Comprehensive assessment of Indian variations in the druggable kinome landscape highlights distinct insights at the sequence, structure and pharmacogenomic stratum

The population diversity in India contains a treasure of clinically relevant rare mutations which may have evolved differently in different subpopulations. While there are many sub-groups present in the nation, the publicly available database like the 1000 Genome data (1KG) contains limited samples for indian ethnicity. Such databases are critical for the pharmaceutical and drug development industry where the diversity plays a crucial role in identifying genetic disposition towards adverse drug reactions. A qualitative and comparative sequence and structural study utilizing variant information present in the recently published, largest curated Indian genome database (Indigen) and the 1000 Genome data was performed for variants belonging to the kinase coding genes, the second most targeted group of drug targets. The sequence level analysis identified similarities and differences among different populations based on the SNVs and amino acid exchange frequencies whereas comparative structural analysis of IndiGen variants was performed with pathogenic variants reported in UniProtKB Humsavar data. The influence of these variations on structural features of the protein, such as structural stability, solvent accessibility, hydrophobicity, and the hydrogen-bond network were investigated. In-silico screening of the known drugs to these Indian variation-containing proteins reveal critical differences imparted in the strength of binding due to the variations present in the Indian population. In conclusion, this study constitutes a comprehensive investigation into the understanding of common variations present in the second largest population in the world, and investigating its implications in the sequence, structural and pharmacogenomic landscape.

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Recent Advances towards Drug Design Targeting the Protease of 2019 novel coronavirus (2019-nCoV)

Current Medicinal Chemistry ◽

10.2174/0929867327666201027153617 ◽

2020 ◽

Vol 27 ◽

Author(s):

Sehrish Bano ◽

Abdul Hameed ◽

Mariya Al-Rashida ◽

Shafia Iftikhar ◽

Jamshed Iqbal

Keyword(s):

Drug Design ◽

Rna Polymerase ◽

Drug Targets ◽

Antiviral Agents ◽

Structural Features ◽

Antiviral Drugs ◽

Rna Dependent Rna Polymerase ◽

Mortality And Morbidity ◽

Functional Relationships ◽

Novel Coronavirus

Background: The 2019 novel coronavirus (2019-nCoV), also known as coronavirus 2 (SARS-CoV-2) acute respiratory syndrome has recently emerged and continued to spread rapidly with high level of mortality and morbidity rates. Currently, no efficacious therapy is available to relieve coronavirus infections. As new drug design and development takes much time, there is a possibility to find an effective treatment from existing antiviral agents. Objective: In this case, there is a need to find out the relationship between possible drug targets and mechanism of action of antiviral drugs. This review discusses about the efforts to develop drug from known or new molecules. Methods: Viruses usually have two structural integrities, proteins and nucleic acids, both of which can be possible drug targets. Herein, we systemically discuss the structural-functional relationships of the spike, 3-chymotrypsin-like protease (3CLpro), papain like protease (PLpro) and RNA-dependent RNA polymerase (RdRp), as these are prominent structural features of corona virus. Certain antiviral drugs such as Remdesivir are RNA dependent RNA polymerase inhibitor. It has the ability to terminate RNA replication by inhibiting ATP. Results: It is reported that ATP is involved in synthesis of coronavirus non-structural proteins from 3CLpro and PLpro. Similarly, mechanisms of action of many other antiviral agents has been discussed in this review. It will provide new insights into the mechanism of inhibition, and let us develop new therapeutic antiviral approaches against novel SARS-CoV-2 coronavirus. Conclusion: In conclusion, this review summarizes recent progress in developing protease inhibitors for SARS-CoV-2.

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Polyamines and Related Nitrogen Compounds in the Chemotherapy of Neglected Diseases Caused by Kinetoplastids

Current Topics in Medicinal Chemistry ◽

10.2174/1568026618666180427151338 ◽

2018 ◽

Vol 18 (5) ◽

pp. 321-368 ◽

Cited By ~ 2

Author(s):

Juan A. Bisceglia ◽

Maria C. Mollo ◽

Nadia Gruber ◽

Liliana R. Orelli

Keyword(s):

Drug Targets ◽

Redox Homeostasis ◽

Cost Effective ◽

Structural Features ◽

Mammalian Host ◽

Neglected Diseases ◽

Nitrogen Compounds ◽

Chemical Structures

Neglected diseases due to the parasitic protozoa Leishmania and Trypanosoma (kinetoplastids) affect millions of people worldwide, and the lack of suitable treatments has promoted an ongoing drug discovery effort to identify novel nontoxic and cost-effective chemotherapies. Polyamines are ubiquitous small organic molecules that play key roles in kinetoplastid parasites metabolism, redox homeostasis and in the normal progression of cell cycles, which differ from those found in the mammalian host. These features make polyamines attractive in terms of antiparasitic drug development. The present work provides a comprehensive insight on the use of polyamine derivatives and related nitrogen compounds in the chemotherapy of kinetoplastid diseases. The amount of literature on this subject is considerable, and a classification considering drug targets and chemical structures were made. Polyamines, aminoalcohols and basic heterocycles designed to target the relevant parasitic enzyme trypanothione reductase are discussed in the first section, followed by compounds directed to less common targets, like parasite SOD and the aminopurine P2 transporter. Finally, the third section comprises nitrogen compounds structurally derived from antimalaric agents. References on the chemical synthesis of the selected compounds are reported together with their in vivo and/or in vitro IC50 values, and structureactivity relationships within each group are analyzed. Some favourable structural features were identified from the SAR analyses comprising protonable sites, hydrophobic groups and optimum distances between them. The importance of certain pharmacophoric groups or amino acid residues in the bioactivity of polyamine derived compounds is also discussed.

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Two Approaches for a Genetic Analysis of Pompe Disease: A Literature Review of Patients with Pompe Disease and Analysis Based on Genomic Data from the General Population

Children ◽

10.3390/children8070601 ◽

2021 ◽

Vol 8 (7) ◽

pp. 601

Author(s):

Kyung-Sun Park

Keyword(s):

General Population ◽

Pompe Disease ◽

Genomic Data ◽

Japanese Patients ◽

Population Database ◽

Genome Database ◽

Genetic Database ◽

Pathogenic Variants ◽

Reference Genome Database ◽

Real Patients

In this study, two different approaches were applied in the analysis of the GAA gene. One was analyzed based on patients with Pompe disease, and the other was analyzed based on GAA genomic data from unaffected carriers in a general population genetic database. For this, GAA variants in Korean and Japanese patients reported in previous studies and in patients reported in the Pompe disease GAA variant database were analyzed as a model. In addition, GAA variants in the Korean Reference Genome Database (KRGDB), the Japanese Multi Omics Reference Panel (jMorp), and the Genome Aggregation Database (gnomAD) were analyzed. Overall, approximately 50% of the pathogenic or likely pathogenic variants (PLPVs) found in unaffected carriers were also found in real patients with Pompe disease (Koreans, 57.1%; Japanese, 46.2%). In addition, there was a moderate positive correlation (Spearman’s correlation coefficient of 0.45–0.69) between the proportion of certain PLPVs in patients and the minor allele frequency of their variants in a general population database. Based on the analysis of general population databases, the total carrier frequency for Pompe disease in Koreans and Japanese was estimated to be 1.7% and 0.7%, respectively, and the predicted genetic prevalence was 1:13,657 and 1:78,013, respectively.

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OGDA: a comprehensive organelle genome database for algae

Database ◽

10.1093/database/baaa097 ◽

2020 ◽

Vol 2020 ◽

Author(s):

Tao Liu ◽

Yutong Cui ◽

Xuli Jia ◽

Jing Zhang ◽

Ruoran Li ◽

...

Keyword(s):

Marine Organism ◽

Structural Characteristics ◽

Genome Structure ◽

Evolutionary Relationship ◽

Uniparental Inheritance ◽

Genome Database ◽

Organelle Genome ◽

Organellar Genomes ◽

Genome Data ◽

Plastid Genomes

Abstract Algae are the oldest taxa on Earth, with an evolutionary relationship that spans prokaryotes (Cyanobacteria) and eukaryotes. A long evolutionary history has led to high algal diversity. Their organelle DNAs are characterized by uniparental inheritance and a compact genome structure compared with nuclear genomes; thus, they are efficient molecular tools for the analysis of gene structure, genome structure, organelle function and evolution. However, an integrated organelle genome database for algae, which could enable users to both examine and use relevant data, has not previously been developed. Therefore, to provide an organelle genome platform for algae, we have developed a user-friendly database named Organelle Genome Database for Algae (OGDA, http://ogda.ytu.edu.cn/). OGDA contains organelle genome data either retrieved from several public databases or sequenced in our laboratory (Laboratory of Genetics and Breeding of Marine Organism [MOGBL]), which are continuously updated. The first release of OGDA contains 1055 plastid genomes and 755 mitochondrial genomes. Additionally, a variety of applications have been integrated into this platform to analyze the structural characteristics, collinearity and phylogeny of organellar genomes for algae. This database represents a useful tool for users, enabling the rapid retrieval and analysis of information related to organellar genomes for biological discovery.

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Affinity Purification of NF1 Protein–Protein Interactors Identifies Keratins and Neurofibromin Itself as Binding Partners

Genes ◽

10.3390/genes10090650 ◽

2019 ◽

Vol 10 (9) ◽

pp. 650 ◽

Cited By ~ 4

Author(s):

Rachel M. Carnes ◽

Robert A. Kesterson ◽

Bruce R. Korf ◽

James A. Mobley ◽

Deeann Wallis

Keyword(s):

Protein Interactions ◽

Drug Targets ◽

Affinity Purification ◽

Neurofibromatosis Type ◽

Hek293 Cells ◽

Ras Signaling ◽

Affinity Tag ◽

Pathogenic Variants ◽

Binding Partners ◽

Keratin Expression

Neurofibromatosis Type 1 (NF1) is caused by pathogenic variants in the NF1 gene encoding neurofibromin. Definition of NF1 protein–protein interactions (PPIs) has been difficult and lacks replication, making it challenging to define binding partners that modulate its function. We created a novel tandem affinity purification (TAP) tag cloned in frame to the 3’ end of the full-length murine Nf1 cDNA (mNf1). We show that this cDNA is functional and expresses neurofibromin, His-Tag, and can correct p-ERK/ERK ratios in NF1 null HEK293 cells. We used this affinity tag to purify binding partners with Strep-Tactin®XT beads and subsequently, identified them via mass spectrometry (MS). We found the tagged mNf1 can affinity purify human neurofibromin and vice versa, indicating that neurofibromin oligomerizes. We identify 21 additional proteins with high confidence of interaction with neurofibromin. After Metacore network analysis of these 21 proteins, eight appear within the same network, primarily keratins regulated by estrogen receptors. Previously, we have shown that neurofibromin levels negatively regulate keratin expression. Here, we show through pharmacological inhibition that this is independent of Ras signaling, as the inhibitors, selumetinib and rapamycin, do not alter keratin expression. Further characterization of neurofibromin oligomerization and binding partners could aid in discovering new neurofibromin functions outside of Ras regulation, leading to novel drug targets.

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Genome Data of Four Pythium insidiosum Strains from the Phylogenetically-Distinct Clades I, II, and III

10.21203/rs.3.rs-308603/v1 ◽

2021 ◽

Author(s):

Theerapong Krajaejun ◽

Weerayuth Kittichotirat ◽

Preecha Patumcharoenpol ◽

Thidarat Rujirawat ◽

Tassanee Lohnoo ◽

...

Keyword(s):

The United States ◽

Open Reading Frames ◽

Genome Database ◽

Pythium Insidiosum ◽

Data Description ◽

Genome Data ◽

Serious Infection ◽

Gdna Sample ◽

Different Strains ◽

Reading Frames

Abstract Objectives: We employed the Illumina NGS platform to sequence genomes of 4 different strains of Pythium insidiosum, an oomycete that causes a serious infection, called pythiosis, in humans and animals. These strains were isolated from humans in Thailand (n=3) and the United States (n=1), and phylogenetically classified into clade-I, -II, and -III. Our study augmented the completeness of the P. insidiosum genome database for exploration of the biology, evolution, and pathogenesis of the pathogen. Data description: Each gDNA sample from the P. insidiosum strains ATCC20026 (clade-I), Pi19 (clade-II), MCC18 (clade-II), and SIMI4763 (clade-III) was processed to prepare one paired-end library (180-bp insert) for whole-genome sequencing by Illumina HiSeq2000/HiSeq2500 NGS platform. A range of 28.4-59.4 million raw reads, accounted for 3.0-7.3 Gb, were obtained and assembled into the genome sizes of 47.1 Mb (15,153 contigs; 85% completeness; 19,329 open reading frames [ORFs]) for strain ATCC20026, 35.4 Mb (14,576 contigs; 83% completeness; 13,895 ORFs) for strain Pi19, 34.5 Mb (11,084 contigs; 84% completeness; 13,249 ORFs) for strain MCC18, and 47.1 Mb (15,162 contigs; 85% completeness; 19,340 ORFs) for strain SIMI4763. The genome data can be downloaded from the NCBI/DDBJ databases under the accessions BCFN00000000.1 (ATCC20026), BCFS00000000.1 (Pi19), BCFT00000000.1 (MCC18), and BCFU00000000.1 (SIMI4763).

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Implementation of homology based and non-homology based computational methods for the identification and annotation of orphan enzymes: using Mycobacterium tuberculosis H37Rv as a case study

BMC Bioinformatics ◽

10.1186/s12859-020-03794-x ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Swati Sinha ◽

Andrew M. Lynn ◽

Dhwani K. Desai

Keyword(s):

Mycobacterium Tuberculosis ◽

Functional Annotation ◽

Drug Targets ◽

Sequence Similarity ◽

Hole Filling ◽

Mycobacterium Tuberculosis H37rv ◽

Genome Data ◽

Candidate Protein ◽

Computational Procedures

Abstract Background Homology based methods are one of the most important and widely used approaches for functional annotation of high-throughput microbial genome data. A major limitation of these methods is the absence of well-characterized sequences for certain functions. The non-homology methods based on the context and the interactions of a protein are very useful for identifying missing metabolic activities and functional annotation in the absence of significant sequence similarity. In the current work, we employ both homology and context-based methods, incrementally, to identify local holes and chokepoints, whose presence in the Mycobacterium tuberculosis genome is indicated based on its interaction with known proteins in a metabolic network context, but have not been annotated. We have developed two computational procedures using network theory to identify orphan enzymes (‘Hole finding protocol’) coupled with the identification of candidate proteins for the predicted orphan enzyme (‘Hole filling protocol’). We propose an integrated interaction score based on scores from the STRING database to identify candidate protein sequences for the orphan enzymes from M. tuberculosis, as a case study, which are most likely to perform the missing function. Results The application of an automated homology-based enzyme identification protocol, ModEnzA, on M. tuberculosis genome yielded 56 novel enzyme predictions. We further predicted 74 putative local holes, 6 choke points, and 3 high confidence local holes in the genome using ‘Hole finding protocol’. The ‘Hole-filling protocol’ was validated on the E. coli genome using artificial in-silico enzyme knockouts where our method showed 25% increased accuracy, compared to other methods, in assigning the correct sequence for the knocked-out enzyme amongst the top 10 ranks. The method was further validated on 8 additional genomes. Conclusions We have developed methods that can be generalized to augment homology-based annotation to identify missing enzyme coding genes and to predict a candidate protein for them. For pathogens such as M. tuberculosis, this work holds significance in terms of increasing the protein repertoire and thereby, the potential for identifying novel drug targets.

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Papain-Like Proteases as Coronaviral Drug Targets: Current Inhibitors, Opportunities, and Limitations

Pharmaceuticals ◽

10.3390/ph13100277 ◽

2020 ◽

Vol 13 (10) ◽

pp. 277 ◽

Cited By ~ 2

Author(s):

Anastasiia I. Petushkova ◽

Andrey A. Zamyatnin

Keyword(s):

Immune Response ◽

Immune System ◽

Severe Acute Respiratory Syndrome ◽

Viral Genome ◽

Drug Targets ◽

Structural Features ◽

The Third ◽

Frequent Mutations ◽

Near Future ◽

Viral Reproduction

Papain-like proteases (PLpro) of coronaviruses (CoVs) support viral reproduction and suppress the immune response of the host, which makes CoV PLpro perspective pharmaceutical targets. Their inhibition could both prevent viral replication and boost the immune system of the host, leading to the speedy recovery of the patient. Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the third CoV outbreak in the last 20 years. Frequent mutations of the viral genome likely lead to the emergence of more CoVs. Inhibitors for CoV PLpro can be broad-spectrum and can diminish present and prevent future CoV outbreaks as PLpro from different CoVs have conservative structures. Several inhibitors have been developed to withstand SARS-CoV and Middle East respiratory syndrome CoV (MERS-CoV). This review summarizes the structural features of CoV PLpro, the inhibitors that have been identified over the last 20 years, and the compounds that have the potential to become novel effective therapeutics against CoVs in the near future.

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Pathogenic NOTCH3 Variants Are Frequent Among the Korean General Population

Neurology Genetics ◽

10.1212/nxg.0000000000000639 ◽

2021 ◽

Vol 7 (6) ◽

pp. e639

Author(s):

Chul-Hoo Kang ◽

Young Mee Kim ◽

Yang-Ji Kim ◽

Su-Jeong Hong ◽

Do Yoon Kim ◽

...

Keyword(s):

Cross Sectional Study ◽

Genome Project ◽

Jeju Island ◽

Cross Sectional ◽

Genome Database ◽

Pathogenic Variants ◽

Number Of Patients ◽

High Prevalence ◽

History Of ◽

Reference Genome Database

ObjectiveThis study aimed to determine the frequency of pathogenic NOTCH3 variants among Koreans.MethodsIn this cross-sectional study, we queried for pathogenic NOTCH3 variants in 2 Korean public genome databases: the Korean Reference Genome Database (KRGDB) and the Korean Genome Project (Korea1K). In addition, we screened the 3 most common pathogenic NOTCH3 variants (p.Arg75Pro, p.Arg544Cys, and p.Arg578Cys) for 1,000 individuals on Jeju Island, where the largest number of patients with cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) have been reported in Korea.ResultsThe pathogenic NOTCH3 variant (p.Arg544Cys) was found in 0.12% of sequences in the KRGDB, and 3 pathogenic variants (p.Arg75Pro, p.Arg182Cys, and p.Arg544Cys) were present in 0.44% of the Korea1K database. Of the 1,000 individuals on Jeju Island, we found 2 cysteine-altering NOTCH3 variants (p.Arg544Cys variant in 9 and p.Arg578Cys in 1 individual) in 1.00% of the participants (95% confidence interval: 0.48%–1.83%). The presence of cysteine-altering NOTCH3 variants was significantly associated with a history of stroke (p < 0.001).DiscussionPathogenic NOTCH3 variants are frequently found in the general Korean population. Such a high prevalence of pathogenic variants could threaten the brain health of tens of thousands to hundreds of thousands of older adults in Korea.

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The human functional genome defined by genetic diversity

10.1101/082362 ◽

2016 ◽

Cited By ~ 3

Author(s):

Julia di Iulio ◽

Istvan Bartha ◽

Emily H.M. Wong ◽

Hung-Chun Yu ◽

Michael Hicks ◽

...

Keyword(s):

Genetic Diversity ◽

Large Scale ◽

Genomic Organization ◽

Population Level ◽

Population Diversity ◽

Sequence Conservation ◽

Pathogenic Variants ◽

Human Genomes ◽

Wide Variability ◽

Context Dependent

ABSTRACTLarge scale efforts to sequence whole human genomes provide extensive data on the non-coding portion of the genome. We used variation information from 11,257 human genomes to describe the spectrum of sequence conservation in the population. We established the genome-wide variability for each nucleotide in the context of the surrounding sequence in order to identify departure from expectation at the population level (context-dependent conservation). We characterized the population diversity for functional elements in the genome and identified the coordination of conserved sequences of distal and cis enhancers, chromatin marks, promoters, coding and intronic regions. The most context-dependent conserved regions of the genome are associated with unique functional annotations and a genomic organization that spreads up to one megabase. Importantly, these regions are enriched by over 100-fold of non-coding pathogenic variants. This analysis of human genetic diversity thus provides a detailed view of sequence conservation, functional constraint and genomic organization of the human genome. Specifically, it identifies highly conserved non-coding sequences that are not captured by analysis of interspecies conservation and are greatly enriched in disease variants.

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