A Short Review of the Generation of Molecular Descriptors and Their Applications in Quantitative Structure Property/Activity Relationships

Graphical Abstracts Current Computer-Aided Drug Design, 2016, Vol. 12, No. 3 i Graphical Abstracts Current Computer-Aided Drug Design, 2016, Vol. 12, No. 3 181 A Short Review of the Generation of Molecular Descriptors and Their Applications in Quantitative Structure Property/Activity Relationships Sagarika Sahoo, Chandana Adhikari, Minati Kuanar and Bijay K. Mishra* *Centre of Studies in Surface Science and Technology, School of Chemistry, Sambalpur University, Jyoti Vihar, 768 019, India Generations of molecular descriptors from the topology and quantum chemical characteristics of organic molecules for potential quantitative structure property/activity relationships have been elaborated. Current Computer-Aided Drug Design, 2016, Vol. 12, No. 3 206 Genome Wide Analysis of Chlamydia pneumoniae for Candidate Vaccine Development Ankita Sharma, Soundhara Rajan G, Rupsi Kharb and Sagarika Whole proteome of Chlamydia pneumoniae * Biswas * CSIR-Institute of Genomics & Integrative Biology, Mall Road, Delhi- Screening of proteins 110007, India Selection of three proteins Prediction of B & T cell epitope Current Computer-Aided Drug Design, 2016, Vol. 12, No. 3 216 Intercorrelation of major DNA/RNA Sequence Descriptors - A Preliminary Study Start with Nucleic Acid Sequences Dwaipayan Sen, Subhadeep Dasgupta, Indrajit Pal, Smarajit Manna, Subhash C. * Basak, Ashesh Nandy and Gregory D. Grunwald * Calculate 7 types of numerical descriptors Centre for Interdisciplinary Research and Education, Jodhpur Park, Kolkata 700068, India Carry out Intercorrelation and Principal Component analysis of data WangZhang 2 epsilon-HBE1-mRNA HBG2-mRNA HBG1-mRNA 1 delta-globin-HBD Randic2 beta-globin-HBB-mRNA SongTang 0 -1 PC2 (40.1% explained var.) zeta-mRNA Polar alpha-globin-HBA1&2 myoglobin -2 Yau Nandy Randic3D -2.5 0.0 2.5 PC1 (49.9% explained var.) Sequence characterization using selected descriptors and PCs. ii Current Computer-Aided Drug Design, 2016, Vol. 12, No. 3 Graphical Abstracts Current Computer-Aided Drug Design, 2016, Vol. 12, No. 3 229 2D QSAR and Virtual Screening based on Pyridopyrimidine Analogs of Epidermal Growth Factor Receptor Tyrosine Kinase S. Sugunakala and S. Selvaraj* Observed Vs Predicted PIC Activity 8 50 * Department of Bioinformatics, School of Life Sciences, Bharathidasan 7.5 University, Tiruchirappalli-620 024, Tamilnadu, India 7 6.5 Activity 50 6 5.5 Predicted PIC Predicted 5 4.5 4 4 4.5 5 5.5 6 6.5 7 7.5 8 Observed PIC50 Activity Current Computer-Aided Drug Design, 2016, Vol. 12, No. 3 241 Quantitative Analysis of Essential Molecular Features of Coumarin Derivatives with Antioxidant Activity Using Chemometric Tools Biplab De, Indrani Adhikari*, Ashis Nandy, Achintya Saha and Binoy B. Goswami *Regional Institute of Pharmaceutical Science and Technology, H Graphical Abstract Abhoynagar, Agartala, Tripura-799005, India O Fragments HN marked O HN essential based on 3D O N pharmacophore model Fragments with maximum contribution determined based on HQSAR model .

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Diagnosis of Sickle Cell Disease and HBB Haplotyping in the Era of Personalized Medicine: Role of Next Generation Sequencing
Journal of Personalized Medicine Article Diagnosis of Sickle Cell Disease and HBB Haplotyping in the Era of Personalized Medicine: Role of Next Generation Sequencing Adekunle Adekile 1,*, Nagihan Akbulut-Jeradi 2, Rasha Al Khaldi 2, Maria Jinky Fernandez 2 and Jalaja Sukumaran 1 1 Department of Pediatrics, Faculty of Medicine, Kuwait University, P.O. Box 24923, Safat 13110, Kuwait; jalajasukumaran@hotmail 2 Advanced Technology Company, Hawali 32060, Kuwait; [email protected] (N.A.-J.); [email protected] (R.A.); [email protected] (M.J.F.) * Correspondence: [email protected]; Tel.: +965-253-194-86 Abstract: Hemoglobin genotype and HBB haplotype are established genetic factors that modify the clinical phenotype in sickle cell disease (SCD). Current methods of establishing these two factors are cumbersome and/or prone to errors. The throughput capability of next generation sequencing (NGS) makes it ideal for simultaneous interrogation of the many genes of interest in SCD. This study was designed to confirm the diagnosis in patients with HbSS and Sβ-thalassemia, identify any ß-thal mutations and simultaneously determine the ßS HBB haplotype. Illumina Ampliseq custom DNA panel was used to genotype the DNA samples. Haplotyping was based on the alleles on five haplotype-specific SNPs. The patients studied included 159 HbSS patients and 68 Sβ-thal patients, previously diagnosed using high performance liquid chromatography (HPLC). There was Citation: Adekile, A.; considerable discordance between HPLC and NGS results, giving a false +ve rate of 20.5% with a S Akbulut-Jeradi, N.; Al Khaldi, R.; sensitivity of 79% for the identification of Sβthal.
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Molecular Epidemiology and Hematologic Characterization of Δβ
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Identification of Novel HPFH-Like Mutations by CRISPR Base Editing That Elevates the Expression of Fetal Hemoglobin
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Normal, C=Critical
Patient Report |FINAL Client: Example Client ABC123 Patient: Patient, Example 123 Test Drive Salt Lake City, UT 84108 DOB 7/22/1970 UNITED STATES Gender: Female Patient Identifiers: 01234567890ABCD, 012345 Physician: Doctor, Example Visit Number (FIN): 01234567890ABCD Collection Date: 00/00/0000 00:00 Hemoglobin Evaluation Reflexive Cascade ARUP test code 2005792 Hemoglobin A 97.1 % (Ref Interval: 95.0-97.9) Hemoglobin A2 2.6 % (Ref Interval: 2.0-3.5) Hemoglobin F 0.3 % (Ref Interval: 0.0-2.1) REFERENCE INTERVAL: Hemoglobin F Access complete set of age- and/or gender-specific reference intervals for this test in the ARUP Laboratory Test Directory (aruplab.com). Hemoglobin S 0.0 % (Ref Interval: 0.0-0.0) Hemoglobin C 0.0 % (Ref Interval: 0.0-0.0) Hemoglobin E 0.0 % (Ref Interval: 0.0-0.0) Hemoglobin - Other 0.0 % (Ref Interval: 0.0-0.0) Sickle Cell Solubility Not Performed Hemoglobin, Capillary Electrophoresis Performed Hemoglobin Evaluation See Note Beta Globin Full Gene Sequencing Not Applicable H=High, L=Low, *=Abnormal, C=Critical Patient: Patient, Example ARUP Accession: 21-048-400496 Patient Identifiers: 01234567890ABCD, 012345 Visit Number (FIN): 01234567890ABCD Page 1 of 4 | Printed: 3/11/2021 11:41:09 AM 4848 Patient Report |FINAL Beta Globin (HBB) Del/Dup Result Not Applicable Alpha Thalassemia HBA1 and HBA2 Seq Not Applicable Gamma Globin (HBG1 and HBG2) Sequencing Not Applicable Hemoglobin Cascade Interpretation See Note H=High, L=Low, *=Abnormal, C=Critical Patient: Patient, Example ARUP Accession: 21-048-400496 Patient Identifiers: 01234567890ABCD, 012345 Visit Number (FIN): 01234567890ABCD Page 2 of 4 | Printed: 3/11/2021 11:41:09 AM 4848 Patient Report |FINAL RESULT Normal hemoglobin evaluation.
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Genome Editing of HBG1/2 Promoter Leads to Robust Hbf Induction in Vivo While Editing of BCL11A Erythroid Enhancer Shows Erythroid Defect
Genome Editing of HBG1/2 Promoter Leads to Robust HbF Induction In Vivo While Editing of BCL11A Erythroid Enhancer Shows Erythroid Defect Kai-Hsin Chang, Minerva Sanchez, Jack Heath, Edouard de Dreuzy, Scott Haskett, Abigail Vogelaar, Kiran Gogi, Jen DaSilva, Tongyao Wang, Andrew Sadowski, Gregory Gotta, Jamaica Siwak, Ramya Viswanathan, Katherine Loveluck, Hoson Chao, Eric Tillotson, Aditi Chalishazar, Abhishek Dass, Frederick Ta, Emily Brennan, Diana Tabbaa, Eugenio Marco, John Zuris, Deepak Reyon, Meltem Isik, Ari Friedland, Terence Ta, Fred Harbinski, Georgia Giannoukos, Sandra Teixeira, Christopher Wilson, Charlie Albright, Haiyan Jiang Editas Medicine, Inc., Cambridge, MA 60th Annual Meeting and Exposition of American Society of Hematology December 2, 2018, San Diego, CA © 2018 Editas Medicine Overview Etiology of Sickle Cell Disease In Vivo Study Design to Evaluate Two Approaches to Increase Fetal Hemoglobin (HbF) Expression Effect of Downregulating BCL11A Expression by Targeting its Erythroid Enhancer Editing Cis-regulatory Elements in b-Globin Locus Conclusion © 2018 Editas Medicine Etiology of Sickle Cell Disease Amino Hemoglobin Low DNA Acid Tetramer O2 a a a a b-globin GLU G A G b b b b HbA a a a a a a a a s s s VAL b b b -globin G T G bs bs bs bs bs bs HbS HbS Fiber • Sickle cell disease (SCD) is caused by a single mutation E6V of the b-globin chain, leading to polymerization of hemoglobin (Hb) and formation of sickle hemoglobin (HbS) fibers when deoxygenated. • Symptoms include anemia, acute chest syndrome, pain crises, and an array of other complications. • Patients suffer significant morbidity and early mortality.
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Identifying Genetic Variants and Pathways Associated with Extreme Levels of Fetal Hemoglobin in Sickle Cell Disease in Tanzania
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