Chimera Software Research Articles

First results of the Hoyle-Gamma experiment: study of the excited levels in carbon-12 gamma decay

Preliminary analysis of the Hoyle-Gamma experiment is presented, where simultaneous gamma-particles detection for the α + 12C → α + (12C* + γ) reaction is used to suppress the background various orders of magnitude. This will allow us to measure very small Γ partial widths of 12C. Details of the method, the implementation and CHIMERA software analysis are presented as well as preliminary results.

Functional and In Silico Assessment of GDF3 Gene Variants in a Chinese Congenital Scoliosis Population.

BackgroundThe present study aimed to evaluate the pathogenicity of 5 GDF3 gene variations using functional and in silico assessment approaches in a Chinese congenital scoliosis population.Material/MethodsWe selected 13 patients carrying 5 variants from a congenital scoliosis cohort. The PCR products of samples were verified by Sanger sequencing. The data and sequence alignment were analyzed using Chromas and ClustalW. SIFT and PolyPhen-2 were used to predict the functional effects of each missense and amino acid substitutions. SWISS-MODEL server and Swiss-PdbViewer were used to analyze conformational changes of GDF3 structure. DUET, UCSF Chimera, and Ligplot software were used to further explore the protein stability, side chains, and hydrophobic interaction changes, respectively. Luciferase reporter gene and Western blot assays were used to perform functional assessments for every variant from the molecular level.ResultsOf the 13 patients, the S212L variant reoccurred in 9 patients. The rest of the patients carried 1 missense mutation each. The variants of R84L and R84C were predicted as probably damaging loci. S212L, N215S, A251T were predicted as benign loci. In functional assays, R84L, S212L, and A251T display inhibitory effects on functional assays. N251S mutation showed a negative effect in protein expression assays but not in luciferase reporter gene assays. The variant of R84C displayed no negative effects on 2 functional assays.ConclusionsOur results suggest that the 4 of the 5 variants in GDF3 gene contribute different pathogenicity in congenital scoliosis, which may provide molecular evidence for clinical genetic testing.

In-Silico Screening of Flavonoids targeted for Death Receptors in Cancer by Using Hex Molecular Docking

Objective: Docking is one of the major tools in the drug development process, here we have selected certain flavonoid molecules such as Formononetin, Tangeritin, Myricetin and Kaempferol and we docked against Death Receptors (DRs) for the prevention of cancer progression. Materials and Methods: In this study, Protein Ligand Docking, we have used HEX as a Docking Software. Receptor structure was obtained from Protein Data Bank (PDB) while the ligand is drawn by using the Chem Draw Software and docking was done according to the specified parameters. Results: All the investigatory molecules except tangeritin (DR5 -212.2; DR 2 -231.1) showed higher energy values on the Death Receptor 5 (Formononetin DR5 -197.8) which states, these flavonoid molecules are having higher affinity and steric compatibility to Death Receptor 5, where DR5 mediates the TRAIL mediated apoptosis. Tangeritin molecule shows higher energy values at DR2 -231.1, it may mediate its effect through the Fas apoptotic path. The Docked molecules are viewed with the help of chimera software to discover the interaction of molecules with the receptors. Conclusion: From the present study, it is confirmed that these investigatory molecules showed a predictable effect over Death Receptors, and further studies will be carried out with ADME/T (Absorption, Distribution, Metabolism, Elimination, Toxicity) Tool. Key words: Flavonoids, Docking, Hex, Death Receptors.

Virtual Screening in Search of Allosteric Modulators of Nav1.1 Channels

Voltage-gated Na+ (Nav) channels provide the basis for neuronal excitability in the brain. Of the nine Nav channel isoforms (Nav1.1-Nav1.9), Nav1.1 exhibits cell-specific distribution in fast-spiking parvalbumin (PV) interneurons in the cortical circuit. Reduced function of PV interneurons results in impairment of the cognitive domain, a bio-signature common to a variety of neuropsychiatric disorders. Thus, selective allosteric modulators targeting Nav1.1 might provide new means to rescue PV interneuron function and improve cognition. Previous studies have identified fibroblast growth factor 14 (FGF14) as a functionally relevant regulator of Nav1.1 channels. Binding of FGF14 to the Nav1.1 C-terminal tail results in modulation of Nav1.1-mediated peak transient currents and biophysical properties of the channel activation and steady-state inactivation. The FGF14:Nav1.1 protein:protein interaction (PPI) interface might therefore provide a novel target for the development of Nav1.1 allosteric modulators.In search of small molecules targeting Nav1.1, we conducted a ligand-based high-throughput virtual screening using a FGF14:Nav1.1 homology model based on available crystal structures of homologous proteins. The UCSF chimera software was used to determine the region of interaction between FGF14 and Nav1.1, and Autodock was used to create a grid box surrounding this area to identify critical amino acids at the PPI surface of FGF14.This region of interest was submitted to the Texas Advanced Computing Center (TACC) drug discovery database, which identified 1001 ZINC compounds out of 642,759 possible ligands against the interaction site. Scores ranged from −13 to 0, with lower scores indicating greater likelihood of binding to the FGF14 surface, and thus interfering with Nav 1.1 binding. On-going counter and orthogonal screenings using in heterologous systems as well as Schrodinger Advanced Drug Discovery Suite are being used to provide in-cell validation of 14 identified hits and understanding of the target-ligand interactions. These small molecules might represent a new class of PPI-based Nav1.1-specific allosteric modulators with applicability as cognitive enhancers.

PrinCCes: Continuity-based geometric decomposition and systematic visualization of the void repertoire of proteins

Grooves and pockets on the surface, channels through the protein, the chambers or cavities, and the tunnels connecting the internal points to each other or to the external fluid environment are fundamental determinants of a wide range of biological functions. PrinCCes (Protein internal Channel & Cavity estimation) is a computer program supporting the visualization of voids. It includes a novel algorithm for the decomposition of the entire void volume of the protein or protein complex to individual entities. The decomposition is based on continuity. An individual void is defined by uninterrupted extension in space: a spherical probe can freely move between any two internal locations of a continuous void. Continuous voids are detected irrespective of their topological complexity, they may contain any number of holes and bifurcations. The voids of a protein can be visualized one by one or in combinations as triangulated surfaces. The output is automatically exported to free VMD (Visual Molecular Dynamics) or Chimera software, allowing the 3D rotation of the surfaces and the production of publication quality images. PrinCCes with graphic user interface and command line versions are available for MS Windows and Linux. The source code and executable can be downloaded at any of the following links:http://scholar.semmelweis.hu/czirjakgabor/s/princces/#t1https://github.com/CzirjakGabor/PrinCCeshttp://1drv.ms/1bP9iJ3

Does topology drive fiber polymerization?

We have developed new procedures to examine the early steps in fibrin polymerization. First, we isolated fibrinogen monomers from plasma fibrinogen by gel filtration. Polymerization of fibrinogen monomers differed from that of plasma fibrinogen. The formation of protofibrils was slower and the transformation of protofibrils to fibers faster for the fibrinogen monomers. Second, we used formaldehyde to terminate the polymerization reactions. The formaldehyde-fixed products obtained at each time point were examined by dynamic light scattering and transmission electron microscopy (TEM). The data showed the formaldehyde-fixed products were stable and representative of the reaction intermediates. TEM images showed monomers, short oligomers, protofibrils, and thin fibers. The amount and length of these species varied with time. Short oligomers were less than 5% of the molecules at all times. Third, we developed models that recapitulate the TEM images. Fibrin monomer models were assembled into protofibrils, and protofibrils were assembled into two-strand fibers using Chimera software. Monomers were based on fibrinogen crystal structures, and the end-to-end interactions between monomers were based on D-dimer crystal structures. Protofibrils assembled from S-shaped monomers through asymmetric D:D interactions were ordered helical structures. Fibers were modeled by duplicating a protofibril and rotating the duplicate 120° around its long axis. No specific interactions were presumed. The two protofibrils simply twisted around one another to form a fiber. This model suggests that the conformation of the protofibril per se promotes the assembly into fibers. These findings introduce a novel mechanism for fibrin assembly that may be relevant to other biopolymers.

Molecular Characteristic and Insilico Analysis of <i>KatG </i>Gene in Isoniazid Resistance <i>Mycobacterium Tuberculosis</i> Isolate from Sudan

The KatG gene of Mycobacterium Tuberculosis has been associated with isoniazid (INH) drug resistance. While isoniazid (INH) considered as corner stone and main chemotherapy used throughout the world to manage tuberculosis, thus the Progress in apprehension of principle concepts associated with resistance to isoniazid (INH) has allowed molecular tests in addition to bioinformatics tool for the detection of drug-resistant tuberculosis to be developed. In Consecutive isolates (n = 20) of multidrug-resistant Mycobacterium tuberculosis, part of the katG was sequenced for INH resistance analysis. BLAST analysis of all sequences revealed 100% identity with the available strain “EGY-K361” Mycobacterium tuberculosis with Accession No: KC49137.1 except 6 isolates :isolate1, 2, 4, 11, 15, and isolate 20 revealed 99% identity. Thosesix isolates (30%) have detected mutation in Catalase-peroxidase enzyme S315T; three isolate from six 3/6 (50%) of mutant isolates have SNP AGC>ACC substitution while others 3/6 have substitution C>G in position 1280 which may contributed in altering gene expression. The secondary structure of wild and mutant proteins had been done using phyre2 software while the three dimensional structures of them had been done by Chimera software. Stability of mutant protein was increased which detected by i-mutant. Phylogenetic tree of the sequences revealed two distinct phylogroups: mutant isolates and wild isolates phylogroups with controls from different countries retrieved from Gene bank. Serine at position 315 is one of potential drug active sites that proved via SiteEngine soft ware, therefore any substitution will change efficiency of INH.

Expanding the spectrum of HEXA mutations in Indian patients with Tay–Sachs disease

Tay–Sachs disease is an autosomal recessive neurodegenerative disorder occurring due to impaired activity of β-hexosaminidase-A (EC 3.2.1.52), resulting from the mutation in HEXA gene. Very little is known about the molecular pathology of TSD in Indian children except for a few mutations identified by us. The present study is aimed to determine additional mutations leading to Tay–Sachs disease in nine patients confirmed by the deficiency of β-hexosaminidase-A (<2% of total hexosaminidase activity for infantile patients) in leucocytes. The enzyme activity was assessed by using substrates 4-methylumbelliferyl-N-acetyl-β-d-glucosamine and 4-methylumbelliferyl-N-acetyl-β-d-glucosamine-6-sulfate for total-hexosaminidase and hexosaminidase-A respectively, and heat inactivation method for carrier detection. The exons and exon–intron boundaries of the HEXA gene were bi-directionally sequenced on an automated sequencer. ‘In silico’ analyses for novel mutations were carried out using SIFT, Polyphen2 and MutationT@ster software programs. The structural study was carried out by UCSF Chimera software using the crystallographic structure of β-hexosaminidase-A (PDB-ID: 2GJX) as the template. Our study identified four novel mutations in three cases. These include a compound heterozygous missense mutation c.524A>C (D175A) and c.805G>C (p.G269R) in one case; and one small 1bp deletion c.426delT (p.F142LfsX57) and one splice site mutation c.459+4A>C in the other two cases respectively. None of these mutations were detected in 100 chromosomes from healthy individuals of the same ethnic group. Three previously reported missense mutations, (i) c.532C>T (p.R178C), (ii) c.964G>T (p.D322Y), and (iii) c.1385A>T (p.E462V); two nonsense mutations (i) c.709C>T (p.Q237X) and (ii) c.1528C>T (p.R510X), one 4bp insertion c.1277_1278insTATC (p.Y427IfsX5) and one splice site mutation c.459+5G>A were also identified in six cases. We observe from this study that novel mutations are more frequently observed in Indian patients with Tay–Sachs disease with clustering of ~73% of disease causing mutations in exons 5 to 12. This database can be used for a carrier rate screening in the larger population of the country.

Characterization of Three Full-length Human Nonmuscle Myosin II Paralogs

Nonmuscle myosin IIs (NM IIs) are a group of molecular motors involved in a wide variety of cellular processes including cytokinesis, migration, and control of cell morphology. There are three paralogs of the NM II heavy chain in humans (IIA, IIB, and IIC), each encoded by a separate gene. These paralogs are expressed at different levels according to cell type and have different roles and intracellular distributions in vivo. Most previous studies on NM II used tissue-purified protein or expressed fragments of the molecule, which presents potential drawbacks for characterizing individual paralogs of the intact protein in vitro. To circumvent current limitations and approach their native properties, we have successfully expressed and purified the three full-length human NM II proteins with their light chains, using the baculovirus/Sf9 system. The enzymatic and structural properties of the three paralogs were characterized. Although each NM II is capable of forming bipolar filaments, those formed by IIC tend to contain fewer constituent molecules than those of IIA and IIB. All paralogs adopt the compact conformation in the presence of ATP. Phosphorylation of the regulatory light chain leads to assembly into filaments, which bind to actin in the presence of ATP. The nature of interactions with actin filaments is shown with different paralogs exhibiting different actin binding behaviors under equivalent conditions. The data show that although NM IIA and IIB form filaments with similar properties, NM IIC forms filaments that are less well suited to roles such as tension maintenance within the cell.

Architecture and Assembly of HIV Integrase Multimers in the Absence of DNA Substrates

We have applied small angle x-ray scattering and protein cross-linking coupled with mass spectrometry to determine the architectures of full-length HIV integrase (IN) dimers in solution. By blocking interactions that stabilize either a core-core domain interface or N-terminal domain intermolecular contacts, we show that full-length HIV IN can form two dimer types. One is an expected dimer, characterized by interactions between two catalytic core domains. The other dimer is stabilized by interactions of the N-terminal domain of one monomer with the C-terminal domain and catalytic core domain of the second monomer as well as direct interactions between the two C-terminal domains. This organization is similar to the "reaching dimer" previously described for wild type ASV apoIN and resembles the inner, substrate binding dimer in the crystal structure of the PFV intasome. Results from our small angle x-ray scattering and modeling studies indicate that in the absence of its DNA substrate, the HIV IN tetramer assembles as two stacked reaching dimers that are stabilized by core-core interactions. These models of full-length HIV IN provide new insight into multimer assembly and suggest additional approaches for enzyme inhibition.

Characterization of the Molecular Architecture of Human Caveolin-3 and Interaction with the Skeletal Muscle Ryanodine Receptor

Caveolin-3 facilitates both caveolae formation and a range of cell signaling pathways, including Ca(2+) homeostasis. Caveolin-3 forms a disc-shaped nonamer that binds the Ca(2+)-release channel, RyR1. Multiple caveolin-3 nonamers bind to a single RyR1 homotetramer. First three-dimensional structural insights into caveolin-3 assembly, interactions with RyR1 suggest a novel role in muscle contraction and/or for channel localization within the membrane. Caveolin-3 (cav-3), an integral membrane protein, is a building block of caveolae as well as a regulator of a number of physiological processes by facilitating the formation of multiprotein signaling complexes. We report that the expression of cav-3 in insect (Sf9) cells induces caveola formation, comparable in size with those observed in native tissue. We have also purified the recombinant cav-3 determining that it forms an oligomer of ∼220 kDa. We present the first three-dimensional structure for cav-3 (using transmission electron microscopy and single particle analysis methods) and show that nine cav-3 monomers assemble to form a complex that is toroidal in shape, ~16.5 nm in diameter and ~ 5.5 nm in height. Labeling experiments and reconstitution of the purified cav-3 into liposomes have allowed a proposal for the orientation of the protein with respect to the membrane. We have identified multiple caveolin-binding motifs within the ryanodine receptor (RyR1) sequence employing a bioinformatic analysis. We have then shown experimentally that there is a direct interaction between recombinant cav-3 nonamers and purified RyR1 homotetramers that would imply that at least one of the predicted cav-3-binding sites is exposed within the fully assembled RyR1 structure. The cav-3 three-dimensional model provides new insights as to how a cav-3 oligomer can bind multiple partners in close proximity to form signaling complexes. Furthermore, a direct interaction with RyR1 suggests a possible role for cav-3 as a modifier of muscle excitation-contraction coupling and/or for localization of the receptor to regions of the sarcoplasmic reticulum.

Structural and Functional Interferences from a Molecular Structural Model of Xenocin&lt;i&gt; &lt;/i&gt;Toxin from&lt;i&gt; Xenorhabdus nematophila&lt;/i&gt;

Bacteriocins constitute the most abundant and diverse family of microbial defense systems. They are pro- duced and secreted to inhib it the gro wth of closely related, co mpeting bacterial species inhabiting a co mmon ecological niche. One such bacteriocin designated as xenocin, is produced by entomopathogenic bacteriu m Xenorhabdus nematophila. In our earlier study, we have shown its regulation under SOS conditions and its activity against wide range of bacteria iso- lated fro m the gut of insect. In this study three dimensional structure of xenocin has been deciphered with the assistance of automated homology modelling and verified by VERIFY-3D program as well as Ramachandran plot 2.0. Three domain organisation; Translocation (T), Receptor (R) and Catalytic do main (C) has been o-0.058 served and their structures were studied by CHIM ERA software (UCSF). Protein disorder structure and Average Area Buried Upon folding (AABUF) in first 100 amino acid residues of Translocation domain is determined by Globplot and ProtScale software respectively. Conserved amino acid residues in the putative active site of the catalytic domain of xenocin have been deciphered with mult iple se- quence alignment.

A Novel p.E311K Mutation of Thyroid Receptor Beta Gene in Resistance to Thyroid Hormone Syndrome, Inherited in Autosomal Recessive Trait

Resistance to thyroid hormone (RTH) syndrome is caused by mutations in THRB gene and is inherited mainly as an autosomal dominant trait with dominant negative effect. Most of up-to-now described RTH cases were heterozygous. We studied a 19-year-old woman presenting severe mental impairment, hyperkinetic behavior, learning disability, hearing loss, tachycardia, goiter, strabismus, nystagmus, and normal stature. The laboratory findings revealed elevated TSH, T3, and T4 serum levels. Her parents were healthy with normal serum level of TSH, fT3, and fT4. Sequence based prediction of a substitution was analyzed by SDM, PolPhen, and SNAP software whereas structural visualizations were performed in UCSF Chimera. We found a novel mutation in THRB gene in position 1216 (G to A transition, codon 311) resulting in novel Glu-311-Lys (p.E311K) substitution, homozygous in proband presenting with severe symptoms of RTH and heterozygous in both of her healthy parents, thus suggesting autosomal recessive mode of inheritance. p.E311K substitution was not found in 50 healthy, unrelated individuals. p.E311K was shown to be deleterious by SDM, PolPhen, and SNAP software. Structural visualizations of mutated protein performed by UCSF Chimera software disclosed a loss of hydrogen bonds between E311, R383, and R429 along with abnormal residue-residue contact between K311 and L377. This is a very rare case of a homozygous mutation in a patient with severe symptoms of RTH and lack of symptoms in both heterozygous parents. Although, computational analyses have provided the evidence that p.E311K substitution may affect THRB function, lack of dominant negative effect typical for THRB mutations could not be explained by structure-based modeling. Further in vitro analysis is required to assess the functional consequences of this substitution.

Functional Implications of an Intermeshing Cogwheel-like Interaction between TolC and MacA in the Action of Macrolide-specific Efflux Pump MacAB-TolC

Macrolide-specific efflux pump MacAB-TolC has been identified in diverse gram-negative bacteria including Escherichia coli. The inner membrane transporter MacB requires the outer membrane factor TolC and the periplasmic adaptor protein MacA to form a functional tripartite complex. In this study, we used a chimeric protein containing the tip region of the TolC α-barrel to investigate the role of the TolC α-barrel tip region with regard to its interaction with MacA. The chimeric protein formed a stable complex with MacA, and the complex formation was abolished by substitution at the functionally essential residues located at the MacA α-helical tip region. Electron microscopic study delineated that this complex was made by tip-to-tip interaction between the tip regions of the α-barrels of TolC and MacA, which correlated well with the TolC and MacA complex calculated by molecular dynamics. Taken together, our results demonstrate that the MacA hexamer interacts with TolC in a tip-to-tip manner, and implies the manner by which MacA induces opening of the TolC channel.

Molecular Rearrangements Involved in the Capsid Shell Maturation of Bacteriophage T7

Maturation of dsDNA bacteriophages involves assembling the virus prohead from a limited set of structural components followed by rearrangements required for the stability that is necessary for infecting a host under challenging environmental conditions. Here, we determine the mature capsid structure of T7 at 1 nm resolution by cryo-electron microscopy and compare it with the prohead to reveal the molecular basis of T7 shell maturation. The mature capsid presents an expanded and thinner shell, with a drastic rearrangement of the major protein monomers that increases in their interacting surfaces, in turn resulting in a new bonding lattice. The rearrangements include tilting, in-plane rotation, and radial expansion of the subunits, as well as a relative bending of the A- and P-domains of each subunit. The unique features of this shell transformation, which does not employ the accessory proteins, inserted domains, or molecular interactions observed in other phages, suggest a simple capsid assembling strategy that may have appeared early in the evolution of these viruses.

Visualization of virtual screening results on tiled display walls (TDW)

Virtual screening has facilitated the drug discovery process through the use of molecular simulations to computationally identify inhibitors and has yielded a tremendous amount of data. These results cannot be utilized in laboratory experiments until they are analyzed manually to identify anomalies, redundant chemical structures, and false positives. For this reason, a new, high‐throughput method to analyze the results of virtual screenings is needed, thereby accelerating the drug discovery process.We have developed, deployed, and tested a modified version of ViewDock (named ViewDock TDW) on two separate TDW configurations. This tool allows a user to simultaneously visualize, group, compare, and analyze dozens of ligand‐receptor interactions on a TDW. To achieve this it was necessary to modify its communication with the molecular visualization program Chimera and create several other shell, python and perl scripts to enable the graphic user interface. ViewDock TDW preserves the functionality of the Chimera software, allowing for rotation, zoom, view angle, protein surface visualization, and calculation of hydrogen bonds. The program also enables global control over all ligand‐receptor models as well as specific control for commands to be sent to individuals or groups of ligand‐receptor pairs on the TDW. This program will help greatly in the visualization and analysis of virtual screening data.

Structural and Functional Fingerprint of the Mitochondrial ATP-binding Cassette Transporter Mdl1 from Saccharomyces cerevisiae

The ATP-binding cassette half-transporter Mdl1 from Saccharomyces cerevisiae has been proposed to be involved in the quality control of misassembled respiratory chain complexes by exporting degradation products generated by the m-AAA proteases from the matrix. Direct functional or structural data of the transport complex are, however, not known so far. After screening expression in various hosts, Mdl1 was overexpressed 100-fold to 1% of total mitochondrial membrane protein in S. cerevisiae. Based on detergent screens, Mdl1 was solubilized and purified to homogeneity. Mdl1 showed a high binding affinity for MgATP (Kd = 0.26 microm) and an ATPase activity with a Km of 0.86 mm (Hill coefficient of 0.98) and a turnover rate of 2.6 ATP/s. Mutagenesis of the conserved glutamate downstream of the Walker B motif (E599Q) or the conserved histidine of the H-loop (H631A) abolished ATP hydrolysis, whereas ATP binding was not affected. Mdl1 reconstituted into liposomes showed an ATPase activity similar to the solubilized complex. By single particle electron microscopy, a first three-dimensional structure of the mitochondrial ATP-binding cassette transporter was derived at 2.3-nm resolution, revealing a homodimeric complex in an open conformation.

Our Hospitals

<h3>Abstract</h3> <h3>Background</h3> HAS (Human Serum Albumin) is a highly water-soluble globular plasma protein, with a relative molecular weight (g/mol) of 67 KDa, consisting of 585 amino acid residues. In this study, we have investigated the interaction of the Crystal structures complexed in human serum albumin at resolutions of 2.8 to 2.0: Camptothecin, 9-amino-camptothecin, Etoposide, Teniposide, Bicalutamide and Idarubicin, using a bioinformatic approach, estimated by Pyrx Virtual Screen Tool and AMDock (AMDock, Assisted Molecular Docking). We have analyzed a validated protocol, studying several parameters, as Binding Affinity, RMSD value, Ligand Efficiency, and Inhibition constant (Ki value). <h3>Methods</h3> Human Serum Albumin protein preparation was characterized with several programs, as Chimera, MGLTools 1.5.6, Swiss PDB Viewer Software to perform docking analysis by Autodock Vina estimated with Pyrx Software. <h3>Results</h3> In this work, we have found crystalized camptothecin, crystalized 9-amino-camptothecin and crystalized teniposide, gave excellent results for Binding Affinity, (kcal/mol), RMSD value (A°), inhibition constant Ki value (nM): -Binding Affinity of 9-amino-camptothecin (ca.−10 kcal/mol), camptothecin (−9 kcal/mol) and teniposide (−11 kcal/mol, -RMSD Value of 9 -amino-camptothecin (ca.1.8 Å), camptothecin (ca.2.2 Å) and teniposide (ca. 3.6 Å), - Ki Value: 9 -amino-camptothecin (ca 59 nM), camptothecin (ca 183 nM) and teniposide (ca 9 nM), -Ligand efficiency: of 9 -amino-camptothecin(ca −0.35 kcal/mol), camptothecin (ca −0.34 kcal/mol) and teniposide (ca −0.24 kcal/mol <h3>Conclusions</h3> We explored the best three crystallized ligand in Human Serum Albumin. Moreover, we observe a complete overlap, during the re-docking analysis phase, estimated by chimera Software. Therefore we have concluded that ID PDB Crystal 4L8U human serum albumin-Crystallised 9 -amino Camptothecin; ID PDB Crystal 4L9K human serum albumin-Crystallised Camptothecin and ID PDB Crystal 4L9Q human serum albumin-crystallized teniposide be used as a possible as a reference template protein to be compared with the target protein, by Docking molecular analysis.