Madhu Sudhana Saddala

Madhu Sudhana Saddala
Johns Hopkins Medicine | JHUSOM · Wilmer Bioinformatics Core

PhD

About

61
Publications
82,707
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348
Citations
Introduction
I am Dr. Madhu Sudhana Saddala working as a Postdoctoral Scientist (Bioinformatics) in Johns Hopkins University School of Medicine, Baltimore, MD. USA.
Additional affiliations
October 2018 - March 2020
University of Missouri School of Medicine
Position
  • PostDoc Position
Description
  • Genomics and Proteomics
January 2018 - October 2018
Johns Hopkins Medicine
Position
  • PostDoc Position
June 2017 - September 2017
ICAR-IASRI
Position
  • Research Associate
Education
July 2010 - July 2016
Sri Venkateswara University
Field of study
  • Bioinformatics
July 2006 - July 2008
Sri Venkateswara University
Field of study
  • Bioinformatics
July 2002 - July 2005
Sri Venkateswara University
Field of study
  • Biotechnology

Publications

Publications (61)
Article
Full-text available
Severe acute respiratory syndrome (SARS) is a severe respiratory infection caused by a recently recognized corona virus (SARS-CoV). Newly innovative machinery for way in of SARS CoV hooked on target cells was reported. The ingress of SARS-CoV necessities for proteases in establishment of viral infection. Cathepsin – L (CTSL) is the prime enzyme con...
Article
Our previous studies found that the C-X-C motif chemokine receptor 5 (CXCR5) loss leads to retinal pigment epithelium (RPE) dysfunction and AMD pathogenesis. The current study aimed to characterize the G protein-coupled receptor (GPCR) structure of CXCR5 and analyze its interactions with AMD-related risk genes. The sequence alignments, homology mod...
Article
Background Retinal microglial cells (RMCs) play crucial roles in maintaining normal visual functions in a healthy eye. However, the underlying mechanisms of RMCs over-activation manifesting the alterations of sensome profile and inflammation state, which contribute to various retinal and neurodegenerative diseases, remain elusive. Here, we aimed to...
Preprint
Full-text available
Placental growth factor (P l GF) and Angiopoietin (Ang)-1 are two angiogenic factors that play vital roles in vascular cell growth and stabilization. The present study's objective is to examine P l GF's regulation of Ang-1 and its Tie-2 receptor expression in human vascular cells and vasculature. We exploited the cocultures of human primary retinal...
Article
Full-text available
Colorectal cancer (CRC) is the third most common cancer diagnosed worldwide making it a serious global challenge. CRC progression results from dysregulated cytoplasmic transcription factors, including signal transducer and activator of transcription (STAT) proteins that are involved in JAK-STAT pathway. The STAT proteins contain a conserved SH2 dom...
Article
Full-text available
Placental growth factor (PlGF or PGF) is a member of the VEGF (vascular endothelial growth factor) family. It plays a pathological role in inflammation, vascular permeability, and pathological angiogenesis. The molecular signaling by which PlGF mediates its effects in non-proliferative diabetic retinopathy (DR) remains elusive. This study aims to c...
Article
To investigate the role of placental growth factor/vascular endothelial growth factor (PlGF-VEGF) heterodimers are involved in the blood-retinal barrier (BRB) breakdown and the associated mechanism, human retinal endothelial cells (HRECs) were treated with recombinant human (rh)PlGF-VEGF heterodimers and rhPlGF and studied in normal and high-glucos...
Article
Full-text available
Homeostasis of the retinal pigment epithelium (RPE) is essential for the health and proper function of the retina. Regulation of RPE homeostasis is, however, largely unexplored, yet dysfunction of this process may lead to retinal degenerative diseases, including age-related macular degeneration (AMD). Here, we report that chemokine receptor CXCR5 r...
Article
Full-text available
Age-related macular degeneration (AMD) is the most common cause of irreversible blindness in the elderly population. In our previous studies, we found that deficiency of CXCR5 causes AMD-like pathological phenotypes in mice, characterized by abnormalities and dysfunction of the retinal pigment epithelium (RPE) cells. The abnormalities included abno...
Article
Full-text available
The CXCR5 (C-X-C motif chemokine receptor 5) is chemokine transmembrane receptor, acting via its ligand CXCL13 and plays a crucial role in controlling the trafficking of inflammatory cells into and from the sub-retinal space, which contributes to the pathogenesis of AMD. We have previously described the genetic ablation of CXCR5 deficiency causes R...
Article
Full-text available
Background: The ways in which microglia activate and promote neovascularization (NV) are not fully understood. Recent in vivo evidence supports the theory that calcium is required for the transition of microglia from a surveillance state to an active one. The objectives of this study were to discover novel L-type voltage-gated channel (L-VGCC) bloc...
Article
Full-text available
Glucose-6-Phosphate Dehydrogenase (G6PD) is a ubiquitous cytoplasmic enzyme converting glucose-6-phosphate into 6-phosphogluconate in the pentose phosphate pathway (PPP). The G6PD deficiency renders the inability to regenerate glutathione due to lack of Nicotine Adenosine Dinucleotide Phosphate (NADPH) and produces stress conditions that can cause...
Article
Full-text available
Background: Retinal degenerative diseases affect millions of people and represent the leading cause of vision loss around the world. Retinal degeneration has been attributed to a wide variety of causes, such as disruption of genes involved in phototransduction, biosynthesis, folding of the rhodopsin molecule, and the structural support of the reti...
Preprint
Full-text available
Background Retinal degenerative diseases affect millions of people and represent the leading cause of vision loss around the world. Retinal degeneration has been attributed to a wide variety of causes, such as disruption of genes involved in phototransduction, biosynthesis, folding of the rhodopsin molecule, and the structural support of the retina...
Preprint
Full-text available
Background: Retinal degenerative diseases affect millions of people and represent the leading cause of vision loss around the world. Retinal degeneration has been attributed to a wide variety of causes, such as disruption of genes involved in phototransduction, biosynthesis, folding of the rhodopsin molecule, and the structural support of the retin...
Article
Xanthomonas oryzae pv. oryzae (Xoo) is an important rice pathogen. This is a vascular pathogen entering the plant via the hydathodes causing rice bacterial blight. It has been known that most regulation of pathogenicity factor F (RpfF) genes in Xanthomonas regulates virulence in response to the diffusible signal factor (DSF). The RpfF recognized as...
Article
A new series of α-thiazolyl aminomethylene bisphosphonates were synthesized by a three component reaction of 4-aryl substituted thiazol-2-amine with different dialkyl/aryl phosphites and triethyl orthoformate in the presence of Ag NPs (nano particles) as a catalyst under solvent free conditions. All the synthesized target compounds were characteriz...
Preprint
Background Retinal degenerative diseases affect millions of people and represent the leading cause of vision loss around the world. Retinal degeneration has been attributed to a wide variety of causes, such as disruption of genes involved in phototransduction, biosynthesis, folding of the rhodopsin molecule, and the structural support of the retina...
Article
Aim: The aim of this study is to synthesize, characterize and biological evaluation of 3-ethyl 5- methyl2-(2-aminoethoxy)-4-(2-chlorophenyl)-1,4-dihydropyridine-3,5-dicarboxylate derivatives. Background: An efficient synthesis of two series of novel carbamate and sulfonamide derivatives of amlodipine, 3-ethyl 5-methyl 2-(2-aminoethoxy)-4-(2-chlo...
Preprint
Retinal degenerative diseases affect millions of people and represent the leading cause of vision loss around the world. Retinal degeneration has been attributed to a wide variety of causes, such as disruption of genes involved in phototransduction, biosynthesis, folding of the rhodopsin molecule, and the structural support of the retina. The molec...
Article
We report that placental growth factor (PlGF) negatively affects the endothelial cell (EC) barrier function through a novel regulatory mechanism. The PlGF mAb promotes (but recombinant protein disrupts) EC barrier function, thus affecting the barrier-forming protein levels, membrane distribution, and EC monolayer impedance by the electrical cell-im...
Article
We report that placental growth factor (PlGF) negatively affects the endothelial cell (EC) barrier function through a novel regulatory mechanism. The PlGF mAb promotes (but recombinant protein disrupts) EC barrier function, thus affecting the barrier-forming protein levels, membrane distribution, and EC monolayer impedance by the electrical cell-im...
Article
Previous research has shown that CXCR5 −/− mice develop retinal degeneration (RD) with age, a characteristic related to age macular degeneration (AMD). RD in these mice is not well-understood, and in this study, we sought to characterize further the RD phenotype and to gain mechanistic insights into the function of CXCR5 in the retina. CXCR5 −/− an...
Preprint
Full-text available
Placental growth factor (PlGF or PGF) is a member of the VEGF family, which is known to play a critical role in pathological angiogenesis, inflammation, and endothelial cell barrier function. However, the molecular mechanisms by which PlGF mediates its effects in non-proliferative diabetic retinopathy (DR) remain elusive. In this study, we performe...
Article
Full-text available
Background: Tumor necrosis factor α (TNFα) is a multifunctional cytokine with a potent pro-inflammatory effect. It is a validated therapeutic target molecule for several disorders related to autoimmunity and inflammation. TNFα-TNF receptor-1 (TNFR1) signaling contributes to the pathological processes of these disorders. The current study is focuse...
Conference Paper
Background: Signal transducer and activator of transcription (STAT) proteins are a seven-member family of cytoplasmic proteins. A conserved SH2 domain facilitates STAT initiation by allowing binding to phosphotyrosine motifs for STAT-receptor interactions and STAT dimerization. STAT proteins (STAT1, STAT2 and STAT3) are promising targets for anti-c...
Preprint
Retinal degenerative diseases affect millions of people and are the leading cause of vision loss. Retinal degeneration has been attributed to a wide variety of causes, such as disruption of genes that are involved in phototransduction, biosynthesis, folding of the rhodopsin molecule and the structural support of the retina. The molecular pathogenes...
Article
Full-text available
Background Age-related macular degeneration (AMD) is the most common, progressive, and polygenic cause of irreversible visual impairment in the world. The molecular pathogenesis of the primary events of AMD is poorly understood. We have investigated a transcriptome-wide analysis of differential gene expression, single-nucleotide polymorphisms (SNPs...
Article
Therapeutic inhibition of hypoxia inducible factor-1α (HIF-1α) action has emerged as a potential approach for managing several diseases including breast cancer (BC). Genistein has been found to exert anti-malignant activity. However, its mechanisms of action remain unknown. Studies indicate that it could act by downregulating HIF-1α. Based on these...
Article
Full-text available
Abstract Placental growth factor (PlGF or PGF), a member of the vascular endothelial growth factor (VEGF) sub-family, plays a crucial role in pathological angiogenesis and inflammation. However, the underlying molecular mechanisms that PlGF mediates regarding the complications of non-proliferative diabetic retinopathy (DR) remain elusive. Using an...
Article
Pancreatic cancer (PC) is an aggressive carcinoma and the fourth cause of cancer deaths in Western countries. Although surgery is the most effective therapeutic option for PC, the management of unresectable, locally advanced disease is highly challenging. Our improved understanding of pancreatic tumor biology and associated pathways has led to the...
Article
Full-text available
Vivapain-3(VP-3) protein is a family of cysteine rich proteases of malaria parasite is extensively reported to participate in a range of wide cellular processes including survival. VP-3 of plasmodium recognized as an attractive drug target in vector-borne diseases like malaria. In the present study we robust a homology model of VP-3 protein and gen...
Article
Full-text available
The precursor compound 3-fluoro-4-morpholinoaniline (7) is an important intermediate of the antibiotic drug linezolid and was synthesized initially by the substitution of morpholine (5) on 1,2-difluoro-4-nitrobenzene (4) under neat conditions, resulting in 4-(2-fluoro-4-nitrophenyl)morpholine (6) followed by its nitro group reduction with Fe/NH4Cl....
Article
Full-text available
Hypoxia inducible factor-1(HIF-1) is a bHLH-family transcription factor that control genes involved in glucolysis, angiogenesis, migration, as well as invasion factors that are important for tumor progression and metastasis. HIF-1, a hetero dimer of HIF-1α and HIF-1β, binds to the hypoxia responsive genes, such as vascular endothelial growth factor...
Article
Full-text available
Synthesis of a series of new ethyl phosphoramidates 9a–j of acyclovir through phosphorylation of hydroxy group followed by substitution of numerous amines/amino acid esters 7a–j was accomplished. The structures of newly synthesized compounds were elucidated by spectroscopic data such as IR, NMR (1H, 13C, and 31P) and mass spectrophotometery, and el...
Article
Full-text available
The present study, we design and synthesize the novel dihydropyridine derivatives, i.e., 3 (a-e) and 5 (a-e) and evaluated, anticonvulsant activity. Initially due to the lacuna of LCC, we modeled the protein through modeller 9.15v and evaluated through servers. Docking studies were performed with the synthesized compounds and resulted two best comp...
Chapter
Full-text available
Cadmium (Cd) is a heavy metal present in air, water, soils and sediments. It is well known that long-term exposure to Cd causes various toxic effects in various organ systems such as cardiovascular, kidneys, liver, brain, lung, bones, immune/haemopoietic, endocrine and reproductive systems. Cd influx mediates voltage-gated L-type calcium channels (...
Article
Full-text available
Background: Cyclooxygenase (COX-2) inhibitors have been developed to provide better anti-inflammatory and analgesic efficacy than those of traditional NSAIDs. Several compounds having selective COX-2 inhibitors such as SC-558, Celecoxib, Rofecoxib, Valdecoxib and Etoricoxib are marketed as new generation NSAIDs and block the production of prostagl...
Article
Full-text available
A series of new urea and thiourea derivatives of lopinavir intermediate 7a–k was designed and synthesized from lopinavir intermediate by treating various biopotent isocyanates and isothiocyanates in the presence of base, 1,4-dimethyl piperazine, and their biological activity was evaluated . The bio-assay revealed that the compounds exhibited modera...
Article
Full-text available
Alzheimer's disease (AD) is a progressive neurodegenerative disorder, encircling the deterioration of cognitive functions and behavioral changes, characterized by the aggregation of amyloid β-protein (Aβ) into fibrillar amyloid plaques in elected areas of the brain with the lipid-carrier protein apolipoprotein E (apoE), the microtubule associated p...
Article
Full-text available
A series of new class of P-heterocycle encompassing urea and thiourea derivatives, N-(substitutedphenyl)-N′-(2-oxo-2,3-dihydro-1H-2λ5-[1,3,2]diazaphospholo[4,5-b]pyridin-2-yl)ureas 11a–e/thioureas 11f–k, was accomplished from the precursor intermediate, 2-amino-2,3-dihydro-1H-2λ5-[1,3,2]diazaphospholo[4,5-b]pyridin-2-one, 9. The compound 9 was obta...
Article
A series of new phosphoramidate derivatives 7a-l were synthesized by reacting 5- nitroindazole with 4-chlorophenyl dichlorophosphate (4), and then further with various biopotent aromatic/hetero/alkyl amines 6a-l. All the newly synthesized compounds were characterized by spectroscopic data (IR, 1H, 13C, 31P NMR and mass) and elemental analysis. The...
Article
In an effort to develop novel anti-inflammatory agents, we synthesized phosphorylated derivatives of febuxostat using various phosphates/phosphonites by Michaelis-Arbuzov reaction. Their inhibitory activity on nitric oxide (NO) production, reactive oxygen species (ROS) production and cytotoxicity were evaluated using lipopolysaccharide (LPS) activa...
Article
VEGFR-2 is a known protein target for antiangiogenic agents, was used in this study. In order to understand of the mechanisms of ligand binding and the interaction between the ligand and the VEGFR-2. A three-dimensional (3D) model of the VEGFR-2 is generated based on the crystal structure of the complex containing KIT and sunitinib (PDB code 3G0E)...
Article
VEGFR-2 is a known protein target for antiangiogenic agents, was used in this study. In order to understand of the mechanisms of ligand binding and the interaction between the ligand and the VEGFR-2. A three-dimensional (3D) model of the VEGFR-2 is generated based on the crystal structure of the complex containing KIT and sunitinib (PDB code 3G0E)...
Article
A series of new phosphoramidate derivatives 7a-l were synthesized by reacting 5- nitroindazole with 4-chlorophenyl dichlorophosphate (4), and then further with various biopotent aromatic/hetero/alkyl amines 6a-l. All the newly synthesized compounds were characterized by spectroscopic data (IR, 1H, 13C, 31P NMR and mass) and elemental analysis. The...
Article
Saddala MS, Babu DK, Bhavani G, Ayisha S, Usha Rani A., Molecular dynamic simulation docking inhibitors of falcipain – 2, Onl J Bioinform., 15 (1): 98-105, 2014. Falcipain-2 promotes intracellular development of the malaria Plasmodium Spp. parasite and degrades the protein hemoglobin. Inhibition of falcipain-2 prevents parasite maturation and there...
Article
Full-text available
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Article
may not store these pages in any form except for your own personal use. All other usage or distribution is illegal under international copyright treaties. Permission to use any of these pages in any other way besides the before mentioned must be gained in writing from the publisher. This article is exclusively copyrighted in its entirety to OJB pub...
Article
not store these pages in any form except for your own personal use. All other usage or distribution is illegal under international copyright treaties. Permission to use any of these pages in any other way besides the beforementioned must be gained in writing from the publisher. This article is exclusively copyrighted in its entirety to OJB publicat...
Article
may not store these pages in any form except for your own personal use. All other usage or distribution is illegal under international copyright treaties. Permission to use any of these pages in any other way besides the before mentioned must be gained in writing from the publisher. This article is exclusively copyrighted in its entirety to OJB pub...
Article
not store these pages in any form except for your own personal use. All other usage or distribution is illegal under international copyright treaties. Permission to use any of these pages in any other way besides the before mentioned must be gained in writing from the publisher. This article is exclusively copyrighted in its entirety to OJB publica...
Article
Cathepsin K (Cat K) is a lysosomal cysteine protease which involves in degradation of bone may lead to severe bone fragility in Osteoporosis patients. Cat K is the primary enzyme involved in osteoclastic bone resorption. Inhibition of Cat K represents a potential drug target for Osteoporosis. Odanacatib (CID 10152654) is a known potent, reversible...

Questions

Questions (29)
Question
Hello guys,
It may seem like a basic question, but this is causing confusion.
What is the difference between fold change and Log fold change?
Question
Given a collection of points in two, three, or higher dimensional space, a "best fitting" line can be defined as one that minimizes the average squared distance from a point to the line. The next best-fitting line can be similarly chosen from directions perpendicular to the first. Repeating this process yields an orthogonal basis in which different individual dimensions of the data are uncorrelated. These basis vectors are called principal components, and several related procedures principal component analysis (PCA).

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