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Clamp loaders ensure processive DNA replication by loading the toroidal shaped sliding clamps onto the DNA. The sliding clamps serve as a platform for the attachment of polymerases and several other proteins associated with the regulation of various cellular processes. Clamp loaders are fascinating as nanomachines that engage in protein-protein and protein-DNA interactions. The loading mechanism of the clamp around dsDNA at the atomic level has not yet been fully explored. We performed microsecond timescale molecular dynamics simulations to reveal the dynamics of two different intermediate complexes involved in loading of the clamps around DNA. We conducted various time-dependent MD-driven analyses including the highly robust Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) calculations to observe changes in the structural elements of the clamp loader-clamp-DNA complexes in open and closed states. Our studies revealed the structural consequences of ATP hydrolysis events at different subunits of the clamp loader. This study would help in a better understanding of the clamp loading mechanism and would allow tackling various complications that might arise due to irregularities in this process.

The enzyme Phosphodiesterase 10A (PDE10A) plays a regulatory role in the cAMP/protein kinase A (PKA) signaling pathway by means of hydrolyzing cAMP and cGMP. PDE10A emerges as a relevant pharmacological drug target for neurological conditions such as psychosis, schizophrenia, Parkinson's, Huntington’s disease, and other memory-related disorders. In the current study, we subjected a set of 1,2,3-triazoles to be explored as PDE10A inhibitors using diverse computational approaches, including molecular docking, classical molecular dynamics (MD) simulations, Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) calculations, steered MD, and umbrella sampling simulations. Molecular docking of cocrystallized ligands papaverine and PFJ, along with a set of in-house synthesized molecules, suggested that molecule 3i haded the highest binding affinity, followed by 3h and 3j. Furthermore, the structural stability studies using MD and MM-PBSA indicated that the 3h and 3j formed stable complexes with PDE10A. The binding free energy of −240.642 kJ/mol and −201.406 kJ/mol was observed for 3h and 3j, respectively. However, the cocrystallized ligands papaverine and PFJ exhibited comparitively higher binding free energy values of −202.030 kJ/mol and −138.764 kJ/mol, respectively. Additionally, steered MD and umbrella sampling simulations provided conclusive evidence that the molecules 3h and 3j could be exploited as promising candidates to target PDE10A. Communicated by Ramaswamy H. Sarma

The quick widespread of the coronavirus and speedy upsurge in the tally of cases demand the fast development of effective drugs. The uridine-directed endoribonuclease activity of nonstructural protein 15 (Nsp15) of the coronavirus is responsible for the invasion of the host immune system. Therefore, developing potential inhibitors against Nsp15 is a promising strategy. In this concern, the in silico approach can play a significant role, as it is fast and cost-effective in comparison to the trial and error approaches of experimental investigations. In this study, six turmeric derivatives (curcuminoids) were chosen for in silico analysis. The molecular interactions, pharmacokinetics, and drug-likeness of all the curcuminoids were measured. Further, the stability of Nsp15-curcuminoids complexes was appraised by employing molecular dynamics (MD) simulations and MM-PBSA approaches. All the molecules were affirmed to have strong interactions and pharmacokinetic profile. The MD simulations data stated that the Nsp15-curcuminoids complexes were stable during simulations. All the curcuminoids showed stable and high binding affinity, and these curcuminoids could be admitted as potential modulators for Nsp15 inhibition.

MEK1 is an attractive target due to its role in selective extracellular-signal-regulated kinase phosphorylation, which plays a pivotal role in regulating cell proliferation. Another benefit of targeting the MEK protein is its unique hydrophobic pocket that can accommodate highly selective allosteric inhibitors. To date, various MEK1 inhibitors have reached clinical trials against several cancers, but they were discarded due to their severe toxicity and low efficacy. Thus, the development of allosteric inhibitors for MEK1 is the demand of the hour. In this in-silico study, molecular docking, long-term molecular dynamics (5 µs), and molecular mechanics Poisson-Boltzmann surface area analysis were undertaken to address the potential of quinolines as allosteric inhibitors. We selected four reference MEK1 inhibitors for the comparative analysis. The drug-likeness and toxicity of these molecules were also examined based on their ADMET and Toxicity Prediction by Komputer Assisted Technology profiles. The outcome of the analysis revealed that the quinolines (4m, 4o, 4s, and 4n) exhibited better stability and binding affinity while being nontoxic compared to reference inhibitors. We have reached the conclusion that these quinoline molecules could be checked by experimental studies to validate their use as allosteric inhibitors against MEK1.

Malaria remains a deadliest disease brought about by Plasmodium species, among one of these species, disease due to Plasmodium falciparum (Pf) is life-threatening. The structures of PfLDH and human LDH are very similar in terms of L-LDH activity, and their biological functions are also equivalent. Therefore, any treatment aiming blocking the functions of PfLDH can affect human LDH. Thus, the main objective of this study is to identify the molecule that exhibits selectivity towards PfLDH without a profound effect on human LDH. In this research, a set of 68 quinolines based molecules were used for molecular docking. From molecular docking, we selected molecules 3j, 4b, 4h, 4m based on their binding affinity, ligand efficiency, lipophilic ligand efficiency, and torsion with selectivity towards PfLDH. The stability of the docked molecules was compared to Chloroquine (reference inhibitor) by applying molecular dynamics simulations and molecular mechanics poisson boltzmann surface area calculations. All the selected molecules showed selectivity for PfLDH with stable dynamic behavior and high binding free energy in comparison to Chloroquine. After examining the molecular mechanics poisson boltzmann surface area ratio results, molecule 3j was reported as a potential and specific inhibitor for PfLDH with a novel mechanism of binding to PfLDH while the remaining molecules 4b, 4h, 4m could further be modified to be used as potent inhibitors against malarial infection.

Cyclin-dependent kinases (CDKs) are known for their vital role in regulating cell cycle progression through protein-kinase interactions. CDKs also help in regulating transcription and development of the central nervous system. Inhibition of CDKs is a very fundamental approach for drug discovery in areas of different types of cancers, Alzheimer's, and HIV infections. The present research focuses on finding a novel, potent, and specific natural inhibitors of CDK isoforms (CDK2, CDK5, CDK7, CDK9). Molecular docking, molecular dynamics (MD) simulations, and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) were carried out to get an in-depth understanding of protein-ligand interactions. Based on our molecular docking results, Ligands-3, 5, 14, and 16 were screened among 17 different Pyrrolone-fused benzosuberene compounds as potent and specific inhibitors without any cross-reactivity against different CDK isoforms. Analysis of MD simulations and MM-PBSA studies, revealed the binding energy profiles of all the selected complexes. Our selected ligands performed better than the standard inhibitor (Roscovitine). Ligands-3 and 14 show specificity for CDK7 and Ligands-5 and 16 were specific against CDK9. These ligands are expected to possess lower risk of side effects due to their natural origin. Moreover, the backbone structure of these ligands could also be exploited to develop specific inhibitors against other CDK isoforms.Communicated by Ramaswamy H. Sarma.

Graphical abstract, Highlights • Nsp15 is involved in viral replication and suppression of host immune response. • Three bioactive molecules of tea showed high binding affinity with Nsp15. • The molecules selected on basis of robust MD simulations and MMPBSA calculations. • Tea bioactive molecules could be developed as inhibitors of Nsp15 to fight the virus., Immensely aggravated situation of COVID-19 has pushed the scientific community towards developing novel therapeutics to fight the pandemic. Small molecules can possibly prevent the spreading infection by targeting specific vital components of the viral genome. Non-structural protein 15 (Nsp15) has emerged as a promising target for such inhibitor molecules. In this investigation, we docked bioactive molecules of tea onto the active site of Nsp15. Based on their docking scores, top three molecules (Barrigenol, Kaempferol, and Myricetin) were selected and their conformational behavior was analyzed via molecular dynamics simulations and MMPBSA calculations. The results indicated that the protein had well adapted the ligands in the binding pocket thereby forming stable complexes. These molecules displayed low binding energy during MMPBSA calculations, substantiating their strong association with Nsp15. The inhibitory potential of these molecules could further be examined by in-vivo and in-vitro investigations to validate their use as inhibitors against Nsp15 of SARS-CoV2.

The coronavirus disease (COVID-19), a worldwide pandemic, is caused by the severe acute respiratory syndrome-corona virus-2 (SARS-CoV-2). At this moment in time, there are no specific therapeutics available to combat COVID-19. Drug repurposing and identification of naturally available bioactive molecules to target SARS-CoV-2 are among the key strategies to tackle the notorious virus. The enzyme RNA-dependent RNA polymerase (RdRp) performs a pivotal role in replicating the virus. RdRp is a prime target for Remdesivir and other nucleotides analog-based antiviral drugs. In this study, we showed three bioactive molecules from tea (epicatechin-3,5-di-O-gallate, epigallocatechin-3,5-di-O-gallate, and epigallocatechin-3,4-di-O-gallate) that showed better interaction with critical residues present at the catalytic center and the NTP entry channel of RdRp than antiviral drugs Remdesivir and Favipiravir. Our computational approach to identify these molecules included molecular docking studies, followed by robust molecular dynamics simulations. All the three molecules are readily available in tea and could be made accessible along with other medications to treat COVID-19 patients. However, these results require validation by furtherin vitroandin vivostudies.

Benzosuberene compounds with a pyrrolone group adhered to it are compounds extracted from the oils of Cedrus deodara plant, that bear inhibitory capabilities. Tobacco mosaic virus is known to affect crop production every year. The currently known inhibitors against TMV have a weak inhibition effect and also tend to be toxic towards non-target living organisms as well as the environment. Thus, the requirement of non-toxic potent inhibitors is the need of the hour, which led us to test our benzosuberene molecules on the binding site of TMV and check their affinity as well as stability. The non-toxic nature of these molecules has already been experimentally established. Through in-silico analysis involving docking and simulation experiments, we compared the interaction pattern of these ligand molecules with the already present inhibitors. Our investigation proved that the reported ligands (ligands 3, 7, 9, and 17 obtained −177.103, −228.632, −184.134, and − 188.075 kJ/mol binding energies, respectively) interacted with the binding site of TMV much efficiently than the known inhibitors (Ribavirin and Zhao et al. 2020 obtained 121.561 and − 221.393 kJ/mol binding energies, respectively). Moreover, they acquired a stable conformation inside the binding pocket, where a higher number of binding site residues contributed towards interaction. Thus, their structural framework can be optimized for the exploration of their antiviral properties to develop potent botanical viricides against plant virus infection.

The human immunodeficiency virus interacts with the cluster of differentiation 4 receptors and one of the two chemokine receptors (CCR5 and CXCR4) to gain entry in human cells. Both the co-receptors are essential for viral entry, replication, and are considered critical targets for antiviral drugs. In this study, bioactive molecules from different Himalayan plants were screened considering their potential to bind with the CCR5 and CXCR4 co-receptors. We utilized computational and thermodynamic parameters to validate the binding of the selected biomolecules to the active site of the co-receptors. The molecules Butyl 2-ethylhexyl phthalate and Dactylorhin-A showed a higher binding affinity with CCR5 co-receptor than the standard antagonist Maraviroc. Moreover, Pseudohypericin, Amarogentin, and Dactylorhin-E exhibited stronger interactions with CXCR4 than the co-crystallized inhibitor Isothiourea-1 t. Hence, we suggest that these molecules could be developed as potential inhibitors of the CCR5 and CXCR4 co-receptors. However, this require further in-vitro and in-vivo validation.

Aurora-A is a novel therapeutic target that belongs to the serine/threonine kinase family of proteins. Several cancers are associated with gene amplification or over-expression of Aurora-A. The somatic mutation (S155R) in Aurora-A results in a loss of interaction with its binding partner TPX2. The S155R mutation thus leads to ectopic expression of Aurora-A, resulting in centrosome amplification, chromosomal instability, aneuploidy, and oncogenic transformations. In order to restore the interaction between mutant Aurora-A and TPX2, we predicted a binding pocket in the interface of the Aurora-A-TPX2 complex. We performed molecular docking of potential bioactive molecules of the Himalayan region at the predicted site. Alantolactone and Dactylose-A were selected as potential molecules that could bind to the interface pocket and restore the lost interaction between mutant Aurora-A and TPX2. The molecular docking results were validated by performing explicit long term molecular dynamics simulations (4.0 μs) and MM-PBSA analysis. The molecular dynamics results confirmed that both the selected molecules could act as potent drugs to tackle the abnormal expression of Aurora-A manifested due to the somatic mutation (S155R). [Formula: see text] Communicated by Ramaswamy H. Sarma.

γ-aminobutyric acid, being a principle neuromediator in humans controlling the inhibition signals, acts on the ligand-gated pentameric type A receptors to transmit their response. Any dysfunction of these receptors leads to neurological disorders and mental illness. Benzodiazepine has been used extensively for the treatment of these disorders, which shows its effect by reducing the threshold concentration of γ-aminobutyric acid required to activate the receptor. Being a central nervous system depressant, benzodiazepine is also a common substance of abuse along with other recreational drugs that show affinity towards the benzodiazepine binding site. Flumazenil is considered the first line of treatment for the overdose of these substances, which competes with them to bind with the receptor having a higher binding affinity towards the receptor. Like most of the synthetic drugs, Flumazenil also has some side-effects associated with it. Here we focus our work towards finding specific naturally originated antagonist of the benzodiazepine binding site to suggest an alternative for Flumazenil by performing various computational analysis like docking experiments followed by simulations and molecular mechanics poisson-boltzmann surface area analysis. Molecular docking experiments filtered out four ligand molecules specific for the benzodiazepine binding site, namely, ligand-1,7,9 and 17. Further, molecular dynamics simulations showed ligand-17 to have stable conformation in the binding site as well as a lower binding free energy as compared to Flumazenil. Due to its natural origin, ligand-17 is supposed to have lower side effects; therefore, its backbone can be further explored to develop specific antagonists of benzodiazepines. Communicated by Ramaswamy H. Sarma.

Stevioside is a natural non-caloric sweetener obtained from Stevia rebaudiana Bertoni plant. The major challenge in the commercialization of stevioside as a natural sweetener is its bitter-off taste. In this study, we prepared molecular models of potential taste receptors of stevioside, both sweet and bitter. With appropriate modifications on the stevioside backbone, we performed molecular docking of prepared ligands with both sweet and bitter taste receptors. Based on binding energy, we found that one of the potential substituents, Kamiya-8, shows a good affinity towards sweet taste and a weak affinity for bitter receptors. Further, we selected Kamiya-8 for molecular dynamics simulations to improve the prediction of binding energy and to check the binding strength of Kamiya-8 with taste receptors. Moreover, we also performed MM-PBSA calculation for calculating the end state free energies of molecules in solvent and found that Kamiya-8 gives a 2-fold effect as it interacts with sweet receptors (T1R2, T1R3) with lowest binding energy conformation (−285.265 kcal/mol, −571.481 kcal/mol). Secondly, it gives high binding energy (–273.319 kcal/mol, −355.500 kcal/mol) with bitter taste receptors (T2R4, T2R14) as compared to stevioside. Based on this study, we found that Kamiya-8 can be the potential substituent that can improve the palatability of stevioside.

From bacteria to mammals, DNA mismatch repair (MMR) pathway plays an essential role in eliminating mismatched nucleotides and insertion-deletion mismatches during the process of DNA replication. Among many of the proteins which participate in the mismatch repair process, proliferating cell nuclear antigen (PCNA) remains the principal conductor at the replication fork. The pol30-201 and pol30-204 are the two mutated alleles which encode for C22Y and C81R mutant forms of PCNA proteins. We performed long term molecular dynamics (MD) simulations analysis (0.8 μs) to understand the dynamic behavior and alterations in the structure of wild type and mutated forms of PCNA at the atomic level. We observed changes in the structural characteristics like length, radius, rise per residue of alpha helices in both the mutated forms of PCNA. Apart from it, disfigurement of the charge distribution which effects binding with the dsDNA due to mutant C22Y and other structural perturbations were also seen in regions significant for the formation of a biologically active trimeric form of PCNA due to mutant C81R. Our analysis of native and mutated forms of PCNA provides an insight into the essential structural and functional features required for proper and well-coordinated DNA mismatch repair process and consequences of the mutation leading to an impaired process of MMR. These structural characteristics are fundamental for the MMR process and hence our analysis likely contributes to or presents the novel mechanism involved in the process of MMR.Communicated by Ramaswamy H. Sarma.

Huntington's disease (HD) is a neurodegenerative disorder that is caused by an abnormal elongation of the polyglutamine (polyQ) chain in the Huntington (Htt) protein. At present, the normal function of Htt of neurons as well as the mechanism by which selective neurodegeneration is caused by the expanded polyQ chain in Htt remains ambiguous. A gain of function as a result of the elongated polyQ chain can lead to abnormal interaction of the Htt protein with its interacting partners, thereby resulting in the neuropathological changes seen in the Huntington's disease. Recent research indicates protein kinase C and casein kinase substrate in neurons protein 1 (PACSIN1) as one of the interacting partners of Htt protein. It has proven experimentally that the mutant Htt and PACSIN1 formed aggregates in the cytoplasm. This aggregation is believed to be a cause for Huntington's disease. In our study, we performed in silico investigations to predict the biomolecular mechanism of Htt/PACSIN1 interaction that could be one of the major triggers of the disease. Biomolecular interaction and molecular dynamics simulation analysis were performed to understand the dynamic behavior of native and mutant structures at the atomic level. Mutant Htt showed more interaction with its biological partner than the native Htt due to its expansion of interaction surface and flexible nature of binding residues. Our investigation of native and mutant Htt clearly shows that the structural and functional consequences of the polyQ elongation cause HD. Because of the central role of the Htt-PACSIN1 complex in maintaining connections between neurons, these differences likely contribute to the mechanism responsible for HD progression.

In this study, we analyzed Coat protein (CP) of Apple chlorotic leaf spot virus (ACLSV), an important latent virus on Apple. Incidence of the virus is upto 60% in various apple cultivars, affecting yield losses of the order of 10–40% (depending upon the cultivar). CP plays an important role as the sole building block of the viral capsid. Homology approach was used to model 193 amino acid sequence of the coat protein. We used various servers such as ConSurf, TargetS, OSML, COACH, COFACTOR for the prediction of active site residues in coat protein. Virtual screening strategy was employed to search potential inhibitors for CP. Top twenty screened molecules considered for drugability, and toxicity analysis and one potential molecule was further analyzed by docking analysis. Here, we reported a potent molecule which could inhibit the formation of viron assembly by targeting the CP protein of virus.

The CEP genes play a pivotal role in the replication of the cell. CEP family proteins form the major constituents of the centrosome and play a prominent role in centriole biogenesis and in cell replication. Alteration in CEP genes will result in disruption of cell cycle that may in turn cause cancer. In our study, we found that 16 of the CEP genes are a potential target to miRNA that binds to complementary sequences in 3'untranslated regions (UTR) of mRNA and stop them from translation. Single nucleotide polymorphisms (SNPs) occurring naturally in such miRNA binding site can alter the miRNA: mRNA interaction and can significantly alter gene expression. We developed a systematic computational pipeline that integrates data from well-established databases, followed stringent selection criteria and identified a panel of 44 high-confidence SNPs that may impair miRNA target sites in the 3'UTR of 16 genes. Further we performed expression analysis to shed light on the potential tissues that might be affected by mutation, enrichment analysis to find the metabolic functions of the gene, and network analysis to highlight the important interactions of CEP genes with other genes to provide insight that complex network will be disturbed upon mutation. In this study, we explored and prioritised the SNPs in CEP gene which could act as a potential target in centrosome-associated human disease. Our analysis would provide a thoughtful insight to wet lab researches to understand the expression pattern of CEP genes and binding phenomenon of mRNA and miRNA upon mutation, which is responsible for inhibition of translation process at genomic levels.

Albinism is an autosomal recessive genetic disorder due to low secretion of melanin. The oculocutaneous albinism (OCA) and ocular albinism (OA) genes are responsible for melanin production and also act as a potential targets for miRNAs. The role of miRNA is to inhibit the protein synthesis partially or completely by binding with the 3'UTR of the mRNA thus regulating gene expression. In this analysis, we predicted the genetic variation that occurred in 3'UTR of the transcript which can be a reason for low melanin production thus causing albinism. The single nucleotide polymorphisms (SNPs) in 3'UTR cause more new binding sites for miRNA which binds with mRNA which leads to inhibit the translation process either partially or completely. The SNPs in the mRNA of OCA and OA genes can create new binding sites for miRNA which may control the gene expression and lead to hypopigmentation. We have developed a computational procedure to determine the SNPs in the 3'UTR region of mRNA of OCA (TYR, OCA2, TYRP1 and SLC45A2) and OA (GPR143) genes which will be a potential cause for albinism. We identified 37 SNPs in five genes that are predicted to create 87 new binding sites on mRNA, which may lead to abrogation of the translation process. Expression analysis confirms that these genes are highly expressed in skin and eye regions. It is well supported by enrichment analysis that these genes are mainly involved in eye pigmentation and melanin biosynthesis process. The network analysis also shows how the genes are interacting and expressing in a complex network. This insight provides clue to wet-lab researches to understand the expression pattern of OCA and OA genes and binding phenomenon of mRNA and miRNA upon mutation, which is responsible for inhibition of translation process at genomic levels.

Amyotrophic lateral sclerosis 6 (ALS6) is an autosomal recessive disorder caused by heterozygous mutation in the Fused in Sarcoma (FUS) gene. ALS6 is a neurodegenerative disorder, which affects the upper and lower motor neurons in the brain and spinal cord, resulting in fatal paralysis. ALS6 is caused by the genetic mutation in the proline/tyrosine-nuclear localization signals of the Fused in sarcoma Protein (FUS). FUS gene also known as TLS (Translocated in liposarcoma), which encodes a protein called RNA-binding protein-Fus (FUS), has a molecular weight of 75 kDa. In this analysis, we applied computational approach to filter the most deleterious and neurodegenerative disease of ALS6-associated mutation on FUS protein. We found H517Q as most deleterious and disease associated using PolyPhen 2.0, I-Mutant 3.0, SIFT, SNPsGO, PhD-SNP, Pmut, and Mutpred tools. Molecular dynamics simulation (MDS) approach was conducted to investigate conformational changes in the mutant protein structure with respect to its native conformation. MDS results showed the flexibility loss in mutant (H517Q) FUS protein. Due to mutation, FUS protein became more rigid in nature and might alter the structural and functional behavior of protein and play a major role in inducing ALS6. The results obtained from this investigation would help in the field of pharmacogenomics to develop a potent drug target against FUS-associated neurodegenerative diseases.

The computational approaches in determining disease-associated Non-synonymous single nucleotide polymorphisms (nsSNPs) have evolved very rapidly. Large number of deleterious and disease-associated nsSNP detection tools have been developed in last decade showing high prediction reliability. Despite of all these highly efficient tools, we still lack the accuracy level in determining the genotype-phenotype association of predicted nsSNPs. Furthermore, there are enormous questions that are yet to be computationally compiled before we might talk about the prediction accuracy. Earlier we have incorporated molecular dynamics simulation approaches to foster the accuracy level of computational nsSNP analysis roadmap, which further helped us to determine the changes in the protein phenotype associated with the computationally predicted disease-associated mutation. Here we have discussed on the present scenario of computational nsSNP characterization technique and some of the questions that are crucial for the proper understanding of pathogenicity level for any disease associated mutations.

Computational prediction of disease-associated non-synonymous polymorphism (nsSNP) has provided a significant platform to filter out the pathological mutations from large pool of SNP datasets at a very low cost input. Several methodologies and complementary protocols have been previously implemented and has provided significant prediction results. Although the previously implicated prediction methods were capable of investigating the most likely deleterious nsSNPs, but due to the lack of genotype-phenotype association analysis, the prediction results lacked in accuracy level. In this work we implemented the computational compilation of protein conformational changes as well as the probable disease-associated phenotypic outcomes. Our result suggested E403K mutation in mitotic centromere-associated kinesin protein as highly damaging and showed strong concordance to the previously observed colorectal cancer mutations aggregation tendency and energy value changes. Moreover, the molecular dynamics simulation results showed major loss in conformation and stability of mutant N-terminal kinesin-like domain structure. The result obtained in this study will provide future prospect of computational approaches in determining the SNPs that may affect the native conformation of protein structure and lead to cancer-associated disorders.

Determining the deleterious non-synonymous single nucleotide polymorphisms (nsSNPs), that might be involved in inducing disease-associated phenomena, is now among the most important field of computational genomic research. The rapid evolution in sequencing technologies has now outranged the limit of available sequence databases and has out-fledged the amount of SNP data that are yet to be characterized. In this article we have performed a comprehensive analysis of deleterious nsSNPs in MyH7 gene associated with cardiomyopathy cases using a set of computational platforms. We implemented a set of computational SNP analysis platforms along with the Bayesian calculations in order to filter the most likely mutation that might be associated with cardiomyopathy associated disorders. The Bayesian calculation depicted 27 fold rises in the likelihood score for causing cardiomyopathy disorder when MyH7 gene mutations were compiled. Furthermore, we reported E466Q mutation in MyH7 motor domain that showed increase in the amyloid propensity of protein, as well as a significant level of pathogenicity was also observed. The prediction roadmap followed in this article has showed a notable range of accuracy and can be used for determining cardiomyopathy associated nsSNPs for other candidate genes.

CK1δ (Casein kinase I isoform delta) is a member of CK1 kinase family protein that mediates neurite outgrowth and the function as brain-specific microtubule-associated protein. ATP binding kinase domain of CK1δ is essential for regulating several key cell cycle signal transduction pathways. Mutation in CK1δ protein is reported to cause cancers and affects normal brain development. S97C mutation in kinase domain of CK1δ protein has been involved to induce breast cancer and ductal carcinoma. We performed molecular docking studies to examine the effect of this mutation on its ATP-binding affinity. Further, we conducted molecular dynamics simulations to understand the structural consequences of S97C mutation over the kinase domain of CK1δ protein. Docking results indicated the loss of ATP-binding affinity of mutant structure, which were further rationalized by molecular dynamics simulations, where a notable loss in 3-D conformation of CK1δ kinase domain was observed in mutant as compared to native. Our results explained the underlying molecular mechanism behind the observed cancer associated phenotype caused by S97C mutation in CK1δ protein.

Centrosomes are the key-regulating element of cell cycle progression. Aberrations in their functional mechanism lead to several cancer-related disorders. Aurora A protein is a centrosome-associated protein that regulates the centriole duplication and its abberations are associated with multiple cases of aneuploidy and cancer-related disorders. S155R mutation in Aurora A is reported to induce cancer like phenotype and disrupt its binding with TPX2 protein. In this study, we have demonstrated the structural consequences of Aurora A S155R mutation and the atomic changes that influenced the loss of TPX2-binding affinity. Docking and molecular dynamics simulation results suggested significant loss in atomic contacts between mutant Aurora A and TPX2 protein. Further, we observed a notable changes in conformation of mutant Aurora A-TPX2 docked complex as compared to the native. Loss of binding affinity rendered the TPX2 domain free which then induced unfolding in its coiled region and enabled the overall expansion of mutant complex as compared to the native. The significant outcomes obtained from this study will facilitate in future cancer researches and in developing the potent drug therapies.

A point mutation (P29S) in the RAS-related C3 botulinum toxin substrate 1 (RAC1) was considered to be a trigger for melanoma, a form of skin cancer with highest mortality rate. In this study, we have investigated the pathogenic role of P29S based on the conformational behavior of RAC1 protein toward guanosine triphosphate (GTP). Molecular interaction, molecular dynamics trajectory analysis (RMSD, RMSF, Rg, SASA, DSSP, and PCA), and shape analysis of binding pocket were performed to analyze the interaction energy and the dynamic behavior of native and mutant RAC1 at the atomic level. Due to this mutation, the RAC1 switch I region acquired more flexibility and, to compensate it, the switch II region becomes rigid in their conformational space, as a result of which the interaction energy of the protein for GTP increased. The overall results strongly implied that the changes in atomic conformation of the switch I and II regions in mutant RAC1 protein were a significant reason for its malignant transformation and tumorigenesis. We raised the opportunity for researchers to design possible therapeutic molecule by considering our findings.

Centrosomes are central regulators of mitosis that are often amplified in cancer cells. Centrosomal protein of 63 kDa (CEP63) is a centrosomal protein that has an effective role in mitotic spindle assembly and cell cycle regulation. Genetic alterations in CEP63 coding gene has been widely studied for inducing aneuploidy and solid tumors in humans. The nonsynonymous single nucleotide polymorphisms (nsSNPs) are a genetic variant resulting in amino acid substitution and are reported in a wide range of human diseases. Here we report one new SNP (rs112926188) in a CEP63 coding region that can potentially disrupt the structure and basic functionality of a CEP63 protein. We used extensive functional and structural level analyses of an available SNP in a CEP63 coding gene. Furthermore the disease-association analysis was carried out to examine the possible pathogenic variant among the available dataset. To understand atomic arrangement in 3D space, native and pathogenic mutant structures were modeled. Molecular dynamics simulations were performed to understand structural consequences of prioritized deleterious mutation. Our analysis showed that rs112926188 allele substituting proline at the 61st residue position (L61P) produced more flexibility in 3D space. Moreover the flexible nature of mutant L61P was validated by a hydrogen bond network. This nature of mutant L61P CEP63 may restrict the recruitment of essential centrosomal proteins to their respective location and may play an active role in inducing aneuploidy.

Genetic variations in oncogenes can often promote uncontrolled cell proliferation by altering the structure of the encoded protein, thereby altering its function. The PI3KCA oncogene that encodes for p110α, the catalytic subunit of phosphatidylinositol 3-kinase (PI3K), is one the most frequently mutated oncogenes in humans. PI3K plays a pivotal role in cell division. PI3K consists of two subunits: the catalytic (p110α) and regulatory (p85α). The regulatory subunit usually controls the catalytic subunit and switches off the enzyme when not required. It is believed that mutations in PI3KCA gene can alter the control of p85α over p110α and can sustain p110α in a prolonged active state. This in turn results in uncontrolled cell division. In this study, we investigate the pathogenic role of two point mutations: E542K and E545K on p110α subunit and how they alter its binding with the regulatory subunit. Molecular interaction and molecular dynamic simulation analysis are performed to study the dynamic behaviour of native and mutant structures at atomic level. Mutant p110α showed less interaction with its regulatory partner p85α than the native did, due to its expanded and rigid structure. Our analysis clearly points out that the structural and functional consequences of the mutations could promote tumour proliferation.

Drug resistant mutations have severely restricted the success of HIV therapy. These mutations frequently involve the aspartic protease encoded by the virus. Knowledge of the molecular mechanisms underlying the conformational changes of HIV-1 protease mutants may be useful in developing more effective and longer lasting treatment regimes. The flap regions of the protease are the target of a particular type of mutations occurring far from the active site, which are able to produce significant resistance against the anti-HIV drug TMC-114. We provide insight into the molecular basis of TMC-114 resistance major flap mutations (I50V and I54M) in HIV-1 protease. It reports the shape complementarity and receptor-ligand interaction analysis supported by unrestrained all-atom molecular dynamics simulations of wild and major flap mutants of HIV-1 protease that sample large conformational changes of the flaps and active site binding residues. Both resistant flap mutants showed less atomic interaction toward TMC-114 and more structural deviation compared to wild HIV-protease. It is due to increasing flexibility at TMC-114 binding cavity and deviation of binding residues in 3-D space. Distortion in binding cavity and deviation in binding residues are the result of alteration in hydrogen bonding. Flap region also exhibited similar behaviour due to changes in number of hydrogen bonds during simulations.

We have investigated and highlighted the behavior of binding residue, Asp25 by computational analysis, which play an important role in understanding docking process with drug molecule, Ritonavir (Norvir®) and the flexibility nature of the Human Immunodeficiency Virus-1 (HIV-1) protease enzyme. It is well known that Ritonavir is a potent and a selective HIV-1 protease inhibitor. Molecular dockings were performed in order to gain insights regarding the binding mode of this inhibitor. In our analysis, we observed Ritonavir had different rank orders of scores against different mutant of this enzyme. Asp25 of the enzyme was found to be the active site for all the mutants. The results clearly suggest that Ritonavir is not able to appropriately bind at the active site of each HIV-1 protease mutant due to RMSD difference of the amino acid (Asp) at the position 25 of all mutants. These findings support the concept that 3D space of active site is a qualitative assessment for binding affinity of inhibitor with an enzyme. The investigation on the flexibility nature of Asp25 by normal mode analysis, show that binding residue posses less flexibility due to its solvation potential. The overall analysis of our study brings clarity to the binding behavior with respect to the different mutants with Ritonavir on the basis RMSD and also on the flexible nature of HIV-1 protease enzyme with respect to Asp25 position.

Huntington's disorder (HD), caused by mutations of the IT-15 gene, is an autosomal genetic disease that causes the breakdown of the nerve cells in the brain. The IT-15 gene encodes the huntingtin (Htt) protein. Htt, along with its interacting partners, are involved in maintaining proper communication among neurons. Our work is based on the interaction behavior between Htt (in three polyglutamine (polyQ) states that is Htt 0Q, 17Q and 36Q) and SH3GL3 interacting protein by using computational methods. We used the HADDOCK docking platform to find out the extent of interaction between Htt polyQ models and SH3GL3. The Htt36Q (mutated) showed higher interaction than Htt17Q (native) with SH3GL3. Molecular dynamics simulation was performed to uncover the structural fluctuations of polyQ models and their complexes. RMSD, Rg, SASA, and total interaction energy graph showed significant results, where as mutant Htt showed higher fluctuations and flexibility than native Htt. The increase in the length of polyQ was found to affect the stability, flexibility, and compactness of the protein and its complex. Our research provided a propitious approach to understand the consequence of polyglutamination in Htt and its relation with HD.

Oculocutaneous albinism (OCA) is an autosomal recessive disorder caused by either complete lack of or a reduction of melanin biosynthesis in the melanocytes. The OCA1A is the most severe type with a complete lack of melanin production throughout life, while the milder forms OCA1B, OCA2, OCA3, and OCA4 show some pigment accumulation over time. Mutations in TYR, OCA2, TYRP1, and SLC45A2 are mainly responsible for causing oculocutaneous albinism. Recently, two new genes SLC24A5 and C10orf11 are identified that are responsible to cause OCA6 and OCA7, respectively. Also a locus has been mapped to the human chromosome 4q24 region which is responsible for genetic cause of OCA5. In this paper, we summarized the clinical and molecular features of OCA genes. Further, we reviewed the screening of pathological mutations of OCA genes and its molecular mechanism of the protein upon mutation byin silicoapproach. We also reviewed TYR (T373K, N371Y, M370T, and P313R), OCA2 (R305W), TYRP1 (R326H and R356Q) mutations and their structural consequences at molecular level. It is observed that the pathological genetic mutations and their structural and functional significance of OCA genes will aid in development of personalized medicine for albinism patients.

AKT1, a serine/threonine-protein kinase also known as AKT kinase, is involved in the regulation of various signalling downstream pathways including metabolism, cell proliferation, survival, growth, and angiogenesis. The AKT kinases pathway stands among the most important components of cell proliferation mechanism. Several approaches have been implemented to design an efficient drug molecule to target AKT kinases, although the promising results have not been confirmed. In this paper we have documented the detailed molecular insight of AKT kinase protein and proposed a probable doxorubicin based approach in inhibiting miR-21 based cancer cell proliferation. Moreover, the inhibition of miR-21 activation by raising the FOXO3A concentration seems promising in reducing miR-21 mediated cancer activation in cell. Furthermore, the use of next generation sequencing and computational drug design approaches will greatly assist in designing a potent drug molecule against the associated cancer cases.

Oculocutaneous albinism type III (OCA3), caused by mutations of TYRP1 gene, is an autosomal recessive disorder characterized by reduced biosynthesis of melanin pigment in the hair, skin, and eyes. The TYRP1 gene encodes a protein called tyrosinase-related protein-1 (Tyrp1). Tyrp1 is involved in maintaining the stability of tyrosinase protein and modulating its catalytic activity in eumelanin synthesis. Tyrp1 is also involved in maintenance of melanosome structure and affects melanocyte proliferation and cell death. In this work we implemented computational analysis to filter the most probable mutation that might be associated with OCA3. We found R326H and R356Q as most deleterious and disease associated by using PolyPhen 2.0, SIFT, PANTHER, I-mutant 3.0, PhD-SNP, SNP&GO, Pmut, and Mutpred tools. To understand the atomic arrangement in 3D space, the native and mutant (R326H and R356Q) structures were modelled. Finally the structural analyses of native and mutant Tyrp1 proteins were investigated using molecular dynamics simulation (MDS) approach. MDS results showed more flexibility in native Tyrp1 structure. Due to mutation in Tyrp1 protein, it became more rigid and might disturb the structural conformation and catalytic function of the structure and might also play a significant role in inducing OCA3. The results obtained from this study would facilitate wet-lab researches to develop a potent drug therapies against OCA3.

Members of the novel SH2-containing protein (NSP3) and Crk-associated substrate (p130Cas) protein families form a multi-domain signalling platforms that mediate cell signalling process. We analysed the damaging consequences of three mutations, each from NSP3 (NSP3(L469R), NSP3(L623E), NSP3(R627E)) and p130Cas (p130Cas(F794R), p130Cas(L787E), p130Cas(D797R)) protein with respect to their native biological partners. Mutations depicted notable loss in interaction affinity towards their corresponding biological partners. NSP3(L469R) and p130Cas(D797R) mutations were predicted as most prominent in docking analysis. Molecular dynamics (MD) studies were conducted to evaluate structural consequences of most prominent mutation in NSP3 and p130Cas obtained from the docking analysis. MD analysis confirmed that mutation in NSP3(L469R) and p130Cas(D797R) showed significant structural deviation, changes in conformations and increased flexibility, which in turn affected the binding affinity with their biological partners. Moreover, the root mean square fluctuation has indicated a rise in fluctuation of residues involved in moderate interaction acquired between the NSP3 and p130Cas. It has significantly affected the binding interaction in mutant complexes. The results obtained in this work present a detailed overview of molecular mechanisms involved in the loss of cell signalling associated with NSP3 and p130Cas protein.

Centrosome forms the backbone of cell cycle progression mechanism. Recent debates have occurred regarding the essentiality of centrosome in cell cycle regulation. CEP family protein is the active component of centrosome and plays a vital role in centriole biogenesis and cell cycle progression control. A total of 31 proteins have been categorized into CEP family protein category and many more are under candidate evaluation. Furthermore, by the recent advancements in genomics and proteomics researches, several new CEP proteins have also been characterized. Here we have summarized the importance of CEP family proteins and their regulation mechanism involved in proper cell cycle progression. Further, we have reviewed the detailed molecular mechanism behind the associated pathological phenotypes and the possible therapeutic approaches. Proteins such as CEP57, CEP63, CEP152, CEP164, and CEP215 have been extensively studied with a detailed description of their molecular mechanisms, which are among the primary targets for drug discovery. Moreover, CEP27, CEP55, CEP70, CEP110, CEP120, CEP135, CEP192, CEP250, CEP290, and CEP350 also seem promising for future drug discovery approaches. Since the overview implicates that the overall researches on CEP proteins are not yet able to present significant details required for effective therapeutics development, thus, it is timely to discuss the importance of future investigations in this field.

Oculocutaneous albinism type 1A (OCA1A) is the most severe form of albinism characterized by a complete lack of melanin production throughout life and is caused by mutations in the TYR gene. TYR gene codes tyrosinase protein to its relation with melanin formation by knowing the function of these SNPs. Based on the computational approaches, we have analyzed the genetic variations that could change the functional behaviour by altering the structural arrangement in TYR protein which is responsible for OCA1A. Consequences of mutation on TYR structure were observed by analyzing the flexibility behaviour of native and mutant tyrosinase protein. Mutations T373K, N371Y, M370T and P313R were suggested as high deleterious effect on TYR protein and it is responsible for OCA1A which were also endorsed with previous in vivo experimental studies. Based on the quantitative assessment and flexibility analysis of OCA1A variants, T373K showed the most deleterious effect. Our analysis determines that certain mutations can affect the dynamic properties of protein and can lead to disease conditions. This study provides a significant insight into the underlying molecular mechanism involved in albinism associated with OCA1A.

Centrosomes are the key regulating element of cell cycle progression. Aberrations in their functional mechanism leads to several cancer related disorders. Although genomic studies in the field of centrosome have been extensively carried out, with the lack of structural conformation, the proteomic analysis of pathological genetic mutation is still a challenging task. Several computational algorithms and high range force fields are used to design the 3D structure conformation of proteins, which has now become the leading platform for in-silico drug discovery approaches. Application of these highly efficient platforms in centrosomics studies will be a novel approach to develop an efficient drug therapy for the treatment of their dysfunction disorders.

Dopamine receptors play a critical role in the cell signalling process responsible for information transfer in neurons functioning in the nervous system. Development of improved therapeutics for disorders like Parkinson's disease and schizophrenia would be significantly enhanced with the availability of the 3D structure for the dopamine receptors. Scorpion neurotoxins are unique source of structural templates from which new therapeutic agents might be developed. We report here the 3D structure of the human D1 dopamine receptor, predicted from primary sequence using computational techniques. The predicted structure of the human D1 dopamine receptor is used to understand the mechanism of interactions between scorpion neurotoxins through the protein–protein docking method. CHARMM force field was used for the energy minimization step before applying the docking method. To cite this article: C. Sudandiradoss et al., C. R. Biologies 331 (2008).

In this study, we identified the most deleterious non-synonymous SNP of ERBB2 (HER2) receptors by its stability and investigated its binding affinity with herceptin. Out of 135 SNPs, 10 are nsSNPs in the coding region, in which one of the nsSNP (SNPid rs4252633) is commonly found to be damaged by I-Mutant 2.0, SIFT and PolyPhen servers. With this effort, we modelled the mutant HER2 protein based on this deleterious nsSNP (rs4252633). The modeled mutant showed less stability than native HER 2 protein, based on both total energy of the mutant and stabilizing residues in the mutant protein. This is due to a deviation between the mutant and the native HER2, having an RMSD of about 2.81 A. Furthermore, we compared the binding efficiency of herceptin with native and mutant HER2 receptors. We found that herceptin has a high binding affinity with mutant HER2 receptor, with a binding energy of -24.40 kcal/mol, as compared to the native type, which has a binding energy of -15.26 kcal/mol due to six-hydrogen bonding and two salt bridges exist between herceptin and the mutant type, whereas the native type establishes four hydrogen bonds and two salt bridges with herceptin. This analysis portrays that mutant type has two additional hydrogen bonds with herceptin compared with the native type. Normal mode analysis also showed that the two amino acids, namely Asp596 and Glu598 of mutant HER2, forming additional hydrogen bonding with herceptin, had a slightly higher flexibility than the native type. Based on our investigations, we propose that SNPid rs4252633 could be the most deleterious nsSNP for HER2 receptor, and that herceptin could be the best drug for mutant compared to the native HER2 target.