Dr. P. K. Krishnan Namboori currently serves as an Associate Professor at the Center for Excellence in Computational Engineering and Networking (CEN) and In-charge of Computational Chemistry Group, Amrita School of Engineering, Amrita VishwaVidyapeetham, Coimbatore campus. He pursued his Ph. D. in Computational Drug Designing from Amrita VishwaVidyapeetham in the year 2010. He is also an Adjuncy Faculty at the School of Biotechnology at Amritapuri Campus. He, focuses on research activities related to theory and computer simulation of chemical and molecular processes. The computational techniques range from ‘ab initio’ electronic structure methods through classical molecular simulation to mesoscale simulation. A number international journal publications, conference proceedings and one international book are to his credit. He is assisted by three research fellows and a number of project students.


Publication Type: Journal Article
Year of Publication Publication Type Title
2015 Journal Article A. E. Silviya, Kavitha, G., K. Kutty, N., and Namboori, P. K. Krishnan, “Insilico modeling of chitosan as a drug delivery system”, International Journal of Drug Delivery, vol. 7, no. 1, pp. 27-31, 2015.[Abstract]

Computational modeling of polymeric nanoparticles as drug carriers have been extensively studied due to their varied functionalities, tunable structures and the capability of controlled drug release. Nano particulate polymeric drug delivery systems enable a cell specific targeting with negligible side effects and drug release based on change in physiological conditions. Eight common polymers are modeled and the various properties have been predicted. ADMET, QSAR, thermodynamic and electronic properties have been predicted and compared using SAR as well as quantum mechanical density functional methods. Comparison of the predicted properties suggests that chitosan, which is a natural polymer and has some advantages over others is a promising drug carrier candidate for tumor. © 2014, Advanced Research Journals. All rights reserved. More »»
2015 Journal Article C. V. Umesh, Jamsheer, A. M., Alex, P. M., and Namboori, P. K. Krishnan, “Perusal of Mbl2 gene -Susceptibility to tuberculosis in different Indian populations”, Journal of Applied Pharmaceutical Science, vol. 5, no. 9, pp. 097-099, 2015.[Abstract]

The tuberculosis (TB) is a major infectious disease in the world, which is still not made under control. Mannose binding lectin (MBL) or MBL2 is a human gene susceptible to Tuberculosis and is used as a tool to investigate the proneness of attack by mycobacterium tuberculosis. MBL2 gene has been found over fifty five different populations in India. Among the identified single-nucleotide polymorphism (SNP) investigated in this work by evaluating the SNPs through computational methods. All identified SNPs are reported as deleterious. The SNP, rs1800450 of MBL2 is commonly reported from all major genomic populations in India, and the individuals holding this SNP are prone to the attack of mycobacterium tuberculosis. © 2015 C.V. Umesh et al. More »»
2013 Journal Article , Sukumaran, Ja, ,, ,, and Namboori, P. K. Krishnan, “Pharmacogenomic analysis of individual variation in prostate cancer”, International Journal of Research in Pharmaceutical Sciences, vol. 4, pp. 70-72, 2013.[Abstract]

Single Nucleotide Polymorphisms (SNPs) are the most common genetic variation among individuals. The work aims at identifying the SNPs associated with prostate cancer. In the present work, pharmacogenomic analysis has been carried out to analyze the impact of functional SNPs in prostate cancer. 11 genes involved in signal transduc-tion in prostate cancer have been subjected to genomic analysis. The genomic analysis protocol includes microsa-tellite analysis, restriction fragment length polymorphism (RFLP) analysis, silent mutation analysis, GC content Analysis and deleterious SNP analysis. From the deleterious SNP analysis, it has been found that the mutations rs28571178 in IL16 (5′ UTR) and rs17854206 in JAZF1 (3′ UTR) cause functional effects on the specific genes. Upon stability analysis of native and mutated proteins, it has been concluded that the above deleterious mutations are supported by nature due to their increased stability. These SNPs have been identified as the most deleterious in causing prostate cancer. © JK Welfare & Pharmascope Foundation.

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2012 Journal Article C. P. Anju, Anusooya, N. J., Deeasree, M., Deepak, O. M., and Namboori, P. K. Krishnan, “De Novo designing of HDAC inhibitors in cancer therapy”, International Journal of Pharmaceutical Science and Health Care, vol. 2, pp. 59–66, 2012.[Abstract]

HDACs are enzymes found in eukaryotes. It removes the acetyl group from the lysine residue on the N-terminal regions of histone proteins and the process is called histone deacetylation. It results in the increased positive charge on histones. The DNA possesses negatively charged sugar-phosphate backbone; therefore the positively charged histones bind more firmly to the DNA. This makes the DNA unavailable for the transcription
factors and eventually leads to the gene silencing. Rather than histone proteins, HDACs ...

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2011 Journal Article P. K. Krishnan Namboori, Vineeth, K. Vb, Rohith, Vb, Hassan, Ia, Sekhar, La, Sekhar, Aa, and Nidheesh, Ma, “The ApoE gene of Alzheimer's disease (AD)”, Functional and Integrative Genomics, vol. 11, pp. 519-522, 2011.[Abstract]

The ApoE gene responsible for the Alzheimer's disease has been examined to identify functional consequences of single-nucleotide polymorphisms (SNPs). Eighty-eight SNPs have been identified in the ApoE gene in which 31 are found to be nonsynonymous, 8 of them are coding synonymous, 33 are found to be in intron, and 3 are in untranslated region. The SNPs found in the untranslated region consisted of two SNPs from 5' and one SNP from the 3'. Twenty-nine percent of the identified nsSNPs have been reported as damaging. In the analysis of SNPs in the UTR regions, it has been recognized that rs72654467 from 5' and rs71673244 from 5' and 3' are responsible for the alteration in levels of expression. Both native and mutant protein structures were analyzed along with the stabilization residues. It has been concluded that among all SNPs of ApoE, the mutation in rs11542041 (R132S) has the most significant effect on functional variation. © Springer-Verlag 2011. More »»
2011 Journal Article K. U. Radhagayathri, Namboori, P. K. Krishnan, Mohandas, V. P., Subeesh, T., Deepa O. S., and Ramachandran, K. I., “Computational modeling and simulation of nanomolecular switch for Alzheimer's disease (A gene silencing technique)”, International Journal of Nanoscience, vol. 10, pp. 319-322, 2011.[Abstract]

The design of artificial gene regulatory networks has paved way for the construction of therapeutic gene circuits that would find application in next generation gene therapy approaches. The main challenge in such designs is in selecting the appropriate genetic components to make up the circuit in order to produce the anticipated or desired behavior. To eliminate this complexity, computational simulation tools are used to guide circuit design. This involves selection and genetic modification of components, until the required system behavior is achieved. In this work, we have designed a model for a synthetic nanogene network. The gene expression involved in diseases caused by mutation, like cancer, Alzheimer's disease (AD), etc., can be effectively controlled by "Nanogene silencing genetic switch". Here, we have considered the case of Alzheimer's disease. Genes that are responsible for genetic AD are APP, PSEN1, and PSEN2. Antimutagenic study of phytochemicals has been carried out with the common AD causing APP gene mutation. By our computational analysis, phytochemicals like curcumin, eugenol, and limonene have been identified as "molecular switch" devices to prevent mutation of AD gene. All these chemicals are found to be strongly interacted with the AD gene without making changes to the remaining part of the sequence. Among the analyzed chemicals, curcumin is found to be most interacting with AD gene protecting it from mutation. Hence, inclusion of curcumin-containing food items in our menu would prevent Alzheimer's disease to a large extent. This technique is a type of gene therapy leading to silencing of the mutated part of the gene and preventing mutation. © 2011 World Scientific Publishing Company.

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2011 Journal Article K. V. Gopal, Namboori, P. K. Krishnan, Premkumar, P., Gopakumar, D., and B, S. Narayanan, “Insilico modeling and simulation of magnetic nanoparticles for the biological cell isolation technique”, International Journal of Nanoscience, vol. 10, no. 1-2, pp. 323-327, 2011.[Abstract]

Magnetic nanoparticles (MNPs) can be used in a wide variety of biomedical applications like contrast agents for magnetic resonance imaging, magnetic labeling, controlled drug release, hyperthermia, and in cell isolation. Most of these applications need distinct and controllable interactions between the MNPs and living cells and can be made possible by a proper functionalization technique. This paper describes a computational approach for the identification of magnetic nanoparticles for the development, design, and demonstration of a novel, incorporated system for selective and rapid removal of biological, chemical, and radioactive biohazards from human body. The attraction between an external magnetic field and the MNPs facilitate separation of a wide variety of biological materials. This principle can be used for the isolation and aggregation of wandering cancer cells from the blood or the bone marrow to make a proper and early diagnosis of leukemia. Similarly, toxins, kidney stones, and other unwanted particles in the human body can be easily diagnosed and removed by the same technique. Nanoparticle-sized iron oxides have been studied in this work by computational modeling and molecular dynamic (MD) simulation techniques. Structural, thermodynamic, and magnetic properties have been formulated. In this work, nanoparticles of size varying from 0.5 to 2.5 nm have been analyzed. Cell isolation ability of the nanoparticles has been compared based on the computational results. MNPs are biologically activated and permitted to bind with the targeted cells through various pathways, thereby allowing certain cellular compartments to be specifically addressed. Once the cells are identified, the preferred cellular compartments can be magnetically isolated and removed with the help of an external magnetic field. Out of the iron oxides analyzed in this work, 1.1 nm Fe 3O 4 is found to be most interacting with leukemia protein. Hence, leukemia cells can be effectively targeted, separated, and removed using Fe 3O 4 of the suggested dimension. © 2011 World Scientific Publishing Company. More »»
2011 Journal Article A. Ranganath, Ashish, G., K Gopal, V., K. Kutty, N., Namboori, P. K. Krishnan, and Gopakumar, D., “Electrical conductivity and thermodynamic stability of single walled carbon nanotube using first principles”, NanoTrends (Nano Science and Technology Consortium), vol. 11, pp. 18-21, 2011.[Abstract]

Single Walled Carbon Nanotube (SWCNT) is known to have unique thermodynamic and electrical properties which mainly depends upon the chiral index values (n,m). Quantum mechanical modeling and simulation studies were conducted for these samples to characterize the above properties. The energy gap of conducting carbon nano tubes has been found to be negligibly small. Armchair configuration with (n=m) is found to be highly stable. All these samples are found to be conducting. Structures with n and m values (8,7), (7,8),(7,6), (7,2), (6,5), (5,3) (4,5) and (3,5) are found to be unstable and are all semiconductors. More »»
2011 Journal Article A. Noushadali, Parimalam, B., R Devi, R., Shilpa, S., A Kumar, S., and Namboori, P. K. Krishnan, “PRE-TRANSCRIPTIONAL GENE SILENCING TECHNIQUE FOR CONTROLLING SKIN CANCER”, International Journal of Pharmaceutical Science and Research, vol. 2, no. 5, pp. 1293-1297, 2011.[Abstract]

Familial cancers, which are in general incapable of exhibiting symptoms at the early onset period of the disease, can become fatal if left undiagnosed. Such cancers turn out to be a great threat through many generations in the long run. The remedial alternative to this is treatment at the genetic level which quite obviously points out to gene therapy. In this work, gene therapy proposed at the pre-transcriptional level intends to silence mutation of the target gene, thereby inhibiting or silencing gene expression in the form of a defective protein. Skin cancer, the second most common type of cancers widespread across the globe, has been considered for our studies. Phytochemicals that have been reported to have anti-skin cancer properties (at the protein level - acting on the defective protein targets), have been further investigated for antimutagenic activity at the gene level (intended to act on gene targets). Lutein and crocetin have been reported to show antimutagenic behavior towards the skin cancer genes considered in the analysis. Considering the drug-likeness of these two molecules, it has been found that the water solubility of lutein and the bioavailability of both lutein and crocetin need to be improved to make them into effective drugs in gene therapy. More »»
2011 Journal Article M. G. Nirmal, K Gopal, V., and Namboori, P. K. Krishnan, “Determination of Protein Subcellular Locations using Support Vector Machines”, Journal of Computational Intelligence in Bioinformatics, vol. 4, pp. 29-35, 2011.
2010 Journal Article R. Radhika, Rohith, V., Kumar, N. C. Anil, K Gopal, V., Namboori, P. K. Krishnan, and Deepak, O. M., “Insilico Analysis of Nano Polyamidoamine (PAMAM) Dendrimers for Cancer Drug Delivery”, Int. J. of Recent Trends in Engineering and Technology, vol. 4, pp. 142-144, 2010.[Abstract]

The treatment of cancer is mainly through chemotherapy, radiational therapy and surgery. However there are many limitations for the conventional use of cytotoxic drugs which may result in lack of selectivity in the body and the intrinsic or acquired multidrug resistance of cancer cells. Hence to end this nano dendritic polymer is used as drug carriers due to their diverse chemistry and safety characteristics in the body. Dendrimers are hyper branched distinctive class of macromolecules having highly branched; three-dimensional architectures with low polydispersity and high functionality .Compared to classical polymers, dendrimers have a sharp degree of molecular uniformity, narrow molecular weight distribution, unambiguous size and shape characteristics, and a high- functionalized terminal surface. Due to their high flexibility, nano-size, and well defined structure dendrimers are used as promising scaffolds and have diverse applications in the field of biomedicine. Different types of interactions like electrostatic, hydrophobic and hydrogen bond interactions take place during entrapment of drugs within the dendritic polymer and the covalent and electrostatic interaction between a drug and the surface of a polymer have been analyzed. Molecular simulations have been used in this work to study the various properties of Polyamidoamine (PAMAM) dendrimers both in equilibrium as well as in the transient or steady-state flows. Hence an insight into these analyses will help us to study how the molecular properties help in anticancer drug delivery. More »»
2010 Journal Article P. K. Krishnan Namboori, Gopakumar, D., Mohan, A., Radhagayathri, K. U., Gopal, V., Vasavi, C. S., Premkumar, P., and Ramachandran, K. I., “Effect of Non-Coding RNA on Post-Transcriptional Gene Silencing of Alzheimer Disease”, Nature Precedings, 2010.[Abstract]

A large amount of hidden biological information is contained in the human genome, which is not expressed or revealed in the form of proteins; the usual end product form of gene expression. Instead, most of such information is in the form of non-coding RNAs (ncRNAs). ncRNAs correspond to genes that are transcribed, but do not get translated into proteins. This part of the genome was, till recently, considered as ‘junk’. The term ‘junk’ implied lack of any discernible function of these RNA. More than 98% of the human genomic size encompasses these non-coding RNAs. But, recent research has evidently brought out the indispensible contribution of non-coding RNA in controlling and regulating gene expression. ncRNA such as siRNAs and microRNAs have been reported to greatly help in causing post-transcriptional gene silencing (PTGS) in cells through RNA interference (RNAi) pathway. In this work, we have investigated the possibility of using siRNAs and microRNAs to aid in gene silencing of early onset Alzheimer’s disease genes… More »»
2010 Journal Article M. S. Kumar, Purushothaman, D., K Gopal, V., Premkumar, P., Gopakumar, D., and Namboori, P. K. Krishnan, “Insilico Analysis of PAC-1 as an Enhancer for Caspase-3 to Promote Apoptosis”, International Journal of Biotechnology and Biochemistry, vol. 6, pp. 595–600, 2010.[Abstract]

Apoptosis is a selective process for deletion of cells. It is generally involved in embryogenesis, tissue remodeling and also to maintain organ size and function. Sequential activation of caspases plays an important role in programmed cell death. In the caspase family, caspase-3 is an important effector protease that cleaves many downstream proteins. Damage in apoptotic pathways promotes uncontrolled growth of cancer cell. Analyses on clinical researches indicate that anticancer drugs activate cascade of apoptotic pathways either by positively or negatively regulating cell death induction. PAC-1 is such a compound, synthesized chemically that selectively induces apoptosis in cancer cells. This article reviews the effect of PAC-1 computationally, as a promoter for caspase-3. Docking of caspase-3 proteins with the specific ligand i.e., compound PAC-1, showed high interaction. The result shows that the PAC-1 facilitates the activation of caspase-3 and thus promotes the activation of apoptotic pathways and prevents the uncontrolled proliferation of cancer cells. More »»
Publication Type: Book
Year of Publication Publication Type Title
2014 Book D. Gopakumar and Namboori, P. K. Krishnan, Bioinformatics Structural and Sequence Analysis. New Delhi: Narosa Publishers, 2014.[Abstract]

Bioinformatics, the application of computers in biological sciences and especially analysis of biological sequence data, is becoming an essential tool in molecular biology as genome projects generate vast quantities of data. With new sequences being added to DNA databases, on average, there is a vital requisite to convert this information into biochemical and biophysical knowledge by explaining the structural, functional of biological sequences. This book begins by introducing the most popular databases (protein and nucleic acid), information resources and analysis methods (sequence alignment and pattern recognition) currently available providing the basis for readers to progress to hands-on practical sequence analysis. It explains some basic algorithms in bioinformatics to readers who have exposure to computer science, mathematics, and statistics. The text also explains the structural bioinformatics that lies at the interface of structural biology and informatics, each of which derive their principles from highly interdisciplinary areas that goes beyond traditional bioinformatics knowledge.

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2008 Book KI Ramachandran, Deepa, G., and Namboori, P. K. Krishnan, Computational Chemistry and Molecular Modeling. Springer, 2008.[Abstract]

Computational chemistry and molecular modeling is a fast emerging area which is used for the modeling and simulation of small chemical and biological systems in order to understand and predict their behavior at the molecular level. It has a wide range of applications in various disciplines of engineering sciences, such as materials science, chemical engineering, biomedical engineering, etc. Knowledge of computational chemistry is essential to understand the behavior of nanosystems; it is probably the easiest route or ...

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Publication Type: Conference Paper
Year of Publication Publication Type Title
2011 Conference Paper P. Da Balakrishnan, Namboori, P. K. Krishnan, Devi, R. Rb, Gopal, K. Vb, and Kumar, A. Sb, “Computational study on metabolomic consequences of antifolate drug treatment and resistance in malarial organisms”, in ICECT 2011 - 2011 3rd International Conference on Electronics Computer Technology, Kanyakumari, 2011, vol. 4, pp. 75-78.[Abstract]

Antimalarial antifolates have been the central drugs for prophylaxis and treatment of malaria. Plasmodium falciparum readily develops resistance to the antifolates pyrimethamine and proguanil through a particular set of mutations in the dihydrofolate reductase (DHFR) gene that results in the less competitive drug binding at the site of the enzyme. Similar mutations can be found in the DHFR gene in Plasmodium vivax (DHFR) also. The aim of this research work is to reveal the interactions of the DHFR inhibitors with the target proteins and to investigate the effect of mutations computationally. Commonly used antifolate drugs against malaria such as trimethoprim, pyrimethamine, proguanil and WR99210 have been considered for the analysis. Proteins which are targeted by the antifolate drugs in malarial organisms have been identified and characterized. Interaction studies of the wild and mutated DHFR proteins with the known drugs have been made. It has been found that the ligand binding to mutated proteins is considerably low compared to that of the wild proteins in most of the cases except WR99210 drug. This discloses the inadequacy of the antifolate drugs and the need to improve the antimalarial antifolate in vivo effectiveness and to recognize powerful novel antifolate agents. From the interaction studies of antifolate drugs against the target DHFR in malarial parasites Plasmodium vivax and Plasmodium falciparum it has been identified that these parasites show resistance to the chemotherapeutic antifolate drugs. A combination of antifolate drugs can be effective against malarial parasites or a designing of a new antifolate drug. © 2011 IEEE. More »»
2011 Conference Paper S. Ca Pillai, Namboori, P. K. Krishnan, Kumar, N. C. Ab, Gopal, K. Vb, Kumar, A. Sb, and Bharath, Pb, “Investigating multi target drug action of aloe vera using computational analysis”, in Proceedings - 2011 2nd National Conference on Emerging Trends and Applications in Computer Science, NCETACS-2011, Shillong, 2011, pp. 174-177.[Abstract]

Aloe vera has an immense role as a natural fighter against all kinds of infection. This is an effective wound healing activator and an efficient anti-oxidant to all type of digestion related problems, arthritis, stress, diabetes, cancer and AIDS. The present study attempts to reveal the multi therapeutic properties of Aloe vera by computational analysis. The interaction analysis of the some of the derived phytochemicals with various targets including proteins involved in Alzheimer's and its role in curing such ailments has been examined. The interaction energy result suggests that Aloe emodin, Emodin, Aloin, Rhein, Coumarin, and Acemannan have an effective role in curing the pandemic conditions. The interaction anlaysis of Acemannan is greatest among all the results, suggesting that this ligand enhance the wound healing capacity. Acemannan was found to be a potent inhibitor of HIV virus replication. Anti inflammatory diseases like arthritis, asthma, hay fever can be cured to some extent by using Emodin, which is an efficient anti-inflammatory agent. Aloe Emodin can be used as an activator of apoptotic pathway in cancer cells as well as an anti sepsis agent. © 2011 IEEE. More »»
2010 Conference Paper P. Premkumar, Namboori, P. K. Krishnan, Gopakumar, D., Mohandas, V. P., and Radhagayathri, K. U., “In-silico characterization of multi walled carbon nanotubes (MWCNTS) to develop gas sensors”, in AIP Conference Proceedings, Guwahati, 2010, vol. 1276, pp. 302-306.[Abstract]

This paper reports the computational modeling and simulation of 'Multi walled carbon nanotube' (MWCNT) to characterize the adsorption of gases. The computational results were properly evaluated experimentally. CNT is known to undergo electrical breakdown on exposure to gases. This unique property has been used in designing CNT-based gas sensors. The electrical resistance of 'large diameter MWCNT' was found to decrease in the presence of air after experiencing electrical breakdown, while 'pristine MWCNTs' were not found to be appreciably sensitive. The deformation and the corresponding mechano electric effects of CNT have been well predicted. Composite electric field guided assembly (CEGA) method was used to locate a single MWCNT between electrodes. The electrical characteristics of the deposited MWCNTs were observed using I-V-curves. The large-diameter MWCNT showed better sensitivity as they possess more distorted shells that can create more adsorption sites for oxygen molecules. The oxidation of CNT begins in the defective or distorted region of the tube separated from the electrodes. The removal of complete shells including the contacts with the electrodes is observed as spikes in the I-V Graph plotted from experimental results. This observation can be due to the presence of two barriers for conductivity along the partially burnt or oxidized MWCNT, the Schottky barrier for carrier injection from the electrodes to the nanotubes and the barrier caused due to the hopping process. © 2010 American Institute of Physics. More »»
2010 Conference Paper A. Ranganath, Ashish, G., K. Gopal, V., Kutty, K. N., Namboori, P. K. Krishnan, and Gopakumar, D., “Quantum mechanical characterization of Single Walled Carbon Nanotube (SWCNT) to evaluate stability and conductivity”, in ACE 2010 - 2010 International Conference on Advances in Computer Engineering, Bangalore, 2010, pp. 39-42.[Abstract]

Single Walled Carbon Nanotube (SWCNT) is known to have unique thermodynamic and electrical properties which mainly depends upon the chiral index values (n, m). Quantum mechanical modeling and simulation studies were conducted for these samples to characterize the above properties. The energy gap of conducting carbon nano tubes has been found to be negligibly small. Armchair configuration with (n=m) is found to be highly stable. All these samples are found to be conducting. Structures with n and m values (8, 7), (7, 8), (7, 6), (7, 2), (6,5), (5,3) (4,5) and (3,5) are found to be unstable and are all semiconductors. © 2010 IEEE. More »»
2009 Conference Paper V. K Gopal, Vasavi, C. S., B, S. Narayanan, Ramachandran, K. I., Gopakumar, D., and Namboori, P. K. Krishnan, “Thermal Analysis of Nanofluids Using Modeling and Molecular Dynamics Simulation”, in International Conference on Artificial Neural Networks, 2009.
2009 Conference Paper A. Prakash, Arun, K. V., Rahul, M., Praveen, T. S., and Namboori, P. K. Krishnan, “Theoretical modeling of aluminium nanofluid to predict chemo-mechanical properties”, in Conference Proceedings RTCSP, Amrita Vishwa Vidyapeetham, Coimbatore, 2009.
2009 Conference Paper P. M. Rajasree and Namboori, P. K. Krishnan, “Characterizing properties of gold nanoparticles by molecular modeling and simulation techniques”, in Conference Proceedings RTCSP, Amrita Vishwa Vidyapeetham, Coimbatore, 2009.
Publication Type: Book Chapter
Year of Publication Publication Type Title
2011 Book Chapter C. R. Athira, Shilpa, S., Parvathy, C. M., Nithya, S., Vinothaa, V., Subashini, S. P., K Gopal, V., Parimalam, B., and Namboori, P. K. Krishnan, “Computational Characterization of CNT-Papain Interactions for Developing a Biosensor”, in Computer Networks and Information Technologies, Springer, 2011, pp. 553–556.[Abstract]

THC and its metabolites are detectable in body fluids and could be used to detect marijuana use. This research work reveals the possibility of using a carbon nano tube (CNT) based enzyme sensor for the detection of 9-carboxy tetrahydrocannabinol (9 THC-COOH) in urine using a cysteine protease obtained from papaya plant called papain. A comparative study of armchair and zigzag conformation of CNTs with the protein was carried out and the suitable conformer of CNT has been identified. The electrostatic energy variations and the thermodynamic energy differences of CNTs have been computed. A characteristic gradient in electrostatic potential has been identified for the CNT-protein complexes which could be effectively sensed using electrochemical sensors. The computational analysis of CNT-papain interaction supports the possibility of developing a biosensor using papain coated carbon nano tubes for the detection of THC-COOH in urine of the suspected marijuana consumed persons. A comparative analysis of the interaction energies of arm-chair and zig-zag conformations of carbon nano tubes with the cysteine protease enzyme papain has been carried out. The arm chair conformation with configuration index 18, 18 (m, n) has been identified as keeping the highest interaction energy of 45.218 kcal/mol. With this conformer designing of an electrochemical sensor has been suggested. More »»
2010 Book Chapter M. S. Kumar, Lainu, K. L., Aghila, V., Purushothaman, D., K Gopal, V., Namboori, P. K. Krishnan, and Harishankar, V., “Designing a Promotor for a Novel Target Site Identified in Caspases for Initiating Apoptosis in Cancer Cells”, in Information and Communication Technologies, Springer, 2010, pp. 62-67.[Abstract]

Caspases are enzymes that can cleave other proteins and control normal and abnormal cell death. Cancer cells generally lack apoptosis. In this research work, a computational approach has been adopted to design a promotor that targets the inactivated caspases particularly Pro-caspase-3 or caspase-7, which are the effector caspases that cleave the downstream substrates like lamin-A, ICAD and PARP. Out of the 38 anti-carcinomic compounds selected for the analysis, some of them are found to have positive charged substituents similar to the known drug; PAC1, which cleaves the safety catch mode that blocks the IETD active site. Site specific interactions of the proteins with these ligands were performed. From the interaction analysis, it was found that 3 compounds; Choline, Glaziovine, Dasatinib can effectively target caspases and activate them. It has been suggested that these compounds favor the activation of the effector caspase proteins, thereby giving a better option in cancer therapy. More »»
2010 Book Chapter C. S. Vasavi, R Devi, R., Anand, L., Varma, M. P., Namboori, P. K. Krishnan, and , “Homology Modeling and Protein Ligand Interaction to Identify Potential Inhibitor for E1 Protein of Chikungunya”, in Information and Communication Technologies, Springer, 2010.[Abstract]

Chikungunya fever is an overwhelming, but non-fatal viral illness that has been reported in many parts of the country. The E1 domain of Q1El92_CHIKV virus that helps in binding with the host has been determined by using comparative homology modeling program MODELLER based on crystal structure of the homotrimer of fusion glycoprotein E1 from Semliki Forest virus as a template protein and it had 63% sequence identity. The modeled structure‘s energy was minimized and validated using structure validation server in which 82.8% of the residues were present in the most favored regions of the Ramachandran plot. Disulphide bonds which help in protein folding of the proteins were analyzed and it was found to be conserved for both the homologous and the modeled structures. The ion pairs which contribute to fusion of viral membranes and that help in solvent protein interactions were analyzed. Docking studies was carried out with various phytochemicals and it was found that osltamivir had the most stable interaction with the E1 domain of the Q1El92_CHIKV virus. Thus from the complex scoring and binding ability it was interpreted that Osltamivir could be a promising inhibitor for E1 domain of Q1El92_CHIKV virus as the drug target yet pharmacological studies have to confirm it. More »»
Publication Type: Conference Proceedings
Year of Publication Publication Type Title
2010 Conference Proceedings P. Harilal, A Krishna, S., K Gopal, V., Jiyesh, M. M., Sankaranarayanan, A., and Namboori, P. K. Krishnan, “Machine learning approaches to determine the drug-likeness of the proteomic targets”, International Conference on Control Communication and Power Engineering - ACEEE. pp. 253-255, 2010.

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