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Article ; Online: Identification of promising anti-DNA gyrase antibacterial compounds using

Islam, Md Ataul / Pillay, Tahir S

Journal of biomolecular structure & dynamics

2019 Volume 38, Issue 6, Page(s) 1798–1809

Abstract: The rapidly increasing rate of antibiotic resistance is of great concern. Approximately two million deaths result annually from bacterial infections worldwide. Therefore, there is a paramount requirement to develop innovative and novel antibacterial ... ...

Abstract	The rapidly increasing rate of antibiotic resistance is of great concern. Approximately two million deaths result annually from bacterial infections worldwide. Therefore, there is a paramount requirement to develop innovative and novel antibacterial agents with new mechanisms of action and activity against resistant bacterial strains. For this purpose, a set of benzothiazole and
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; DNA Gyrase/metabolism ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Topoisomerase II Inhibitors/pharmacology
Chemical Substances	Anti-Bacterial Agents ; Topoisomerase II Inhibitors ; DNA Gyrase (EC 5.99.1.3)
Language	English
Publishing date	2019-05-24
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2019.1617785
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Article ; Online: Pharmacoinformatics-based identification of chemically active molecules against Ebola virus.

Islam, Md Ataul / Pillay, Tahir S

Journal of biomolecular structure & dynamics

2018 Volume 37, Issue 15, Page(s) 4104–4119

Abstract: Ebola is a dangerous virus transmitted by animals and humans and to date there is no curable agent for such a deadly infectious disease. In this study, pharmacoinformatics-based methods were adopted to find effective novel chemical entities against Ebola ...

Abstract	Ebola is a dangerous virus transmitted by animals and humans and to date there is no curable agent for such a deadly infectious disease. In this study, pharmacoinformatics-based methods were adopted to find effective novel chemical entities against Ebola virus. A well predictive and statistical robust pharmacophore model was developed from known Ebola virus inhibitors collected from the literature. The model explained the significance of each of hydrogen bond acceptor and donor, and two hydrophobic regions for activity. The National Cancer Institute and Asinex (Antiviral library) databases were screened using the final validated pharmacophore model. Initial hits were further screened with a set of criteria and finally eight molecules from both databases were proposed as promising anti Ebola agents. Further molecular docking and molecular dynamics studies were carried out and it was found that the proposed molecules possessed capability to interact with amino residues of Ebola protein as well as retaining equilibrium of protein-ligand systems. Finally, the binding energies were calculated using molecular mechanics Poisson-Boltzmann surface area approach and all proposed molecules showed strong binding affinity towards the Ebola protein receptor. Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Area Under Curve ; Computational Biology/methods ; Ebolavirus/drug effects ; Humans ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Molecular Structure ; Quantitative Structure-Activity Relationship ; Reproducibility of Results
Chemical Substances	Antiviral Agents ; Ligands
Language	English
Publishing date	2018-12-24
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2018.1544509
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Article ; Online: β-secretase inhibitors for Alzheimer's disease: identification using pharmacoinformatics.

Islam, Md Ataul / Pillay, Tahir S

Journal of biomolecular structure & dynamics

2018 Volume 37, Issue 2, Page(s) 503–522

Abstract: In this study we searched for potential β-site amyloid precursor protein cleaving enzyme1 (BACE1) inhibitors using pharmacoinformatics. A large dataset containing 7155 known BACE1 inhibitors was evaluated for pharmacophore model generation. The final ... ...

Abstract	In this study we searched for potential β-site amyloid precursor protein cleaving enzyme1 (BACE1) inhibitors using pharmacoinformatics. A large dataset containing 7155 known BACE1 inhibitors was evaluated for pharmacophore model generation. The final model (R = 0.950, RMSD = 1.094, Q
MeSH term(s)	Algorithms ; Alzheimer Disease/drug therapy ; Amyloid Precursor Protein Secretases/antagonists & inhibitors ; Amyloid Precursor Protein Secretases/chemistry ; Drug Discovery/methods ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Molecular Structure ; Quantitative Structure-Activity Relationship ; ROC Curve ; Reproducibility of Results
Chemical Substances	Enzyme Inhibitors ; Amyloid Precursor Protein Secretases (EC 3.4.-)
Language	English
Publishing date	2018-02-01
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2018.1430619
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Article ; Online: Identification of promising DNA GyrB inhibitors for Tuberculosis using pharmacophore-based virtual screening, molecular docking and molecular dynamics studies.

Islam, Md Ataul / Pillay, Tahir S

Chemical biology & drug design

2017 Volume 90, Issue 2, Page(s) 282–296

Abstract: In this study, we searched for potential DNA GyrB inhibitors using pharmacophore-based virtual screening followed by molecular docking and molecular dynamics simulation approaches. For this purpose, a set of 248 DNA GyrB inhibitors was collected from the ...

Abstract	In this study, we searched for potential DNA GyrB inhibitors using pharmacophore-based virtual screening followed by molecular docking and molecular dynamics simulation approaches. For this purpose, a set of 248 DNA GyrB inhibitors was collected from the literature and a well-validated pharmacophore model was generated. The best pharmacophore model explained that two each of hydrogen bond acceptors and hydrophobicity regions were critical for inhibition of DNA GyrB. Good statistical results of the pharmacophore model indicated that the model was robust in nature. Virtual screening of molecular databases revealed three molecules as potential antimycobacterial agents. The final screened promising compounds were evaluated in molecular docking and molecular dynamics simulation studies. In the molecular dynamics studies, RMSD and RMSF values undoubtedly explained that the screened compounds formed stable complexes with DNA GyrB. Therefore, it can be concluded that the compounds identified may have potential for the treatment of TB.
MeSH term(s)	DNA Gyrase/metabolism ; Drug Discovery ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Mycobacterium smegmatis/drug effects ; Mycobacterium smegmatis/enzymology ; Topoisomerase II Inhibitors/chemistry ; Topoisomerase II Inhibitors/pharmacology ; Tuberculosis/drug therapy
Chemical Substances	Topoisomerase II Inhibitors ; DNA Gyrase (EC 5.99.1.3)
Language	English
Publishing date	2017-02-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2216600-2
ISSN	1747-0285 ; 1747-0277
ISSN (online)	1747-0285
ISSN	1747-0277
DOI	10.1111/cbdd.12949
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Article ; Online: Insight into the screening of potential beta-lactamase inhibitors as anti-bacterial chemical agents through pharmacoinformatics study.

Parida, Pratap / Bhowmick, Shovonlal / Saha, Achintya / Islam, Md Ataul

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 3, Page(s) 923–942

Abstract: Drug resistance is an unsolved and major concern in the bacterial infection. Continuous development of drug-resistance to the antibiotics exponentially rises the danger of bacterial infections. Chemical components from the plants are becoming a major ... ...

Abstract	Drug resistance is an unsolved and major concern in the bacterial infection. Continuous development of drug-resistance to the antibiotics exponentially rises the danger of bacterial infections. Chemical components from the plants are becoming a major resource of potentially effective therapeutic chemical agents for the wide range of diseases including bacterial infections. In the current study, pharmacoinformatics methodologies were implemented on more than two hundred known phytochemicals to find promising beta-lactamase inhibitors for therapeutically effective anti-bacterial agents. Initially, the molecular docking-based score was used to reduce the chemical space of the selected dataset. Fourteen molecules were found to have more affinity towards the beta-lactamase in compared to the well-known anti-bacterial agent, Avibactam. Binding interactions analysis revealed the strong binding interactions between phytochemicals and catalytic amino residues. For further analysis, molecular dynamics (MD) simulations, density functional theory (DFT) and
MeSH term(s)	Anti-Bacterial Agents ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; beta-Lactamase Inhibitors ; beta-Lactamases/metabolism
Chemical Substances	Anti-Bacterial Agents ; beta-Lactamase Inhibitors ; beta-Lactamases (EC 3.5.2.6)
Language	English
Publishing date	2020-02-12
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1720819
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Article ; Online: Structural requirements for potential HIV-integrase inhibitors identified using pharmacophore-based virtual screening and molecular dynamics studies.

Islam, Md Ataul / Pillay, Tahir S

Molecular bioSystems

2016 Volume 12, Issue 3, Page(s) 982–993

Abstract: Acquired immunodeficiency syndrome (AIDS) is a life-threatening disease which is a collection of symptoms and infections caused by a retrovirus, human immunodeficiency virus (HIV). There is currently no curative treatment and therapy is reliant on the ... ...

Abstract	Acquired immunodeficiency syndrome (AIDS) is a life-threatening disease which is a collection of symptoms and infections caused by a retrovirus, human immunodeficiency virus (HIV). There is currently no curative treatment and therapy is reliant on the use of existing anti-retroviral drugs. Pharmacoinformatics approaches have already proven their pivotal role in the pharmaceutical industry for lead identification and optimization. In the current study, we analysed the binding preferences and inhibitory activity of HIV-integrase inhibitors using pharmacoinformatics. A set of 30 compounds were selected as the training set of a total 540 molecules for pharmacophore model generation. The final model was validated by statistical parameters and further used for virtual screening. The best mapped model (R = 0.940, RMSD = 2.847, Q(2) = 0.912, se = 0.498, Rpred(2) = 0.847 and rm(test)(2) = 0.636) explained that two hydrogen bond acceptor and one aromatic ring features were crucial for the inhibition of HIV-integrase. From virtual screening, initial hits were sorted using a number of parameters and finally two compounds were proposed as promising HIV-integrase inhibitors. Drug-likeness properties of the final screened compounds were compared to FDA approved HIV-integrase inhibitors. HIV-integrase structure in complex with the most active and final screened compounds were subjected to 50 ns molecular dynamics (MD) simulation studies to check comparative stability of the complexes. The study suggested that the screened compounds might be promising HIV-integrase inhibitors. The new chemical entities obtained from the NCI database will be subjected to experimental studies to confirm potential inhibition of HIV integrase.
MeSH term(s)	Drug Approval ; Drug Evaluation, Preclinical ; HIV Integrase Inhibitors/chemistry ; HIV Integrase Inhibitors/pharmacology ; Humans ; Inhibitory Concentration 50 ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; ROC Curve ; Time Factors ; User-Computer Interface
Chemical Substances	HIV Integrase Inhibitors
Language	English
Publishing date	2016-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2188635-0
ISSN	1742-2051 ; 1742-206X
ISSN (online)	1742-2051
ISSN	1742-206X
DOI	10.1039/c5mb00767d
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Article ; Online: Structure-based identification of SARS-CoV-2 main protease inhibitors from anti-viral specific chemical libraries: an exhaustive computational screening approach.

Bhowmick, Shovonlal / Saha, Achintya / Osman, Sameh Mohamed / Alasmary, Fatmah Ali / Almutairi, Tahani Mazyad / Islam, Md Ataul

Molecular diversity

2021 Volume 25, Issue 3, Page(s) 1979–1997

Abstract: Worldwide coronavirus disease 2019 (COVID-19) outbreak is still threatening global health since its outbreak first reported in the late 2019. The causative novel virus has been designated as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). ... ...

Abstract	Worldwide coronavirus disease 2019 (COVID-19) outbreak is still threatening global health since its outbreak first reported in the late 2019. The causative novel virus has been designated as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although COVID-19 emergent with significant mortality, there is no availability of definite treatment measures. It is now extremely desirable to identify potential chemical entities against SARS-CoV-2 for the treatment of COVID-19. In the present study, a state-of-art virtual screening protocol was implemented on three anti-viral specific chemical libraries against SARS-CoV-2 main protease (M
MeSH term(s)	Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Computer Simulation ; Coronavirus 3C Proteases/antagonists & inhibitors ; Drug Evaluation, Preclinical ; Molecular Dynamics Simulation ; Protease Inhibitors/chemistry ; Protease Inhibitors/pharmacology ; Protein Conformation ; SARS-CoV-2/drug effects ; SARS-CoV-2/enzymology ; Thermodynamics
Chemical Substances	Antiviral Agents ; Protease Inhibitors ; Coronavirus 3C Proteases (EC 3.4.22.28)
Language	English
Publishing date	2021-04-12
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1376507-3
ISSN	1573-501X ; 1381-1991
ISSN (online)	1573-501X
ISSN	1381-1991
DOI	10.1007/s11030-021-10214-6
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Article ; Online: Design, synthesis, molecular modelling and antiproliferative evaluation of novel benzothiazole trihybrids.

Bhoi, Pradip / Thorat, Sonali G / Alasmary, Fatmah Ali / Wabaidur, Saikh Mohammad / Islam, Md Ataul

Biophysical chemistry

2021 Volume 278, Page(s) 106664

Abstract: Colorectal cancer is the third most commonly occurring cancer with very less treatment options in case surgery fails to cure the disease. The emergence of drug resistant colon cancer poses a new threat and calls for better drugs for treatment of colon ... ...

Abstract	Colorectal cancer is the third most commonly occurring cancer with very less treatment options in case surgery fails to cure the disease. The emergence of drug resistant colon cancer poses a new threat and calls for better drugs for treatment of colon cancer patients. Novel substituted benzo[d]thiazol-2-yl)-5-(pyridin-2-yl) penta-1,4-dien-3-one trihybrid molecules were synthesized following appropriate synthetic route. These compounds were tested for their efficacy in colon cancer and drug resistant colon cancer cell lines. Their toxicity was studied on the ICR mice model and the selectivity study was performed in calorimetric assay and xenograft mice model. An attempt was also made to chalk out the feasible mechanism of action based on molecular docking and molecular dynamics simulation studies. Compounds 4f, 4h and 4i were found to be highly effective and selective towards the inhibition of the colon cancer and drug resistant colon cancer cell lines and in the xenograft method. Selective compounds from this study can be developed into potential drug candidates for the possible treatment of drug resistant colorectal cancer.
MeSH term(s)	Animals ; Antineoplastic Agents/chemistry ; Benzothiazoles/chemistry ; Benzothiazoles/pharmacology ; Cell Line, Tumor ; Cell Proliferation ; Drug Design ; Humans ; Mice ; Mice, Inbred ICR ; Molecular Docking Simulation ; Molecular Structure ; Structure-Activity Relationship
Chemical Substances	Antineoplastic Agents ; Benzothiazoles
Language	English
Publishing date	2021-08-08
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	185052-0
ISSN	1873-4200 ; 0301-4622
ISSN (online)	1873-4200
ISSN	0301-4622
DOI	10.1016/j.bpc.2021.106664
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Article ; Online: Identification of Novel Ribonucleotide Reductase Inhibitors for Therapeutic Application in Bile Tract Cancer: An Advanced Pharmacoinformatics Study.

Islam, Md Ataul / Barshetty, Mayuri Makarand / Srinivasan, Sridhar / Dudekula, Dawood Babu / Rallabandi, V P Subramanyam / Mohammed, Sameer / Natarajan, Sathishkumar / Park, Junhyung

Biomolecules

2022 Volume 12, Issue 9

Abstract: Biliary tract cancer (BTC) is constituted by a heterogeneous group of malignant tumors that may develop in the biliary tract, and it is the second most common liver cancer. Human ribonucleotide reductase M1 (hRRM1) has already been proven to be a ... ...

Abstract	Biliary tract cancer (BTC) is constituted by a heterogeneous group of malignant tumors that may develop in the biliary tract, and it is the second most common liver cancer. Human ribonucleotide reductase M1 (hRRM1) has already been proven to be a potential BTC target. In the current study, a de novo design approach was used to generate novel and effective chemical therapeutics for BTC. A set of comprehensive pharmacoinformatics approaches was implemented and, finally, seventeen potential molecules were found to be effective for the modulation of hRRM1 activity. Molecular docking, negative image-based ShaEP scoring, absolute binding free energy, in silico pharmacokinetics, and toxicity assessments corroborated the potentiality of the selected molecules. Almost all molecules showed higher affinity in comparison to gemcitabine and naphthyl salicylic acyl hydrazone (NSAH). On binding interaction analysis, a number of critical amino acids was found to hold the molecules at the active site cavity. The molecular dynamics (MD) simulation study also indicated the stability between protein and ligands. High negative MM-GBSA (molecular mechanics generalized Born and surface area) binding free energy indicated the potentiality of the molecules. Therefore, the proposed molecules might have the potential to be effective therapeutics for the management of BTC.
MeSH term(s)	Amino Acids ; Bile ; Biliary Tract Neoplasms/drug therapy ; Humans ; Hydrazones/therapeutic use ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Ribonucleotide Reductases
Chemical Substances	Amino Acids ; Hydrazones ; Ribonucleotide Reductases (EC 1.17.4.-)
Language	English
Publishing date	2022-09-10
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom12091279
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Article ; Online: Design of a Structurally Novel Multipotent Drug Candidate by the Scaffold Architecture Technique for ACE-II, NSP15, and M

Pakrashy, Sourav / Mandal, Prakash K / Dey, Surya Kanta / Choudhury, Sujata Maiti / Alasmary, Fatmah Ali / Almalki, Amani Salem / Islam, Md Ataul / Dolai, Malay

ACS omega

2022 Volume 7, Issue 37, Page(s) 33408–33422

Abstract: Scaffold architecture in the sectors of biotechnology and drug discovery research include scaffold hopping and molecular modelling techniques and helps in searching for potential drug candidates containing different core structures using computer-based ... ...

Abstract	Scaffold architecture in the sectors of biotechnology and drug discovery research include scaffold hopping and molecular modelling techniques and helps in searching for potential drug candidates containing different core structures using computer-based software, which greatly aids medicinal and pharmaceutical chemistry. Going ahead, the computational method of scaffold architecture is thought to produce new scaffolds, and the method is capable of helping search engines toward producing new scaffolds that are likely to represent potent compounds with high therapeutic applications, which is a possibility in this case as well. Here we probate a different interactive design by natural product hopping, molecular modelling, pharmacophore modelling, modification, and combination of the phytoconstituents present in different medicinal plants for developing a pharmacophore-guided good drug candidate for the variants of SARS-CoV-2 or Covid 19. In the modern era, these approaches are carried out at every level of development of scaffold queries, which are increasingly summarized from chemical structures. In this context, we report on a successfully designed drug-like candidate having a high-binding-affinity "compound SLP" by understanding the relationships between the compounds' pharmacophores, scaffold functional groups, and biological activities beyond their individual applications that abide by Lipinski's rule of five, Ghose rule, Veber rule etc. The new scaffold generated by altering the core of the known phyto-compounds holds a good predicted ADMET profile and is examined with iMODS server to check the molecular dynamics simulation with normal mode analysis (NMA). The scaffold's three-dimensional (3D) structure yields a searchable natural product koenimbine from a conformer database having good ADMET property and high availability in spice
Language	English
Publishing date	2022-09-10
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.2c04051
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