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Article: An Evolutionary Insight Into the Heterogeneous Severity Pattern of the SARS-CoV-2 Infection.

Raza, Rabail Zehra / Abbasi, Sumra Wajid

2022 Volume 13, Page(s) 859508

Abstract: The ongoing pandemic of COVID-19 has elaborated an idiosyncratic pattern of SARS-CoV-2-induced symptoms in the human host. Some populations have succumbed to the SARS-CoV-2 infection in large numbers during this pandemic, whereas others have shown a ... ...

Abstract	The ongoing pandemic of COVID-19 has elaborated an idiosyncratic pattern of SARS-CoV-2-induced symptoms in the human host. Some populations have succumbed to the SARS-CoV-2 infection in large numbers during this pandemic, whereas others have shown a resilient side by manifesting only milder or no symptoms at all. This observation has relayed the onus of the heterogeneous pattern of SARS-CoV-2-induced critical illness among different populations to the host genetic factors. Here, the evolutionary route was explored and three genetic loci, i.e., rs10735079, rs2109069, and rs2236757, associated with COVID-19 were analyzed. Among the three, the risk allele A at genetic locus rs2236757 residing in the
Language	English
Publishing date	2022-03-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2022.859508
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Article ; Online: Correction to: Exploring Novel 1-Hydroxynaphthalene-2-Carboxanilides Based Inhibitors Against C-Jun N-Terminal Kinases Through Molecular Dynamic Simulation and WaterSwap Analysis.

Jamal, Syed Babar / Ismail, Saba / Yousaf, Rimsha / Qazi, Asma Saleem / Iftkhar, Saba / Abbasi, Sumra Wajid

Applied biochemistry and biotechnology

2023

Language	English
Publishing date	2023-09-16
Publishing country	United States
Document type	Published Erratum
ZDB-ID	392344-7
ISSN	1559-0291 ; 0273-2289
ISSN (online)	1559-0291
ISSN	0273-2289
DOI	10.1007/s12010-023-04720-6
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Article ; Online: Exploring Novel 1-Hydroxynaphthalene-2-Carboxanilides Based Inhibitors Against C-Jun N-Terminal Kinases Through Molecular Dynamic Simulation and WaterSwap Analysis.

Jamal, Syed Babar / Ismail, Saba / Yousaf, Rimsha / Qazi, Asma Saleem / Iftkhar, Saba / Abbasi, Sumra Wajid

Applied biochemistry and biotechnology

2023 Volume 196, Issue 4, Page(s) 1803–1819

Abstract: Cancer is a disease of mutation and lifestyle modifications. A large number of normal genes can transform normal cells to cancer cells due to their deregulations including overexpression and loss of expression. Signal transduction is a complex signaling ... ...

Abstract	Cancer is a disease of mutation and lifestyle modifications. A large number of normal genes can transform normal cells to cancer cells due to their deregulations including overexpression and loss of expression. Signal transduction is a complex signaling process that involves multiple interactions and different functions. C-Jun N-terminal kinases (JNKs) is an important protein involved in signaling process. JNK mediated pathways can detect, integrate, and amplify various external signals that may cause alterations in gene expression, enzyme activities, and different cellular functions that affect cellular behavior like metabolism, proliferation, differentiation, and cell survival. In this study, we performed molecular docking protocol (MOE) to predict the binding interactions of some known anticancer 1-hydroxynaphthalene-2-carboxanilides candidates. A set of 10 active compounds was retrieved after initial screening on the basis of docking scores, binding energies, and number of interactions and was re-docked in the active site of JNK protein. The results were further validated through molecular dynamics simulation and MMPB/GBSA calculations. The active compounds 4p and 5 k were ranked on top. After computationally exploring interactions of 1-hydroxynaphthalene-2-carboxanilides with JNK protein, we believe compounds 4p and 5 k can serve as potential inhibitors of JNK protein. It is believed that the results of current research would help to develop novel and structurally diverse anticancer compounds that will be useful not only treat cancer but also for the medication for the other diseases caused by protein deregulation.
MeSH term(s)	JNK Mitogen-Activated Protein Kinases/metabolism ; JNK Mitogen-Activated Protein Kinases/chemistry ; JNK Mitogen-Activated Protein Kinases/antagonists & inhibitors ; Molecular Dynamics Simulation ; Humans ; Molecular Docking Simulation ; Protein Kinase Inhibitors/pharmacology ; Protein Kinase Inhibitors/chemistry ; Anilides/pharmacology ; Anilides/chemistry ; Naphthols/chemistry ; Naphthols/pharmacology ; Naphthols/metabolism
Chemical Substances	JNK Mitogen-Activated Protein Kinases (EC 2.7.11.24) ; Protein Kinase Inhibitors ; Anilides ; Naphthols
Language	English
Publishing date	2023-07-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	392344-7
ISSN	1559-0291 ; 0273-2289
ISSN (online)	1559-0291
ISSN	0273-2289
DOI	10.1007/s12010-023-04638-z
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Article ; Online: Stilbene-based natural compounds as promising drug candidates against COVID-19.

Wahedi, Hussain Mustatab / Ahmad, Sajjad / Abbasi, Sumra Wajid

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 9, Page(s) 3225–3234

Abstract: The pandemic coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a great threat to public health. Currently, no potent medicine is available to treat COVID-19. Quest for new drugs especially from ...

Abstract	The pandemic coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a great threat to public health. Currently, no potent medicine is available to treat COVID-19. Quest for new drugs especially from natural plant sources is an area of immense potential. The current study aimed to repurpose stilbenoid analogs, reported for some other biological activities, against SARS-CoV-2 spike protein and human ACE2 receptor complex for their affinity and stability using molecular dynamics simulation and binding free energy analysis based on molecular docking. Four compounds in total were probed for their binding affinity using molecular docking. All of the compounds showed good affinity (> -7 kcal/mol). However, fifty nanoseconds molecular dynamic simulation in aqueous solution revealed highly stable bound conformation of resveratrol to the viral protein: ACE2 receptor complex. Net free energy of binding using MM-PBSA also affirmed the stability of the resveratrol-protein complex. Based on the results, we report that stilbene based compounds in general and resveratrol, in particular, can be promising anti-COVID-19 drug candidates acting through disruption of the spike protein. Our findings in this study are promising and call for further
MeSH term(s)	Antiviral Agents/pharmacology ; COVID-19 ; Humans ; Molecular Docking Simulation ; Pharmaceutical Preparations ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Stilbenes/pharmacology
Chemical Substances	Antiviral Agents ; Pharmaceutical Preparations ; Spike Glycoprotein, Coronavirus ; Stilbenes ; spike protein, SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-05-12
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1762743
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Zs.A 2093: Show issues

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Article: Effect of

Qazi, Neelam Gul / Khan, Arif-Ullah / Abbasi, Sumra Wajid / Malik, Imran / Naeem, Komal

Frontiers in pharmacology

2022 Volume 13, Page(s) 936161

Abstract: This present study aims to ... ...

Abstract	This present study aims to delineate
Language	English
Publishing date	2022-08-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587355-6
ISSN	1663-9812
ISSN	1663-9812
DOI	10.3389/fphar.2022.936161
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Article: Design of a Multi-Epitopes Vaccine against Hantaviruses: An Immunoinformatics and Molecular Modelling Approach.

Ismail, Saba / Abbasi, Sumra Wajid / Yousaf, Maha / Ahmad, Sajjad / Muhammad, Khalid / Waheed, Yasir

Vaccines

2022 Volume 10, Issue 3

Abstract: Hantaviruses are negative-sense, enveloped, single-stranded RNA viruses of the family Hantaviridae. In recent years, rodent-borne hantaviruses have emerged as novel zoonotic viruses posing a substantial health issue and socioeconomic burden. In the ... ...

Abstract	Hantaviruses are negative-sense, enveloped, single-stranded RNA viruses of the family Hantaviridae. In recent years, rodent-borne hantaviruses have emerged as novel zoonotic viruses posing a substantial health issue and socioeconomic burden. In the current research, a reverse vaccinology approach was applied to design a multi-epitope-based vaccine against hantavirus. A set of 340 experimentally reported epitopes were retrieved from Virus Pathogen Database and Analysis Resource (ViPR) and subjected to different analyses such as antigenicity, allergenicity, solubility, IFN gamma, toxicity, and virulent checks. Finally, 10 epitopes which cleared all the filters used were linked with each other through specific GPGPG linkers to construct a multi-antigenic epitope vaccine. The designed vaccine was then joined to three different adjuvants-TLR4-agonist adjuvant, β-defensin, and 50S ribosomal protein L7/L12-using an EAAAK linker to boost up immune-stimulating responses and check the potency of vaccine with each adjuvant. The designed vaccine structures were modelled and subjected to error refinement and disulphide engineering to enhance their stability. To understand the vaccine binding affinity with immune cell receptors, molecular docking was performed between the designed vaccines and TLR4; the docked complex with a low level of global energy was then subjected to molecular dynamics simulations to validate the docking results and dynamic behaviour. The docking binding energy of vaccines with TLR4 is -29.63 kcal/mol (TLR4-agonist), -3.41 kcal/mol (β-defensin), and -11.03 kcal/mol (50S ribosomal protein L7/L12). The systems dynamics revealed all three systems to be highly stable with a root-mean-square deviation (RMSD) value within 3 Å. To test docking predictions and determine dominant interaction energies, binding free energies of vaccine(s)-TLR4 complexes were calculated. The net binding energy of the systems was as follows: TLR4-agonist vaccine with TLR4 (MM-GBSA, -1628.47 kcal/mol and MM-PBSA, -37.75 kcal/mol); 50S ribosomal protein L7/L12 vaccine with TLR4 complex (MM-GBSA, -194.62 kcal/mol and MM-PBSA, -150.67 kcal/mol); β-defensin vaccine with TLR4 complex (MM-GBSA, -9.80 kcal/mol and MM-PBSA, -42.34 kcal/mol). Finally, these findings may aid experimental vaccinologists in developing a very potent hantavirus vaccine.
Language	English
Publishing date	2022-02-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2703319-3
ISSN	2076-393X
ISSN	2076-393X
DOI	10.3390/vaccines10030378
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Article ; Online: An in silico study to unveil potential drugs and vaccine chimera for HBV capsid assembly protein: combined molecular docking and dynamics simulation approach.

Ismail, Saba / Waheed, Yasir / Ahmad, Sajjad / Ahsan, Omar / Abbasi, Sumra Wajid / Sadia, Khulah

Journal of molecular modeling

2022 Volume 28, Issue 2, Page(s) 51

Abstract: Humans are a major reservoir of the hepatitis B virus (HBV), therefore promising treatment and control vaccination strategies are needed to eradicate the virus. Though promising drugs and vaccines are available against HBV, still efforts are required to ... ...

Abstract	Humans are a major reservoir of the hepatitis B virus (HBV), therefore promising treatment and control vaccination strategies are needed to eradicate the virus. Though promising drugs and vaccines are available against HBV, still efforts are required to enrich the therapy options. Herein, the HBV assembly protein was explored to identify novel targets for future use against HBV. Computer-aided drug designing and immune-informatics techniques were employed for the identification of putative inhibitors and vaccine ensemble against HBV using capsid assembly protein. The identified drug molecule binds with high affinity to the active pocket of the protein, and several epitopes are scanned in the protein sequence. The drug molecule, besides being a good putative inhibitor, has acceptable drug-like properties. A multi-epitope vaccine is also constructed to overcome the limitations of weakly immunogenic epitopes. In contrast to the MHC II level, the set of predicted epitopes has been recognized to interact with significant numbers of HLA alleles of MHC I. Selected epitopes are extremely virulent, antigenic, nontoxic, nonallergic, have suitable affinity to bind with the prevailing DRB*0101 allele, and also spectacle 86% mediocre population coverage. A multi-epitope peptide-based vaccine chimera having 73 amino acids was designed. It emerged as substantially immunogenic, thermally stable, robust in producing cellular as well as humoral immune responses, and had competent physicochemical properties to analyze in vitro and in vivo studies. The capsid assembly protein is a in more stable nature in the presence of the drug molecule compared to the TLR3 receptor in the vaccine presence. These particulars were confirmed by exposing the docked molecules to absolute and relative binding free energy approaches of MMGBSA/PBSA. The purpose to investigate the interactions between the vaccine and a representative TLR3 immune receptor can reveal the intermolecular affinity and possible presentation mechanism of the vaccine by TLR3 to the host immune system. It was revealed that the vaccine is showing a very good affinity of binding for the TLR3 and forming a network of hydrophobic and hydrophilic interactions. Overall, the findings of this study are promising and might be useful for further experimental validations.
MeSH term(s)	Amino Acid Sequence ; Antiviral Agents/chemistry ; Binding Sites ; Capsid Proteins/chemistry ; Capsid Proteins/immunology ; Catalytic Domain ; Cluster Analysis ; Computational Biology/methods ; Databases, Factual ; Drug Design ; Epitopes, T-Lymphocyte/chemistry ; Epitopes, T-Lymphocyte/immunology ; Hepatitis B Vaccines/chemistry ; Hepatitis B Vaccines/immunology ; Hepatitis B virus/immunology ; Humans ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Binding ; Structure-Activity Relationship
Chemical Substances	Antiviral Agents ; Capsid Proteins ; Epitopes, T-Lymphocyte ; Hepatitis B Vaccines ; Ligands
Language	English
Publishing date	2022-02-02
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-022-05042-w
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Article: Immunoinformatics Approach to Design a Multi-Epitope Vaccine against Cutaneous Leishmaniasis.

Naz, Shumaila / Aroosh, Aiman / Caner, Ayse / Şahar, Esra Atalay / Toz, Seray / Ozbel, Yusuf / Abbasi, Sumra Wajid

Vaccines

2023 Volume 11, Issue 2

Abstract: Cutaneous Leishmaniasis (CL), a neglected vector-borne disease caused by protozoan parasite Leishmania major ( ...

Abstract	Cutaneous Leishmaniasis (CL), a neglected vector-borne disease caused by protozoan parasite Leishmania major (
Language	English
Publishing date	2023-02-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2703319-3
ISSN	2076-393X
ISSN	2076-393X
DOI	10.3390/vaccines11020339
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Article ; Online: Repurposing FIASMAs against Acid Sphingomyelinase for COVID-19: A Computational Molecular Docking and Dynamic Simulation Approach.

Naz, Aliza / Asif, Sumbul / Alwutayd, Khairiah Mubarak / Sarfaraz, Sara / Abbasi, Sumra Wajid / Abbasi, Asim / Alenazi, Abdulkareem M / Hasan, Mohamed E

Molecules (Basel, Switzerland)

2023 Volume 28, Issue 7

Abstract: Over the past few years, COVID-19 has caused widespread suffering worldwide. There is great research potential in this domain and it is also necessary. The main objective of this study was to identify potential inhibitors against acid sphingomyelinase ( ... ...

Abstract	Over the past few years, COVID-19 has caused widespread suffering worldwide. There is great research potential in this domain and it is also necessary. The main objective of this study was to identify potential inhibitors against acid sphingomyelinase (ASM) in order to prevent coronavirus infection. Experimental studies revealed that SARS-CoV-2 causes activation of the acid sphingomyelinase/ceramide pathway, which in turn facilitates the viral entry into the cells. The objective was to inhibit acid sphingomyelinase activity in order to prevent the cells from SARS-CoV-2 infection. Previous studies have reported functional inhibitors against ASM (FIASMAs). These inhibitors can be exploited to block the entry of SARS-CoV-2 into the cells. To achieve our objective, a drug library containing 257 functional inhibitors of ASM was constructed. Computational molecular docking was applied to dock the library against the target protein (PDB: 5I81). The potential binding site of the target protein was identified through structural alignment with the known binding pocket of a protein with a similar function. AutoDock Vina was used to carry out the docking steps. The docking results were analyzed and the inhibitors were screened based on their binding affinity scores and ADME properties. Among the 257 functional inhibitors, Dutasteride, Cepharanthine, and Zafirlukast presented the lowest binding affinity scores of -9.7, -9.6, and -9.5 kcal/mol, respectively. Furthermore, computational ADME analysis of these results revealed Cepharanthine and Zafirlukast to have non-toxic properties. To further validate these findings, the top two inhibitors in complex with the target protein were subjected to molecular dynamic simulations at 100 ns. The molecular interactions and stability of these compounds revealed that these inhibitors could be a promising tool for inhibiting SARS-CoV-2 infection.
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2 ; Molecular Docking Simulation ; Drug Repositioning ; Sphingomyelin Phosphodiesterase ; Protease Inhibitors/chemistry ; Molecular Dynamics Simulation ; Antiviral Agents/pharmacology
Chemical Substances	zafirlukast (XZ629S5L50) ; Sphingomyelin Phosphodiesterase (EC 3.1.4.12) ; Protease Inhibitors ; Antiviral Agents
Language	English
Publishing date	2023-03-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules28072989
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Article ; Online: In-silico

Shahid, Izzah / Shoaib, Muhammad / Raza, Rabail Zehra / Jahangir, Muhammad / Abbasi, Sumra Wajid / Riasat, Areej / Akbar, Ansa / Mehnaz, Samina

Anti-cancer agents in medicinal chemistry

2023 Volume 23, Issue 12, Page(s) 1388–1396

Abstract: Background: Breast cancer is characterized by uncontrolled cell growth in the breast tissue and is a leading cause of death globally. Cytotoxic effects and reduced efficacy of currently used therapeutics insist to look for new chemo-preventive ... ...

Abstract	Background: Breast cancer is characterized by uncontrolled cell growth in the breast tissue and is a leading cause of death globally. Cytotoxic effects and reduced efficacy of currently used therapeutics insist to look for new chemo-preventive strategies against breast cancer. Objective: The utilization of drug-likeness filters and molecular simulation has helped evaluate the pharmacological activity and binding abilities of selected drug candidates to the target proteins in many cancer studies. Methods: The current Results: Among the three honokiol derivatives, ligand-protein binding energy of 3' formylhonokiol with Conclusion: It was further established that 3'- formylhonokiol displays an excellent profile of distribution, metabolism, and absorption, indicating it is an anticipated future drug candidate.
MeSH term(s)	Humans ; Female ; Breast Neoplasms/pathology ; Molecular Docking Simulation ; Protein Serine-Threonine Kinases/metabolism ; Biphenyl Compounds/pharmacology ; Molecular Dynamics Simulation
Chemical Substances	honokiol (11513CCO0N) ; Protein Serine-Threonine Kinases (EC 2.7.11.1) ; Biphenyl Compounds
Language	English
Publishing date	2023-04-03
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2217610-X
ISSN	1875-5992 ; 1871-5206
ISSN (online)	1875-5992
ISSN	1871-5206
DOI	10.2174/1871520623666230330083630
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