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Article ; Online: Oxadiazole Derivatives of Diclofenac as an Anti-proliferative Agent for B-cell Non-Hodgkin Lymphoma: An In vitro and In Silico Studies.

Qayyum, Shaista / Jabeen, Almas / Ashraf, Sajda / Seraj, Faiza / Mohammad Khan, Khalid / Siddiqui, Rafat Ali / Zaheer Ul-Haq

Medicinal chemistry (Shariqah (United Arab Emirates))

2024

Abstract: Background: Non-Hodgkin lymphoma of B cell origin is the common type of lymphoma- related malignancy with poor response rate with conventional front-line therapies.: Aim: The aim of the present study was to investigate the potential of new anti- ... ...

Abstract	Background: Non-Hodgkin lymphoma of B cell origin is the common type of lymphoma- related malignancy with poor response rate with conventional front-line therapies. Aim: The aim of the present study was to investigate the potential of new anti-inflammatory oxadiazole derivatives of Diclofenac as an anti-lymphoma agent through in vitro and in silico approaches. Method: The compound (II) showed anti-lymphoma activity against both follicular and Burkitt's lymphoma cells, whereas compound (V) inhibited follicular lymphoma cells only. The diclofenac (I) and derivatives (III, IV and VI) exhibited no anti-proliferative effects. The (II) significantly inhibited the expression of BCL-2, p-38 MAPK and TGF-β in both follicular and Burkitt's lymphoma cells and was non-toxic against normal human fibroblast cells (BJ). Result: The in silico studies against BCL-2 revealed that the unsubstituted Sulphur group in compound (II) is involved in the crucial interactions with the binding site residue. Conclusion: The compound (II) can be a potential therapeutic candidate for B-cell non-Hodgkin lymphoma and deserves further development as a novel anti-lymphoma agent.
Language	English
Publishing date	2024-01-25
Publishing country	Netherlands
Document type	Journal Article
ISSN	1875-6638
ISSN (online)	1875-6638
DOI	10.2174/0115734064290905231228110023
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Article ; Online: Computational Overview of Mycobacterial Thymidine Monophosphate Kinase.

Gul, Sana / Khalil, Ruqaiya / Zaheer Ul-Haq / Mubarak, Mohammad S

Current pharmaceutical design

2020 Volume 26, Issue 15, Page(s) 1676–1681

Abstract: Tuberculosis (TB) ranks among the diseases with the highest morbidity rate with significantly high prevalence in developing countries. Globally, tuberculosis poses the most substantial burden of mortality. Further, a partially treated tuberculosis ... ...

Abstract	Tuberculosis (TB) ranks among the diseases with the highest morbidity rate with significantly high prevalence in developing countries. Globally, tuberculosis poses the most substantial burden of mortality. Further, a partially treated tuberculosis patient is worse than untreated; they may lead to standing out as a critical obstacle to global tuberculosis control. The emergence of multi-drug resistant (MDR) and extremely drug-resistant (XDR) strains, and co-infection of HIV further worsen the situation. The present review article discusses validated targets of the bacterial enzyme thymidine monophosphate kinase (TMPK). TMPKMTB enzyme belongs to the nucleoside monophosphate kinases (NMPKs) family. It is involved in phosphorylation of TMP to TDP, and TDP is phosphorylated to TTP. This review highlights structure elucidation of TMP enzymes and their inhibitors study on TMP scaffold, and it also discusses different techniques; including molecular docking, virtual screening, 3DPharmacophore, QSAR for finding anti-tubercular agents.
MeSH term(s)	Antitubercular Agents/pharmacology ; Humans ; Molecular Docking Simulation ; Mycobacterium tuberculosis ; Nucleoside-Phosphate Kinase ; Tuberculosis/drug therapy ; Tuberculosis, Multidrug-Resistant
Chemical Substances	Antitubercular Agents ; Nucleoside-Phosphate Kinase (EC 2.7.4.4) ; dTMP kinase (EC 2.7.4.9)
Language	English
Publishing date	2020-04-03
Publishing country	United Arab Emirates
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1304236-1
ISSN	1873-4286 ; 1381-6128
ISSN (online)	1873-4286
ISSN	1381-6128
DOI	10.2174/1381612826666200403114152
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Article ; Online: Discovery of Potential Chemical Probe as Inhibitors of CXCL12 Using Ligand-Based Virtual Screening and Molecular Dynamic Simulation

Sajjad Haider / Assem Barakat / Zaheer Ul-Haq

Molecules, Vol 25, Iss 4829, p

2020 Volume 4829

Abstract: CXCL12 are small pro-inflammatory chemo-attractant cytokines that bind to a specific receptor CXCR4 with a role in angiogenesis, tumor progression, metastasis, and cell survival. Globally, cancer metastasis is a major cause of morbidity and mortality. In ...

Abstract	CXCL12 are small pro-inflammatory chemo-attractant cytokines that bind to a specific receptor CXCR4 with a role in angiogenesis, tumor progression, metastasis, and cell survival. Globally, cancer metastasis is a major cause of morbidity and mortality. In this study, we targeted CXCL12 rather than the chemokine receptor (CXCR4) because most of the drugs failed in clinical trials due to unmanageable toxicities. Until now, no FDA approved medication has been available against CXCL12. Therefore, we aimed to find new inhibitors for CXCL12 through virtual screening followed by molecular dynamics simulation. For virtual screening, active compounds against CXCL12 were taken as potent inhibitors and utilized in the generation of a pharmacophore model, followed by validation against different datasets. Ligand based virtual screening was performed on the ChEMBL and in-house databases, which resulted in successive elimination through the steps of pharmacophore-based and score-based screenings, and finally, sixteen compounds of various interactions with significant crucial amino acid residues were selected as virtual hits. Furthermore, the binding mode of these compounds were refined through molecular dynamic simulations. Moreover, the stability of protein complexes, Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), and radius of gyration were analyzed, which led to the identification of three potent inhibitors of CXCL12 that may be pursued in the drug discovery process against cancer metastasis.
Keywords	chemokines ; metastasis ; cancer ; pharmacophore based virtual screening ; CXCR4 ; molecular dynamic simulation ; Organic chemistry ; QD241-441
Subject code	540
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: Unraveling the versatility of human serum albumin – A comprehensive review of its biological significance and therapeutic potential

Sajda Ashraf / Hina Qaiser / Sumayya Tariq / Asaad Khalid / Hafiz A. Makeen / Hassan A. Alhazmi / Zaheer Ul-Haq

Current Research in Structural Biology, Vol 6, Iss , Pp 100114- (2023)

2023

Abstract: Human serum albumin (HSA) is a multi-domain macromolecule with diverse ligand binding capability because of its ability to allow allosteric modulation despite being a monomeric protein. Physiologically, HSA act as the primary carrier for various ... ...

Abstract	Human serum albumin (HSA) is a multi-domain macromolecule with diverse ligand binding capability because of its ability to allow allosteric modulation despite being a monomeric protein. Physiologically, HSA act as the primary carrier for various exogenous and endogenous compounds and fatty acids, and alter the pharmacokinetic properties of several drugs. It has antioxidant properties and is utilized therapeutically to improve the drug delivery of pharmacological agents for the treatment of several disorders. The flexibility of albumin in holding various types of drugs coupled with a variety of modifications makes this protein a versatile drug carrier with incalculable potential in therapeutics. This review provides a brief outline of the different structural properties of HSA, and its various binding sites, moreover, an overview of the genetic, biomedical, and allosteric modulation of drugs and drug delivery aspects of HSA is also included, which may be helpful in guiding advanced clinical applications and further research on the therapeutic potential of this extraordinary protein.
Keywords	Human serum albumin ; Allosteric modulation ; Drug delivery ; Drug specificity ; Albumin fusion proteins ; Biology (General) ; QH301-705.5
Subject code	500
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Effects of Smokeless Tobacco Samples from Tabuk Saudi Arabia on Nitric Oxide Production: A Potential Risk for Cancer and Cardiovascular Diseases.

Mesaik, Muhammed Ahmed / Jabeen, Almas / Saeed, Maria / Zaheer Ul-Haq / Ahmed, Izzaddinn Elawad / Ibrahim Mohammed, Yassin / Mirghani, Hyder Osman / Khalid, Asaad

Current computer-aided drug design

2021 Volume 18, Issue 2, Page(s) 110–119

Abstract: Background: Smokeless tobacco (SLT) is traditionally used in Middle East countries. The several toxic constituents with potential carcinogenicity make it a serious human health risk. Literature regarding their effects on cardiac and cancer disease is ... ...

Abstract	Background: Smokeless tobacco (SLT) is traditionally used in Middle East countries. The several toxic constituents with potential carcinogenicity make it a serious human health risk. Literature regarding their effects on cardiac and cancer disease is lacking in Saudi Arabia. Objective: This study was conducted to investigate the adverse effect of 11 different samples of widely used SLT varieties from the Tabuk region - Saudi Arabia, on Nitric Oxide (NO) level and their potential risk on cardiovascular health, etiology and/or progression of cancers. Methods: Samples were collected from Tabuk, KSA and analyzed by the GC-MS technique. Nitric oxide inhibition was performed using J774.2 macrophages by the Griess method. The retrieved crystallized structure of human inducible nitric oxide synthase (iNOS) from Brookhaven Protein Data Bank Repository PDB I.D: 3E7G with 2.20Å resolution was further prepared by structure using the MOE.2019 tool. The compounds abstracted from 11 different Shammah varieties were sketched by the MOE-Builder tool. Minimization for both receptor and compounds was performed via AMBER99 and MMFF99X force field implemented in MOE. Results: Nine samples (4 - 11) showed a potent suppressive effect on NO production with IC50 values ranging between (16.9-20.4 μg/mL), respectively. The samples (1 & 2) exhibited a moderate level of inhibition with IC50 ranging between 33.2 and 57.4 μg/mL, respectively. Interestingly, sample 4 consisting of compounds (13-15, 19-26, 28) that mostly belongs to the group fatty acid ester and phthalic acid ester showed the most potent suppressive effect. Molecular docking results revealed that the current local SLT constituents presented noticeable potency in different extract samples. Conclusion: Variable suppressive effects on NO were detected in the current SLT samples, where sample 4 was the most potent among all. The extract of the latter exhibited molecular interaction with the first shell amino acid residues of Inducible nitric oxide synthase (iNOS), which may anchor the plasticity and selectivity of the compounds present in it. The samples (4 -11) showed a potent inhibitory effect on the NO, where compound 26 (Phthalic acid ester) is common, and its adequate concentration may account for augmented biological activity. These results may effectively highlight their adverse effects on cardiovascular health and etiology and/or progression of cancer and may help in strengthening the social and governmental efforts in minimizing the use of these substances.
MeSH term(s)	Cardiovascular Diseases ; Esters ; Humans ; Molecular Docking Simulation ; Neoplasms ; Nitric Oxide/metabolism ; Nitric Oxide Synthase Type II/metabolism ; Plant Extracts/pharmacology ; Saudi Arabia ; Tobacco, Smokeless/adverse effects
Chemical Substances	Esters ; Plant Extracts ; Nitric Oxide (31C4KY9ESH) ; Nitric Oxide Synthase Type II (EC 1.14.13.39)
Language	English
Publishing date	2021-11-17
Publishing country	United Arab Emirates
Document type	Journal Article
ISSN	1875-6697
ISSN (online)	1875-6697
DOI	10.2174/1573409917666211118094840
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Book ; Online: An in-silico evaluation of COVID-19 main protease with clinically approved drugs

TACHOUA Wafa / KABRINE Mohamed / Mamona Mushtaq / Zaheer Ul-Haq

2020

Abstract: A novel strain of coronavirus, namely, SARS-CoV-2 identified in Wuhan city of China in December 2019, continues to spread at a rapid rate worldwide. There are no specific therapies available and investigations regarding the treatment of this disease are ... ...

Abstract	A novel strain of coronavirus, namely, SARS-CoV-2 identified in Wuhan city of China in December 2019, continues to spread at a rapid rate worldwide. There are no specific therapies available and investigations regarding the treatment of this disease are still lacking. In order to identify a novel potent inhibitor, we performed blind docking studies on the main virus protease M pro with eight approved drugs belonging to four pharmacological classes such as: anti-malarial, anti-bacterial, anti-infective and anti-histamine. Among the eight studied compounds, Lymecycline and Mizolastine appear as potential inhibitors of this protease. When docked against M pro crystal structure, these two compounds revealed a minimum binding energy of -8.87 and -8.71 kcal/mol with 168 and 256 binding modes detected in the binding substrate pocket, respectively. Further, to study the interaction mechanism and conformational dynamics of protein-ligand complexes, Molecular dynamic simulation and MM/PBSA binding free calculations were performed. Our results showed that both Lymecycline and Mizolastine bind in the active site. And exhibited good binding affinities towards target protein. Moreover, the ADMET analysis also indicated drug-likeness properties. Thus it is suggested that the identified compounds can inhibit Chymotrypsin-like protease (3CL pro ) of SARS-CoV-2.
Keywords	Biochemistry ; Bioinformatics and Computational Biology ; Coronavirus ; COVID-19 Main protease ; SwissDock Web server ; Molecular docking analysis ; approved drugs ; molecular dynamics ; ADMET ; covid19
Subject code	540
Publishing date	2020-05-19T13:56:51Z
Document type	Book ; Online
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Article ; Online: Quantum mechanics and 3D-QSAR studies on thienopyridine analogues

Zaheer Ul-Haq / Alamgir Khan / Sajda Ashraf / Alejandro Morales-Bayuelo

Heliyon, Vol 6, Iss 6, Pp e04125- (2020)

inhibitors of IKKβ

2020

Abstract: Inhibitor of kappa B kinase subunit β (IKKβ) is a main regulator of nuclear factor kappa B (NF-κB) and has received considerable attention as an attractive therapeutic target for the treatment of lung cancer or other inflammatory disease. A group of ... ...

Abstract	Inhibitor of kappa B kinase subunit β (IKKβ) is a main regulator of nuclear factor kappa B (NF-κB) and has received considerable attention as an attractive therapeutic target for the treatment of lung cancer or other inflammatory disease. A group of diversified thienopyridine derivatives exhibited a wide range of biological activity was used to investigate its structural requirements by using DFT and 3D-Quantitative structure activity relationship. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were established using the experimental activity of thienopyridine derivatives. The cross-validation coefficient (q2) values for CoMFA and CoMSIA are 0.671 and 0.647 respectively, were achieved, demonstrating high predictive capability of the model. The contour analysis indicate that presence of hydrophobic and electrostatic field is highly desirable for biological activity. The results indicate that substitution of hydrophobic group with electron withdrawing effect at R4 and R6 position have more possibility to increase the biological activity of thienopyridine derivatives. Subsequently molecular docking and DFT calculation were performed to assess the potency of the compounds.
Keywords	Pharmaceutical chemistry ; Theoretical chemistry ; Inhibitors of IKKβ ; Thienopyridine analogues ; Quantum mechanics ; 3D-QSAR Studies ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	540
Language	English
Publishing date	2020-06-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Exploration of the structural requirements of Aurora Kinase B inhibitors by a combined QSAR, modelling and molecular simulation approach

Sajda Ashraf / Kara E. Ranaghan / Christopher J. Woods / Adrian J. Mulholland / Zaheer Ul-Haq

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 19

Abstract: Abstract Aurora kinase B plays an important role in the cell cycle to orchestrate the mitotic process. The amplification and overexpression of this kinase have been implicated in several human malignancies. Therefore, Aurora kinase B is a potential drug ... ...

Abstract	Abstract Aurora kinase B plays an important role in the cell cycle to orchestrate the mitotic process. The amplification and overexpression of this kinase have been implicated in several human malignancies. Therefore, Aurora kinase B is a potential drug target for anticancer therapies. Here, we combine atom-based 3D-QSAR analysis and pharmacophore model generation to identify the principal structural features of acylureidoindolin derivatives that could potentially be responsible for the inhibition of Aurora kinase B. The selected CoMFA and CoMSIA model showed significant results with cross-validation values (q2) of 0.68, 0.641 and linear regression values (r2) of 0.971, 0.933 respectively. These values support the statistical reliability of our model. A pharmacophore model was also generated, incorporating features of reported crystal complex structures of Aurora kinase B. The pharmacophore model was used to screen commercial databases to retrieve potential lead candidates. The resulting hits were analyzed at each stage for diversity based on the pharmacophore model, followed by molecular docking and filtering based on their interaction with active site residues and 3D-QSAR predictions. Subsequently, MD simulations and binding free energy calculations were performed to test the predictions and to characterize interactions at the molecular level. The results suggested that the identified compounds retained the interactions with binding residues. Binding energy decomposition identified residues Glu155, Trp156 and Ala157 of site B and Leu83 and Leu207 of site C as major contributors to binding affinity, complementary to 3D-QSAR results. To best of our knowledge, this is the first comparison of WaterSwap field and 3D-QSAR maps. Overall, this integrated strategy provides a basis for the development of new and potential AK-B inhibitors and is applicable to other protein targets.
Keywords	Medicine ; R ; Science ; Q
Subject code	540
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Structure based 3D-QSAR studies of Interleukin-2 inhibitors: Comparing the quality and predictivity of 3D-QSAR models obtained from different alignment methods and charge calculations.

Halim, Sobia Ahsan / Zaheer-ul-Haq

Chemico-biological interactions

2015 Volume 238, Page(s) 9–24

Abstract: Interleukin-2 is an essential cytokine in an innate immune response, and is a promising drug target for several immunological disorders. In the present study, structure-based 3D-QSAR modeling was carried out via Comparative Molecular Field Analysis ( ... ...

Abstract	Interleukin-2 is an essential cytokine in an innate immune response, and is a promising drug target for several immunological disorders. In the present study, structure-based 3D-QSAR modeling was carried out via Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Index Analysis (CoMSIA) methods. Six different partial charge calculation methods were used in combination with two different alignment methods to scrutinize their effects on the predictive power of 3D-QSAR models. The best CoMFA and CoMSIA models were obtained with the AM1 charges when used with co-conformer based substructure alignment (CCBSA) method. The obtained models posses excellent correlation coefficient value and also exhibited good predictive power (for CoMFA: q(2)=0.619; r(2)=0.890; r(2)Pred=0.765 and for CoMSIA: q(2)=0.607; r(2)=0.884; r(2)Pred=0.655). The developed models were further validated by using a set of another sixteen compounds as external test set 2 and both models showed strong predictive power with r(2)Pred=>0.8. The contour maps obtained from these models better interpret the structure activity relationship; hence the developed models would help to design and optimize more potent IL-2 inhibitors. The results might have implications for rational design of specific anti-inflammatory compounds with improved affinity and selectivity.
MeSH term(s)	Binding Sites ; Crystallography, X-Ray ; Interleukin-2/chemistry ; Interleukin-2/metabolism ; Least-Squares Analysis ; Ligands ; Lymphokines/chemistry ; Lymphokines/metabolism ; Molecular Docking Simulation ; Protein Binding ; Protein Structure, Tertiary ; Quantitative Structure-Activity Relationship ; Static Electricity
Chemical Substances	Interleukin-2 ; Ligands ; Lymphokines ; interleukin 2 inhibitor
Language	English
Publishing date	2015-08-05
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	218799-1
ISSN	1872-7786 ; 0009-2797
ISSN (online)	1872-7786
ISSN	0009-2797
DOI	10.1016/j.cbi.2015.05.018
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Article ; Online: Identification of Selective BRD9 Inhibitor via Integrated Computational Approach

Maria Mushtaq Ali / Sajda Ashraf / Mohammad Nure-e-Alam / Urooj Qureshi / Khalid Mohammed Khan / Zaheer Ul-Haq

International Journal of Molecular Sciences, Vol 23, Iss 13513, p

2022 Volume 13513

Abstract: Bromodomain-containing protein 9 (BRD9), a member of the bromodomain and extra terminal domain (BET) protein family, works as an epigenetic reader. BRD9 has been considered an essential drug target for cancer, inflammatory diseases, and metabolic ... ...

Abstract	Bromodomain-containing protein 9 (BRD9), a member of the bromodomain and extra terminal domain (BET) protein family, works as an epigenetic reader. BRD9 has been considered an essential drug target for cancer, inflammatory diseases, and metabolic disorders. Due to its high similarity among other isoforms, no effective treatment of BRD9-associated disorders is available. For the first time, we performed a detailed comparative analysis among BRD9, BRD7, and BRD4. The results indicate that residues His42, Gly43, Ala46, Ala54, Val105, and Leu109 can confer the BRD9 isoform selectivity. The predicted crucial residues were further studied. The pharmacophore model’s features were precisely mapped with some key residues including, Gly43, Phe44, Phe45, Asn100, and Tyr106, all of which play a crucial role in BRD9 inhibition. Docking-based virtual screening was utilized with the consideration of the conserved water network in the binding cavity to identify the potential inhibitors of BRD9. In this workflow, 714 compounds were shortlisted. To attain selectivity, 109 compounds were re-docked to BRD7 for negative selection. Finally, four compounds were selected for molecular dynamics studies. Our studies pave the way for the identification of new compounds and their role in causing noticeable, functional differences in isoforms and between orthologues.
Keywords	BRD9 ; cancer ; structure-based pharmacophore ; molecular docking ; molecular dynamic simulation ; MM-GBSA ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2022-11-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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