Papers by Md. Anayet Hasan
MicroRNAs (miRNAs) are a type of interfering RNAs which are small, ~22 nucleotides long and remai... more MicroRNAs (miRNAs) are a type of interfering RNAs which are small, ~22 nucleotides long and remain evolutionary conserved. They have been reported in a large number of plants including other organisms like viruses, insects and higher vertebrates where they have biological and metabolic activities. Their pivotal role in gene silencing has been correlated with a number of diseases; therefore miRNA prediction is an important and challenging field. In spite of being a significant medicinal plant, no specific work has been done yet on the microRNAs (miRNAs) and their potential targets in Cannabis sativa. In vitro prediction of miRNAs is a slow and laborious process as it is hard to isolate them. In our current study a well-developed, faster and powerful in silico approach, EST-based homology search is followed to identify potential miRNA of C. sativa. Here, the Expressed Sequence Tag (EST) database of Cannabis sativa was BLASTed against the previously identified plant miRNAs and following a series of filtration criteria, a total of 2 potential miRNAs were identified. Furthermore, 14 potential mRNA targets were tagged in C. sativa genome based on the complementarity between miRNAs and their targeted mRNA sequences. The predicted target genes encode mainly transcriptional regulators including R2R3-Myb transcription factor, GRAS family transcription factor, Scarecrow protein, Transcriptional regulator family protein and DNA binding protein. Some other targets have more specific functions in the developmental process of C. sativa and are associated with diverse metabolic processes for stress management as well as other metabolic functions. These include Leucine rich protein kinase family protein, Retro element pol polyprotein, Pectin acetyl Esterase, SET domain protein, HXXXD-type acyl-transferase family protein, Ankyrin repeat family protein, Hypersensitiv-ity related protein. Overall, findings from our study will pave the way for further researches on C. sativa miRNAs and their functions.
Chagas is a parasitic disease with major threat to public health due to its resistance against c... more Chagas is a parasitic disease with major threat to public health due to its resistance against commonly available drugs. Trypanothione reductase (TryR) is the key enzyme to develop this disease. Though this enzyme is well thought-out as potential drug target, the accurate structure of enzyme-inhibitor complex is required to design a potential inhibitor which is less available for TryR. In this research, we aimed to investigate the advanced drug over the available existing drugs by designing inhibitors as well as to identify a new enzyme-inhibitor complex that may act as a template for drug design. A set of analogues were designed from a known inhibitor Quinacrine Mustard (QUM) to identify the effective inhibitor against this enzyme. Further, the pharmacoinformatics elucidation and structural properties of designed inhibitor proposed effective drug candidates against Chagas disease. Molecular docking study suggests that a designed inhibitor has higher binding affinity in both crystal and modeled TryR and also poses similar interacting residues as of crystal TryR-QUM complex structure. The comparative studies based on in silico prediction proposed an enzyme-inhibitor complex which could be effective to control the disease activity. So our in silico analysis based on TryR built model, Pharmacophore and docking analysis might play an important role for the development of novel therapy for Chagas disease. But both animal model experiments and clinical trials must be done to confirm the efficacy of the therapy.
Vancomycin-resistant Staphylococcus aureus (VRSA) is a Gram-positive, facultative aerobic bacteri... more Vancomycin-resistant Staphylococcus aureus (VRSA) is a Gram-positive, facultative aerobic bacterium which is evolved from the extensive exposure of Vancomycin to Methicillin resistant S. aureus (MRSA) that had become the most common cause of hospital and community-acquired infections. Due to the emergence of different antibiotic resistance strains, there is an exigency to develop novel drug targets to address the provocation of multidrug-resistant bacteria. In this study, in-silico genome subtraction methodology was used to design potential and pathogen specific drug targets against VRSA. Our study divulged 1987 proteins from the proteome of 34,549 proteins, which have no homologues in human genome after sequential analysis through CD-HIT and BLASTp. The high stringency analysis of the remaining proteins against database of essential genes (DEG) resulted in 169 proteins which are essential for S. aureus. Metabolic pathway analysis of human host and pathogen by KAAS at the KEGG server sorted out 19 proteins involved in unique metabolic pathways. 26 human non-homologous membrane-bound essential proteins including 4 which were also involved in unique metabolic pathway were deduced through PSORTb, CELLO v.2.5, ngLOC. Functional classification of uncharacterized proteins through SVMprot derived 7 human non-homologous membrane-bound hypothetical essential proteins. Study of potential drug target against Drug Bank revealed pbpA-penicillin-binding protein 1 and hypothetical protein MQW_01796 as the best drug target candidate. 2D structure was predicted by PRED-TMBB, 3D structure and functional analysis was also performed. Protein–protein interaction network of potential drug target proteins was analyzed by using STRING. The identified drug targets are expected to have great potential for designing novel drugs against VRSA infections and further screening of the compounds against these new targets may result in the discovery of novel therapeutic compounds that can be effective against Vancomycin resistant S. aureus.
Purpose
Ebola virus (EBOV) is such kind of virus which is responsible for 23,825 cases and 9675 ... more Purpose
Ebola virus (EBOV) is such kind of virus which is responsible for 23,825 cases and 9675 deaths worldwide only in 2014 and with an average diseases fatality rate between 25 % and 90 %. Although, medical technology has tried to handle the problems, there is no Food and Drug Administration (FDA)-approved therapeutics or vaccines available for the prevention, post exposure, or treatment of Ebola virus disease (EVD).
Methods
In the present study, we used the immunoinformatics approach to design a potential epitope-based vaccine against the RNA-dependent RNA polymerase-L of EBOV. BioEdit v7.2.3 sequence alignment editor, Jalview v2 and CLC Sequence Viewer v7.0.2 were used for the initial sequence analysis for securing the conservancy from the sequences. Later the Immune Epitope Database and Analysis Resource (IEDB-AR) was used for the identification of T-cell and B-cellepitopes associated with type I and II major histocompatibility complex molecules analysis. Finally, the population coverage analysis was employed.
Results
The core epitope “FRYEFTAPF” was found to be the most potential one, with 100 % conservancy among all the strains of EBOV. It also interacted with both type I and II major histocompatibility complex molecules and is considered as nonallergenic in nature. Finally, with impressive cumulative population coverage of 99.87 % for the both MHC-I and MHC-II class throughout the world population was found for the proposed epitope.
Conclusion
To end, the projected peptide gave us a solid stand to propose for vaccine consideration and that might be experimented for its potency in eliciting immunity through humoral and cell mediated immune responses in vitro and in vivo.
In developing countries threat of cholera is a significant health concern whenever water purifica... more In developing countries threat of cholera is a significant health concern whenever water purification and sewage disposal systems are inadequate. Vibrio cholerae is one of the responsible bacteria involved in cholera disease. The complete genome sequence of V. cholerae deciphers the presence of various genes and hypothetical proteins whose function are not yet understood. Hence analyzing and annotating the structure and function of hypothetical proteins is important for understanding the V. cholerae. V. cholerae O139 is the most common and pathogenic bacterial strain among various V. cholerae strains. In this study sequence of six hypothetical proteins of V. cholerae O139 has been annotated from NCBI. Various computational tools and databases have been used to determine domain family, protein-protein interaction, solubility of protein, ligand binding sites etc. The three dimensional structure of two proteins were modeled and their ligand binding sites were identified. We have found domains and families of only one protein. The analysis revealed that these proteins might have antibiotic resistance activity, DNA breaking-rejoining activity, integrase enzyme activity, restriction endonuclease, etc. Structural prediction of these proteins and detection of binding sites from this study would indicate a potential target aiding docking studies for therapeutic designing against cholera.
A commonly diagnosed cancer, prostate cancer (PrCa), is being regulated by the gene RNASEL previo... more A commonly diagnosed cancer, prostate cancer (PrCa), is being regulated by the gene RNASEL previously known as PRCA1 codes for ribonuclease L which is an integral part of interferon regulated system that mediates antiviral and antiproliferative role of the interferons. Both somatic and germline mutations have been implicated to cause prostate cancer. With an array of available Single Nucleotide Polymorphism data on dbSNP this study is designed to sort out functional SNPs in RNASEL by implementing different authentic computational tools such as SIFT, PolyPhen, SNPs&GO, Fathmm, ConSurf, UTRScan, PDBsum, Tm-Align, I-Mutant, and Project HOPE for functional and structural assessment, solvent accessibility, molecular dynamics, and energy minimization study. Among 794 RNASEL SNP entries 124 SNPs were found nonsynonymous from which SIFT predicted 13 nsSNPs as nontolerable whereas PolyPhen-2 predicted 28. SNPs found on the 3′ and 5′ UTR were also assessed. By analyzing six tools having different perspectives an aggregate result was produced where nine nsSNPs were found to be most likely to exert deleterious effect. 3D models of mutated proteins were generated to determine the functional and structural effect of the mutations on ribonuclease L. The initial findings were reinforced by the results from I-Mutant and Project HOPE as these tools predicted significant structural and functional instability of the mutated proteins. Expasy-ProSit tool defined the mutations to be situated in the functional domains of the protein. Considering previous analysis this study revealed a conclusive result deducing the available SNP data on the database by identifying the most damaging three nsSNP rs151296858 (G59S), rs145415894 (A276V), and rs35896902 (R592H). As such studies involving polymorphisms of RNASEL were none to be found, the results of the current study would certainly be helpful in future prospects concerning prostate cancer in males.
Background
Malaria has been a major life threatening mosquito borne disease from long since. Una... more Background
Malaria has been a major life threatening mosquito borne disease from long since. Unavailability of any effective vaccine and recent emergence of multi drug resistant strains of malaria pathogen Plasmodium falciparum continues to cause persistent deaths in the tropical and sub-tropical region. As a result, demands for new targets for more effective anti-malarial drugs are escalating. Transketolase is an enzyme of the pentose phosphate pathway; a novel pathway which is involved in energy generation and nucleic acid synthesis. Moreover, significant difference in homology between Plasmodium falciparum transketolase (Pftk) and human (Homo sapiens) transketolase makes it a suitable candidate for drug therapy. Our present study is aimed to predict the 3D structure of Plasmodium falciparum transketolase and design an inhibitor against it.
Results
The primary and secondary structural features of the protein is calculated by ProtParam and SOPMA respectively which revealed the protein is composed of 43.3 % alpha helix and 33.04 % random coils along with 15.62 % extended strands, 8.04 % beta turns. The three dimensional structure of the transketolase is constructed using homology modeling tool MODELLAR utilizing several available transketolase structures as templates. The structure is then subjected to deep optimization and validated by structure validation tools PROCHECK, VERIFY 3D, ERRAT, QMEAN. The predicted model scored 0.74 for global model reliability in PROCHECK analysis, which ensures the quality of the model. According to VERIFY 3D the predicted model scored 0.77 which determines good environmental profile along with ERRAT score of 78.313 which is below 95 % rejection limit. Protein-protein and residue–residue interaction networks are generated by STRING and RING server respectively. CASTp server was used to analyze active sites and His 109, Asn 108 and His 515 are found to be more positive site to dock the substrate, in addition molecular docking simulation with Autodock vina determined the estimated free energy of molecular binding was of −6.6 kcal/mol for most favorable binding of 6′-Methyl-Thiamin Diphosphate.
Conclusion
This predicted structure of Pftk will serve first hand in the future development of effective Pftk inhibitors with potential anti-malarial activity. However, this is a preliminary study of designing an inhibitor against Plasmodium falciparum 3D7; the results await justification by in vitro and in vivo experimentations.
Background: Analyzing the structures and functions of different proteins of Wuchereria bancrofti ... more Background: Analyzing the structures and functions of different proteins of Wuchereria bancrofti is very important because till date no effective drug or vaccine has been discovered to treat lymphatic filariasis (LF). ATPase is one of the most important proteins of Wuchereria bancrofti. Adenosine triphosphate (ATP) converts into adenosine diphosphate (ADP) and a free phosphate ion by the action of these ATPase enzymes. Energy releases from these dephosphorylation reactions drive the other chemical reactions in the cell. Materials and Methods: In
this study we worked on the protein ATPase of Wuchereria bancrofti which has been annotated from National Center for Biotechnology Information (NCBI). Various computational tools and databases have been used to determine the various characteristics of that enzyme such as physiochemical properties, secondary structure, three‑dimensional (3D) structure, conserved domain, epitope, and their molecular evolutionary relationship. Result: Subcellular localization of ATPase was identified and we have found that 55.5% are localized in the cytoplasm. Secondary and 3D structure of this protein was also predicted. Both structure and function analysis of ATPase of Wuchereria bancrofti showed unique nonhomologous epitope sites and nonhomologous antigenicity sites. Moreover, it resulted in 15 ligand drug‑binding sites in its tertiary structure. Conclusion: Structure prediction of these proteins and detection of binding sites and antigenicity sites from this study would indicate a potential target aiding docking studies for therapeutic designing against filariasis.
Recent concerning facts of Chikungunya virus (CHIKV); a Togaviridae family alphavirus has proved ... more Recent concerning facts of Chikungunya virus (CHIKV); a Togaviridae family alphavirus has proved this as a worldwide emerging threat which causes Chikungunya fever and devitalizing arthritis. Despite severe outbreaks and lack of antiviral drug, a mere progress has been made regarding to an epitope-based vaccine designed for CHIKV. In this study, we aimed to design an epitope-based vaccine that can trigger a significant immune response as well as to prognosticate inhibitor that can bind with potential drug target sites by using various immunoinformatics and docking simulation tools. Initially, whole proteome of CHIKV was retrieved from database and perused to identify the most immunogenic protein. Structural properties of the selected protein were analyzed. The capacity to induce both humoral and cell-mediated immunity by T cell and B cell were checked for the selected protein. The peptide region spanning 9 amino acids from 397 to 405 and the sequence YYYELYPTM were found as the most potential B cell and T cell epitopes respectively. This peptide could interact with as many as 19 HLAs and showed high population coverage ranging from 69.50% to 84.94%. By using in silico docking techniques the epitope was further assessed for binding against HLA molecules to verify the binding cleft interaction. In addition with this, the allergenicity of the epitopes was also evaluated. In the post therapeutic strategy, three dimensional structure was predicted along with validation and verification that resulted in molecular docking study to identify the potential drug binding sites and suitable therapeutic inhibitor against targeted protein. Finally, pharmacophore study was also performed in quest of seeing potent drug activity. However, this computational epitope-based peptide vaccine designing and target site prediction against CHIKV opens up a new horizon which may be the prospective way in Chikungunya virus research; the results require validation by in vitro and in vivo experiments.
The harshness of legionellosis differs from mild Pontiac fever to potentially fatal Legionnaire’s... more The harshness of legionellosis differs from mild Pontiac fever to potentially fatal Legionnaire’s disease. The increasing
development of drug resistance against legionellosis has led to explore new novel drug targets. It has been found that
phosphoglucosamine mutase, phosphomannomutase, and phosphoglyceromutase enzymes can be used as the most
probable therapeutic drug targets through extensive data mining. Phosphoglucosamine mutase is involved in amino sugar
and nucleotide sugar metabolism. The purpose of this study was to predict the potential target of that specific drug. For this,
the 3D structure of phosphoglucosamine mutase of Legionella pneumophila (strain Paris) was determined by means of
homology modeling through Phyre2 and refined by ModRefiner. Then, the designed model was evaluated with a structure
validation program, for instance, PROCHECK, ERRAT, Verify3D, and QMEAN, for further structural analysis. Secondary
structural features were determined through self-optimized prediction method with alignment (SOPMA) and interacting
networks by STRING. Consequently, we performed molecular docking studies. The analytical result of PROCHECK showed
that 95.0% of the residues are in the most favored region, 4.50% are in the additional allowed region and 0.50% are in the
generously allowed region of the Ramachandran plot. Verify3D graph value indicates a score of 0.71 and 89.791, 1.11 for
ERRAT and QMEAN respectively. Arg419, Thr414, Ser412, and Thr9 were found to dock the substrate for the most favorable
binding of S-mercaptocysteine. However, these findings from this current study will pave the way for further extensive
investigation of this enzyme in wet lab experiments and in that way assist drug design against legionellosis.
The Middle East respiratory syndrome coronavirus (MERS-CoV) is a virus that manifests itself in
... more The Middle East respiratory syndrome coronavirus (MERS-CoV) is a virus that manifests itself in
viral infection with fever, cough, shortness of breath, renal failure and severe acute pneumonia, which often result
in a fatal outcome. MERS-CoV has been shown to spread between people who are in close contact. Transmission
from infected patients to healthcare personnel has also been observed and is irredeemable with present technology.
Genetic studies on MERS-CoV have shown that ORF 1ab encodes replicase polyproteins and play a foremost role
in viral infection. Therefore, ORF 1ab replicase polyprotein may be used as suitable target for disease control.
Viral activity can be controlled by RNA interference (RNAi) technology, a leading method for post transcriptional
gene silencing in a sequence specific manner. However, there is a genetic inconsistency in different viral isolates;
it is a great challenge to design potential RNAi (miRNA and siRNA) molecules which can silence the respective
target genes rather than any other viral gene simultaneously. In current study four effective miRNA and five
siRNA molecules for silencing of nine different strains of MERS-CoV were rationally designed and corroborated
using computational methods, which might lead to knockdown the activity of virus. siRNA and miRNA molecules
were predicted against ORF1ab gene of different strains of MERS-CoV as effective candidate using computational
methods. Thus, this method may provide an insight for the chemical synthesis of antiviral RNA molecule for the
treatment of MERS-CoV, at genomic level.
Bacillus anthracis substractive genome analysis, Sep 18, 2014
Background
Bacillus anthracis is a gram positive, spore forming, rod shaped bacteria which is th... more Background
Bacillus anthracis is a gram positive, spore forming, rod shaped bacteria which is the etiologic agent of anthrax – cutaneous, pulmonary and gastrointestinal. A recent outbreak of anthrax in a tropical region uncovered natural and in vitro resistance against penicillin, ciprofloxacin, quinolone due to over exposure of the pathogen to these antibiotics. This fact combined with the ongoing threat of using B. anthracis as a biological weapon proves that the identification of new therapeutic targets is urgently needed.
Methods
In this computational approach various databases and online based servers were used to detect essential proteins of B. anthracis A0248. Protein sequences of B. anthracis A0248 strain were retrieved from the NCBI database which was then run in CD-hit suite for clustering. NCBI BlastP against the human proteome and similarity search against DEG were done to find out essential human non-homologous proteins. Proteins involved in unique pathways were analyzed using KEGG genome database and PSORTb, CELLO v.2.5, ngLOC – these three tools were used to deduce putative cell surface proteins.
Results
Successive analysis revealed 116 proteins to be essential human non-homologs among which 17 were involved in unique metabolic pathways and 28 were predicted as membrane associated proteins. Both types of proteins can be exploited as they are unlikely to have homologous counterparts in the human host.
Conclusion
Being human non-homologous, these proteins can be targeted for potential therapeutic drug development in future. Targets on unique metabolic and membrane-bound proteins can block cell wall synthesis, bacterial replication and signal transduction respectively.
Molecular Characterization of Eimeria spp, Jan 14, 2014
Coccidiosis in chickens is one of the major problems of poultry industry that is caused by protoz... more Coccidiosis in chickens is one of the major problems of poultry industry that is caused by protozoan parasites of genus Eimeria . Present study was conducted to characterize the Eimeria species infecting poultry in different regions of Chittagong district of Bangladesh. Seven species of Eimeria including E. tenella, E. necatrix, E. acervulina, E. maxima, E. brunetti, E. mitis, and E. praecox have been characterized using conventional PCR analysis through amplifying unique single copy sequences derived from sequence characterized amplified region (SCAR) markers. The present study is the first of its type to use molecular tools to identify Eimeria spp. infecting chicken in Bangladesh. The study indicates that the modern molecular technique involving PCR to detect the Eimeria species are more reliable and accurate than the traditional morphology-based technique.
Molecular characterization of YopT, Jan 13, 2014
Plague is a major health concern and Yersinia pestis plays the central causal role in this diseas... more Plague is a major health concern and Yersinia pestis plays the central causal role in this disease. Yersinia pestis has developed resistance against the commonly available drugs. So, it is now a key concern to find a new drug target. Cysteine protease YopT enzyme is an important factor used by Yersinia pestis for pathogenesis in its host and it has the anti-phagocytic function of removal of C-termini lipid modification. The 3D structure of cysteine protease YopT of Yersinia pestis was determined by means of homology modeling through multiple alignments followed by intensive optimization and validation. The modeling was done by Phyre 2 and refined by ModRefiner. The obtained model was verified with structure validation programs such as PROCHECK, verify 3D and ERRAT for reliability. Interacting partners and active sites were also determined. PROCHECK analysis showed that 93% of the residues are in the most favored region, 5.9% are in the additional allowed region and 1.1% are in the generously allowed region of the Ramachandran plot. The verify 3D value of 0.78 indicates that the environmental profile of the model is good. SOPMA is employed for calculation of the secondary structural features of cysteine protease YopT. Active site determination through CASTp proposes that this protein can be utilized as a potential drug target. However, these findings should further be confirmed by wet lab studies for a targeted therapeutic agent design against Yersinia pestis.
Background: Averrhoa bilimbi, Gymnema sylvestre and Capsicum frutescens are medicinal plants comm... more Background: Averrhoa bilimbi, Gymnema sylvestre and Capsicum frutescens are medicinal plants commonly used as traditional medicine for the treatment of various diseases. The present study was designed to investigate the antioxidant activities of Ethanolic extract of A. bilimbi, G. sylvestre and C. frutescens. Materials and Methods: The antioxidant activity of the extracts were evaluated using total phenolic and fl avonoid contents, ferric reducing power and the free radical scavenging activity against 1,1-diphenyl-2-picrylhydrazyl (DPPH). Results: Total phenolic and flavonoid contents were higher in G. sylvestre (53.63636 ± 0.454545 mg/g
gallic acid equivalent) and C. frutescens (26.66667 ± 2.081666 mg/g quercetin equivalent) respectively. Reducing power of the crude ethanol extracts increased with the concentrations of the extracts and all the extracts showed moderate free radical scavenging activity against DPPH. The plant extract displayed moderate phenolic and fl avonoid contents compared to gallic acid and quercetin equivalent respectively, whereas also exhibited signifi cant scavenging of DPPH radical and reducing power compared with ascorbic acid as standard. Conclusion:
Our study suggests that G. sylvestre has signifi cant antioxidant activity. The antioxidant compound of this plant might be a therapeutic candidate against oxidative stress related diseases. Different sub-fraction of A. bilimbi and C. frutescens should be studied further to assess the effect. Further study is necessary for isolation and characterization of the active antioxidant agents for better treatment.
Epitope design against SLEV, Nov 24, 2013
Saint Louis encephalitis virus, a member of the flaviviridae subgroup, is a culex mosquito-borne ... more Saint Louis encephalitis virus, a member of the flaviviridae subgroup, is a culex mosquito-borne pathogen. Despite severe epidemic outbreaks on several occasions, not much progress has been made with regard to an epitope-based vaccine designed for Saint Louis encephalitis virus. The envelope proteins were collected from a protein database and analyzed with an in silico tool to identify the most immunogenic protein. The protein was then verified through several parameters to predict the T-cell and B-cell epitopes. Both T-cell and B-cell immunity were assessed to determine that the protein can induce humoral as well as cell-mediated immunity. The peptide sequence from 330–336 amino acids and the sequence REYCYEATL from the position 57 were found as the most potential B-cell and T-cell epitopes, respectively. Furthermore, as an RNA virus, one important thing was to establish the epitope as a conserved one; this was also done by in silico tools, showing 63.51% conservancy. The epitope was further tested for binding against the HLA molecule by computational docking techniques to verify the binding cleft epitope interaction. However, this is a preliminary study of designing an epitope-based peptide vaccine against Saint Louis encephalitis virus; the results awaits validation by in vitro and in vivo experiments.
siRNA against HSV-1, Jun 20, 2013
""Abstract
Background
The herpes simplex virus (HSV-1) is a virus that manifests itself in vira... more ""Abstract
Background
The herpes simplex virus (HSV-1) is a virus that manifests itself in viral infection with painful, watery blisters in the skin or on the genitals as well as mucous membrane such as the mouth or lips. During an outbreak, the disease is contagious particularly and is irredeemable with present technology. Genetic studies of HSV-1 have shown that ICP22 (US1) gene is an immediate early gene and is responsible for genome replication and also has contribution in viral infection.
Method
For disease diagnosis, ICP22 (US1) gene may be suitable target. Viral activity can be controlled through RNA interference technology, a significant method for the post-transcriptional gene silencing. However, in different viral isolates there is a genetic variability; it is very challenging to design possible siRNA molecules which can silence the respective target genes. The work was done by using various computational tools as similarity search, target alignment, secondary structure prediction and RNA interaction evaluation.
Result
In our study two effective siRNA molecules for ICP22 (US1) gene silencing of seven different strains of HSV-1 were rationally designed and authenticated using computational methods, which might lead to knockdown the viral activity.
Conclusion
siRNA molecules were foreseen against ICP22 (US1) gene of different strains of HSV-1 as effective aspirant using computational methods. Thus, the approach may deliver a vision for the chemical synthesis of antiviral RNA molecule for treatment of HSV-1, at genomic level.""
Pulse nutrition value, Feb 28, 2012
The issue of balanced nutrition is of great concern to human. Meat and fish are the best sources ... more The issue of balanced nutrition is of great concern to human. Meat and fish are the best sources of protein. The affordability of these resources for people in developing countries is less. Thus, there is an increasing interest in pulses and its derivates as an alternative to fish and meat. Lectin and histone H1 are the most common proteins in various pulses and our interest is in identifying the dominant essential amino acids in them for use as supplements. However, actin and lectin are common among Oryza Sativa and cicer arietinum. We describe the amount of lectin and histone H1 in cicer arietinum, Lens culinaris and Pisum sativum in a comparative manner. cicer arietinum was found to contain more essential amino acids than Lens culinaris and Pisum sativum. The secondary structures of lectin and histone H1 protein were analyzed to gain functional inferences in these species. The comparative study shows the relatively poor presence of the amino acid methionine in most pulses. However, Oryza Sativa was found to contain sufficient methionine. The study shows that pulses (especially cicer arietinum) were a suitable alternative source to meat and fish for Lectin and Histone H1 balance. Hence, pulses could be suggested with rice for balanced protein diet.
Conference Presentations by Md. Anayet Hasan
Background: Analyzing the structures and functions of different proteins of Wuchereria bancrofti ... more Background: Analyzing the structures and functions of different proteins of Wuchereria bancrofti is very important because till date no effective drug or vaccine has been discovered to treat lymphatic filariasis (LF). ATPase is one of the most important proteins of Wuchereria bancrofti. Adenosine triphosphate (ATP) converts into adenosine diphosphate (ADP) and a free phosphate ion by the action of these ATPase enzymes. Energy releases from these dephosphorylation reactions drive the other chemical reactions in the cell. Materials and Methods: In this study we worked on the protein ATPase of Wuchereria bancrofti which has been annotated from National Center for Biotechnology Information (NCBI). Various computational tools and databases have been used to determine the various characteristics of that enzyme such as physiochemical properties, secondary structure, three‑dimensional (3D) structure, conserved domain, epitope, and their molecular evolutionary relationship. Result: Subcellular localization of ATPase was identified and we have found that 55.5% are localized in the cytoplasm. Secondary and 3D structure of this protein was also predicted. Both structure and function analysis of ATPase of Wuchereria bancrofti showed unique nonhomologous epitope sites and nonhomologous antigenicity sites. Moreover, it resulted in 15 ligand drug‑binding sites in its tertiary structure. Conclusion: Structure prediction of these proteins and detection of binding sites and antigenicity sites from this study would indicate a potential target aiding docking studies for therapeutic designing against filariasis.
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Papers by Md. Anayet Hasan
Ebola virus (EBOV) is such kind of virus which is responsible for 23,825 cases and 9675 deaths worldwide only in 2014 and with an average diseases fatality rate between 25 % and 90 %. Although, medical technology has tried to handle the problems, there is no Food and Drug Administration (FDA)-approved therapeutics or vaccines available for the prevention, post exposure, or treatment of Ebola virus disease (EVD).
Methods
In the present study, we used the immunoinformatics approach to design a potential epitope-based vaccine against the RNA-dependent RNA polymerase-L of EBOV. BioEdit v7.2.3 sequence alignment editor, Jalview v2 and CLC Sequence Viewer v7.0.2 were used for the initial sequence analysis for securing the conservancy from the sequences. Later the Immune Epitope Database and Analysis Resource (IEDB-AR) was used for the identification of T-cell and B-cellepitopes associated with type I and II major histocompatibility complex molecules analysis. Finally, the population coverage analysis was employed.
Results
The core epitope “FRYEFTAPF” was found to be the most potential one, with 100 % conservancy among all the strains of EBOV. It also interacted with both type I and II major histocompatibility complex molecules and is considered as nonallergenic in nature. Finally, with impressive cumulative population coverage of 99.87 % for the both MHC-I and MHC-II class throughout the world population was found for the proposed epitope.
Conclusion
To end, the projected peptide gave us a solid stand to propose for vaccine consideration and that might be experimented for its potency in eliciting immunity through humoral and cell mediated immune responses in vitro and in vivo.
Malaria has been a major life threatening mosquito borne disease from long since. Unavailability of any effective vaccine and recent emergence of multi drug resistant strains of malaria pathogen Plasmodium falciparum continues to cause persistent deaths in the tropical and sub-tropical region. As a result, demands for new targets for more effective anti-malarial drugs are escalating. Transketolase is an enzyme of the pentose phosphate pathway; a novel pathway which is involved in energy generation and nucleic acid synthesis. Moreover, significant difference in homology between Plasmodium falciparum transketolase (Pftk) and human (Homo sapiens) transketolase makes it a suitable candidate for drug therapy. Our present study is aimed to predict the 3D structure of Plasmodium falciparum transketolase and design an inhibitor against it.
Results
The primary and secondary structural features of the protein is calculated by ProtParam and SOPMA respectively which revealed the protein is composed of 43.3 % alpha helix and 33.04 % random coils along with 15.62 % extended strands, 8.04 % beta turns. The three dimensional structure of the transketolase is constructed using homology modeling tool MODELLAR utilizing several available transketolase structures as templates. The structure is then subjected to deep optimization and validated by structure validation tools PROCHECK, VERIFY 3D, ERRAT, QMEAN. The predicted model scored 0.74 for global model reliability in PROCHECK analysis, which ensures the quality of the model. According to VERIFY 3D the predicted model scored 0.77 which determines good environmental profile along with ERRAT score of 78.313 which is below 95 % rejection limit. Protein-protein and residue–residue interaction networks are generated by STRING and RING server respectively. CASTp server was used to analyze active sites and His 109, Asn 108 and His 515 are found to be more positive site to dock the substrate, in addition molecular docking simulation with Autodock vina determined the estimated free energy of molecular binding was of −6.6 kcal/mol for most favorable binding of 6′-Methyl-Thiamin Diphosphate.
Conclusion
This predicted structure of Pftk will serve first hand in the future development of effective Pftk inhibitors with potential anti-malarial activity. However, this is a preliminary study of designing an inhibitor against Plasmodium falciparum 3D7; the results await justification by in vitro and in vivo experimentations.
this study we worked on the protein ATPase of Wuchereria bancrofti which has been annotated from National Center for Biotechnology Information (NCBI). Various computational tools and databases have been used to determine the various characteristics of that enzyme such as physiochemical properties, secondary structure, three‑dimensional (3D) structure, conserved domain, epitope, and their molecular evolutionary relationship. Result: Subcellular localization of ATPase was identified and we have found that 55.5% are localized in the cytoplasm. Secondary and 3D structure of this protein was also predicted. Both structure and function analysis of ATPase of Wuchereria bancrofti showed unique nonhomologous epitope sites and nonhomologous antigenicity sites. Moreover, it resulted in 15 ligand drug‑binding sites in its tertiary structure. Conclusion: Structure prediction of these proteins and detection of binding sites and antigenicity sites from this study would indicate a potential target aiding docking studies for therapeutic designing against filariasis.
development of drug resistance against legionellosis has led to explore new novel drug targets. It has been found that
phosphoglucosamine mutase, phosphomannomutase, and phosphoglyceromutase enzymes can be used as the most
probable therapeutic drug targets through extensive data mining. Phosphoglucosamine mutase is involved in amino sugar
and nucleotide sugar metabolism. The purpose of this study was to predict the potential target of that specific drug. For this,
the 3D structure of phosphoglucosamine mutase of Legionella pneumophila (strain Paris) was determined by means of
homology modeling through Phyre2 and refined by ModRefiner. Then, the designed model was evaluated with a structure
validation program, for instance, PROCHECK, ERRAT, Verify3D, and QMEAN, for further structural analysis. Secondary
structural features were determined through self-optimized prediction method with alignment (SOPMA) and interacting
networks by STRING. Consequently, we performed molecular docking studies. The analytical result of PROCHECK showed
that 95.0% of the residues are in the most favored region, 4.50% are in the additional allowed region and 0.50% are in the
generously allowed region of the Ramachandran plot. Verify3D graph value indicates a score of 0.71 and 89.791, 1.11 for
ERRAT and QMEAN respectively. Arg419, Thr414, Ser412, and Thr9 were found to dock the substrate for the most favorable
binding of S-mercaptocysteine. However, these findings from this current study will pave the way for further extensive
investigation of this enzyme in wet lab experiments and in that way assist drug design against legionellosis.
viral infection with fever, cough, shortness of breath, renal failure and severe acute pneumonia, which often result
in a fatal outcome. MERS-CoV has been shown to spread between people who are in close contact. Transmission
from infected patients to healthcare personnel has also been observed and is irredeemable with present technology.
Genetic studies on MERS-CoV have shown that ORF 1ab encodes replicase polyproteins and play a foremost role
in viral infection. Therefore, ORF 1ab replicase polyprotein may be used as suitable target for disease control.
Viral activity can be controlled by RNA interference (RNAi) technology, a leading method for post transcriptional
gene silencing in a sequence specific manner. However, there is a genetic inconsistency in different viral isolates;
it is a great challenge to design potential RNAi (miRNA and siRNA) molecules which can silence the respective
target genes rather than any other viral gene simultaneously. In current study four effective miRNA and five
siRNA molecules for silencing of nine different strains of MERS-CoV were rationally designed and corroborated
using computational methods, which might lead to knockdown the activity of virus. siRNA and miRNA molecules
were predicted against ORF1ab gene of different strains of MERS-CoV as effective candidate using computational
methods. Thus, this method may provide an insight for the chemical synthesis of antiviral RNA molecule for the
treatment of MERS-CoV, at genomic level.
Bacillus anthracis is a gram positive, spore forming, rod shaped bacteria which is the etiologic agent of anthrax – cutaneous, pulmonary and gastrointestinal. A recent outbreak of anthrax in a tropical region uncovered natural and in vitro resistance against penicillin, ciprofloxacin, quinolone due to over exposure of the pathogen to these antibiotics. This fact combined with the ongoing threat of using B. anthracis as a biological weapon proves that the identification of new therapeutic targets is urgently needed.
Methods
In this computational approach various databases and online based servers were used to detect essential proteins of B. anthracis A0248. Protein sequences of B. anthracis A0248 strain were retrieved from the NCBI database which was then run in CD-hit suite for clustering. NCBI BlastP against the human proteome and similarity search against DEG were done to find out essential human non-homologous proteins. Proteins involved in unique pathways were analyzed using KEGG genome database and PSORTb, CELLO v.2.5, ngLOC – these three tools were used to deduce putative cell surface proteins.
Results
Successive analysis revealed 116 proteins to be essential human non-homologs among which 17 were involved in unique metabolic pathways and 28 were predicted as membrane associated proteins. Both types of proteins can be exploited as they are unlikely to have homologous counterparts in the human host.
Conclusion
Being human non-homologous, these proteins can be targeted for potential therapeutic drug development in future. Targets on unique metabolic and membrane-bound proteins can block cell wall synthesis, bacterial replication and signal transduction respectively.
gallic acid equivalent) and C. frutescens (26.66667 ± 2.081666 mg/g quercetin equivalent) respectively. Reducing power of the crude ethanol extracts increased with the concentrations of the extracts and all the extracts showed moderate free radical scavenging activity against DPPH. The plant extract displayed moderate phenolic and fl avonoid contents compared to gallic acid and quercetin equivalent respectively, whereas also exhibited signifi cant scavenging of DPPH radical and reducing power compared with ascorbic acid as standard. Conclusion:
Our study suggests that G. sylvestre has signifi cant antioxidant activity. The antioxidant compound of this plant might be a therapeutic candidate against oxidative stress related diseases. Different sub-fraction of A. bilimbi and C. frutescens should be studied further to assess the effect. Further study is necessary for isolation and characterization of the active antioxidant agents for better treatment.
Background
The herpes simplex virus (HSV-1) is a virus that manifests itself in viral infection with painful, watery blisters in the skin or on the genitals as well as mucous membrane such as the mouth or lips. During an outbreak, the disease is contagious particularly and is irredeemable with present technology. Genetic studies of HSV-1 have shown that ICP22 (US1) gene is an immediate early gene and is responsible for genome replication and also has contribution in viral infection.
Method
For disease diagnosis, ICP22 (US1) gene may be suitable target. Viral activity can be controlled through RNA interference technology, a significant method for the post-transcriptional gene silencing. However, in different viral isolates there is a genetic variability; it is very challenging to design possible siRNA molecules which can silence the respective target genes. The work was done by using various computational tools as similarity search, target alignment, secondary structure prediction and RNA interaction evaluation.
Result
In our study two effective siRNA molecules for ICP22 (US1) gene silencing of seven different strains of HSV-1 were rationally designed and authenticated using computational methods, which might lead to knockdown the viral activity.
Conclusion
siRNA molecules were foreseen against ICP22 (US1) gene of different strains of HSV-1 as effective aspirant using computational methods. Thus, the approach may deliver a vision for the chemical synthesis of antiviral RNA molecule for treatment of HSV-1, at genomic level.""
Conference Presentations by Md. Anayet Hasan
Ebola virus (EBOV) is such kind of virus which is responsible for 23,825 cases and 9675 deaths worldwide only in 2014 and with an average diseases fatality rate between 25 % and 90 %. Although, medical technology has tried to handle the problems, there is no Food and Drug Administration (FDA)-approved therapeutics or vaccines available for the prevention, post exposure, or treatment of Ebola virus disease (EVD).
Methods
In the present study, we used the immunoinformatics approach to design a potential epitope-based vaccine against the RNA-dependent RNA polymerase-L of EBOV. BioEdit v7.2.3 sequence alignment editor, Jalview v2 and CLC Sequence Viewer v7.0.2 were used for the initial sequence analysis for securing the conservancy from the sequences. Later the Immune Epitope Database and Analysis Resource (IEDB-AR) was used for the identification of T-cell and B-cellepitopes associated with type I and II major histocompatibility complex molecules analysis. Finally, the population coverage analysis was employed.
Results
The core epitope “FRYEFTAPF” was found to be the most potential one, with 100 % conservancy among all the strains of EBOV. It also interacted with both type I and II major histocompatibility complex molecules and is considered as nonallergenic in nature. Finally, with impressive cumulative population coverage of 99.87 % for the both MHC-I and MHC-II class throughout the world population was found for the proposed epitope.
Conclusion
To end, the projected peptide gave us a solid stand to propose for vaccine consideration and that might be experimented for its potency in eliciting immunity through humoral and cell mediated immune responses in vitro and in vivo.
Malaria has been a major life threatening mosquito borne disease from long since. Unavailability of any effective vaccine and recent emergence of multi drug resistant strains of malaria pathogen Plasmodium falciparum continues to cause persistent deaths in the tropical and sub-tropical region. As a result, demands for new targets for more effective anti-malarial drugs are escalating. Transketolase is an enzyme of the pentose phosphate pathway; a novel pathway which is involved in energy generation and nucleic acid synthesis. Moreover, significant difference in homology between Plasmodium falciparum transketolase (Pftk) and human (Homo sapiens) transketolase makes it a suitable candidate for drug therapy. Our present study is aimed to predict the 3D structure of Plasmodium falciparum transketolase and design an inhibitor against it.
Results
The primary and secondary structural features of the protein is calculated by ProtParam and SOPMA respectively which revealed the protein is composed of 43.3 % alpha helix and 33.04 % random coils along with 15.62 % extended strands, 8.04 % beta turns. The three dimensional structure of the transketolase is constructed using homology modeling tool MODELLAR utilizing several available transketolase structures as templates. The structure is then subjected to deep optimization and validated by structure validation tools PROCHECK, VERIFY 3D, ERRAT, QMEAN. The predicted model scored 0.74 for global model reliability in PROCHECK analysis, which ensures the quality of the model. According to VERIFY 3D the predicted model scored 0.77 which determines good environmental profile along with ERRAT score of 78.313 which is below 95 % rejection limit. Protein-protein and residue–residue interaction networks are generated by STRING and RING server respectively. CASTp server was used to analyze active sites and His 109, Asn 108 and His 515 are found to be more positive site to dock the substrate, in addition molecular docking simulation with Autodock vina determined the estimated free energy of molecular binding was of −6.6 kcal/mol for most favorable binding of 6′-Methyl-Thiamin Diphosphate.
Conclusion
This predicted structure of Pftk will serve first hand in the future development of effective Pftk inhibitors with potential anti-malarial activity. However, this is a preliminary study of designing an inhibitor against Plasmodium falciparum 3D7; the results await justification by in vitro and in vivo experimentations.
this study we worked on the protein ATPase of Wuchereria bancrofti which has been annotated from National Center for Biotechnology Information (NCBI). Various computational tools and databases have been used to determine the various characteristics of that enzyme such as physiochemical properties, secondary structure, three‑dimensional (3D) structure, conserved domain, epitope, and their molecular evolutionary relationship. Result: Subcellular localization of ATPase was identified and we have found that 55.5% are localized in the cytoplasm. Secondary and 3D structure of this protein was also predicted. Both structure and function analysis of ATPase of Wuchereria bancrofti showed unique nonhomologous epitope sites and nonhomologous antigenicity sites. Moreover, it resulted in 15 ligand drug‑binding sites in its tertiary structure. Conclusion: Structure prediction of these proteins and detection of binding sites and antigenicity sites from this study would indicate a potential target aiding docking studies for therapeutic designing against filariasis.
development of drug resistance against legionellosis has led to explore new novel drug targets. It has been found that
phosphoglucosamine mutase, phosphomannomutase, and phosphoglyceromutase enzymes can be used as the most
probable therapeutic drug targets through extensive data mining. Phosphoglucosamine mutase is involved in amino sugar
and nucleotide sugar metabolism. The purpose of this study was to predict the potential target of that specific drug. For this,
the 3D structure of phosphoglucosamine mutase of Legionella pneumophila (strain Paris) was determined by means of
homology modeling through Phyre2 and refined by ModRefiner. Then, the designed model was evaluated with a structure
validation program, for instance, PROCHECK, ERRAT, Verify3D, and QMEAN, for further structural analysis. Secondary
structural features were determined through self-optimized prediction method with alignment (SOPMA) and interacting
networks by STRING. Consequently, we performed molecular docking studies. The analytical result of PROCHECK showed
that 95.0% of the residues are in the most favored region, 4.50% are in the additional allowed region and 0.50% are in the
generously allowed region of the Ramachandran plot. Verify3D graph value indicates a score of 0.71 and 89.791, 1.11 for
ERRAT and QMEAN respectively. Arg419, Thr414, Ser412, and Thr9 were found to dock the substrate for the most favorable
binding of S-mercaptocysteine. However, these findings from this current study will pave the way for further extensive
investigation of this enzyme in wet lab experiments and in that way assist drug design against legionellosis.
viral infection with fever, cough, shortness of breath, renal failure and severe acute pneumonia, which often result
in a fatal outcome. MERS-CoV has been shown to spread between people who are in close contact. Transmission
from infected patients to healthcare personnel has also been observed and is irredeemable with present technology.
Genetic studies on MERS-CoV have shown that ORF 1ab encodes replicase polyproteins and play a foremost role
in viral infection. Therefore, ORF 1ab replicase polyprotein may be used as suitable target for disease control.
Viral activity can be controlled by RNA interference (RNAi) technology, a leading method for post transcriptional
gene silencing in a sequence specific manner. However, there is a genetic inconsistency in different viral isolates;
it is a great challenge to design potential RNAi (miRNA and siRNA) molecules which can silence the respective
target genes rather than any other viral gene simultaneously. In current study four effective miRNA and five
siRNA molecules for silencing of nine different strains of MERS-CoV were rationally designed and corroborated
using computational methods, which might lead to knockdown the activity of virus. siRNA and miRNA molecules
were predicted against ORF1ab gene of different strains of MERS-CoV as effective candidate using computational
methods. Thus, this method may provide an insight for the chemical synthesis of antiviral RNA molecule for the
treatment of MERS-CoV, at genomic level.
Bacillus anthracis is a gram positive, spore forming, rod shaped bacteria which is the etiologic agent of anthrax – cutaneous, pulmonary and gastrointestinal. A recent outbreak of anthrax in a tropical region uncovered natural and in vitro resistance against penicillin, ciprofloxacin, quinolone due to over exposure of the pathogen to these antibiotics. This fact combined with the ongoing threat of using B. anthracis as a biological weapon proves that the identification of new therapeutic targets is urgently needed.
Methods
In this computational approach various databases and online based servers were used to detect essential proteins of B. anthracis A0248. Protein sequences of B. anthracis A0248 strain were retrieved from the NCBI database which was then run in CD-hit suite for clustering. NCBI BlastP against the human proteome and similarity search against DEG were done to find out essential human non-homologous proteins. Proteins involved in unique pathways were analyzed using KEGG genome database and PSORTb, CELLO v.2.5, ngLOC – these three tools were used to deduce putative cell surface proteins.
Results
Successive analysis revealed 116 proteins to be essential human non-homologs among which 17 were involved in unique metabolic pathways and 28 were predicted as membrane associated proteins. Both types of proteins can be exploited as they are unlikely to have homologous counterparts in the human host.
Conclusion
Being human non-homologous, these proteins can be targeted for potential therapeutic drug development in future. Targets on unique metabolic and membrane-bound proteins can block cell wall synthesis, bacterial replication and signal transduction respectively.
gallic acid equivalent) and C. frutescens (26.66667 ± 2.081666 mg/g quercetin equivalent) respectively. Reducing power of the crude ethanol extracts increased with the concentrations of the extracts and all the extracts showed moderate free radical scavenging activity against DPPH. The plant extract displayed moderate phenolic and fl avonoid contents compared to gallic acid and quercetin equivalent respectively, whereas also exhibited signifi cant scavenging of DPPH radical and reducing power compared with ascorbic acid as standard. Conclusion:
Our study suggests that G. sylvestre has signifi cant antioxidant activity. The antioxidant compound of this plant might be a therapeutic candidate against oxidative stress related diseases. Different sub-fraction of A. bilimbi and C. frutescens should be studied further to assess the effect. Further study is necessary for isolation and characterization of the active antioxidant agents for better treatment.
Background
The herpes simplex virus (HSV-1) is a virus that manifests itself in viral infection with painful, watery blisters in the skin or on the genitals as well as mucous membrane such as the mouth or lips. During an outbreak, the disease is contagious particularly and is irredeemable with present technology. Genetic studies of HSV-1 have shown that ICP22 (US1) gene is an immediate early gene and is responsible for genome replication and also has contribution in viral infection.
Method
For disease diagnosis, ICP22 (US1) gene may be suitable target. Viral activity can be controlled through RNA interference technology, a significant method for the post-transcriptional gene silencing. However, in different viral isolates there is a genetic variability; it is very challenging to design possible siRNA molecules which can silence the respective target genes. The work was done by using various computational tools as similarity search, target alignment, secondary structure prediction and RNA interaction evaluation.
Result
In our study two effective siRNA molecules for ICP22 (US1) gene silencing of seven different strains of HSV-1 were rationally designed and authenticated using computational methods, which might lead to knockdown the viral activity.
Conclusion
siRNA molecules were foreseen against ICP22 (US1) gene of different strains of HSV-1 as effective aspirant using computational methods. Thus, the approach may deliver a vision for the chemical synthesis of antiviral RNA molecule for treatment of HSV-1, at genomic level.""