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Article ; Online: Phenolic compounds as α-glucosidase inhibitors: a docking and molecular dynamics simulation study.

Swargiary, Ananta / Roy, Mritunjoy Kumar / Mahmud, Shafi

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 9, Page(s) 3862–3871

Abstract: Phenolic compounds possess significant biological activity. Several pieces of research emphasize the medicinal importance of phenolic compounds, including diabetes. The present study investigated the α-glucosidase inhibitory activity of phenolic ... ...

Abstract	Phenolic compounds possess significant biological activity. Several pieces of research emphasize the medicinal importance of phenolic compounds, including diabetes. The present study investigated the α-glucosidase inhibitory activity of phenolic compounds reported from several plants. The phenolic compounds reported in different literature were collected. Molecular docking was carried out using AutoDock Vina. Various physicochemical properties such as size, LogP, molecular complexity, hydrogen bonding properties of phenolic compounds were correlated with the binding affinities. Furthermore, MD simulation was carried out to study the structural stability of the docking complexes. A total of 155 phenolic compounds were reported from different plants. Amentoflavone showed the strongest binding affinity with α-glucosidase, much more potent than reference acarbose. The binding energy showed a good correlation with the molecular complexity, hydrogen bond donor and acceptor property and heavy atom counts of the compounds. The polarity of the surface area also showed a positive correlation with the binding affinity of the compounds. The best docking phenolic compound, amentoflavone, showed stable binding affinity and conformation during the simulation period compared to apoprotein and acarbose-docking complex. The top ten phenolic compounds, including amentoflavone, showed considerable drug-likeness properties with fewer toxicity effects. The study suggests that the amentoflavone could be a potential therapeutic drug as an α-glucosidase inhibitor and help control postprandial hyperglycemia.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Glycoside Hydrolase Inhibitors/pharmacology ; Glycoside Hydrolase Inhibitors/chemistry ; Acarbose/pharmacology ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; alpha-Glucosidases/chemistry ; Phenols/pharmacology
Chemical Substances	Glycoside Hydrolase Inhibitors ; Acarbose (T58MSI464G) ; alpha-Glucosidases (EC 3.2.1.20) ; Phenols
Language	English
Publishing date	2022-04-01
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2058092
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Screening of phytochemicals as potent inhibitor of 3-chymotrypsin and papain-like proteases of SARS-CoV2: an in silico approach to combat COVID-19.

Swargiary, Ananta / Mahmud, Shafi / Saleh, Md Abu

Journal of biomolecular structure & dynamics

2020 Volume 40, Issue 5, Page(s) 2067–2081

Abstract: COVID-19 and its causative organism SARS-CoV2 that emerged from Wuhan city, China have paralyzed the world. With no clinically approved drugs, the global health system is struggling to find an effective treatment measure. At this crucial juncture, ... ...

Abstract	COVID-19 and its causative organism SARS-CoV2 that emerged from Wuhan city, China have paralyzed the world. With no clinically approved drugs, the global health system is struggling to find an effective treatment measure. At this crucial juncture, screening of plant-derived compounds may be an effective strategy to combat COVID-19. The present study investigated the binding affinity of phytocompounds with 3-Chymotrypsin-like (3CLpro) and Papain-like proteases (PLpro) of SARS-CoV2 using
MeSH term(s)	COVID-19 ; Chymotrypsin ; Humans ; Molecular Docking Simulation ; Papain ; Peptide Hydrolases ; Phytochemicals/pharmacology ; RNA, Viral ; SARS-CoV-2
Chemical Substances	Phytochemicals ; RNA, Viral ; Peptide Hydrolases (EC 3.4.-) ; Chymotrypsin (EC 3.4.21.1) ; Papain (EC 3.4.22.2)
Keywords	covid19
Language	English
Publishing date	2020-10-22
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1835729
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Article: Biochemical and

Paul, Gobindo Kumar / Mahmud, Shafi / Hasan, Md Mehedi / Zaman, Shahriar / Uddin, Md Salah / Saleh, Md Abu

Saudi journal of biological sciences

2021 Volume 28, Issue 11, Page(s) 6592–6605

Abstract: Aphanamixis ... ...

Abstract	Aphanamixis polystachya
Language	English
Publishing date	2021-07-16
Publishing country	Saudi Arabia
Document type	Journal Article
ZDB-ID	2515206-3
ISSN	2213-7106 ; 1319-562X
ISSN (online)	2213-7106
ISSN	1319-562X
DOI	10.1016/j.sjbs.2021.07.032
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Article: Identification of Zinc-Binding Inhibitors of Matrix Metalloproteinase-9 to Prevent Cancer Through Deep Learning and Molecular Dynamics Simulation Approach.

Mathpal, Shalini / Sharma, Priyanka / Joshi, Tushar / Pande, Veena / Mahmud, Shafi / Jeong, Mi-Kyung / Obaidullah, Ahmad J / Chandra, Subhash / Kim, Bonglee

Frontiers in molecular biosciences

2022 Volume 9, Page(s) 857430

Abstract: The overexpression of matrix metalloproteinase-9 (MMP-9) is associated with tumor development and angiogenesis, and hence, it has been considered an attractive drug target for anticancer therapy. To assist in drug design endeavors for MMP-9 targets, ... ...

Abstract	The overexpression of matrix metalloproteinase-9 (MMP-9) is associated with tumor development and angiogenesis, and hence, it has been considered an attractive drug target for anticancer therapy. To assist in drug design endeavors for MMP-9 targets, an
Language	English
Publishing date	2022-03-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2022.857430
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Article ; Online: Designing potential siRNA molecules for silencing the gene of the nucleocapsid protein of Nipah virus: A computational investigation.

Mahfuz, Amub / Khan, Md Arif / Sajib, Emran Hossain / Deb, Anamika / Mahmud, Shafi / Hasan, Mahmudul / Saha, Otun / Islam, Ariful / Rahaman, Md Mizanur

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

2022 Volume 102, Page(s) 105310

Abstract: Nipah virus (NiV), a zoonotic virus, engenders severe infections with noticeable complications and deaths in humans and animals. Since its emergence, it is frightening, this virus has been causing regular outbreaks in various countries, particularly in ... ...

Abstract	Nipah virus (NiV), a zoonotic virus, engenders severe infections with noticeable complications and deaths in humans and animals. Since its emergence, it is frightening, this virus has been causing regular outbreaks in various countries, particularly in Bangladesh, India, and Malaysia. Unfortunately, no efficient vaccine or drug is available now to combat this baneful virus. NiV employs its nucleocapsid protein for genetic material packaging, which is crucial for viral replication inside the host cells. The small interfering RNAs (siRNAs) can play a central role in inhibiting the expression of disease-causing viral genes by hybridization and subsequent inactivation of the complementary target viral mRNAs through the RNA interference (RNAi) pathway. Therefore, potential siRNAs as molecular therapeutics against the nucleocapsid protein gene of NiV were designed in this study. First, ten prospective siRNAs were identified using the conserved nucleocapsid gene sequences among all available NiV strains collected from various countries. After that, off-target binding, GC (guanine-cytosine) content, secondary structure, binding affinity with the target, melting temperature, efficacy analysis, and binding capacity with the human argonaute protein 2 (AGO2) of these siRNAs were evaluated to predict their suitability. These designed siRNA molecules bear promise in silencing the NiV gene encoding the nucleocapsid protein and thus can alleviate the severity of this dangerous virus. Further in vivo experiments are recommended before using these designed siRNAs as alternative and effective molecular therapeutic agents against NiV.
MeSH term(s)	Animals ; Henipavirus Infections ; Nipah Virus/genetics ; Nucleocapsid Proteins/genetics ; Prospective Studies ; RNA, Small Interfering/genetics
Chemical Substances	Nucleocapsid Proteins ; RNA, Small Interfering
Language	English
Publishing date	2022-05-28
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2037068-4
ISSN	1567-7257 ; 1567-1348
ISSN (online)	1567-7257
ISSN	1567-1348
DOI	10.1016/j.meegid.2022.105310
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Article ; Online: A conserved subunit vaccine designed against SARS-CoV-2 variants showed evidence in neutralizing the virus.

Kibria, K M Kaderi / Faruque, Md Omar / Islam, Md Shaid Bin / Ullah, Hedayet / Mahmud, Shafi / Miah, Mojnu / Saleh, Amani Ali

Applied microbiology and biotechnology

2022 Volume 106, Issue 11, Page(s) 4091–4114

Abstract: Novel coronavirus (SARS-CoV-2) leads to coronavirus disease 19 (COVID-19), declared as a pandemic that outbreaks within almost 225 countries worldwide. For the time being, numerous mutations have been reported that led to the generation of numerous ... ...

Abstract	Novel coronavirus (SARS-CoV-2) leads to coronavirus disease 19 (COVID-19), declared as a pandemic that outbreaks within almost 225 countries worldwide. For the time being, numerous mutations have been reported that led to the generation of numerous variants spread more rapidly. This study aims to establish an efficient multi-epitope subunit vaccine that could elicit both T-cell and B-cell responses sufficient to recognize three confirmed surface proteins of the virus. The sequences of the viral surface proteins, e.g., an envelope protein (E), membrane glycoprotein (M), and S1 and S2 domain of spike surface glycoprotein (S), were analyzed by an immunoinformatic approach. Top immunogenic epitopes have been selected based on the assessment of the affinity with MHC class-I and MHC class-II, population coverage, along with conservancy among wild type and new variants of SARS-CoV-2 genomes. Molecular docking and molecular dynamic simulation suggest that the proposed top peptides have the potential to interact with the highest number of both the MHC class I and MHC class II. The epitopes were assembled by the appropriate linkers to form a multi-epitope vaccine. Epitopes used in the vaccine construct are conserved in all the variants evolved till now. This in silico-designed multi-epitope vaccine is highly immunogenic and induces levels of SARS-CoV2-neutralizing antibodies in mice, which is detected by inhibition of cytopathic effect in Vero cell monolayer. Further studies are required to improve its efficiency in the prevention of virus replication in lung tissue, in addition to safety validation as a step for human application to combat SARS-CoV-2 variants. KEY POINTS: • We discovered five T-cell epitopes from three surface proteins of SARS-CoV-2. • These are conserved in the wild-type virus and variants, e.g., beta, delta, and omicron. • The multi-epitope vaccine can induce IgG in mice that can neutralize the virus.
MeSH term(s)	Animals ; COVID-19/prevention & control ; COVID-19 Vaccines/genetics ; Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte/genetics ; Humans ; Mice ; Molecular Docking Simulation ; RNA, Viral ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics ; Vaccines, Subunit/genetics ; Viral Vaccines
Chemical Substances	COVID-19 Vaccines ; Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte ; RNA, Viral ; Spike Glycoprotein, Coronavirus ; Vaccines, Subunit ; Viral Vaccines ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-05-25
Publishing country	Germany
Document type	Journal Article
ZDB-ID	392453-1
ISSN	1432-0614 ; 0171-1741 ; 0175-7598
ISSN (online)	1432-0614
ISSN	0171-1741 ; 0175-7598
DOI	10.1007/s00253-022-11988-x
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Article ; Online: Missense mutations in spike protein of SARS-CoV-2 delta variant contribute to the alteration in viral structure and interaction with hACE2 receptor.

Mahmood, Tousif Bin / Hossan, Mohammad Imran / Mahmud, Shafi / Shimu, Mst Sharmin Sultana / Alam, Md Jahidul / Bhuyan, Md Mahfuzur Rahman / Emran, Talha Bin

Immunity, inflammation and disease

2022 Volume 10, Issue 9, Page(s) e683

Abstract: Introduction: Many of the global pandemics threaten human existence over the decades among which coronavirus disease (COVID-19) is the newest exposure circulating worldwide. The RNA encoded severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ... ...

Abstract	Introduction: Many of the global pandemics threaten human existence over the decades among which coronavirus disease (COVID-19) is the newest exposure circulating worldwide. The RNA encoded severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus is referred as the pivotal agent of this deadly disease that induces respiratory tract infection by interacting host ACE2 receptor with its spike glycoprotein. Rapidly evolving nature of this virus modified into new variants helps in perpetrating immune escape and protection against host defense mechanism. Consequently, a new isolate, delta variant originated from India is spreading perilously at a higher infection rate. Methods: In this study, we focused to understand the conformational and functional significance of the missense mutations found in the spike glycoprotein of SARS-CoV-2 delta variant performing different computational analysis. Results: From physiochemical analysis, we found that the acidic isoelectric point of the virus elevated to basic pH level due to the mutations. The targeted mutations were also found to change the interactive bonding pattern and conformational stability analyzed by the molecular dynamic's simulation. The molecular docking study also revealed that L452R and T478K mutations found in the RBD domain of delta variant spike protein contributed to alter interaction with the host ACE2 receptor. Conclusions: Overall, this study provided insightful evidence to understand the morphological and attributive impact of the mutations on SARS-CoV-2 delta variant.
MeSH term(s)	Angiotensin-Converting Enzyme 2/chemistry ; Angiotensin-Converting Enzyme 2/genetics ; Angiotensin-Converting Enzyme 2/metabolism ; COVID-19/genetics ; Humans ; Molecular Docking Simulation ; Mutation, Missense ; Peptidyl-Dipeptidase A/metabolism ; Protein Binding ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics ; Viral Structures/metabolism
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2022-08-30
Publishing country	England
Document type	Journal Article
ZDB-ID	2740382-8
ISSN	2050-4527 ; 2050-4527
ISSN (online)	2050-4527
ISSN	2050-4527
DOI	10.1002/iid3.683
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Screening of phytochemicals as potent inhibitor of 3-chymotrypsin and papain-like proteases of SARS-CoV2: an in silico approach to combat COVID-19

Swargiary, Ananta / Mahmud, Shafi / Saleh, Md Abu

J Biomol Struct Dyn

Abstract	COVID-19 and its causative organism SARS-CoV2 that emerged from Wuhan city, China have paralyzed the world. With no clinically approved drugs, the global health system is struggling to find an effective treatment measure. At this crucial juncture, screening of plant-derived compounds may be an effective strategy to combat COVID-19. The present study investigated the binding affinity of phytocompounds with 3-Chymotrypsin-like (3CLpro) and Papain-like proteases (PLpro) of SARS-CoV2 using in-silico techniques. A total of 32 anti-protease phytocompounds were investigated for the binding affinity to the proteins. Docking was performed in Autodock Vina. Pharmacophore descriptors of best ligands were studied using LigandScout. Molecular dynamics (MD) simulation of apo-protein and ligand-bound complexes was carried out in YASARA software. The druglikeness properties of phytocompounds were studied using ADMETlab. Out of 32 phytochemicals, amentoflavone and gallocatechin gallate showed the best binding affinity to 3CLpro (-9.4 kcal/mol) and PLpro (-8.8 kcal/mol). Phytochemicals such as savinin, theaflavin-3,3-digallate, and kazinol-A also showed strong affinity. MD simulation revealed ligand-induced conformational changes in the protein with decreased surface area and higher stability. The RMSD/F of proteins and ligands showed stability of the protein suggesting the effective binding of the ligand in both the proteins. Both amentoflavone and gallocatechin gallate possess promising druglikeness property. The present study thus suggests that Amentoflavone and Gallocatechin gallate may be potential inhibitors of 3CLpro and PLpro proteins and effective drug candidates for SARS-CoV2. However, the findings of in silico study need to be supported by in vivo studies to establish the exact mode of action. Communicated by Ramaswamy H. Sarma.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #885576
Database	COVID19

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Article ; Online: Screening of phytochemicals as potent inhibitor of 3-chymotrypsin and papain-like proteases of SARS-CoV2

Swargiary, Ananta / Mahmud, Shafi / Saleh, Md. Abu

Journal of Biomolecular Structure and Dynamics

an in silico approach to combat COVID-19

2020 , Page(s) 1–15

Keywords	Molecular Biology ; Structural Biology ; General Medicine ; covid19
Language	English
Publisher	Informa UK Limited
Publishing country	uk
Document type	Article ; Online
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1835729
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Designing potential siRNA molecules for silencing the gene of the nucleocapsid protein of Nipah virus: A computational investigation

Mahfuz, A.M.U.B. / Khan, Md. Arif / Sajib, Emran Hossain / Deb, Anamika / Mahmud, Shafi / Hasan, Mahmudul / Saha, Otun / Islam, Ariful / Rahaman, M. Mizanur

Infection, genetics, and evolution. 2022 May 24,

2022

Abstract: Nipah virus (NiV), a zoonotic virus, engenders severe infections with noticeable complications and deaths in humans and animals. Since its emergence, it is frightening that this virus has been causing regular outbreaks in various countries, particularly ... ...

Abstract	Nipah virus (NiV), a zoonotic virus, engenders severe infections with noticeable complications and deaths in humans and animals. Since its emergence, it is frightening that this virus has been causing regular outbreaks in various countries, particularly Bangladesh, India, and Malaysia. Unfortunately, no efficient vaccine or drug is available to combat this baneful virus. It employs the nucleocapsid protein in its genetic material encapsidation, which is a crucial for viral replication. The small interfering RNAs (siRNAs) play a central role in inhibiting the expression of human disease-causing viral genes by hybridization and inactivation of complementary target viral mRNAs through the RNA interference (RNAi) pathway. Therefore, potential siRNAs as molecular therapeutics against the nucleocapsid protein gene of NiV were designed in this study. First, ten prospective siRNAs were identified using the conserved nucleocapsid gene sequences of all available NiV strains collected from various countries. After that, off-target binding, GC content, secondary structure, binding affinity with the target, melting temperature, efficacy analysis, and binding capacity with the human argonaute protein 2 (AGO2) of these siRNAs were evaluated to predict their suitability. These designed siRNA molecules bear promise in silencing the NiV gene encoding the nucleocapsid protein and thus can alleviate the severity of this dangerous virus. Further in vivo experiments are recommended before using these designed siRNAs as alternative and effective molecular therapeutic agents against NiV.
Keywords	Nipah henipavirus ; RNA interference ; evolution ; genes ; humans ; infection ; nucleocapsid ; nucleocapsid proteins ; temperature ; therapeutics ; vaccines ; virus replication ; viruses ; Bangladesh ; India ; Malaysia
Language	English
Dates of publication	2022-0524
Publishing place	Elsevier B.V.
Document type	Article
Note	Pre-press version
ZDB-ID	2037068-4
ISSN	1567-1348
ISSN	1567-1348
DOI	10.1016/j.meegid.2022.105310
Database	NAL-Catalogue (AGRICOLA)

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