Atomic Contact Energy Research Articles

Synthesis, physicochemical characterization and structural studies of new Schiff base ligand and its metal (II) complexes: In silico molecular docking analysis, antimicrobial activity and cytotoxicity

A new Schiff base ligand, namely 2‐((4‐(diethylamino)phenylimino)methyl)‐4,6‐di‐tert‐butylphenol (HL), and its derived metal (II) complexes [Cu (L)2] (1), [Co (L)2] (2) and [Zn (L)2] (3) have been synthesized and characterized using various physicochemical techniques. Single‐crystal X‐ray diffraction studies confirm the structure of newly synthesized HL and complex 2. Density functional theory analysis was used to investigate their electronic structures and properties. In silico docking analysis revealed that complex 1 has significant DNA binding ability (atomic contact energy of −1008.26 kcal mol−1) and complex 2 has a greater affinity with human serum albumin (binding energy of −901.61 kcal mol−1). Complex 2 reveals the highest antimicrobial activity against both fungi and bacteria, whereas complex 1 shows greater cytotoxicity (IC50 = 14.3 ±0.9 μg ml−1) to MCF‐7 cancer cells.

In vitro and in silico analyses of Vicia faba L. on Peroxisome proliferator–activated receptor gamma

The agonists of peroxisome proliferator-activated receptor gamma (PPARγ) from natural victual products were used as antidiabetic agents. Faba bean (Vicia faba L.) is a consequential legume that was known to possess potential antidiabetic activity, whose mechanism of action was unknown. The current study was focused to ascertain gene expression of the nuclear receptor PPARγ by Faba bean pod extract in rat cell lines (RINm5F).The real-time polymerase chain reaction analysis demonstrated that Faba bean pod extract in concentrations of 160 µg/mL have shown4.97-fold stimulation compared with control. The cells treated with 320 µg/mL has shown 5.89-fold upregulation, respectively. Furthermore, in silico docking analysis was carried out against PPARγ, using the bioactive compounds identified from Faba bean pod extracts, which were known reported compounds from the literature. The results suggest that gene expression of PPARγ was inhibited by the constituents in Faba bean. In silico analysis prognosticates, butein has a high binding energy (-8.6 kcal/mol) with an atomic contact energy of -214.10, followed by Apigenin and Quercetin against PPARγ. Similarly, the percentage of interaction was high for butein, followed by Apigenin and Quercetin than other compounds comparatively. Hence, the results conclude inhibition of PPARγ by the bioactive compounds from Faba bean, which may provide insights into developing future therapeutic molecules for diabetes mellitus.

PREDICTING THE BIODEGRADABILITY NATURE OF IMIDAZOLE AND ITS DERIVATIVES BY MODULATING TWO HISTIDINE DEGRADATION ENZYMES (UROCANASE AND FORMIMINOGLUTAMASE) ACTIVITIES

Objectives: The biodegradation pathway of substituted imidazole ring compounds has been reported to have close analogy to the histidine degradation pathway. This prompted the present study to be carried out on 12 selected imidazole and its derivatives which are 1-imidazole, 1, 2-dimethylimidazole, 1-ethyl imidazole, 2-ethyl-4-methylimidazole, 2-isopropylimidazole, 2-Isopropyl-4-nitro-1H-imidazole, 1-methylimidazole, 2-methyl-5-nitroimidazole, 2-methyl-1-vinylimidazole, 1-nitro imidazole, 1-phenyl imidazole, and 1-vinylimidazole.Methods: The imidazole and its derivatives were evaluated on the docking behavior of urocanase and formiminoglutamase using PatchDock. In addition, molecular physicochemical, drug-likeness, absorption, distribution, metabolism, and excretion analyses (ADME) were done.Results: The molecular physicochemical analysis revealed that all the tested ligands showed nil violation and complied well with the Lipinski’s rule of five. ADME analysis showed that 1-phenylimidazole alone predicated to have cytochrome P450 1A2 inhibition effect. Docking studies revealed that 1-nitroimidazole showed the least atomic contact energy with both targeted enzymes (urocanase and FIGase).Conclusion: Inhibition of both enzymes (urocanase and FIGase) might show poor biodegradability nature. Thus, we can predict biodegradability nature of imidazloe and its derivatives by modulating two histidine degradation enzymes activities.

Natural alkaloid Luotonin A and its affixed acceptor molecules: Serum albumin binding studies

Effective interaction of natural alkaloid Luotonin A (L) and its affixed acceptor molecules 1 and 2 with donor molecule as Bovine serum albumin (BSA) at various pH (4.0, 7.4 and 10.0) medium have been demonstrated using various conventional spectroscopic techniques. These analyses provide some valuable features on the interaction between BSA and acceptor molecules (L, 1 and 2). From the absorption and fluorescence spectral titration studies, the formation of ground-state complexes between the acceptor molecules (L, 1 and 2) and the BSA have been confirmed. The results of the afore titrations analysis reveal that, the strong binding of receptor 1 with BSA (Kapp 5.68×104M−1; KSV 1.86×106Lmol−1; Ka 6.42×105Lmol−1; Kass 8.09×106M−1; ΔG −33.35kJ/mol) at physiological pH medium (7.4) than other receptor molecules 2 and L. The Förster resonance energy transfer (FRET) efficiency between the tryptophan (Trp) residues of BSA and acceptor molecules L, 1 and 2 during the interaction, are 28.85, 85.24 and 53.25 % respectively. The superior binding efficacy of acceptor 1 at physiological pH condition has been further confirmed by FT-IR and Raman spectral analysis methods. Moreover, theoretical docking studies of acceptors L, 1 and 2 towards HSA have been demonstrated to differentiate their binding behaviours. It reveals that, acceptor 1 has the strongest binding ability with HSA through two hydrogen bonding and the Atomic contact energy (ACE) value of −483.96kcal/mol.

Pairwise contact energy statistical potentials can help to find probability of point mutations.

To adopt a particular fold, a protein requires several interactions between its amino acid residues. The energetic contribution of these residue-residue interactions can be approximated by extracting statistical potentials from known high resolution structures. Several methods based on statistical potentials extracted from unrelated proteins are found to make a better prediction of probability of point mutations. We postulate that the statistical potentials extracted from known structures of similar folds with varying sequence identity can be a powerful tool to examine probability of point mutation. By keeping this in mind, we have derived pairwise residue and atomic contact energy potentials for the different functional families that adopt the (α/β)8 TIM-Barrel fold. We carried out computational point mutations at various conserved residue positions in yeast Triose phosphate isomerase enzyme for which experimental results are already reported. We have also performed molecular dynamics simulations on a subset of point mutants to make a comparative study. The difference in pairwise residue and atomic contact energy of wildtype and various point mutations reveals probability of mutations at a particular position. Interestingly, we found that our computational prediction agrees with the experimental studies of Silverman et al. (Proc Natl Acad Sci 2001;98:3092-3097) and perform better prediction than iMutant and Cologne University Protein Stability Analysis Tool. The present work thus suggests deriving pairwise contact energy potentials and molecular dynamics simulations of functionally important folds could help us to predict probability of point mutations which may ultimately reduce the time and cost of mutation experiments. Proteins 2016; 85:54-64. © 2016 Wiley Periodicals, Inc.

Durantol - a phytosterol antifungal contributor from Duranta repens Linn. For organic Management of Sorghum Downy Mildew

Downy mildew of sorghum (DMS) has serious implications agronomically worldwide and to-date the search for a potent fungicide is a high priority and necessity. Phytochemicals have proven to be effective against various plant pathogens with minimal or no side effects. Duranta repens aqueous extract exhibited a promising potential as an organic fungicide for management of sorghum downy mildew (Peronosclerospora sorghi) in greenhouse conditions, at low concentration of 5 %. Activity guided bio-prospecting lead to the isolation of active principle which could control the DMS at as low as 0.1 % concentration. Spectral studies identified the bioactive contributor as a phytosterol namely 16-Hydroxy-8,10,13-trimethyl-1,2,8,10,12,13,14,15-octahydro cyclopenta [a] phenanthren-3-one, designated as Durantol. The results of microscopy exhibited the inhibition of conidial germ-tube growth by formation of bulb-like swellings at the tip, suggesting the mechanism of action of Durantol was via hampering the membrane integrity of the pathogen. Further, the same was virtually predicted using molecular docking for structure-activity relationship (SAR) against four best known membrane receptors namely 1-UDP-glycosyltransferases (UGT), cytochromes P450 (P450), oxidosqualene cyclase (OSC) and serine carboxypeptidase-like acyltransferase (SCPL), proposing that glycosylation onto the membrane would be a reason for inhibition and which is evident from atomic contact energy (ACE) values. The results of the study indicate that, organic management of airborne inoculum of downy mildew of sorghum is feasible and preferable, as compared to the use of chemical fungicides, considering human and environmental health concerns.

Geometric Simulation Approach for Grading and Assessing the Thermostability of CALBs.

Candida antarctica lipase B (CALB) is a known stable and highly active enzyme used widely in biodiesel synthesis. In this work, the stability of native (4K6G) and mutant (4K5Q) CALB was studied through various structural parameters using conformational sampling approach. The contours of polar surface area and surface area of mutant CALB were 11357.67 Å2 and 30007.4 Å2, respectively, showing an enhanced stability compared to native CALB with a statistically significant P value of < 0.0001. Moreover, simulated thermal denaturation of CALB, a process involving dilution of hydrogen bond, significantly shielded against different intervals of energy application in mutant CALB revealing its augmentation of structural rigidity against native CALB. Finally, computational docking analysis showed an increase in the binding affinity of CALB and its substrate (triglyceride) in mutant CALB with Atomic Contact Energy (ACE) of −91.23 kcal/mol compared to native CALB (ACE of −70.3 kcal/mol). The computational observations proposed that the use of mutant CALB (4K5Q) could serve as a best template for production of biodiesel in the future. Additionally, it can also be used as a template to identify efficient thermostable lipases through further mutations.

Evaluating the inhibitory potential of Withania somnifera on platelet aggregation and inflammation enzymes: An in vitro and in silico study

Context Withania somnifera (L.) Dunal is traditionally used for treating various ailments, but lacks scientific evaluation.Objective This study evaluates Withania somnifera (WS) for its effect on platelet activity and inflammatory enzymes.Materials and methods Aqueous and ethanolic (1:1) leaf extracts were subjected to in vitro indirect haemolytic activity using Naja naja venom, human platelet aggregation was quantified for lipid peroxidation using arachidonic acid (AA) as agonist and 5-lipoxygenase (5-LOX) levels were determined using standard spectrometric assays. Further, molecular docking was performed by the ligand fit method using molegro software package (Molegro ApS, Aarhus, Denmark).Results The study found that aqueous and ethanol extracts have very negligible effect (15%) with an IC50 value of 13.8 mg/mL on PLA2 from Naja naja venom. Further, extracts of WS also had very little effect (18%) with an IC50 value of 16.6 mg/mL on malondialdehyde (MDA) formation. However, a 65% inhibition of 5-LOX with an IC50 value of 0.92 mg/mL was observed in 1:1 ethanol extracts. The same was evident from SAR model with the active ingredient withaferin A binding predominantly on Phe 77, Tyr 98, Arg 99, Asp 164, Leu 168, Ser 382, Arg 395, Tyr 396 and Tyr 614 with an atomic contact energy value of −128.96 compared to standard phenidone (−103.61). Thus, the current study validates the application of WS for inflammatory diseases.Conclusion This study reveals the inhibitory potential of W. somnifera on inflammatory enzymes and platelet aggregation. Thus, WS can serve as a newer, safer and affordable medicine for inflammatory diseases.

3,5-Disubstituted Isoxazole Derivatives: Potential Inhibitors of Inflammation and Cancer.

The products of arachidonic acid metabolism by lipoxygenase (LOX) and cyclooxygenase (COX) significantly contribute to inflammation and carcinogenesis. Particularly, overproduction of leukotrienes and prostaglandins contribute to tumor growth by inducing formation of new blood vessels that sustain tumor cell viability and growth. Hence, search for novel anticancer drug via inhibition of LOX and COX enzymes constitutes an impressive strategy till date. In this context, a series of isoxazole derivatives were synthesized and screened for their anti-inflammatory activity via LOX and COX inhibition. Among these, 3-(3-methylthiophen-2-yl)-5-(3,4,5-trimethoxyphenyl)isoxazole (2b) showed significant inhibitory activity toward LOX and COX-2. Additionally, 2b showed a good inhibition of tumor growth, peritoneal angiogenesis, and ascite formation in Ehrlich ascites carcinoma (EAC) cell mouse model. Further, the in silico molecular studies also revealed that the compound 2b binds to the catalytic domain of LOX and COX-1 and COX-2 strongly with high atomic contact energy (ACE) score compared to standard drug. These initial pharmacological data support the fact that the compound 2b serves as the basis in developing anti-inflammatory and anticancer agents.

Anti-Cancer Activity of 2,4-Disubstituted Thiophene Derivatives: Dual Inhibitors of Lipoxygenase and Cyclooxygenase.

2,4-Disubstituted thiophene derivatives were synthesized and assessed for antiinflammatory and anti-cancer activities by targeting two important enzymes of the arachidonic acid metabolism. Both lipoxygenase and cyclooxygenase enzymes play vital role in chronic inflammation and carcinogenesis. Previous studies have proved that COX-2 and 5-LOX are highly activated in various types of cancers; hence inhibition of these clinically important enzymes constitutes the essential criterion for the suppression of tumor progression and metastasis. Among the tested derivatives, 2d and 2g compounds emerged as potent inhibitors of lipoxygenase and cyclooxygenase enzymes. The potent inhibitor of cyclooxygenase was further tested for in vitro cytotoxicity on cervical cancer (HeLa) cells and in vivo tumor model studies using EAT bearing mice where 2-(3,4,5- trimethoxyphenyl)-4-(N-methylindol-3-yl) thiophene (2g) showed eloquent activity. Further, in silico modeling results confirmed the active catalytic ligand binding pockets, which is evident from higher atomic contact energy values of 2d and 2g than compared to standard drug. Thus, 2g may find better application in management of inflammation and in proapoptotic therapeutic engineering.

Azamacrocycle Complexes: Synthesis and Xanthine Oxidase and Antioxidant Activity

Aims: Gout is caused by high uric acid in the blood that leads to excess uric acid crystallizing in the joints causing swelling and pain. Uric acid is produced from the breakdown of the purine which is released when cells die or introduced from the food we eat. The enzyme that helps in breakdown of purine to uric acid is xanthine oxidase (XO). Since XO makes the conversion of purine into uric acid happen, preventing its activity results to slow down of uric acid production. Such is the role of xanthine oxidase inhibitors (XOI). In this context we aimed to synthesize new complex which can be potent towards XOI and antioxidant properties.Study Design: Based on the literature we have designed azamacrocyclic complexes for advanced biological applications.Place and Duration of Study: Department of Chemistry, Research Laboratory, Yuvaraj’s College, University of Mysore, Mysore for synthesis and for biological activities Mahajana Life Science Research Laboratory, Department of Biotechnology, Microbiology and Biochemistry. June 2012-may 2013.Methodology: The macrocyclic metal complexes were synthesized by the template condensation of diamine and formaldehyde in MeOH. After stirring for 10 min a solution of 1, 4-diaminobutane, metallic salt and 2, 4-pentanedione in MeOH was added and the resulting mixture was refluxed.Results: Macrocylic metal complexes containing phenylene bridges have been synthesized and subjected to biological activities. Among the four synthesized complexes (3a-3d), 3d exhibited 83.2% of XO inhibition and also showed potent antioxidant activity. The same was also evident from structure activity relationship with atomic contact energy values of -285.78 compared to allopurinol with -200.02.Conclusion: From the present study, we infer that, aza macrocyclic metal complexes could lead to the development of newer therapeutics for gout and other inflammatory diseases which are caused by oxidative stress.

Protein-protein binding site identification by enumerating the configurations

BackgroundThe ability to predict protein-protein binding sites has a wide range of applications, including signal transduction studies, de novo drug design, structure identification and comparison of functional sites. The interface in a complex involves two structurally matched protein subunits, and the binding sites can be predicted by identifying structural matches at protein surfaces.ResultsWe propose a method which enumerates “all” the configurations (or poses) between two proteins (3D coordinates of the two subunits in a complex) and evaluates each configuration by the interaction between its components using the Atomic Contact Energy function. The enumeration is achieved efficiently by exploring a set of rigid transformations. Our approach incorporates a surface identification technique and a method for avoiding clashes of two subunits when computing rigid transformations. When the optimal transformations according to the Atomic Contact Energy function are identified, the corresponding binding sites are given as predictions. Our results show that this approach consistently performs better than other methods in binding site identification.ConclusionsOur method achieved a success rate higher than other methods, with the prediction quality improved in terms of both accuracy and coverage. Moreover, our method is being able to predict the configurations of two binding proteins, where most of other methods predict only the binding sites. The software package is available at http://sites.google.com/site/guofeics/dobi for non-commercial use.

In Silico Identification and Analysis of Drug Resistant Mutants of ABL Tyrosine Kinase Based on Detrimental Missense Mutations

In this work, we computationally identified the most detrimental missense mutations of ABL tyrosine kinase in Chronic Myelogenous Leukemia (CML) and analyzed the drug resistance from these detrimental missense mutations. Out of 45 missense mutations, 20 variants were commonly found less stable, deleterious and damaging by I-Mutant2.0, SIFT and PolyPhen programs respectively. Subsequently, we performed modeling of these 20 variants to understand their change in conformations with respect to native ABL tyrosine kinase by computing their RMSD (Root Mean Square Deviation). Further, the native and 20 mutants were docked with the drug ‘imatinib’ to find out the drug resistance of these detrimental missense mutations. Among the 20 mutants, we found by docking studies that 12 mutants, namely M244V, Q252H, Y253H, K285N, T315I, F317L, F317I, S349L, M351T, E355G, S417Y and W430L had less binding affinity with imatinib than the native type. Finally, we analyzed that the loss of binding affinity of these 12 mutants were due to altered flexibility in their binding amino acids with imatinib as compared with native type by normal mode analysis. In our work, we found the novel data that majority of the drug binding amino acids in those 12 mutants had encountered the loss of flexibility which could be the theoretical basis for the cause of drug resistance. Keywords: Missense mutation, ABL tyrosine kinase, Imatinib, Modeling, Docking, Flexibility, Chronic Myelogenous Leukemia, Adenosine triphosphate, Swissprot, Protein Data Bank, I-Mutant 2.0, SIFT, PolyPhen, DDG, Tolerance index, PSIC SD, RMSD, Force Field, Gromacs, Atomic Contact Energy, PatchDock, Normal mode analysis, B-factors, ElNemo, Ligand Contact Tool

Identification of EPAC (Exchange Protein Activated by cAMP) bioinformatically as a potential signalling biomarker in Cardiovascular Disease (CVD) and its molecular docking by a lead molecule.

The present work delineates the combinatorial approach of firstly, creation of a centralized data-set comprising signalling proteins identified on the basis of altered expression, such as over-expression or repression of a set of signalling protein(s) leading to the cause of the disease, which is based on published reports screened through Pubmed and secondly, in the in silico creation of novel lead (drug) molecules and docking of identified signalling biomarkers using such drugs to investigate possibility of their future application in the model systems eventually. EPAC (Exchange Protein Activated by cAMP) emerges as a signalling biomarker in cases studied presently. Brefeldin, the known inhibitor of EPAC, though the mechanism yet unexplored, has been the molecule used as the pharmacophore for creation of lead drug molecule. Various modifications have been incorporated into the pharmacophore to increase the hydrophobic interactions for increasing the binding efficiency of the generated lead molecule. Side-chain modifications of the pharmacophore and refinement of data through firedock upon docking of EPAC with the modified pharmacophore yielded best results on the bases of atomic contact energy, van der Waal and partial electrostatic interactions as well as additional estimations of the binding free energy. Modifications of CH3 at C15 with COOH and H at C2 with OH in brefeldin showed the best docking results on the basis of protein-drug interaction parameters. The present work provides a clue in rational design of EPAC inhibitors which could be developed as drug lead in combating CVD.

Molecular docking study of tripeptides VPP and IPP inhibiting angiotensin I converting enzyme to alleviate high altitude pulmonary edema

High altitude pulmonary edema (HAPE) remains the major cause of death related to high altitude exposure with a high mortality in absence of emergency treatment. Due to the deprival of oxygen in higher altitudes, the blood vessels constricts and squeezes blood in the vessels. This makes pressure to go up which in turn forces blood into air pockets in lungs that can kill people with HAPE. Angiotensin Converting Enzyme (ACE) is found in lung capillaries. It catalyses conversion of angiotensin I to angiotensin II which is a potent vasoconstrictor and inactivates bradykinin which is a potent vasodilator thereby causing HAPE. Tripeptides Val-Pro-Pro (VPP) and Ile-Pro-Pro (IPP) act as ACE inhibitors, that reduce vasoconstriction and facilitate vasodilation, so that they can be used in the treatment of HAPE. Enzyme-inhibitor docking is performed between Angiotensin I Converting Enzyme ACE and two natural inhibitors, tripeptides Val-Pro-Pro (VPP) and Ile-Pro-Pro (IPP) using the Patchdock Software. The docking study provided a quantitative energetic measure (Atomic Contact Energy) of 262.56 and 147.73 for ACE inhibition by VPP and IPP respectively. This ensures that the tripeptides Val-Pro-Pro (VPP) and Ile-Pro-Pro (IPP) are able to inhibit the activity of the ACE which in turn can induce decreased formation of Angiotensin II and decreased inactivation of bradykinin thereby it can alleviate HAPE. Key words: High altitude pulmonary edema (HAPE), angiotensin converting enzyme, Val-Pro-Pro, Ile-Pro-Pro, patchdock

ReplicOpter: A replicate optimizer for flexible docking

We present a computationally efficient method for flexible refinement of docking predictions that reflects observed motions within a protein's structural class. Using structural homologs, we derive deformation models that capture likely motions. The models or "replicates" typically align along a rigid core, with a handful of flexible loops, linkers and tails. A few replicates can generate a much larger number of conformers, by exchanging each flexible region independently of the others. In this way, 10 replicates of a protein having 6 flexible regions can be used to generate a million conformations of a molecule. While this has obvious advantages in terms of sampling, the cost of assessing energies at every conformer is prohibitive, particularly when both molecules are flexible. Our approach addresses this combinatorial explosion, using key assumptions to compress the sampling by many orders of magnitude. ReplicOpter can perform hierarchical clustering from a list of rigid docking predictions and find nearby structures to any promising cluster representatives. These predicted complexes can then be refined and rescored. ReplicOpter's scoring function includes a Lennard-Jones potential softened using the Anderson-Chandler-Weeks decomposition, a desolvation term derived from the Atomic Contact Energy function, Coulombic electrostatics, hydrogen bonding, and terms to model pi-pi and pi-cation interactions. ReplicOpter has performed well on several recent CAPRI systems. We are presently benchmarking ReplicOpter on the complete docking benchmark set to fully establish its utility in refining rigid docking predictions and identifying near-native solutions.

Monte Carlo refinement of rigid‐body protein docking structures with backbone displacement and side‐chain optimization

Structures of hitherto unknown protein complexes can be predicted by docking the solved protein monomers. Here, we present a method to refine initial docking estimates of protein complex structures by a Monte Carlo approach including rigid-body moves and side-chain optimization. The energy function used is comprised of van der Waals, Coulomb, and atomic contact energy terms. During the simulation, we gradually shift from a novel smoothed van der Waals potential, which prevents trapping in local energy minima, to the standard Lennard-Jones potential. Following the simulation, the conformations are clustered to obtain the final predictions. Using only the first 100 decoys generated by a fast Fourier transform (FFT)-based rigid-body docking method, our refinement procedure is able to generate near-native structures (interface RMSD <2.5 A) as first model in 14 of 59 cases in a benchmark set. In most cases, clear binding funnels around the native structure can be observed. The results show the potential of Monte Carlo refinement methods and emphasize their applicability for protein-protein docking.

A filter enhanced sampling and combinatorial scoring study for protein docking in CAPRI

Protein-protein docking is usually exploited with a two-step strategy, i.e., conformational sampling and decoy scoring. In this work, a new filter enhanced sampling scheme was proposed and added into the RosettaDock algorithm to improve the conformational sampling efficiency. The filter term is based on the statistical result that backbone hydrogen bonds in the native protein structures are wrapped by more than nine hydrophobic groups to shield them from attacks of water molecules (Fernandez and Scheraga, Proc Natl Acad Sci USA 2003;100:113-118). A combinatorial scoring function, ComScore, specially designed for the other-type protein-protein complexes was also adopted to select the near native docked modes. ComScore was composed of the atomic contact energy, van der Waals, and electrostatic interaction energies, and the weight of each item was fit through the multiple linear regression approach. To analyze our docking results, the filter enhanced sampling scheme was applied to targets T12, T20, and T21 after the CAPRI blind test, and improvements were obtained. The ligand least root mean square deviations (L_rmsds) were reduced and the hit numbers were increased. ComScore was used in the scoring test for CAPRI rounds 9-12 with good success in rounds 9 and 11.

Complex-type-dependent scoring functions in protein–protein docking

A major challenge in the field of protein–protein docking is to discriminate between the many wrong and few near-native conformations, i.e. scoring. Here, we introduce combinatorial complex-type-dependent scoring functions for different types of protein–protein complexes, protease/inhibitor, antibody/antigen, enzyme/inhibitor and others. The scoring functions incorporate both physical and knowledge-based potentials, i.e. atomic contact energy (ACE), the residue pair potential (RP), electrostatic and van der Waals' interactions. For different type complexes, the weights of the scoring functions were optimized by the multiple linear regression method, in which only top 300 structures with ligand root mean square deviation (L_RMSD) less than 20 Å from the bound (co-crystallized) docking of 57 complexes were used to construct a training set. We employed the bound docking studies to examine the quality of the scoring function, and also extend to the unbound (separately crystallized) docking studies and extra 8 protein–protein complexes. In bound docking of the 57 cases, the first hits of protease/inhibitor cases are all ranked in the top 5. For the cases of antibody/antigen, enzyme/inhibitor and others, there are 17/19, 5/6 and 13/15 cases with the first hits ranked in the top 10, respectively. In unbound docking studies, the first hits of 9/17 protease/inhibitor, 6/19 antibody/antigen, 1/6 enzyme/inhibitor and 6/15 others' complexes are ranked in the top 10. Additionally, for the extra 8 cases, the first hits of the two protease/inhibitor cases are ranked in the top for the bound and unbound test. For the two enzyme/inhibitor cases, the first hits are ranked 1st for bound test, and the 119th and 17th for the unbound test. For the others, the ranks of the first hits are the 1st for the bound test and the 12th for the 1WQ1 unbound test. To some extent, the results validated our divide-and-conquer strategy in the docking study, which might hopefully shed light on the prediction of protein–protein interactions.

Despite Having a Common P1 Leu, Eglin C Inhibits α-Lytic Proteinase a Million-fold More Strongly than Does Turkey Ovomucoid Third Domain

Results of the inhibition of alpha-lytic proteinase by two standard mechanism serine proteinase inhibitors, turkey ovomucoid third domain (OMTKY3) and eglin C, and many of their variants are presented. Despite similarities, including an identical P1 residue (Leu) in their primary contact regions, OMTKY3 and eglin C have vastly different association equilibrium constants toward alpha-lytic proteinase, with Ka values of 1.8 x 10(3) and 1.2 x 10(9) M(-1), respectively. Although 12 of the 13 serine proteinases tested in our laboratory for inhibition by OMTKY3 and eglin C are more strongly inhibited by the latter, the million-fold difference observed here with alpha-lytic proteinase is the largest we have seen. The million-fold stronger inhibition by eglin C is retained when the Ka values of the P1 Gly, Ala, Ser, and Ile variants of OMTKY3 and eglin C are compared. Despite the small size of the S1 pocket in alpha-lytic proteinase, interscaffolding additivity for OMTKY3 and eglin C holds well for the four P1 residues tested here. To better understand this difference, we measured Ka values for other OMTKY3 variants, including some that had residues elsewhere in their contact region that corresponded to those of eglin C. Assuming intrascaffolding additivity and using the Ka values obtained for OMTKY3 variants, we designed an OMTKY3-based inhibitor of alpha-lytic proteinase that was predicted to inhibit 10,000-fold more strongly than wild-type OMTKY3. This variant (K13A/P14E/L18A/R21T/N36D OMTKY3) was prepared, and its Ka value was measured against alpha-lytic proteinase. The measured Ka value was in excellent agreement with the predicted one (1.1 x 10(7) and 2.0 x 10(7) M(-1), respectively). Computational protein docking results are consistent with the view that the backbone conformation of eglin C is not significantly altered in the complex with alpha-lytic proteinase. They also show that the strong binding for eglin C correlates well with more favorable atomic contact energy and desolvation energy contributions as compared to OMTKY3.