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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] [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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Faisal S, Tariq MH, Ullah R, Zafar S, Rizwan M, Bibi N, Khattak A, Amir N, Abdullah. Exploring the antibacterial, antidiabetic, and anticancer potential of Mentha arvensis extract through in-silico and in-vitro analysis. BMC Complement Med Ther 2023; 23:267. [PMID: 37496047 PMCID: PMC10373235 DOI: 10.1186/s12906-023-04072-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/06/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND Mentha arvensis has been utilized in diverse traditional medicines as an antidiabetic, anticarcinogenic, antiallergic, antifungal, and antibacterial agent. In this work, we have explored the phytochemical analyses and pharmacological potential of Mentha arvensis using both in silico and in vitro approaches for drug discovery. METHODS To determine the extract with the highest potential for powerful bioactivity, ethanol was used as the solvent. The phytochemical components of the extracts were quantified using liquid chromatography-mass spectrometry analysis. The potential bioactivities of extracts and lead phytocompounds, including their antibacterial, cytotoxic, and anti-diabetic effects, were evaluated. RESULTS The compounds oleanolic acid, rosmarinic acid, luteolin, isoorientin, and ursolic acid have been identified through liquid chromatography mass spectrometry analysis. Based on antimicrobial research, it has been found that the Mentha arvensis extract shows potential activity against K. pneumoniae which was 13.39 ± 0.16. Mentha arvensis has demonstrated a greater degree of efficacy in inhibiting α-glucosidase, with an inhibition rate of 58.36 ± 0.12, and in inhibiting α-amylase, with an inhibition rate of 42.18 ± 0.83. The growth of HepG2 cells was observed to be significantly suppressed upon treatment with extracts obtained from Mentha arvensis. Finally, In-silico methods demonstrated that the Luteolin and Rosmarinic acid exhibit acceptable drug-like characteristics. Furthermore, Molecular docking studies further demonstrated that both compounds have strong potential to inhibit the active sites of therapeutically relevant enzymes involved in Diabetes, Bacterial infections, and Cancer. CONCLUSIONS The results of this study suggest that the Mentha arvensis extract possesses potent pharmacological potentials, particularly in terms of antibacterial, anti-diabetic, and cytotoxic effects. Particularly, Luteolin and Rosmarinic acid were identified as the top contenders for potential bioactivity with acceptable drug-like properties.
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Affiliation(s)
- Shah Faisal
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda, 24460, Pakistan.
| | | | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Sania Zafar
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Rizwan
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Nadia Bibi
- Department of Microbiology, Shaheed Benazir Bhutto Women University, Peshawar, Pakistan
| | - Aishma Khattak
- Department of Bioinformatics, Shaheed Benazir Bhutto Women University, Peshawar, Pakistan
| | - Noora Amir
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Abdullah
- Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, M. Strzody 9, 44-100, Gliwice, Poland
- Joint Doctoral School, Silesian University of Technology, Akademicka 2A, 44-100, Gliwice, Poland
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Isolation, Structural Elucidation, In Vitro Anti-α-Glucosidase, Anti-β-Secretase, and In Silico Studies of Bioactive Compound Isolated from Syzygium cumini L. Processes (Basel) 2023. [DOI: 10.3390/pr11030880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
Abstract
Diabetes is one of the main health issues worldwide because of its lifetime duration. To overcome this health problem, the current study was conducted. This investigation aims to explore the α-glucosidase and β-secretase potential of extract/fractions and pure isolated compounds of Syzygium cumini bark. The chloroform extract of Syzygium cumini bark was subjected to chromatographic analysis to yield compound 1. The structure of isolated phytochemical (1) was conducted using advanced spectroscopic analysis. Among test extracts, the chloroform fraction exhibited a significant effect against α-glucosidase with a % activity of 86.20% and an IC50 of 77.09 µM, while the isolated compound exhibited a promising effect with a % activity of 91.54 and an IC50 value of 17.54 μM. The extract/fractions and isolated compound 1 also showed promising effects against the β-secretase enzyme, having % effects of 83.21 and 91.54% with IC50 values of 318.76 and 17.54 μM, respectively. The extract/fractions and compound 1 were found to possess promising inhibitory activity against α-glucosidase and β-secretase. This research project opens a new avenue for research into detailed chemical and biological studies on Syzygium cumini to isolate bioactive enzyme inhibitors. Furthermore, the isolated compound 1 friedelin was docked into the active site of β-secretase and α-glucosidase. The molecular docking was assessed using molecular docking via the MOE-Dock tool. The docking results showed good docking scores of −6.84 and −6.46 when docked against β-secretase and α-glucosidase, respectively, and strong interactions.
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Tevyashova AN, Chudinov MV. Progress in the medicinal chemistry of organoboron compounds. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4977] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The review aims to draw attention to the latest advances in the organoboron chemistry and therapeutic use of organoboron compounds. The synthetic strategies towards boron-containing compounds with proven in vitro and/or in vivo biological activities, including derivatives of boronic acids, benzoxaboroles, benzoxaborines and benzodiazaborines, are summarized. Approaches to the synthesis of hybrid structures containing an organoboron moiety as one of the pharmacophores are considered, and the effect of this modification on the pharmacological activity of the initial molecules is analyzed. On the basis of analysis of the published data, the most promising areas of research in the field of organoboron compounds are identified, including the latest methods of synthesis, modification and design of effective therapeutic agents.
The bibliography includes 246 references.
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Zhang C, Lu M, Lin L, Huang Z, Zhang R, Wu X, Chen Y. Riboflavin Is Directly Involved in N-Dealkylation Catalyzed by Bacterial Cytochrome P450 Monooxygenases. Chembiochem 2020; 21:2297-2305. [PMID: 32243060 DOI: 10.1002/cbic.202000071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/01/2020] [Indexed: 11/09/2022]
Abstract
Like a vast number of enzymes in nature, bacterial cytochrome P450 monooxygenases require an activated form of flavin as a cofactor for catalytic activity. Riboflavin is the precursor of FAD and FMN that serves as indispensable cofactor for flavoenzymes. In contrast to previous notions, herein we describe the identification of an electron-transfer process that is directly mediated by riboflavin for N-dealkylation by bacterial P450 monooxygenases. The electron relay from NADPH to riboflavin and then via activated oxygen to heme was proposed based on a combination of X-ray crystallography, molecular modeling and molecular dynamics simulation, site-directed mutagenesis and biochemical analysis of representative bacterial P450 monooxygenases. This study provides new insights into the electron transfer mechanism in bacterial P450 enzyme catalysis and likely in yeasts, fungi, plants and mammals.
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Affiliation(s)
- Chengchang Zhang
- Laboratory of Chemical Biology and State Key Laboratory of Natural Medicines, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu Province, 211198, P. R. China
| | - Meiling Lu
- Laboratory of Chemical Biology and State Key Laboratory of Natural Medicines, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu Province, 211198, P. R. China
| | - Lin Lin
- National Center for Protein Science and Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, P. R. China
| | - Zhangjian Huang
- Laboratory of Chemical Biology and State Key Laboratory of Natural Medicines, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu Province, 211198, P. R. China
| | - Rongguang Zhang
- National Center for Protein Science and Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, P. R. China
| | - Xuri Wu
- Laboratory of Chemical Biology and State Key Laboratory of Natural Medicines, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu Province, 211198, P. R. China
| | - Yijun Chen
- Laboratory of Chemical Biology and State Key Laboratory of Natural Medicines, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu Province, 211198, P. R. China
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Wang J, Liu J, Guo Y. Cell Growth Stimulation, Cell Cycle Alternation, and Anti-Apoptosis Effects of Bovine Bone Collagen Hydrolysates Derived Peptides on MC3T3-E1 Cells Ex Vivo. Molecules 2020; 25:E2305. [PMID: 32422931 PMCID: PMC7287833 DOI: 10.3390/molecules25102305] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/27/2020] [Accepted: 05/12/2020] [Indexed: 01/30/2023] Open
Abstract
Bovine bone collagen hydrolysates promote bone formation through regulating bone growth. However, the peptide sequences within these isolates have not been characterized. In this study, twenty-nine peptides from bovine bone collagen hydrolysates were purified and identified using nano-HPLC-MS-MS and Peak Studio analysis. HHGDQGAPGAVGPAGPRGPAGPSGPAGKDGR (Deamidation) and GPAGANGDRGEAGPAGPAGPAGPR (Deamidation) enhanced cell viability, inhibited apoptosis, and significantly altered the cell cycle of MC3T3-E1 osteoblast cells. These peptides were selected to perform molecular docking analysis to examine the mechanism underlying these bioactivities. Molecular docking analysis showed that these two peptides formed hydrophobic interactions and hydrogen bonds with epidermal growth factor receptor (EGFR) to activate the EGFR-signaling pathway, which may explain their bioactivity. These findings indicate that these and other similar peptides might be candidates for the treatment of osteoporosis.
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Affiliation(s)
- Jianing Wang
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (J.W.); (J.L.)
- School of Chemical Sciences, University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - Junli Liu
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (J.W.); (J.L.)
| | - Yanchuan Guo
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China; (J.W.); (J.L.)
- School of Chemical Sciences, University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
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Xu XT, Deng XY, Chen J, Liang QM, Zhang K, Li DL, Wu PP, Zheng X, Zhou RP, Jiang ZY, Ma AJ, Chen WH, Wang SH. Synthesis and biological evaluation of coumarin derivatives as α-glucosidase inhibitors. Eur J Med Chem 2020; 189:112013. [DOI: 10.1016/j.ejmech.2019.112013] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 12/26/2019] [Accepted: 12/26/2019] [Indexed: 12/13/2022]
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Majeed A, Ranjha NM, Hussain M, Rasool MF. Fabrication and evaluation of pH-dependent polymeric microspheres of ivabradine and their in vitro and in vivo studies. Polym Bull (Berl) 2019. [DOI: 10.1007/s00289-018-2546-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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9
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Abbasi MA, Ramzan MS, Aziz-ur-Rehman, Siddiqui SZ, Shah SAA, Hassan M, Seo SY, Ashraf M, Mirza B, Ismail H. N-(5-Methyl-1,3-Thiazol-2-yl)-2-{[5-((Un)Substituted- Phenyl)1,3,4-Oxadiazol-2-yl]Sulfanyl}acetamides. Unique Biheterocycles as Promising Therapeutic Agents. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s106816201806002x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Majeed A, Ranjha NM. Ivabradine HCL-Loaded Polymeric Microspheres Consisting of Ethyl Cellulose and Eudragit FS30D for Controlled Drug Release. ADVANCES IN POLYMER TECHNOLOGY 2018. [DOI: 10.1002/adv.21715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Abdul Majeed
- Faculty of Pharmacy; Bahauddin Zakariya University; Multan 60800 Pakistan
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Majeed A, Ranjha NM, Rasool MF, Hussain M. Development and evaluation of ivabradine microspheres for controlled release. BIOINSPIRED BIOMIMETIC AND NANOBIOMATERIALS 2018. [DOI: 10.1680/jbibn.17.00001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The objective of this study was to formulate and evaluate controlled release formulations of ivabradine hydrochloride (HCl)-loaded microspheres consisting of Kollicoat MAE 100 P and ethyl cellulose prepared by the oil-in-oil solvent evaporation method. The drug was encapsulated into microspheres by an in situ method by varying the polymer contents. The resultant microspheres were characterized with respect to drug loading, flow properties, Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), X-ray diffractometry (XRD), thermal analysis and release behavior. Chemically stable loaded microspheres were confirmed by FTIR, differential scanning calorimetry (DSC), thermogravimetric analysis and XRD. SEM images showed that the microspheres were spherical with smooth surfaces. FTIR spectra confirmed the presence of the drug in pure form and revealed no interaction between the drug and polymers. XRD and DSC were conducted to determine the nature of the drug in drug-loaded microspheres, and the results revealed that the drug was present in amorphous form. The maximum percentage entrapment efficiency was found to be 82 ± 2·11%, and the percentage yield was 89 ± 3·31%. The maximum in vitro drug release was more than 90% for pH 7·4, which demonstrated that drug-loaded formulations had a pH-dependent drug release. Cumulative drug release data were analyzed by using different kinetic models. The Korsmeyer–Peppas equation was used to determine the value of n which follows non-Fickian diffusion.
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Affiliation(s)
- Abdul Majeed
- Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
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12
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Aray Y, Aguilera-García R, Izquierdo DR. Exploring the nature of the H-bonds between the human class II MHC protein, HLA-DR1 (DRB*0101) and the influenza virus hemagglutinin peptide, HA306-318, using the quantum theory of atoms in molecules. J Biomol Struct Dyn 2017; 37:48-64. [PMID: 29246090 DOI: 10.1080/07391102.2017.1418432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The nature of the H-bonds between the human protein HLA-DR1 (DRB*0101) and the hemagglutinin peptide HA306-318 has been studied using the Quantum Theory of Atoms in Molecules for the first time. We have found four H-bond groups: one conventional CO··HN bond group and three nonconventional CO··HC, π··HC involving aromatic rings and HN··HCaliphatic groups. The calculated electron density at the determined H-bond critical points suggests the follow protein pocket binding trend: P1 (2,311) >> P9 (1.109) > P4 (0.950) > P6 (0.553) > P7 (0.213) which agrees and reveal the nature of experimental findings, showing that P1 produces by a long way the strongest binding of the HLA-DR1 human protein molecule with the peptide backbone as consequence of the vast number of H-bonds in the P1 area and at the same time the largest specific binding of the peptide Tyr308 residue with aromatic residues located at the binding groove floor. The present results suggest the topological analysis of the electronic density as a valuable tool that allows a non-arbitrary partition of the pockets binding energy via the calculated electron density at the determined critical points.
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Affiliation(s)
- Yosslen Aray
- a Facultad de Ciencias , Universidad de Ciencias Aplicadas y Ambientales, UDCA , Bogotá , Colombia
| | - Ricardo Aguilera-García
- a Facultad de Ciencias , Universidad de Ciencias Aplicadas y Ambientales, UDCA , Bogotá , Colombia
| | - Daniel R Izquierdo
- a Facultad de Ciencias , Universidad de Ciencias Aplicadas y Ambientales, UDCA , Bogotá , Colombia
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Salar U, Taha M, Khan KM, Ismail NH, Imran S, Perveen S, Gul S, Wadood A. Syntheses of new 3-thiazolyl coumarin derivatives, in vitro α-glucosidase inhibitory activity, and molecular modeling studies. Eur J Med Chem 2016; 122:196-204. [PMID: 27371923 DOI: 10.1016/j.ejmech.2016.06.037] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 06/02/2016] [Accepted: 06/20/2016] [Indexed: 11/26/2022]
Abstract
3-Thiazolylcoumarin derivatives 1-14 were synthesized via one-pot two step reactions, and screened for in vitro α-glucosidase inhibitory activity. All compounds showed inhibitory activity in the range of IC50 = 0.12 ± 0.01-16.20 ± 0.23 μM as compared to standard acarbose (IC50 = 38.25 ± 0.12 μM), and also found to be nontoxic. Molecular docking study was carried out in order to establish the structure-activity relationship (SAR) which demonstrated that electron rich centers at one and electron withdrawing centers at the other end of the molecules showed strong inhibitory activity. All the synthesized compounds were characterized by spectroscopic techniques such as EI-MS, HREI-MS, (1)H NMR and (13)C NMR. CHN analysis was also performed.
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Affiliation(s)
- Uzma Salar
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Muhammad Taha
- Atta-ur-Rahman Institute for Natural Product Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam Campus, 42300 Bandar Puncak Alam, Selangor D. E., Malaysia; Faculty of Applied Science Universiti Teknologi MARA, Shah Alam 40450, Selangor D. E., Malaysia.
| | - Khalid Mohammed Khan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Nor Hadiani Ismail
- Atta-ur-Rahman Institute for Natural Product Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam Campus, 42300 Bandar Puncak Alam, Selangor D. E., Malaysia; Faculty of Applied Science Universiti Teknologi MARA, Shah Alam 40450, Selangor D. E., Malaysia
| | - Syahrul Imran
- Atta-ur-Rahman Institute for Natural Product Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam Campus, 42300 Bandar Puncak Alam, Selangor D. E., Malaysia; Faculty of Applied Science Universiti Teknologi MARA, Shah Alam 40450, Selangor D. E., Malaysia
| | - Shahnaz Perveen
- PCSIR Laboratories Complex, Karachi, Shahrah-e-Dr. Salimuzzaman Siddiqui, Karachi 75280, Pakistan
| | - Sahib Gul
- Department of Biochemistry, Computational Medicinal Chemistry Laboratory, UCSS, Abdul Wali Khan University, Mardan, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Computational Medicinal Chemistry Laboratory, UCSS, Abdul Wali Khan University, Mardan, Pakistan
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Dehghanian F, Kay M, Kahrizi D. A novel recombinant AzrC protein proposed by molecular docking and in silico analyses to improve azo dye's binding affinity. Gene 2015; 569:233-8. [PMID: 26026905 DOI: 10.1016/j.gene.2015.05.063] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/23/2015] [Accepted: 05/25/2015] [Indexed: 10/23/2022]
Abstract
Azo dyes are broadly used in different industries through their chemical stability and ease of synthesis. These dyes are usually identified as critical environmental pollutants and many attentions were performed to degradation of azo dyes using biological systems. In this study, the interactions of an azoreductase from mesophilic gram-positive Bacillus sp. B29, AzrC, with four common azo dyes (orange I, orange II, orange G and acid red 88) were investigated. Fifteen points, double, triple and quadruple mutant forms of AzrC were made using Molegro Virtual Docker 6.0 in order to improve the binding affinity of azo dyes to AzrC. The impact of 15 different mutations on azo dye affinity potency of AzrC was computationally analyzed using AzrC-azo dye molecular docking, and each interaction was scored based on AutoDock 4.2 free binding energy. Our results have indicated that Asn 104 (A), Asn 187 (B), and Tyr 151 (A) make stable hydrogen bond between AzrC and azo dyes. The hydrophobic amino acids like Phe105 (A), Phe 125 (B), and Phe 172 (B) in wild type form make hydrophobic interactions. In addition, the presence of more hydrophobic residues F60 (B), I119 (B), I121 (B) and F132 (B) in mutant forms made more powerful hydrophobic pocket in the active site. In conclusion, recombinant AzrC with quadruple mutations was suggested in order to increase the biodegradation capacity of AzrC through improving its affinity to four studied azo dyes. This study would be promising for future experimental analyses in order to produce recombinant form of AzrC.
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Affiliation(s)
- Fariba Dehghanian
- Division of Genetics, Biology Department, Faculty of Sciences, University of Isfahan, Isfahan, Iran.
| | - Maryam Kay
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Danial Kahrizi
- Department of Agronomy and Plant Breeding, Razi University, Kermanshah, Iran; Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Poly(ADP-ribose) polymerase (PARP)-based pharmacophore model development and its application in designing antitumor inhibitors. J Taiwan Inst Chem Eng 2015. [DOI: 10.1016/j.jtice.2014.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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16
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Riaz S, Khan IU, Yar M, Ashraf M, Rehman TU, Shaukat A, Jamal SB, Duarte VC, Alves MJ. Novel pyridine-2,4,6-tricarbohydrazide derivatives: Design, synthesis, characterization and in vitro biological evaluation as α- and β-glucosidase inhibitors. Bioorg Chem 2014; 57:148-154. [DOI: 10.1016/j.bioorg.2014.10.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 10/25/2014] [Accepted: 10/29/2014] [Indexed: 10/24/2022]
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17
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Wadood A, Jamal SB, Riaz M, Mir A. Computational analysis of benzofuran-2-carboxlic acids as potent Pim-1 kinase inhibitors. PHARMACEUTICAL BIOLOGY 2014; 52:1170-1178. [PMID: 24766364 DOI: 10.3109/13880209.2014.880488] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
CONTEXT The three Pim serine/threonine kinases (Pim-1, Pim-2, and Pim-3) belong to a small family of kinases that regulate numerous signaling pathways fundamental to the development of tumors. Pim kinases' overexpression has been reported in numerous solid and hematological tumors and, in particular, prostate cancer (Pim-1). OBJECTIVES This study investigated the binding modes of benzofuran-2-carboxlic acids against Pim-1 kinase, hence providing useful information for the active inhibition of it. MATERIALS AND METHODS In present study, molecular docking approach via MOE-Dock program was applied to predict the binding interactions of some known Pim-1 kinase inhibitors. First validation of the docking protocol was carried out by calculating RMSD for the co-crystallized and docked ligands. Using the same protocol, all the compounds were docked into the active site of Pim-1 kinase. RESULTS All the compounds showed significant interactions and good correlation with the experimental data. The results illustrate that compounds with optimum basicity and relevant distance between the acidic and basic groups showed optimum interactions with the active site residues of Pim-1 kinase. CONCLUSION We hope that this study will be helpful in designing new, structurally diverse and more potent compounds for the active treatment of prostate cancer and other related diseases caused by deregulation of Pim-1 kinase.
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Affiliation(s)
- Abdul Wadood
- Computational Medicinal Chemistry Laboratory, Department of Biochemistry, Abdul Wali Khan University , Mardan , Pakistan and
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Wadood A, Riaz M, Uddin R, ul-Haq Z. In silico identification and evaluation of leads for the simultaneous inhibition of protease and helicase activities of HCV NS3/4A protease using complex based pharmacophore mapping and virtual screening. PLoS One 2014; 9:e89109. [PMID: 24551230 PMCID: PMC3923879 DOI: 10.1371/journal.pone.0089109] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/17/2014] [Indexed: 01/09/2023] Open
Abstract
Hepatitis C virus (HCV) infection is an alarming and growing threat to public health. The present treatment gives limited efficacy and is poorly tolerated, recommending the urgent medical demand for novel therapeutics. NS3/4A protease is a significant emerging target for the treatment of HCV infection. This work reports the complex-based pharmacophore modeling to find out the important pharmacophoric features essential for the inhibition of both protease and helicase activity of NS3/4A protein of HCV. A seven featured pharmacophore model of HCV NS3/4A protease was developed from the crystal structure of NS3/4A protease in complex with a macrocyclic inhibitor interacting with both protease and helicase sites residues via MOE pharmacophore constructing tool. It consists of four hydrogen bond acceptors (Acc), one hydrophobic (Hyd), one for lone pair or active hydrogen (Atom L) and a heavy atom feature (Atom Q). The generated pharmacophore model was validated by a test database of seventy known inhibitors containing 55 active and 15 inactive/least active compounds. The validated pharmacophore model was used to virtually screen the ChemBridge database. As a result of screening 1009 hits were retrieved and were subjected to filtering by Lipinski’s rule of five on the basis of which 786 hits were selected for further assessment using molecular docking studies. Finally, 15 hits of different scaffolds having interactions with important active site residues were predicted as lead candidates. These candidates having unique scaffolds have a strong likelihood to act as further starting points in the development of novel and potent NS3/4A protease inhibitors.
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Affiliation(s)
- Abdul Wadood
- Computational Medicinal Chemistry Laboratory, Department of Biochemistry Abdul Wali Khan University Mardan, Mardan, Khyber Pakhthunkhwa, Pakistan
- * E-mail:
| | - Muhammad Riaz
- Computational Medicinal Chemistry Laboratory, Department of Biochemistry Abdul Wali Khan University Mardan, Mardan, Khyber Pakhthunkhwa, Pakistan
| | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, University of Karachi, Karach, Sindh, Pakistan
| | - Zaheer ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, University of Karachi, Karach, Sindh, Pakistan
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