the consensus residue having a tendency to form a H-bond with withanolide Q, too. Molecular dynamics simulations were used to validate the top-ranked docked complexes for the stability of the modeled protein. We also predicted the pharmacokinetic properties of binding affinity-based top-ranked compounds and concluded that they could be used as potential inhibitors of Hmgcr. However, further in vitro and in vivo studies are essential to completing the drug development process.
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Affiliation(s)
- Muhammad Bilal Azmi
- Department
of Biochemistry, Dow Medical College, Dow
University of Health Sciences, Karachi 74200, Pakistan
| | - Fearoz Khan
- Department
of Biochemistry, University of Karachi, Karachi 75270, Pakistan
- Rahman
Medical College, Peshawar 25000, Pakistan
| | - Uzma Asif
- Department
of Biochemistry, Medicine Program, Batterjee
Medical College, Jeddah 21442, Saudi Arabia
| | - Beenish Khurshid
- Department
of Biochemistry, Abdul Wali Khan University
Mardan, Mardan 23200, Pakistan
| | - Abdul Wadood
- Department
of Biochemistry, Abdul Wali Khan University
Mardan, Mardan 23200, Pakistan
| | | | - Syed Danish Haseen Ahmed
- Department
of Biochemistry, Dow Medical College, Dow
University of Health Sciences, Karachi 74200, Pakistan
| | - Hina Akram Mudassir
- Department
of Biochemistry, Federal Urdu University
of Arts, Science and Technology, Karachi 75300, Pakistan
| | - Sadia Ikhlaque Sheikh
- Department
of Biochemistry, Dow Medical College, Dow
University of Health Sciences, Karachi 74200, Pakistan
| | - Nazia Feroz
- Department
of Biochemistry, Dow Medical College, Dow
University of Health Sciences, Karachi 74200, Pakistan
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Mahmood A, Samad A, Shah AA, Wadood A, Alkathiri A, Alshehri MA, Alam MZ, Hussain T, He P, Umair M. A novel biallelic variant in the Popeye domain-containing protein 1 (POPDC1) underlies limb girdle muscle dystrophy type 25. Clin Genet 2023; 103:219-225. [PMID: 36155908 DOI: 10.1111/cge.14238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/13/2022] [Accepted: 09/21/2022] [Indexed: 01/13/2023]
Abstract
POPDC1 also known as BVES, is a highly conserved transmembrane protein, important for striated muscle function and homeostasis. Pathogenic variants in the POPDC1 gene are associated with limb-girdle muscular dystrophy type 25 (LGMDR25). In the present study, we performed trio-whole exome sequencing (WES) followed by Sanger sequencing on a single family having LGMD clinical features. Protein modeling of all POPDC1 missense variants (POPDC1Pro134Leu , POPDC1Ile193Ser , and POPDC1Ser201Phe ) associated with LGMDR25 were performed using Molecular Dynamics (MD) simulation. We identified a homozygous missense variant (c.401C>T; p.Pro134Leu) in the POPDC1 gene. Altered 3D structure, disruptive fluctuation, less compactness, and instability were observed in all the three variants of POPDC1 protein models. In comparison, POPDC1Ser201Phe protein dynamics were more unstable than other variants. Functional study of newly identified variant would add key answers to underlying mechanisms of the disease.
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Affiliation(s)
- Arif Mahmood
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Abdus Samad
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Abid Ali Shah
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Afnan Alkathiri
- Medical Genetics, Laboratory Medicine Department, Faculty of Applied Medical Sciences, Albaha University, Albaha, Saudi Arabia
| | - Mohammed Ali Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Mohammad Zubair Alam
- Pre-Clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Taimur Hussain
- Department of Cardiology, Medical Teaching Institute, Bacha Khan Medical Complex, Swabi, Pakistan
| | - Pei He
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
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Adalat B, Rahim F, Rehman W, Ali Z, Rasheed L, Khan Y, Farghaly TA, Shams S, Taha M, Wadood A, Shah SAA, Abdellatif MH. Biologically Potent Benzimidazole-Based-Substituted Benzaldehyde Derivatives as Potent Inhibitors for Alzheimer's Disease along with Molecular Docking Study. Pharmaceuticals (Basel) 2023; 16:208. [PMID: 37259358 PMCID: PMC9958709 DOI: 10.3390/ph16020208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 09/29/2023] Open
Abstract
Twenty-one analogs were synthesized based on benzimidazole, incorporating a substituted benzaldehyde moiety (1-21). These were then screened for their acetylcholinesterase and butyrylcholinesterase inhibition profiles. All the derivatives except 13, 14, and 20 showed various inhibitory potentials, ranging from IC50 values of 0.050 ± 0.001 µM to 25.30 ± 0.40 µM against acetylcholinesterase, and 0.080 ± 0.001 µM to 25.80 ± 0.40 µM against butyrylcholinesterase, when compared with the standard drug donepezil (0.016 ± 0.12 µM and 0.30 ± 0.010 µM, against acetylcholinesterase and butyrylcholinesterase, respectively). Compound 3 in both cases was found to be the most potent compound due to the presence of chloro groups at the 3 and 4 positions of the phenyl ring. A structure-activity relationship study was performed for all the analogs except 13, 14, and 20, further, molecular dynamics simulations were performed for the top two compounds as well as the reference compound in a complex with acetylcholinesterase and butyrylcholinesterase. The molecular dynamics simulation analysis revealed that compound 3 formed the most stable complex with both acetylcholinesterase and butyrylcholinesterase, followed by compound 10. As compared to the standard inhibitor donepezil both compounds revealed greater stabilities and higher binding affinities for both acetylcholinesterase and butyrylcholinesterase.
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Affiliation(s)
- Bushra Adalat
- Department of Chemistry, Hazara University, Mansehra 21300, Pakistan
| | - Fazal Rahim
- Department of Chemistry, Hazara University, Mansehra 21300, Pakistan
| | - Wajid Rehman
- Department of Chemistry, Hazara University, Mansehra 21300, Pakistan
| | - Zarshad Ali
- Department of Chemistry, Hazara University, Mansehra 21300, Pakistan
| | - Liaqat Rasheed
- Department of Chemistry, Hazara University, Mansehra 21300, Pakistan
| | - Yousaf Khan
- Department of Chemistry, COMSATS University, Islamabad 45550, Pakistan
| | - Thoraya A. Farghaly
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, P.O. Box 715, Makkah Almukkarramah 24382, Saudi Arabia
| | - Sulaiman Shams
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Muhammad Taha
- Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdul Rahman Bin Faisal University, P.O. Box 31441, Dammam 11099, Saudi Arabia
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Syed A. A. Shah
- Faculty of Pharmacy, Universiti Teknologi MARA Cawangan Selangor Kampus Puncak Alam, Bandar, Puncak Alam 42300, Malaysia
| | - Magda H. Abdellatif
- Department of Chemistry, College of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
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Riaz M, Rehman AU, Waqas M, Khalid A, Abdalla AN, Mahmood A, Hu J, Wadood A. A Novel Approach to Develop New and Potent Inhibitors for the Simultaneous Inhibition of Protease and Helicase Activities of HCV NS3/4A Protease: A Computational Approach. Molecules 2023; 28:molecules28031300. [PMID: 36770965 PMCID: PMC9918934 DOI: 10.3390/molecules28031300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 02/03/2023] Open
Abstract
Infection of hepatitis C (HCV) is a major threat to human health throughout the world. The current therapy program suffers from restricted efficiency and low tolerance, and there is serious demand frr novel medication. NS3/4A protease is observed to be very effective target for the treatment of HCV. A data set of the already reported HCV NS3/4A protease inhibitors was first docked into the NS3/4A protease (PDB ID: 4A92A) active sites of both protease and helicase sites for calculating the docking score, binding affinity, binding mode, and solvation energy. Then the data set of these reported inhibitors was used in a computer-based program "RECAP Analyses" implemented in MOE to fragment every molecule in the subset according to simple retrosynthetic analysis rules. The RECAP analysis fragments were then used in another computer-based program "RECAP Synthesis" to randomly recombine and generate synthetically reasonable novel chemical structures. The novel chemical structures thus produced were then docked against HCV NS3/4A. After a thorough validation of all undertaken steps, based on Lipinski's rule of five, docking score, binding affinity, solvation energy, and Van der Waal's interactions with HCV NS3/4A, 12 novel chemical structures were identified as inhibitors of HCV NS3/4A. The novel structures thus designed are hoped to play a key role in the development of new effective inhibitors of HCV.
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Affiliation(s)
- Muhammad Riaz
- Computational Medicinal Chemistry Laboratory, Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Ashfaq Ur Rehman
- School of Biological Science, University of California, Irvine, CA 92697, USA
| | - Muhammad Waqas
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat Al Mauz, P.O. Box 33, Nizwa 616, Oman
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia
- Medicinal and Aromatic Plants and Traditional Medicine Research Institute, National Center for Research, Khartoum P.O. Box 2404, Sudan
| | - Ashraf N. Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Arif Mahmood
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Junjian Hu
- Department of Central Laboratory, SSL, Central Hospital of Dongguan City, Affiliated Dongguan Shilong People’s Hospital of Southern Medical University, Dongguan 523000, China
- Correspondence: (J.H.); (A.W.)
| | - Abdul Wadood
- Computational Medicinal Chemistry Laboratory, Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
- Correspondence: (J.H.); (A.W.)
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Taha M, Rahim F, Khan IU, Uddin N, Farooq RK, Wadood A, Rehman AU, Khan KM. Synthesis of thiazole-based-thiourea analogs: as anticancer, antiglycation and antioxidant agents, structure activity relationship analysis and docking study. J Biomol Struct Dyn 2023; 41:12077-12092. [PMID: 36695088 DOI: 10.1080/07391102.2023.2171134] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/27/2022] [Indexed: 01/26/2023]
Abstract
This work reports the convenient approach for the synthesis of thiazole based thiourea derivatives (1-21) from 2-bromo-1-(4-fluorophenyl)thiazole-1-one and phenyl isothiocyanates. The scope and diversity were achieved from readily available phenyl isothiocyanates. This protocol involves an oxidative C-S bond formation. Moreover, hybrid thiazole based thiourea scaffolds (1-21) according to literature known protocol were screened in vitro for anticancer Potential against breast cancer, antiglycation and antioxidant inhibitory profile. All newly developed scaffolds were showed moderate to good inhibitory potentials ranging from 0.10 ± 0.01 µM to 11.40 ± 0.20 µM, 64.20 ± 0.40 µM to 385.10 ± 1.70 µM and 8.90 ± 0.20 µM to 39.20 ± 0.50 µM against anticancer, antiglycation and antioxidant respectively. Among the series, compounds 12 (IC50 = 0.10 ± 0.01 µM), 10 (IC50 = 64.20 ± 0.40 µM) and 12 (IC50 = 8.90 ± 0.20 µM) with flouro substitution at phenyl ring of thiourea were identified to be the most potent among the series having excellent anticancer, antiglycation and antioxidant potential. The structure of all the newly synthetics scaffolds were confirmed by using different types of spectroscopic techniques such as HREI-MS, 1H- and 13C-NMR spectroscopy. To find structure-activity relationship, molecular docking studies were carried out to understand the binding mode of active inhibitors with active site of enzymes and results supported the experimental data.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muhammad Taha
- Department of clinical pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Fazal Rahim
- Department of Chemistry, Hazara University, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - Ihsan Ullah Khan
- Department of Chemistry, Hazara University, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - Nizam Uddin
- Department of Chemistry, University of Karachi, Karachi, Pakistan
| | - Rai Khalid Farooq
- Department of Neuroscience Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Ashfaq Ur Rehman
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Khalid Mohammed Khan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
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Samad A, Ajmal A, Mahmood A, Khurshid B, Li P, Jan SM, Rehman AU, He P, Abdalla AN, Umair M, Hu J, Wadood A. Identification of novel inhibitors for SARS-CoV-2 as therapeutic options using machine learning-based virtual screening, molecular docking and MD simulation. Front Mol Biosci 2023; 10:1060076. [PMID: 36959979 PMCID: PMC10028080 DOI: 10.3389/fmolb.2023.1060076] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/11/2023] [Indexed: 03/09/2023] Open
Abstract
The new coronavirus SARS-COV-2, which emerged in late 2019 from Wuhan city of China was regarded as causing agent of the COVID-19 pandemic. The primary protease which is also known by various synonymous i.e., main protease, 3-Chymotrypsin-like protease (3CLPRO) has a vital role in the replication of the virus, which can be used as a potential drug target. The current study aimed to identify novel phytochemical therapeutics for 3CLPRO by machine learning-based virtual screening. A total of 4,000 phytochemicals were collected from deep literature surveys and various other sources. The 2D structures of these phytochemicals were retrieved from the PubChem database, and with the use of a molecular operating environment, 2D descriptors were calculated. Machine learning-based virtual screening was performed to predict the active phytochemicals against the SARS-CoV-2 3CLPRO. Random forest achieved 98% accuracy on the train and test set among the different machine learning algorithms. Random forest model was used to screen 4,000 phytochemicals which leads to the identification of 26 inhibitors against the 3CLPRO. These hits were then docked into the active site of 3CLPRO. Based on docking scores and protein-ligand interactions, MD simulations have been performed using 100 ns for the top 5 novel inhibitors, ivermectin, and the APO state of 3CLPRO. The post-dynamic analysis i.e,. Root means square deviation (RMSD), Root mean square fluctuation analysis (RMSF), and MM-GBSA analysis reveal that our newly identified phytochemicals form significant interactions in the binding pocket of 3CLPRO and form stable complexes, indicating that these phytochemicals could be used as potential antagonists for SARS-COV-2.
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Affiliation(s)
- Abdus Samad
- Department of Biochemistry, Abdul Wali Khan University, Mardan, KPK, Pakistan
| | - Amar Ajmal
- Department of Biochemistry, Abdul Wali Khan University, Mardan, KPK, Pakistan
| | - Arif Mahmood
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Beenish Khurshid
- Department of Biochemistry, Abdul Wali Khan University, Mardan, KPK, Pakistan
| | - Ping Li
- Institutes of Biomedical Sciences, Shanxi university, Taiyuan, China
| | - Syed Mansoor Jan
- Department of Biochemistry, Abdul Wali Khan University, Mardan, KPK, Pakistan
| | - Ashfaq Ur Rehman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Pei He
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ashraf N. Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Muhammad Umair
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
| | - Junjian Hu
- Department of Central Laboratory, SSL Central Hospital of Dongguan City, Affiliated Dongguan Shilong People’s Hospital of Southern Medical University, Dongguan, China
- *Correspondence: Junjian Hu, ; Abdul Wadood,
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan, KPK, Pakistan
- *Correspondence: Junjian Hu, ; Abdul Wadood,
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Saleem F, Khan KM, Ullah N, Özil M, Baltaş N, Hameed S, Salar U, Wadood A, Rehman AU, Kumar M, Taha M, Haider SM. Bioevaluation of synthetic pyridones as dual inhibitors of α-amylase and α-glucosidase enzymes and potential antioxidants. Arch Pharm (Weinheim) 2023; 356:e2200400. [PMID: 36284484 DOI: 10.1002/ardp.202200400] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022]
Abstract
Herein, a library of novel pyridone derivatives 1-34 was designed, synthesized, and evaluated for α-amylase and α-glucosidase inhibitory as well as antioxidant activities. Pyridone derivatives 1-34 were synthesized via a one-pot multi-component reaction of variously substituted aromatic aldehydes, acetophenone, ethyl cyanoacetate, and ammonium acetate in absolute ethanol. Synthetic compounds 1-34 were structurally characterized by different spectroscopic techniques. Most of the tested compounds showed more promising inhibition potential than the standard acarbose (IC50 = 14.87 ± 0.16 µM) but compounds 13 and 12 were found to be the most potent compounds with IC50 values of 9.20 ± 0.14 µM and 3.05 ± 0.18 µM against α-amylase and α-glucosidase enzymes, respectively. Compounds 1-34 also displayed moderate antioxidant potential in the range of IC50 = 96.50 ± 0.45 to 189.98 ± 1.00 µM in comparison to the control butylated hydroxytoluene (BHT) (IC50 = 66.50 ± 0.36 µM), in DPPH radical scavenging activities. Additionally, all synthetic derivatives were subjected to a molecular docking study to investigate the interaction details of compounds 1-34 (ligands) with the active site of enzymes (receptors). These results indicate that the newly synthesized pyridone class may serve as promising lead candidates for controlling diabetes mellitus and as antioxidants.
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Affiliation(s)
- Faiza Saleem
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Khalid Mohammed Khan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.,Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Nisar Ullah
- Chemistry Department, King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia
| | - Musa Özil
- Department of Chemistry, Recep Tayyip Erdogan University, Rize, Turkey
| | - Nimet Baltaş
- Department of Chemistry, Recep Tayyip Erdogan University, Rize, Turkey
| | - Shehryar Hameed
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Uzma Salar
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Ashfaq Ur Rehman
- School of Biological Sciences, University of California, Irvine, California, USA
| | - Mukesh Kumar
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Muhammad Taha
- Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Syed Moazzam Haider
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
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Arshad N, Jawaid S, Hashim J, Ullah I, Gul S, Aziz A, Wadood A, Khan A. Highly potent anti-inflammatory, analgesic and antioxidant activities of 3,5-disubstituted tetrahydro-2H-1,3,5-thiadiazine thiones. Bioorg Med Chem Lett 2023; 79:129068. [PMID: 36395994 DOI: 10.1016/j.bmcl.2022.129068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/11/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022]
Abstract
Four series of tetrahydro-2H-1,3,5-thiadiazine-2-thiones (series A and B including two novel enantiopure isomers), tetrahydro-2H-1,3,5-thiadiazine-6-thiones (series C) and N-3 ester derivatives of tetrahydro-2H-1,3,5-thiadiazine-6-thiones (series D) were synthesized and evaluated for their anti-inflammatory, analgesic and anti-oxidant activities. These THTT analogues specially series D were first time examined for their in vitro anti-inflammatory, in vivo analgesic and anti-oxidant activities. Among them lipophilic compounds (series B and D) were found to be highly active for anti-inflammatory evaluation with IC50 values between 5.1-16.9 and 4.1-32.4 μM, respectively when compared with the standard drug ibuprofen IC50 = 11.2 μM. The structure-activity relationship exposed the importance of lipophilic substituents especially ester and n-propyl group for inhibition of inflammation. The molecular docking studies demonstrated that all the active analogues of THTT have notable binding relations with Arg120 of the active sites of COX-1 enzyme either through CS moiety of the THTT nucleus or with COO attached at N-3 of THTT nucleus. In vivo analgesic activity of the selected THTT compounds 14, 17, 18, 19 (series B) and 28 (series D) were also carried out by acetic acid-induced writhing procedure. The compound 28 showed significant anti-nociceptive/analgesic activity at the oral dose of 5 mg/kg body weight with the percent protection (32.05 %) when compared with standard indomethacin at 10 mg/kg (48.83 %). Additionally, these compounds demonstrated the moderate level of antioxidant potential with IC50 values in the range of 60.9 to 93.6 μM (standard butylated hyroxyanisole; IC50 = 44.2 μM). These results indicated that this class of heterocyclic compounds may be a template specially to design better anti-inflammatory and analgesic agents.
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Affiliation(s)
- Nuzhat Arshad
- Department of Chemistry, NED University of Engineering and Technology, Karachi 75270, Pakistan.
| | - Shumaila Jawaid
- Department of Chemistry, NED University of Engineering and Technology, Karachi 75270, Pakistan
| | - Jamshed Hashim
- Department of Chemistry, NED University of Engineering and Technology, Karachi 75270, Pakistan; H.E.J. Research Institute of Chemistry, ICCBS, University of Karachi, Karachi 75270, Pakistan; Department of Chemical Sciences, University of Lakki Marwat, Lakki Marwat 28420, Pakistan.
| | - Irfan Ullah
- H.E.J. Research Institute of Chemistry, ICCBS, University of Karachi, Karachi 75270, Pakistan; Institute of Chemical Sciences, University of Peshawar, Peshawar 25120, Pakistan
| | - Somia Gul
- Faculty of Pharmacy, Jinnah University for Women, Karachi 74600, Pakistan
| | - Aisha Aziz
- Faculty of Pharmacy, Jinnah University for Women, Karachi 74600, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Alamzeb Khan
- Department of Pediatrics, Yale School of Medicine, Yale University, New Haven CT-06511, United States
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Abbas G, Usman M, Salman ZE, Wadood A, Halim SA, Shams S, Ullah MS, Al-Harrasi A. Biological evaluation and in silico molecular docking studies of newly synthesized homoleptic and heteroleptic Cd(II) carboxylates. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.133991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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