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Shad M, Rehman HM, Akhtar MW, Sajjad M. Structural and functional insights of starch processing α-amylase from hyperthermophilic archaeon Pyrococcusabyssi. Carbohydr Res 2024; 539:109122. [PMID: 38657354 DOI: 10.1016/j.carres.2024.109122] [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: 01/19/2024] [Revised: 03/26/2024] [Accepted: 04/16/2024] [Indexed: 04/26/2024]
Abstract
The genomic screening of hyper-thermophilic Pyrococcus abyssi showed uncharacterized novel α-amylase sequences. Homology modelling analysis revealed that the α-amylase from P. abyssi consists of an N-terminal GH57 catalytic domain, α-amylase central, and C-terminal domain. Current studies emphasize in-silico structural and functional analysis, recombinant expression, characterization, structural studies through CD spectroscopy, and ligand binding studies of the novel α-amylase from P. abyssi. The soluble expression of PaAFG was observed in the E. coli Rosetta™ (DE3) pLysS strain upon incubation overnight at 18 °C in an orbital shaker. The optimum temperature and pH of the PaAFG were observed at 90 °C in 50 mM phosphate buffer pH 6. The Km value for PaAFG against wheat starch was determined as 0.20 ± 0.053 mg while the corresponding Vmax value was 25.00 ± 0.67 μmol min-1 mg-1 in the presence of 2 mM CaCl2 and 12.5 % glycerol. The temperature ramping experiments through CD spectroscopy reveal no significant change in the secondary structures and positive and negative ellipticities of the CD spectra showing the proper folding and optimal temperature of PaAFG protein. The RMSD and RMSF of the PaAFG enzyme determined through molecular dynamic simulation show the significant protein's stability and mobility. The soluble production, thermostability and broad substrate specificity make this enzyme a promising choice for various industrial applications.
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Affiliation(s)
- Mohsin Shad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, P.O. 54590, Lahore, Pakistan; Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Quaid-e-Azam Campus, P.O. 54590, Lahore, Pakistan
| | - Muhammad Waheed Akhtar
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, P.O. 54590, Lahore, Pakistan
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, P.O. 54590, Lahore, Pakistan.
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2
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El-Mernissi R, Khaldan A, Bouamrane S, Rehman HM, Alaqarbeh M, Ajana MA, Lakhlifi T, Bouachrine M. 3D-QSAR, molecular docking, simulation dynamic and ADMET studies on new quinolines derivatives against colorectal carcinoma activity. J Biomol Struct Dyn 2024; 42:3682-3699. [PMID: 37227776 DOI: 10.1080/07391102.2023.2214233] [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: 12/09/2022] [Accepted: 05/10/2023] [Indexed: 05/27/2023]
Abstract
Cancer is the uncontrolled spread of abnormal cells that results in abnormal tissue growth in the affected organ. One of the most important organs is exposed to the growth of colon cancer cells, which start in the large intestine (colon) or the rectum. Several therapeutic protocols were used to treat different kinds of cancer. Recently, several studies have targeted tubulin and microtubules due to their remarkable prefoliation. Also, recent research shows that quinoline compounds have significant efficacy against human colorectal cancer. So, the present work investigated the potential of thirty quinoline compounds as tubulin inhibitors using computational methods. A 3D-QSAR approach using two contours (CoMFA and CoMSIA), molecular docking simulation to determine the binding type of the complexes (ligand-receptor), molecular dynamics simulation and identifying pharmacokinetic characteristics were used to design molecules. For all compounds designed (T1-5), molecular docking was used to compare the stability by type of binding. The ADMET has been utilized for molecules with good stability in molecular docking (T1-3); these compounds have good medicinal characteristics. Furthermore, a molecular dynamics simulation (MD) at 100 ns was performed to confirm the stability of the T1-3 compounds; the molecules (T1-3) remained the most stable throughout the simulation. The compounds T1, T2 and T3 are the best-designed drugs for colorectal carcinoma treatments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Reda El-Mernissi
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - Ayoub Khaldan
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - Soukaina Bouamrane
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | | | | | - Mohammed Aziz Ajana
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - Tahar Lakhlifi
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - Mohammed Bouachrine
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
- EST Khenifra, Sultan Moulay Sliman University, Beni mellal, Morocco
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Mohamed SK, Ahsin A, Rehman HM, Mohammed HH, Mague JT, Al-Salahi R, El Bakri Y, Hussein BRM. XRD/DFT, Hirshfeld surface analysis and molecular modelling simulations for unfolding reactivity of newly synthesized vanillin derivatives: excellent optical, NLO and protein binding efficiency. J Biomol Struct Dyn 2024:1-19. [PMID: 38305762 DOI: 10.1080/07391102.2024.2308774] [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: 08/27/2023] [Accepted: 01/14/2024] [Indexed: 02/03/2024]
Abstract
New vanillin derivatives, namely, ethyl (4-formyl-2-methoxyphenoxy)acetate (2a) and 2-(4-formyl-2-methoxyphenoxy)-N-phenylacetamide (2b), respectively, were synthesized and characterized by NMR (1H and 13C), IR, mass spectra and confirmed by single-crystal X-ray analysis. Hirshfeld surface (HS) analysis was performed to probe intra- and intermolecular interactions and surface reactivity. 2D fingerprint plots (FP) were used to study the nature and percentage contribution of intermolecular interactions leading to the formation of the crystal unit. Density functional theory (DFT) simulations were used to obtain the electronic structure and reactivity of the new molecules. Natural population analysis (NPA) and frontier molecular orbital (FMO) calculations reveal significant charge transfer and a reduced HOMO-LUMO gap up to 4.34 eV for 2b. Bader's quantum theory of atoms in molecules (QTAIM) study is utilized to understand the surface topological and bonding nature of 2a and 2b. The performed molecular electrostatic potential (MESP) and density of states (DOS) study further suggest sites likely to be attractive to incoming reagents. At the same time, hyperpolarizability (βo) is used to characterize the nonlinear optical properties, and TD-DFT study shows the excitation energy and absorption behavior. In silico studies were performed, including docking, binding free energies (MMBGSA) and molecular dynamics simulations. Compounds 2a and 2b were docked with RdRp of SARS-Cov-2, and the MMBGSA for 2a and 2b were -30.70 and -28.47 kcal/mol, respectively, while MD simulation showed the stability of protein-ligand complexes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shaaban K Mohamed
- Chemistry and Environmental Division, Manchester Metropolitan University, Manchester, UK
| | - Atazaz Ahsin
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Hayam H Mohammed
- Department of Chemistry, Faculty of Science, Sohag University, Sohag, Egypt
| | - Joel T Mague
- Department of Chemistry, Tulane University, New Orleans, LA, USA
| | - Rashad Al-Salahi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russian Federation
| | - Bahgat R M Hussein
- Department of Chemistry, Faculty of Science, Sohag University, Sohag, Egypt
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Kaur G, Bansal M, Rehman HM, Kaur M, Kaur A. Synthesis and studies of new purines/pyrimidine derivatives as multi-targeted agents involving various receptor sites in the immune system. Mol Divers 2024; 28:97-110. [PMID: 36853528 PMCID: PMC9972316 DOI: 10.1007/s11030-023-10616-8] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 01/23/2023] [Indexed: 03/01/2023]
Abstract
Pro-inflammation, which is developed due to the increased production of cytokines, mainly interleukin-6 (IL-6), during the working of immune system pathways, becomes a major concern these days for many researchers. So, it is desired to design, screen, and synthesize new molecules with multi-parametric features showing their efficacy for Toll-like receptors (TLRs) and inhibiting the disease-causing receptor sites like viral infections, cancers, etc. along with controlling inflammation, fever, and other side effects during such pathways. Further, looking at the literature, curcumin a multi-targeted agent is showing its efficiency toward various receptor sites involved in many diseases as mentioned above. This fascinated us to build up new molecules which behave like curcumin with minimum side effects. In silico studies, involving ADMET studies, toxicological data, and docking analyses, of newly synthesized compounds (3-5) along with tautomers of curcumin i.e., (1-2), and some reported compounds like 9 and 10 have been studied in detail. Great emphasis has been made on analyzing binding energies, protein-ligand structural interactions, stabilization of newly synthesized molecules against various selected receptor sites using such computational tools. Compound 3 is the most efficient multifunctional agent, which has shown its potential toward most of the receptor sites in docking analysis. It has also responded well in Molecular dynamics (MD) simulation toward 5ZLN, 4RJ3, 4YO9, 4YOJ, and 1I1R sites. Finally, studies were extended to understand in vitro anti-inflammatory activity for particularly compound 3 in comparison to diclofenac and curcumin, which signifies the efficiency of compound 3.
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Affiliation(s)
- Gurmeet Kaur
- Synthetic and Medicinal Chemistry Laboratory, Department of Chemistry, Punjabi University, Patiala, 147002, India
| | - Manisha Bansal
- Department of Chemistry, Punjabi University, Patiala, 147002, India.
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Mandeep Kaur
- Synthetic and Medicinal Chemistry Laboratory, Department of Chemistry, Punjabi University, Patiala, 147002, India
| | - Amandeep Kaur
- Synthetic and Medicinal Chemistry Laboratory, Department of Chemistry, Punjabi University, Patiala, 147002, India
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Hosen MA, El Bakri Y, Rehman HM, Hashem HE, Saki M, Kawsar SMA. A computational investigation of galactopyranoside esters as antimicrobial agents through antiviral, molecular docking, molecular dynamics, pharmacokinetics, and bioactivity prediction. J Biomol Struct Dyn 2024; 42:1015-1030. [PMID: 37027788 DOI: 10.1080/07391102.2023.2198606] [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: 11/22/2022] [Accepted: 03/25/2023] [Indexed: 04/09/2023]
Abstract
One of the most common viral infections worldwide is the Human Papilloma Virus (HPV) which has been linked to cancer and other diseases in many countries. Monosaccharide esters are significant in the field of carbohydrate chemistry because they are efficient in the synthesis of pharmacologically active compounds. Therefore, the present study aimed to perform thermodynamic, molecular docking and molecular dynamics study of a series of previously designed monosaccharaides, methyl β-d-galactopyranoside (MGP, 1) esters (2-10) with along with their physicochemical and pharmacokinetic properties. We have optimized the MGP esters employing the DFT study at the B3LYP/6-311 + G (d,p) level of theory. The subsequent analysis also investigated the electronic energies, enthalpies, entropies, polarizability, and natural bond orbital (NBO) of these modified esters. Then, MGP esters were docked into CTX-M-15 extended-spectrum beta-lactamase from Escherichia coli (PDB: 4HBT) and E2 DNA-binding domain from human papillomavirus type 31 (PDB: 1A7G), and the results revealed that most of the esters can efficiently bind to the target. Desmond was used to doing molecular dynamics simulations at 200 ns in addition to molecular docking to look at the binding conformational stability of the protein-ligand complex. Based on RMSD and RMSF, it was determined that the stability of the protein-ligand combination was maintained during the whole 200 ns simulations for all compounds. Finally, a pharmacokinetic study suggests that modified esters of MGP exhibited better pharmacokinetic characteristics and were less hazardous than the parent drug. This work demonstrated that potential MGP esters can efficiently bind to 4HBT and 1A7G proteins and opened avenues for the development of newer antimicrobial agents that can target dangerous pathogens.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammed A Hosen
- Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
| | - Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russian Federation
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
- Alnoorians Group of Institutes, Lahore, Pakistan
| | - Heba E Hashem
- Department of Chemistry, Faculty of Women, Ain Shams University, Cairo, Egypt
| | - Morteza Saki
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sarkar M A Kawsar
- Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
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Naveed M, Jabeen K, Aziz T, Mughual MS, Ul-Hassan J, Sheraz M, Rehman HM, Alharbi M, Albekairi TH, Alasmari AF. Whole proteome analysis of MDR Klebsiella pneumoniae to identify mRNA and multiple epitope based vaccine targets against emerging nosocomial and lungs associated infections. J Biomol Struct Dyn 2023:1-14. [PMID: 38141172 DOI: 10.1080/07391102.2023.2293266] [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: 05/21/2023] [Accepted: 11/29/2023] [Indexed: 12/25/2023]
Abstract
Klebsiella pneumonia is a Gram negative facultative anaerobic bacterium involved in various community-acquired pneumonia, nosocomial and lungs associated infections. Frequent usage of several antibiotics and acquired resistance mechanisms has made this bacterium multi-drug resistance (MDR), complicating the treatment of patients. To avoid the spread of this bacterium, there is an urgent need to develop a vaccine based on immuno-informatics approaches that is more efficient than conventional method of vaccine prediction or development. Initially, the complete proteomic sequence of K. pneumonia was picked over for specific and prospective vaccine targets. From the annotation of the whole proteome, eight immunogenic proteins were selected, and these shortlisted proteins were interpreted for CTL, B-cells, and HTL epitopes prediction, to construct mRNA and multi-epitope vaccines. The Antigenicity, allergenicity and toxicity analysis validate the vaccine's design, and its molecular docking was done with immuno-receptor the TLR-3. The docking interaction showed a stronger binding affinity with a minimum energy of -1153.2 kcal/mol and established 23 hydrogen bonds, 3 salt bridges, 1 disulfide bond, and 340 non-binding contacts. Further validation was done using In-silico cloning which shows the highest CAI score of 0.98 with higher GC contents of 72.25% which represents a vaccine construct with a high value of expression in E. coli. Immune Simulation shows that the antibodies (IgM, IgG1, and IgG2) production exceeded 650,000 in 2 to 3 days but the response was completely neutralized in the 5th day. In conclusion, the study provides the effective, safe and stable vaccine construct against Klebsiella pneumonia, which further needs in vitro and in vivo validations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muhammad Naveed
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Khizra Jabeen
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Tariq Aziz
- Department of Agriculture, University of Ioannina, Arta, Greece
| | - Muhammad Saad Mughual
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Jawad Ul-Hassan
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Mohsin Sheraz
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | | | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Thamer H Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah F Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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Belghalia E, Ouabane M, El Bahi S, Rehman HM, Sbai A, Lakhlifi T, Bouachrine M. In silico research on new sulfonamide derivatives as BRD4 inhibitors targeting acute myeloid leukemia using various computational techniques including 3D-QSAR, HQSAR, molecular docking, ADME/Tox, and molecular dynamics. J Biomol Struct Dyn 2023:1-19. [PMID: 37656159 DOI: 10.1080/07391102.2023.2250460] [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: 06/20/2023] [Accepted: 08/15/2023] [Indexed: 09/02/2023]
Abstract
Acute myeloid leukemia, a serious condition affecting stem cells, drives uncontrollable myeloblast proliferation, leading to accumulation. Extensive research seeks rapid, effective chemotherapeutics. A potential option is a BRD4 inhibitor, known for suppressing cell proliferation. Sulfonamide derivatives probed essential structural elements for potent BRD4 inhibitors. To achieve this goal, we employed 3D-QSAR molecular modeling techniques, including CoMFA, CoMSIA, and HQSAR models, along with molecular docking and molecular dynamics simulations. The validation of the 2D/3D QSAR models, both internally and externally, underscores their robustness and reliability. The contour plots derived from CoMFA, CoMSIA, and HQSAR analyses played a pivotal role in shaping the design of effective BRD4 inhibitors. Importantly, our findings highlight the advantageous impact of incorporating bulkier substituents on the pyridinone ring and hydrophobic/electrostatic substituents on the methoxy-substituted phenyl ring, enhancing interactions with the BRD4 target. The interaction mode of the new compounds with the BRD4 receptor (PDB ID: 4BJX) was investigated using molecular docking simulations, revealing favorable binding energies, supported by the formation of hydrogen and hydrophobic bonds with key protein residues. Moreover, these novel inhibitors exhibited good oral bioavailability and demonstrated non-toxic properties based on ADMET analysis. Furthermore, the newly designed compounds along with the most active one from series 58, underwent a molecular dynamics simulation to analyze their behavior. The simulation provided additional evidence to support the molecular docking results, confirming the sustained stability of the analyzed molecules over the trajectory. This outcome could serve as a valuable reference for designing and developing novel and effective BRD4 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Etibaria Belghalia
- Molecular chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - Mohamed Ouabane
- Molecular chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
- Chemistry- Biologie Applied to the Environment URL CNRT 13, Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Salma El Bahi
- Molecular chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | | | - Abdelouahid Sbai
- Molecular chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - Tahar Lakhlifi
- Molecular chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - Mohammed Bouachrine
- Higher School of Technology - Khenifra (EST-Khenifra), University of Sultan My Slimane, Beni Mellal, Morocco
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Hassan HA, Abdelwahab SF, Al-Khdhairawi A, Al Zrkani MK, Rehman HM, Abdel-Rahman IM, El-Sheikh AAK, Abdelhamid MM. Exploring the therapeutic potential of galidesivir analogs against Zaire ebolavirus protein 24 (V24): database screening, molecular docking, drug-relevant property evaluation and molecular dynamics simulations. J Biomol Struct Dyn 2023:1-11. [PMID: 37477257 DOI: 10.1080/07391102.2023.2236720] [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] [Indexed: 07/22/2023]
Abstract
The recent outbreak of the Ebola virus (EBOV) has marked it as one of the most severe health threats globally. Among various anti-EBOV inhibitors studied, galidesivir (BCX4430) has shown remarkable efficacy. This study aims to identify novel potential anti-EBOV drugs among galidesivir analogs, focusing on the Zaire ebolavirus (Z-EBOV), which exhibits a mortality rate of 90%. We subjected 200 candidate compounds to molecular docking calculations, followed by an evaluation of the bioactivity of the top 25 compounds using the OSIRIS Property Explorer. Initial 50 ns molecular dynamics (MD) simulations were then performed. According to our findings, only six compounds exhibited positive drug scores. We further performed molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) calculations of binding energy over 50 ns, selecting the two top-performing compounds for extended 150 ns MD simulations. CID 117698807 and CID 117712809 showed higher binding stability compared to galidesivir, with ΔGbinding values of -36.7 and -53.4 kcal/mol, respectively. Both compounds demonstrated high stability within the Z-EBOV-V24 active site over the 150 ns MD simulations. Hence, our study proposes CID 117698807 and CID 117712809 as potential anti-Z-EBOV-V24 drug candidates, warranting further investigation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Heba Ali Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Sohag University, Sohag, Egypt
| | - Sayed F Abdelwahab
- Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Ahmad Al-Khdhairawi
- Department of Biological Science and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Mrtatha K Al Zrkani
- Institute of Genetic Engineering & Biotechnology Research, Baghdad University, Iraq
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore, Pakistan
| | - Islam M Abdel-Rahman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, New-Minia, Egypt
| | - Azza A K El-Sheikh
- Basic Health Sciences Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mahmoud M Abdelhamid
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut, Egypt
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Huang X, Liu Y, Wang Q, Rehman HM, Horváth D, Zhou S, Fu R, Zhang L, Szöllősi AG, Li Z. Brief literature review and comprehensive bioinformatics analytics unravel the potential mechanism of curcumin in the treatment of periodontitis. BMC Oral Health 2023; 23:469. [PMID: 37422651 PMCID: PMC10329799 DOI: 10.1186/s12903-023-03181-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 06/28/2023] [Indexed: 07/10/2023] Open
Abstract
OBJECTIVE Periodontitis is a chronic oral disease prevalent worldwide, and natural products are recommended as adjunctive therapy due to their minor side effects. Curcumin, a widely used ancient compound, has been reported to possess therapeutic effects in periodontitis. However, the exact mechanism underlying its activity remains unclear. In this context, the present study aimed to conduct computational simulations to uncover the potential mechanism of action of Curcumin in the treatment of periodontitis. MATERIALS AND METHODS Single-cell analysis was conducted using a dataset (i.e., GSE164241) curated from the Gene Expression Omnibus (GEO) database through an R package "Seurat package." Bulk RNA sequencing data were curated from GSE10334 and GSE16134 and processed by R package "Limma." Then, the marker genes in the single-cell transcriptome and differentially expressed genes (DEGs) in the bulk transcriptome were integrated. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were also carried out to reveal their functionalities. Key targets were mined from their protein-protein interaction (PPI) network topologically. Afterward, molecular docking was performed. The top-ranked pose was subjected to molecular dynamics simulations to investigate the stability of the docking result. RESULTS FOS, CXCL1, CXCL8, and IL1B, were filtered after a series of selected processes. The results of molecular modeling suggested that except for IL1B, the Vena Scores of the rest exceeded -5 kcal/mol. Furthermore, the molecular dynamic simulation indicated that the binding of the CXCL8-Curcumin complex was stable over the entire 100 ns simulation. CONCLUSION The present study unlocked the binding modes of CXCL1, FOS, and CXCL8 with the Curcumin molecule, which were relatively stable, especially for CXCL8, hindering its promising potential to serve as the critical targets of Curcumin in periodontitis treatment.
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Affiliation(s)
- Xufeng Huang
- Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
- Department of Immunology, University of Debrecen, Debrecen, Hungary
| | - Ying Liu
- Department of Cardiology, Sixth Medical Center, PLA General Hospital, Beijing, China
| | - Qi Wang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, LahorePunjab, 54590 Pakistan
- Alnoorians Group of Institutes, 55-Elahi Bukhsh Park, Amir Road, Shad Bagh, Lahore, 54000 Pakistan
| | - Dorottya Horváth
- Department of Immunology, University of Debrecen, Debrecen, Hungary
| | - Shujing Zhou
- Department of Immunology, University of Debrecen, Debrecen, Hungary
| | - Rao Fu
- Department of Oral and Maxillofacial-Head and Neck Oncology, College of Stomatology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology and National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Ling Zhang
- Department of Oral and Maxillofacial-Head and Neck Oncology, College of Stomatology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology and National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | | | - Zhengrui Li
- Department of Oral and Maxillofacial-Head and Neck Oncology, College of Stomatology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology and National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
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Aslam S, Rehman HM, Sarwar MZ, Ahmad A, Ahmed N, Amirzada MI, Rehman HM, Yasmin H, Nadeem T, Bashir H. Computational Modeling, High-Level Soluble Expression and In Vitro Cytotoxicity Assessment of Recombinant Pseudomonas aeruginosa Azurin: A Promising Anti-Cancer Therapeutic Candidate. Pharmaceutics 2023; 15:1825. [PMID: 37514012 PMCID: PMC10383417 DOI: 10.3390/pharmaceutics15071825] [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: 05/10/2023] [Revised: 05/31/2023] [Accepted: 06/13/2023] [Indexed: 07/30/2023] Open
Abstract
Azurin is a natural protein produced by Pseudomonas aeruginosa that exhibits potential anti-tumor, anti-HIV, and anti-parasitic properties. The current study aimed to investigate the potential of azurin protein against breast cancer using both in silico and in vitro analyses. The amino acid sequence of Azurin was used to predict its secondary and tertiary structures, along with its physicochemical properties, using online software. The resulting structure was validated and confirmed using Ramachandran plots and ERRAT2. The mature azurin protein comprises 128 amino acids, and the top-ranked structure obtained from I-TASSER was shown to have a molecular weight of 14 kDa and a quality factor of 100% by ERRAT2, with 87.4% of residues in the favored region of the Ramachandran plot. Docking and simulation studies of azurin protein were conducted using HDOCK and Desmond servers, respectively. The resulting analysis revealed that Azurin docked against p53 and EphB2 receptors demonstrated maximum binding affinity, indicating its potential to cause apoptosis. The recombinant azurin gene was successfully cloned and expressed in a BL21 (DE3) strain using a pET20b expression vector under the control of the pelB ladder, followed by IPTG induction. The azurin protein was purified to high levels using affinity chromatography, yielding 70 mg/L. In vitro cytotoxicity assay was performed using MCF-7 cells, revealing the significant cytotoxicity of the azurin protein to be 105 µg/mL. These findings highlight the potential of azurin protein as an anticancer drug candidate.
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Affiliation(s)
- Shakira Aslam
- Centre for Applied Molecular Biology, University of the Punjab, Lahore 54590, Pakistan
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Pakistan
- Department of Human Genetics and Molecular Biology, University of Health Science, Lahore 54600, Pakistan
| | | | - Ajaz Ahmad
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Nadeem Ahmed
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 54000, Pakistan
- International Center for Genetic Engineering and Biotechnology, Galleria Padriciano, 99, 34149 Trieste, TS, Italy
| | - Muhammad Imran Amirzada
- Department of Pharmacy, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22010, Pakistan
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214082, China
| | - Hafiz Muhammad Rehman
- Centre for Applied Molecular Biology, University of the Punjab, Lahore 54590, Pakistan
- University Institute of Medical Laboratory Technology, Faculty of Allied Health Sciences, The University of Lahore, Lahore 54000, Pakistan
| | - Humaira Yasmin
- Department of Infectious Diseases, Faculty of Medicine, South Kensington Campus, Imperial College, London W2 1NY, UK
- Department of Biosciences, COMSATS University Islamabad, Islamabad 54000, Pakistan
| | - Tariq Nadeem
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 54000, Pakistan
| | - Hamid Bashir
- Centre for Applied Molecular Biology, University of the Punjab, Lahore 54590, Pakistan
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Muhammad Rehman H, Rehman HM, Naveed M, Khan MT, Shabbir MA, Aslam S, Bashir H. In Silico Investigation of a Chimeric IL24-LK6 Fusion Protein as a Potent Candidate Against Breast Cancer. Bioinform Biol Insights 2023; 17:11779322231182560. [PMID: 37377793 PMCID: PMC10291407 DOI: 10.1177/11779322231182560] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Targeted delivery of therapeutic anticancer chimeric molecules enhances the efficacy of drug by improving cellular uptake and circulation time. Engineering the molecules to facilitate the specific interaction between chimeric protein and its receptor is critical to elucidate biological mechanism as well as accuracy in modeling of complexes. A theoretically designed novel protein-protein interfaces can serve as a bottom-up method for comprehensive understanding of interacting protein residues. This study was aimed for in silico analyses of a chimeric fusion protein against breast cancer. The amino acid sequences of the interleukin 24 (IL-24) and LK-6 peptide were used to design the chimeric fusion protein via a rigid linker. The secondary and tertiary structures along with physicochemical properties by ProtParam and solubility were predicted using online software. The validation and quality of the fusion protein was confirmed by Rampage and ERRAT2. The newly designed fusion construct has a total length of 179 amino acids. The top-ranked structure from alpha fold2 showed 18.1 KD molecular weight by ProtParam, quality factor of 94.152 by ERRAT, and a valid structure by a Ramachandran plot with 88.5% residues in the favored region. Finally, the docking and simulation studies were performed using HADDOCK and Desmond module of Schrodinger. The quality, validity, interaction analysis, and stability of the fusion protein depict a functional molecule. The fusion gene IL24-LK6 after cloning and expression in a suitable prokaryotic cell might be a useful candidate for developing a novel anticancer therapy.
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Affiliation(s)
- Hafiz Muhammad Rehman
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
- University Institute of Medical Lab Technology, Faculty of Allied Health Sciences, The University of Lahore, Pakistan
| | - Hafiz Muzzammel Rehman
- School of Biochemistry & Biotechnology, University of the Punjab, Lahore, Pakistan
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore, Pakistan
| | - Muhammad Naveed
- Department of Biotechnology, Faculty of Science & Technology, University of Central Punjab, Lahore, Pakistan
| | - Muhammad Tahir Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Aqib Shabbir
- Department of Biotechnology, Faculty of Science & Technology, University of Central Punjab, Lahore, Pakistan
| | - Shakira Aslam
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
| | - Hamid Bashir
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
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12
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Shinwari K, Wu Y, Rehman HM, Xiao N, Bolkov M, Tuzankina I, Chereshnev V. In-silico assessment of high-risk non-synonymous SNPs in ADAMTS3 gene associated with Hennekam syndrome and their impact on protein stability and function. BMC Bioinformatics 2023; 24:251. [PMID: 37322437 DOI: 10.1186/s12859-023-05361-6] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/25/2023] [Indexed: 06/17/2023] Open
Abstract
Hennekam Lymphangiectasia-Lymphedema Syndrome 3 (HKLLS3) is a rare genetical disorder caused by mutations in a few genes including ADAMTS3. It is characterized by lymphatic dysplasia, intestinal lymphangiectasia, severe lymphedema and distinctive facial appearance. Up till now, no extensive studies have been conducted to elucidate the mechanism of the disease caused by various mutations. As a preliminary investigation of HKLLS3, we sorted out the most deleterious nonsynonymous single nucleotide polymorphisms (nsSNPs) that might affect the structure and function of ADAMTS3 protein by using a variety of in silico tools. A total of 919 nsSNPs in the ADAMTS3 gene were identified. 50 nsSNPs were predicted to be deleterious by multiple computational tools. 5 nsSNPs (G298R, C567Y, A370T, C567R and G374S) were found to be the most dangerous and can be associated with the disease as predicted by different bioinformatics tools. Modelling of the protein shows it can be divided into segments 1, 2 and 3, which are connected by short loops. Segment 3 mainly consists of loops without substantial secondary structures. With prediction tools and molecular dynamics simulation, some SNPs were found to significantly destabilize the protein structure and disrupt the secondary structures, especially in segment 2. The deleterious effects of mutations in segment 1 are possibly not from destabilization but from other factors such as the change in phosphorylation as suggested by post-translational modification (PTM) studies. This is the first-ever study of ADAMTS3 gene polymorphism, and the predicted nsSNPs in ADAMST3, some of which have not been reported yet in patients, will serve for diagnostic purposes and further therapeutic implications in Hennekam syndrome, contributing to better diagnosis and treatment.
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Affiliation(s)
- Khyber Shinwari
- Institute of Chemical Engineering, Department of Immunochemistry, Ural Federal University, Yekaterinburg, Russia.
- Insitutite of Immunology and Physiology, Russian Academy of Science, Yekaterinburg, Russia.
| | - Yurong Wu
- Department of Chemistry, Hong Kong University of Science and Technology, Hong Kong, China
| | | | - Ningkun Xiao
- Department of Psychology, Ural Federal University, Yekaterinburg, Russia
| | - Mikhail Bolkov
- Insitutite of Immunology and Physiology, Russian Academy of Science, Yekaterinburg, Russia
| | - Irina Tuzankina
- Insitutite of Immunology and Physiology, Russian Academy of Science, Yekaterinburg, Russia
| | - Valery Chereshnev
- Insitutite of Immunology and Physiology, Russian Academy of Science, Yekaterinburg, Russia
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13
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Kaur M, Muzzammel Rehman H, Kaur G, Kaur A, Bansal M. Switching of newly synthesized linker-based derivatives of non-steroidal anti-inflammatory drugs toward anti-inflammatory and anticancer activity. Bioorg Chem 2023; 133:106406. [PMID: 36773455 DOI: 10.1016/j.bioorg.2023.106406] [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: 12/01/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023]
Abstract
A new series of linker-based derivatives of non-steroidal anti-inflammatory drugs were designed and synthesized. All the compounds were well characterized with the help of various spectroscopic techniques such as FT-IR, 1H NMR, 13C NMR, and HRMS. The main emphasis of this paper is to understand the switching of the most promising compounds 8 and 10 towards anti-inflammatory and anticancer activity in terms of in-silico and in-vitro studies in detail. During the molecular docking study, compounds 8 and 10 demonstrated the importance of hetero atoms as well as the perfect alignment of a compound in the binding pocket of a target site, which may affect their bioactivity. Here, the presence of 1,3‑dicarbonyl interactions with ASN 351 in compound 8 (not found in compound 10) may be responsible for its better inhibitory activity against the COX-2 target site. On the other hand, a slight increase in the potency of compound 10 towards anticancer activity may be due to the instantaneous participation of the OH group and carbonyl group to give conventional hydrogen bonds towards THR 149 amino acid residue, which was missing in compound 8. Molecular dynamics simulation was also performed for compounds 10 and 8 toward COX-2 and HER-2 protein sites. Further, compounds 8 and 10 were subjected to in-vitro COX-2 inhibition and cytotoxicity assay and the results obtained were in accordance with the in-silico study. Thus, compound 8 become more potent towards COX-2 inhibition with IC50 value of 48.51 µg/ml and compound 10 showed good bioactivity toward cytotoxic activity with IC50 value of 93.03 µg/ml.
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Affiliation(s)
- Mandeep Kaur
- Synthetic and Medicinal Chemistry Laboratory, Department of Chemistry, Punjabi University, Patiala 147002, India
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Gurmeet Kaur
- Synthetic and Medicinal Chemistry Laboratory, Department of Chemistry, Punjabi University, Patiala 147002, India
| | - Amandeep Kaur
- Synthetic and Medicinal Chemistry Laboratory, Department of Chemistry, Punjabi University, Patiala 147002, India
| | - Manisha Bansal
- Synthetic and Medicinal Chemistry Laboratory, Department of Chemistry, Punjabi University, Patiala 147002, India.
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14
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Tariq N, Yaseen M, Xu D, Rehman HM, Bibi M, Uzair M. Rice anther tapetum: a vital reproductive cell layer for sporopollenin biosynthesis and pollen exine patterning. Plant Biol (Stuttg) 2023; 25:233-245. [PMID: 36350096 DOI: 10.1111/plb.13485] [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] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
The tapetum is the innermost layer of the four layers of the rice anther that provides protection and essential nutrients to pollen grain development and delivers precursors for pollen exine formation. The tapetum has a key role in the normal development of pollen grains and tapetal programmed cell death (PCD) that is linked with sporopollenin biosynthesis and transport. Recently, many genes have been identified that are involved in tapetum formation in rice and Arabidopsis. Genetic mutation in PCD-associated genes could affect normal tapetal PCD, which finally leads to aborted pollen grains and male sterility in rice. In this review, we discuss the most recent research on rice tapetum development, including genomic, transcriptomic and proteomic studies. Furthermore, tapetal PCD, sporopollenin biosynthesis, ROS activity for tapetum function and its role in male reproductive development are discussed in detail. This will improve our understanding of the role of the tapetum in male fertility using rice as a model system, and provide information that can be applied in rice hybridization and that of other major crops.
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Affiliation(s)
- N Tariq
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - M Yaseen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Institute of Rice Research, Sichuan Agricultural University, Sichuan, China
| | - D Xu
- School of Agronomy, Anhui Agricultural University, Hefei, China
| | - H M Rehman
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - M Bibi
- Department of Bioindustry and Bioresource Engineering, Sejong University, Seoul, Korea
| | - M Uzair
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
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15
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Moukhliss Y, Koubi Y, Alaqarbeh M, Muzzammel Rehman H, Maghat H, Sbai A, Bouachrine M, Lakhlifi T. Computational and Retrosynthetic Investigation of Isoxazole‐Bearing Chalcones as Antioxidant Activate Compounds. ChemistrySelect 2023. [DOI: 10.1002/slct.202203908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Affiliation(s)
- Youness Moukhliss
- Molecular Chemistry and Natural Substances Laboratory (MCNSL) Department of Chemistry Faculty of Science University of Moulay Ismail Meknes Morocco
| | - Yassine Koubi
- Molecular Chemistry and Natural Substances Laboratory (MCNSL) Department of Chemistry Faculty of Science University of Moulay Ismail Meknes Morocco
| | | | | | - Hamid Maghat
- Molecular Chemistry and Natural Substances Laboratory (MCNSL) Department of Chemistry Faculty of Science University of Moulay Ismail Meknes Morocco
| | - Abdelouahid Sbai
- Molecular Chemistry and Natural Substances Laboratory (MCNSL) Department of Chemistry Faculty of Science University of Moulay Ismail Meknes Morocco
| | - Mohammed Bouachrine
- Molecular Chemistry and Natural Substances Laboratory (MCNSL) Department of Chemistry Faculty of Science University of Moulay Ismail Meknes Morocco
- EST Khenifra Sultan Moulay Slimane University Beni Mellal Morocco
| | - Tahar Lakhlifi
- Molecular Chemistry and Natural Substances Laboratory (MCNSL) Department of Chemistry Faculty of Science University of Moulay Ismail Meknes Morocco
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16
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Al-Taifi EA, Rehman HM, Bakhite EA, Mohamed SK, Yeap GY, Lai CH, Mague JT, El Bakri Y. Synthesis, X-Ray Crystal Structure, and Identification of Potential Drug Candidate against COVID-19 Main Protease through Structure-Guided Modeling and Simulation Approach. Polycycl Aromat Compd 2023. [DOI: 10.1080/10406638.2023.2165512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Elham A. Al-Taifi
- Chemistry Department, Faculty of Science, Sana’a University, Sana’a, Yemen
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
- Alnoorians Group of Institutes, Lahore, Pakistan
| | - Etify A. Bakhite
- Chemistry Department, Faculty of Science, Assiut University, Assiut, Egypt
| | - Shaaban K. Mohamed
- Chemistry and Environmental Division, Manchester Metropolitan University, Manchester, UK
- Chemistry Department, Faculty of Science, Minia University, El-Minia, Egypt
| | - Guan-Yeow Yeap
- Liquid Crystal Research Laboratory, School of Chemical Sciences, Universiti Sains Malaysia, Minden, Malaysia
| | - Chin-Hung Lai
- Department of Medical Applied Chemistry, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Education, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Joel T. Mague
- Department of Chemistry, Tulane University, New Orleans, LA, USA
| | - Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russia
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17
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Rehman HM, Sajjad M, Ali MA, Gul R, Irfan M, Naveed M, Bhinder MA, Ghani MU, Hussain N, Said ASA, Al Haddad AHI, Saleem M. Identification of NS2B-NS3 Protease Inhibitors for Therapeutic Application in ZIKV Infection: A Pharmacophore-Based High-Throughput Virtual Screening and MD Simulations Approaches. Vaccines (Basel) 2023; 11:vaccines11010131. [PMID: 36679976 PMCID: PMC9862652 DOI: 10.3390/vaccines11010131] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Zika virus (ZIKV) pandemic and its implication in congenital malformations and severe neurological disorders had created serious threats to global health. ZIKV is a mosquito-borne flavivirus which spread rapidly and infect a large number of people in a shorter time-span. Due to the lack of effective therapeutics, this had become paramount urgency to discover effective drug molecules to encounter the viral infection. Various anti-ZIKV drug discovery efforts during the past several years had been unsuccessful to develop an effective cure. The NS2B-NS3 protein was reported as an attractive therapeutic target for inhibiting viral proliferation, due to its central role in viral replication and maturation of non-structural viral proteins. Therefore, the current in silico drug exploration aimed to identify the novel inhibitors of Zika NS2B-NS3 protease by implementing an e-pharmacophore-based high-throughput virtual screening. A 3D e-pharmacophore model was generated based on the five-featured (ADPRR) pharmacophore hypothesis. Subsequently, the predicted model is further subjected to the high-throughput virtual screening to reveal top hit molecules from the various small molecule databases. Initial hits were examined in terms of binding free energies and ADME properties to identify the candidate hit exhibiting a favourable pharmacokinetic profile. Eventually, molecular dynamic (MD) simulations studies were conducted to evaluate the binding stability of the hit molecule inside the receptor cavity. The findings of the in silico analysis manifested affirmative evidence for three hit molecules with -64.28, -55.15 and -50.16 kcal/mol binding free energies, as potent inhibitors of Zika NS2B-NS3 protease. Hence, these molecules holds the promising potential to serve as a prospective candidates to design effective drugs against ZIKV and related viral infections.
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Affiliation(s)
- Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Quaid e Azam Campus, Lahore 54590, Punjab, Pakistan
| | - Muhammad Akhtar Ali
- School of Biological Sciences, University of the Punjab, Quaid e Azam Campus, Lahore 54590, Punjab, Pakistan
| | - Roquyya Gul
- Faculty of Life Sciences, Gulab Devi Educational Complex, Lahore 54590, Punjab, Pakistan
| | - Muhammad Irfan
- Kauser Abdulla Malik School of Life Sciences, Forman Christian College (A Chartered University), Lahore 54600, Punjab, Pakistan
| | - Muhammad Naveed
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab Lahore, Lahore 54590, Punjab, Pakistan
| | - Munir Ahmad Bhinder
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan
| | - Muhammad Usman Ghani
- Center for Applied Molecular Biology, University of the Punjab, Lahore 54590, Punjab, Pakistan
| | - Nadia Hussain
- Department of Pharmaceutical Sciences, College of Pharmacy, Al Ain University, Al Ain 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 112612, United Arab Emirates
| | - Amira S. A. Said
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 112612, United Arab Emirates
- Department of Clinical Pharmacy, College of Pharmacy, Al Ain University, Al Ain 64141, United Arab Emirates
- Clinical Pharmacy Department, Faculty of Pharmacy, Beni Suef University, Beni Suef 62521, Egypt
| | - Amal H. I. Al Haddad
- Chief Operations Office, Sheikh Shakhbout Medical City (SSMC) in Partnership with Mayo Clinic, Abu Dhabi 11001, United Arab Emirates
| | - Mahjabeen Saleem
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan
- School of Medical Lab Technology, Minhaj University Lahore, Lahore 54770, Punjab, Pakistan
- Correspondence:
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Shinwari K, Rehman HM, Xiao N, Guojun L, Khan MA, Bolkov MA, Tuzankina IA, Chereshnev VA. Novel high-risk missense mutations identification in FAT4 gene causing Hennekam syndrome and Van Maldergem syndrome 2 through molecular dynamics simulation. Informatics in Medicine Unlocked 2023. [DOI: 10.1016/j.imu.2023.101160] [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: 01/15/2023] Open
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19
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Serseg T, Benarous K, Serseg M, Rehman HM, El Bakri Y, Goumri-Said S. Discovery of inhibitors against SARS-CoV-2 associated fungal coinfections via virtual screening, ADMET evaluation, PASS, molecular docking, dynamics and pharmacophore studies. Arab Journal of Basic and Applied Sciences 2022. [DOI: 10.1080/25765299.2022.2126588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Affiliation(s)
- Talia Serseg
- Natural Sciences department, Ecole Normale Supérieure Taleb Abderrahmane, Laghouat, Algeria
- Fundamental Sciences Laboratory, Amar Telidji University, Laghouat, Algeria
| | - Khedidja Benarous
- Fundamental Sciences Laboratory, Amar Telidji University, Laghouat, Algeria
- Biology department, Amar Telidji University, Laghouat, Algeria
| | - Menaouar Serseg
- Laboratory of Hematology, Central Hospital of Army, Ain Naadja, Algiers, Algeria
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
- Alnoorians Group of Institutes 55-Elahi Bukhsh Park, Amir Road, Shad Bagh, Shad Bagh, Lahore, Pakistan
| | - Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russian Federation
| | - Souraya Goumri-Said
- College of Science, Physics Department, Alfaisal University, Riyadh, Saudi Arabia
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Aziz M, Ejaz SA, Rehman HM, Alsubaie ASA, Mahmoud KH, Siddique F, Al-Buriahi MS, Alrowaili ZA. Identification of NEK7 inhibitors: structure based virtual screening, molecular docking, density functional theory calculations and molecular dynamics simulations. J Biomol Struct Dyn 2022:1-15. [PMID: 35983608 DOI: 10.1080/07391102.2022.2113563] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 10/15/2022]
Abstract
NEK7 is a NIMA related-protein kinase that plays a crucial role in spindle assembly and cell division. Dysregulation of NEK7 protein leads to development and progression of different types of malignancies including colon and breast cancers. Therefore, NEK7 could be considered as an attractive target for anti-cancer drug discovery. However, few efforts have been made for the development of selective inhibitors of NIMA-related kinase but still no FDA approved drug is known to selectively inhibit the NEK7 protein. Dacomitinib and Neratinib are two Enamide derivatives that were approved for treatment against non-small cell lung cancer and breast cancer respectively. Drug repurposing is a time and cost-efficient method for re-evaluating the activities of previously authorized medications. Thus, the present research involves the repurposing of two FDA-approved medications via comprehensive in silico approach including Density functional theory (DFTs) studies which were conducted to determine the electronic properties of the Dacomitinib and Neratinib. Afterward, binding orientation of selected drugs inside NEK7 activation loop was evaluated through molecular docking approach. Selected drugs exhibited potential molecular interactions engaging important amino acid residues of active site. The docking score of Dacomitinib and Neratinib was -30.77 and -26.78 kJ/mol, respectively. The top ranked pose obtained from molecular docking was subjected to Molecular Dynamics (MD) Simulations for investigating the stability of protein-ligand complex. The RMSD pattern revealed the stability of protein-ligand complex throughout simulated trajectory. In conclusion, both drugs displayed inhibitory efficacy against NEK7 protein and provide a prospective therapy option for malignant malignancies linked with NEK7. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mubashir Aziz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Pakistan
| | - Syeda Abida Ejaz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Pakistan
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan.,Alnoorians Group of Institutes, Lahore, Pakistan
| | - A S A Alsubaie
- Department of Physics, College of Khurma University College, Taif University, Taif, Saudi Arabia
| | - K H Mahmoud
- Department of Physics, College of Khurma University College, Taif University, Taif, Saudi Arabia
| | - Farhan Siddique
- Department of Pharmacy, Royal Institute of Medical Sciences (RIMS), Multan, Pakistan.,Department of Science and Technology, Laboratory of Organic Electronics, Linköping University, Norrköping, Sweden
| | - M S Al-Buriahi
- Department of Physics, Sakarya University, Sakarya, Turkey
| | - Z A Alrowaili
- Department of Physics, College of Science, Jouf University, Sakaka, Saudi Arabia
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Al-Fahad D, Alyaseen F, Al-Amery A, Singh G, Srinath M, Rehman HM, Abbas Y. Kinetic Changes of Ptdins (3,4,5) P3 within Fast and Slow Turnover Rates of Focal Adhesion. Rep Biochem Mol Biol 2022; 11:262-269. [PMID: 36164635 PMCID: PMC9455192 DOI: 10.52547/rbmb.11.2.262] [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: 01/02/2022] [Accepted: 01/02/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The assembly and disassembly of the focal adhesions (FA) components occurs throughout life cycle of adhesion, with conservation of balance between removal and recruitment rate during temporal stages. Previous studies have demonstrated that phosphotidyilinositols play a role in regulating FA turnover. However, a little attention has been given to quantify the dynamics changes of Phosphatidylinositol 3,4,5-trisphosphate (PtdIns (3,4,5) P3) within and during fast and slow turnover rates of FA. METHODS In this study, we developed a protein purification MDA-MB-231 breast cancer cell line was used as a model in this study due to high metastatic and motile. These cells were co-transfected with GFP- paxillin/vinculin, as FA marker, and the GFP/mCherry-Btk-PH, as a biosensor to visualize PtdIns (3,4,5) P3. Confocal time-lapse images were used to monitor changes or differences in the local generation of PtdIns (3,4,5) P3 within and during assembly and disassembly of FA. Following transfection, immunostaining was used to examine the spatial co-localization between FA and PtdIns (3,4,5) P3. RESULTS Our data demonstrated that PtdIns (3,4,5) P3 co-localized with FAs and increase during assembly and decline during disassembly of FA which exhibits slow turnover rates and was in a constant level during assembly and disassembly of FA that displays fast turnover rates. DISCUSSION Our result suggested that the dynamic changes of PtdIns (3,4,5) P3, it may depend on components undergo turnover, such that early, nascent FA displays fast turnover rates and mature FA exhibits slow turnover rates. Thus, the local enrichment of PtdIns (3,4,5) P3 enhances FA assembly and disassembly activation.
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Affiliation(s)
- Dhurgham Al-Fahad
- Department of Pharmaceutical Sciences, College of Pharmacy University of Thi-Qar, Thi-Qar 64001, Iraq.
| | - Firas Alyaseen
- Department of Pharmaceutical Sciences, College of Pharmacy University of Thi-Qar, Thi-Qar 64001, Iraq.
| | - Ahmed Al-Amery
- Department of Physiology, College of Medicine, University of Thi-Qar, Iraq.
| | - Gagandeep Singh
- Viral Research and Diagnostic Laboratory, Department of Microbiology, Osmanian Medical College, Hyderabad, Telangana, India.
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India.
| | - Mote Srinath
- Viral Research and Diagnostic Laboratory, Department of Microbiology, Osmanian Medical College, Hyderabad, Telangana, India.
| | | | - Yahya Abbas
- Department of Biology, College of Science, University of Thi-Qar, Thi-Qar, 64001 Iraq.
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22
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Liu Y, Zhou S, Huang X, Rehman HM. Mechanistic insight of the potential of geraniol against Alzheimer's disease. Eur J Med Res 2022; 27:93. [PMID: 35701806 PMCID: PMC9199166 DOI: 10.1186/s40001-022-00699-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/26/2021] [Accepted: 05/07/2022] [Indexed: 12/12/2022] Open
Abstract
Background Alzheimer’s disease (AD) as a neurodegenerative disease occupies 3/5–4/5 cases among patients with dementia, yet its pathogenetic mechanism remains unclear. Geraniol, on the other hand, is a well-known extract from essential oils of aromatic plants and has been proven that it has outstanding neuroprotective effects as well as ameliorating influence in memory impairment. Therefore, the present study aims to elucidate the potential of geraniol against AD by network pharmacology-based approach combined with molecular modeling study. Materials and methods Firstly, we evaluated the druggability of geraniol by ADME method. Then, we obtained the geraniol targets and AD-related targets from multiple open data sources. Afterward, we calculated the intersection through a Venn diagram to find common targets, and via Panther classification system to categorize them. In order to gain a macroscopic understanding of these common targets, we carried out GO terms and KEGG pathways enrichment analyses, according to which we constructed a compound–target–pathway–disease network. In addition, we built a preliminary PPI network which was further analyzed both functionally and topologically. Consequently, five hub targets were sorted out. Finally, we conducted molecular docking and molecular dynamic simulation to validate our findings. Results In the present study, the pharmacological properties of geraniol were assessed according to ADME and Lipinski’s rule, which demonstrate promising druggability. Then, from 10,972 AD-related targets and 33 geraniol targets, 29 common targets were identified, among which 38.1% of them are metabolite interconversion enzymes, 23.8% are protein modifying enzymes, 33.3% are transmembrane receptors, and the rest are transporters. Enrichment analyses hint that geraniol is involved in cholinergic synapse, serotonergic synapse, and neuroactive ligand–receptor interaction. We also built a preliminary PPI network to investigate the interplay between these targets and their extensive interactions. Then, by functionally clustering the preliminary PPI network, we gained a cluster of proteins which formed a subnetwork with score of 8.476, and 22 nodes. Its results of GO terms and KEGG pathways enrichment analyses once again suggests that geraniol actively participates in cholinergic synapse, serotonergic synapse, and neuroactive ligand–receptor interaction, which are believed to be strongly associated with AD pathogenesis. Besides, topological analyses of the preliminary PPI network helped find 5 hub targets (i.e., CHRM3, PRKCA, PRKCD, JAK1, JAK2). To verify their interaction with geraniol molecule, we conducted molecular docking, and found that CHRM3 possesses the highest affinity in binding, indicating that geraniol molecules are closely bound to each hub target, and CHRM3 may serve as a key target of geraniol against AD. It was then further confirmed by molecular dynamic simulation, the result of which supports our hypothesis. Conclusion The present study shares a mechanistic insight of the potential of geraniol against AD, giving a reference to future experimental studies. Supplementary Information The online version contains supplementary material available at 10.1186/s40001-022-00699-8.
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Affiliation(s)
- Ying Liu
- Department of Cardiology, 6th Medical Centre, Chinese PLA General Hospital, Beijing, China.
| | - Shujing Zhou
- Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary
| | - Xufeng Huang
- Faculty of Dentistry, University of Debrecen, Debrecen, 4032, Hungary
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Punjab, Pakistan.,Alnoorians Group of Institutes, 55-Elahi Bukhsh Park, Amir Road, Shad Bagh, Lahore, 54000, Pakistan
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23
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Shinwari K, Rehman HM, Liu G, Bolkov MA, Tuzankina IA, Chereshnev VA. Novel Disease-Associated Missense Single-Nucleotide Polymorphisms Variants Predication by Algorithms Tools and Molecular Dynamics Simulation of Human TCIRG1 Gene Causing Congenital Neutropenia and Osteopetrosis. Front Mol Biosci 2022; 9:879875. [PMID: 35573728 PMCID: PMC9095858 DOI: 10.3389/fmolb.2022.879875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/04/2022] [Indexed: 12/16/2022] Open
Abstract
T Cell Immune Regulator 1, ATPase H + Transporting V0 Subunit A3 (TCIRG1 gene provides instructions for making one part, the a3 subunit, of a large protein complex known as a vacuolar H + -ATPase (V-ATPase). V-ATPases are a group of similar complexes that act as pumps to move positively charged hydrogen atoms (protons) across membranes. Single amino acid changes in highly conserved areas of the TCIRG1 protein have been linked to autosomal recessive osteopetrosis and severe congenital neutropenia. We used multiple computational approaches to classify disease-prone single nucleotide polymorphisms (SNPs) in TCIRG1. We used molecular dynamics analysis to identify the deleterious nsSNPs, build mutant protein structures, and assess the impact of mutation. Our results show that fifteen nsSNPs (rs199902030, rs200149541, rs372499913, rs267605221, rs374941368, rs375717418, rs80008675, rs149792489, rs116675104, rs121908250, rs121908251, rs121908251, rs149792489 and rs116675104) variants are likely to be highly deleterious mutations as by incorporating them into wild protein they destabilize the wild protein structure and function. They are also located in the V-ATPase I domain, which may destabilize the structure and impair TCIRG1 protein activation, as well as reduce its ATPase effectiveness. These mutants have not yet been identified in patients suffering from CN and osteopetrosis while (G405R, R444L, and D517N) reported in our study are already associated with osteopetrosis. Mutation V52L reported in our study was identified in a patient suspected for CN. Finally, these mutants can help to further understand the broad pool of illness susceptibilities associated with TCIRG1 catalytic kinase domain activation and aid in the development of an effective treatment for associated diseases.
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Affiliation(s)
- Khyber Shinwari
- Institute of Chemical Engineering, Department of Immunochemistry, Ural Federal University, Yekaterinburg, Russia
- *Correspondence: Khyber Shinwari,
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
- Alnoorians Group of Institutes, Shad Bagh, Lahore, Pakistan
| | - Guojun Liu
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Mikhail A. Bolkov
- Institute of Chemical Engineering, Department of Immunochemistry, Ural Federal University, Yekaterinburg, Russia
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
| | - Irina A. Tuzankina
- Institute of Chemical Engineering, Department of Immunochemistry, Ural Federal University, Yekaterinburg, Russia
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
| | - Valery. A. Chereshnev
- Institute of Chemical Engineering, Department of Immunochemistry, Ural Federal University, Yekaterinburg, Russia
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
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24
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Huang X, Rehman HM, Szöllősi AG, Zhou S. Network Pharmacology-Based Approach Combined with Bioinformatic Analytics to Elucidate the Potential of Curcumol against Hepatocellular Carcinoma. Genes (Basel) 2022; 13:genes13040653. [PMID: 35456457 PMCID: PMC9028201 DOI: 10.3390/genes13040653] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/28/2022] [Accepted: 03/28/2022] [Indexed: 12/04/2022] Open
Abstract
Purpose: Modern, open-source databases provide an unprecedented wealth of information to help drug development. By combining data available in these databases with the proper bioinformatical tools, we can elucidate the molecular targets of natural compounds. One such molecule is curcumol, a guaiane-type sesquiterpenoid hemiketal isolated from Rhizoma Curcumae, which is used for a broad range of diseases in traditional Chinese and Indian medicine. It has been reported to exert anti-tumor activity, but the intrinsic molecular mechanism in hepatocellular carcinoma (HCC) is unclear. Therefore, the present study was designed to reveal the predictive targets and biological mechanisms of curcumol against HCC via a network pharmacology-based approach combined with bioinformatic analytics and to provide proof of concept for further similar investigations. Methods: Data available from open-source databases (Traditional Chinese Medicine Systems Pharmacology, Comparative Toxicogenomic Database, The Cancer Genome Atlas, the Human Protein Atlas project) was processed with the help of a variety of open-source tools (SwissADME, SwissTargetPrediction, JVenn, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, GeneMANIA, Cytoscape). Results: In the present study, the potential of curcumol against HCC was unraveled by network pharmacology-based elucidation. It suggests that curcumol shows exciting druggability with 44 potent homo sapiens biotargets against HCC. The GO terms and KEGG pathways enrichment analyses, curcumol-targets-pathways-HCC network, PPI network, and corresponding in-depth topological analyses, as well as survival analysis, molecular docking simulation indicate that the potential mechanism of curcumol against HCC is complicated, as it may act in various ways, mainly by inducing apoptosis and modulating the inflammatory response, increasing presentation of HCC-specific protein. Conclusion: The present study highlights the potential of curcumol against HCC, giving reference to further experimental study. It also presents a roadmap that can be followed to conduct in silico prescreening of other compounds of interest.
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Affiliation(s)
- Xufeng Huang
- Faculty of Dentistry, University of Debrecen, 4032 Debrecen, Hungary;
| | - Hafiz Muzzammel Rehman
- Alnoorians Group of Institutes 55-Elahi Bukhsh Park, Amir Road, Shad Bagh, Lahore 54000, Pakistan;
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Pakistan
| | - Attila Gábor Szöllősi
- Department of Immunology, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence:
| | - Shujing Zhou
- Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
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25
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Tariq A, Rehman HM, Mateen RM, Ali M, Mutahir Z, Afzal MS, Sajjad M, Gul R, Saleem M. A computer aided drug discovery based discovery of lead-like compounds against KDM5A for cancers using pharmacophore modeling and high-throughput virtual screening. Proteins 2021; 90:645-657. [PMID: 34642975 DOI: 10.1002/prot.26262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 03/22/2021] [Revised: 09/17/2021] [Accepted: 10/03/2021] [Indexed: 12/11/2022]
Abstract
KDM5A over-expression mediates cancer cell proliferation and promotes resistance toward chemotherapy through epigenetic modifications. As its complete mechanism of action is still unknown, there is no KDM5A specific drug available at clinical level. In the current study, lead compounds for KDM5A were determined through pharmacophore modeling and high-throughput virtual screening from Asinex libraries containing 0.5 million compounds. These virtual hits were further evaluated and filtered for ADMET properties. Finally, 726 compounds were used for docking analysis against KDM5A. On the basis of docking score, 10 top-ranked compounds were selected and further evaluated for non-central nervous system (CNS) and CNS drug-like properties. Among these compounds, N-{[(7-Methyl-4-oxo-1,2,3,4-tetrahydrocyclopenta [c] chromen-9-yl) oxy]acetyl}-l-phenylalanine (G-score: -11.363 kcal/mol) was estimated to exhibit non-CNS properties while 2-(3,4-Dimethoxy-phenyl)-7-methoxy-chromen-4-one (G-score: -7.977 kcal/mol) was evaluated as CNS compound. Docked complexes of both compounds were finally selected for molecular dynamic simulation to examine the stability. This study concluded that both these compounds can serve as lead compounds in the quest of finding therapeutic agents against KDM5A associated cancers.
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Affiliation(s)
- Asma Tariq
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Rana Muhammad Mateen
- Department of Life sciences, School of Science, University of Management and Technology, Lahore, Punjab, Pakistan
| | - Moazzam Ali
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Zeeshan Mutahir
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Muhammad Sohail Afzal
- Department of Life sciences, School of Science, University of Management and Technology, Lahore, Punjab, Pakistan
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Lahore, Punjab, Pakistan
| | - Roquyya Gul
- Faculty of Life Sciences, Gulab Devi Educational Complex, Lahore, Punjab, Pakistan
| | - Mahjabeen Saleem
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
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26
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Shafique QUA, Rehman HM, Zaheer T, Tahir RA, Bhinder MA, Gul R, Saleem M. A Computational Approach to Modeling an Antagonistic Angiogenic VEGFR1-IL2 Fusion Protein for Cancer Therapy. Bioinform Biol Insights 2021; 15:11779322211043297. [PMID: 34566410 PMCID: PMC8458685 DOI: 10.1177/11779322211043297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 04/01/2021] [Accepted: 08/13/2021] [Indexed: 11/17/2022] Open
Abstract
In cancer treatment, immunotherapy has great potential for improving the prognosis of patients with hematologic and solid malignancies. In this study, various bioinformatics tools and servers were used to design an antiangiogenic fusion protein. After comprehensive evaluation, an antiangiogenic fusion protein was designed using a soluble extracellular domain of human vascular endothelial growth factor receptor 1 (sVEGFR-1) and human interleukin-2 (IL-2) joined by a flexible linker. The final construct was composed of 875 amino acids. The secondary structure of the fusion protein, obtained by CFSSP, PSIPRED, and SOPMA tools, consisted of 14.17% helices, 29.71% extended strands, 4.69% beta turns and 51.43% random coils. Tertiary structure prediction by Raptor X showed that the fusion protein comprises 3 domains with 875 modeled amino acids, out of which 26 positions (2%) were considered disordered. The Ramachandran plot revealed 89.3%, 7.1%, and 3.6% amino acid residues in favored, allowed, and outlier regions, respectively. Physical features of the Molecular Dynamic (MD) simulated system such as root mean square deviation, root mean square fluctuation, solvent-on hand surface region, and radius of gyration identified the fusion construct as a stable and compact protein with few fluctuations in its overall structure. Docking of the fusion protein showed that interaction between sVEGFR-1/VEGFA and IL-2/IL-2R still exists. In silico analysis revealed that the fusion protein comprising IL-2 and sVEGFR-1 has stable structure and the selected linker can efficiently separate the two domains. These observations may be helpful in determining protein stability prior to protein expression.
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Affiliation(s)
| | - Hafiz Muzzammel Rehman
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan.,Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore, Pakistan
| | - Tahreem Zaheer
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Rana Adnan Tahir
- Department of Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Munir Ahmad Bhinder
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore, Pakistan
| | - Roquyya Gul
- Faculty of Life Sciences, Gulab Devi Educational Complex, Lahore, Pakistan
| | - Mahjabeen Saleem
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
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27
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Nazir Z, Chohan R, Mahmood MS, Rehman HM, Gul R, Saleem M. Molecular Cloning and Characterization of an Acidic Polygalacturonase from Grapes and Its Potential in Industry. Crit Rev Eukaryot Gene Expr 2021; 30:411-425. [PMID: 33389878 DOI: 10.1615/critreveukaryotgeneexpr.2020034410] [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] [Indexed: 11/13/2022]
Abstract
Pectinase enzymes from different plants have many possible biotechnological applications in various industries. Considering industrial significance of pectinolytic enzymes, the polygalacturonase (PG) gene from grapes was cloned into Escherichia coli DH5α using pTZ57R/T vector. Homologous sequences established a close link to Vitis vinifera. Conserve domain analysis predicted PLN02218 domain belongs to the cl31843 superfamily, showing its function as polygalacturonase. After confirmation by PCR and restriction analysis, the PG gene was expressed in E. coli BL21 and induced by IPTG. Expression level was assessed by 12% SDS-PAGE, which showed a 47 kDa protein. High expression level in the soluble fraction indicated that the protein is intracellular or transmembrane. Maximum expression was obtained with 1 mM IPTG and 6 hour induction time, and autoinduction with lactose increased production of the recombinant enzyme. Zymogram analysis revealed that the induced protein was an active enzyme. Expressed PG showed pectinolytic effect on the physiochemical properties of lemon juice. Natural biopolymers are greatly needed because synthetic fibers can negatively affect health. Pectin hydrolysis of banana pseudostem by the PG enzyme produced better quality fiber. Morphological studies by scanning electron microscopy revealed pectin degradation within the fiber cell architecture, showing the effectiveness of PG treatment on banana pseudostem.
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Affiliation(s)
- Zahra Nazir
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Riffat Chohan
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | | | | | - Roquyya Gul
- Institute of Biological Sciences, Gulab Devi Educational Complex, Lahore, Pakistan
| | - Mahjabeen Saleem
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
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28
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Rehman HM, Mirza MU, Ahmad MA, Saleem M, Froeyen M, Ahmad S, Gul R, Alghamdi HA, Aslam MS, Sajjad M, Bhinder MA. A Putative Prophylactic Solution for COVID-19: Development of Novel Multiepitope Vaccine Candidate against SARS-COV-2 by Comprehensive Immunoinformatic and Molecular Modelling Approach. Biology (Basel) 2020; 9:E296. [PMID: 32962156 PMCID: PMC7563440 DOI: 10.3390/biology9090296] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/04/2020] [Accepted: 09/05/2020] [Indexed: 12/13/2022]
Abstract
The outbreak of 2019-novel coronavirus (SARS-CoV-2) that causes severe respiratory infection (COVID-19) has spread in China, and the World Health Organization has declared it a pandemic. However, no approved drug or vaccines are available, and treatment is mainly supportive and through a few repurposed drugs. The urgency of the situation requires the development of SARS-CoV-2-based vaccines. Immunoinformatic and molecular modelling are time-efficient methods that are generally used to accelerate the discovery and design of the candidate peptides for vaccine development. In recent years, the use of multiepitope vaccines has proved to be a promising immunization strategy against viruses and pathogens, thus inducing more comprehensive protective immunity. The current study demonstrated a comprehensive in silico strategy to design stable multiepitope vaccine construct (MVC) from B-cell and T-cell epitopes of essential SARS-CoV-2 proteins with the help of adjuvants and linkers. The integrated molecular dynamics simulations analysis revealed the stability of MVC and its interaction with human Toll-like receptors (TLRs), which trigger an innate and adaptive immune response. Later, the in silico cloning in a known pET28a vector system also estimated the possibility of MVC expression in Escherichia coli. Despite that this study lacks validation of this vaccine construct in terms of its efficacy, the current integrated strategy encompasses the initial multiple epitope vaccine design concepts. After validation, this MVC can be present as a better prophylactic solution against COVID-19.
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Affiliation(s)
- Hafiz Muzzammel Rehman
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan; (H.M.R.); (M.S.A.)
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan; (M.A.A.); (M.A.B.)
| | - Muhammad Usman Mirza
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000 Leuven, Belgium; (M.U.M.); (M.F.)
| | - Mian Azhar Ahmad
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan; (M.A.A.); (M.A.B.)
- Department of Health, Government of the Punjab, Lahore 54590, Punjab, Pakistan
| | - Mahjabeen Saleem
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan; (H.M.R.); (M.S.A.)
| | - Matheus Froeyen
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000 Leuven, Belgium; (M.U.M.); (M.F.)
| | - Sarfraz Ahmad
- Drug Design and Development Research Group (DDDRG), Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - Roquyya Gul
- Faculty of Life Sciences, Gulab Devi Educational Complex, Lahore 54590, Punjab, Pakistan;
| | - Huda Ahmed Alghamdi
- Department of Biology, College of Sciences, King Khalid University, Abha 61413, Saudi Arabia;
| | - Muhammad Shahbaz Aslam
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan; (H.M.R.); (M.S.A.)
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Quaid e Azam Campus, Lahore 54590, Punjab, Pakistan;
| | - Munir Ahmad Bhinder
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan; (M.A.A.); (M.A.B.)
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Rehman HM, Mahmood R, Razaq M, Saeed R, Jamil M, Reddy GVP. Varietal Preferences and Within-Orchard and Tree Distribution of Newly Recorded Gall Midges, Dasineura amaramanjarae and Procontarinia mangiferae (Diptera: Cecidomyiidae), From Commercial Mango Cultivars in Pakistan. Environ Entomol 2017; 46:826-830. [PMID: 28531303 DOI: 10.1093/ee/nvx095] [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] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Indexed: 06/07/2023]
Abstract
Gall midges (Diptera: Cecidomyiidae) damage mango by feeding on flowers and fruit tissues, inducing galls on leaves, and providing inoculums of anthracnose. Dasineura amaramanjarae Grover and Procontarinia mangiferae (Felt), two gall midges that damage flowers in all mango-growing areas of the world, have recently been recorded in Pakistan, and studies were conducted in 2011 and 2012 on the within-tree and orchard distribution patterns and cultivar preference of both species in Pakistan at one location (Rahim Yar Khan). Both gall midge species were found on all mango cultivars examined (Chaunsa, Fajri, Dusehri, Surkha, Sindhri, and Anwar Ratul), with the most damage occurring to Surkha and Dusehri. Research on midge distribution patterns in different parts of mango orchards (central, southern, northern, eastern, and western sides) showed these species to be found in all areas, with the greatest numbers in the central and southern regions. In addition, both species were most abundant on the lower parts of the mango tree canopy.
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Affiliation(s)
- H M Rehman
- Department of Entomology, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
- CABI Central and West Asia, Opposite 1-A, Data Gunj Bukhsh Rd., Satellite Town, Rawalpindi, Pakistan
| | - R Mahmood
- CABI Central and West Asia, Opposite 1-A, Data Gunj Bukhsh Rd., Satellite Town, Rawalpindi, Pakistan
| | - M Razaq
- Department of Entomology, Faculty of Agriculture Sciences and Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - R Saeed
- Entomology Section, Central Cotton Research Institute, Multan, Punjab, Pakistan
| | - M Jamil
- Department of Soil Science, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - G V P Reddy
- Department of Research Centers, Western Triangle Agricultural Research Center, Montana State University, P. O. Box 656, Conrad, MT 59425
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