Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

Sastry, G. Madhavi; Adzhigirey, Matvey; Day, Tyler; Annabhimoju, Ramakrishna; Sherman, Woody

doi:10.1007/s10822-013-9644-8

Cited by 4,400 publications

(2,163 citation statements)

References 77 publications

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“…As the optimum pH for peroxygenase activity is 7, the structure was prepared accordingly using Schrodinger's Protein Preparation Wizard (24) and Hϩϩ web server (25). Histidines were ␦-protonated, with the exception of His-82 (ε-protonated) and His-118 and His-251 (double protonated).…”

Section: Methodsmentioning

confidence: 99%

Steroid Hydroxylation by Basidiomycete Peroxygenases: a Combined Experimental and Computational Study

Babot

Río

Cañellas

et al. 2015

Appl Environ Microbiol

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The goal of this study is the selective oxyfunctionalization of steroids under mild and environmentally friendly conditions using fungal enzymes. With this purpose, peroxygenases from three basidiomycete species were tested for the hydroxylation of a variety of steroidal compounds, using H 2 O 2 as the only cosubstrate. Two of them are wild-type enzymes from Agrocybe aegerita and Marasmius rotula, and the third one is a recombinant enzyme from Coprinopsis cinerea. The enzymatic reactions on free and esterified sterols, steroid hydrocarbons, and ketones were monitored by gas chromatography, and the products were identified by mass spectrometry. Hydroxylation at the side chain over the steroidal rings was preferred, with the 25-hydroxyderivatives predominating. Interestingly, antiviral and other biological activities of 25-hydroxycholesterol have been reported recently (M. Blanc et al., Immunity 38:106 -118, 2013, http://dx.doi.org/10.1016/j.immuni.2012.11.004). However, hydroxylation in the ring moiety and terminal hydroxylation at the side chain also was observed in some steroids, the former favored by the absence of oxygenated groups at C-3 and by the presence of conjugated double bonds in the rings. To understand the yield and selectivity differences between the different steroids, a computational study was performed using Protein Energy Landscape Exploration (PELE) software for dynamic ligand diffusion. These simulations showed that the active-site geometry and hydrophobicity favors the entrance of the steroid side chain, while the entrance of the ring is energetically penalized. Also, a direct correlation between the conversion rate and the side chain entrance ratio could be established that explains the various reaction yields observed.

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Section: Methodsmentioning

confidence: 99%

Steroid Hydroxylation by Basidiomycete Peroxygenases: a Combined Experimental and Computational Study

Babot

Río

Cañellas

et al. 2015

Appl Environ Microbiol

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“…[91][92][93][94][95] Initial CODV models are designed by the following 3D-modeling strategy (Fig. S1).…”

Section: Initial Design Of Codv Proteinsmentioning

confidence: 99%

CODV-Ig, a universal bispecific tetravalent and multifunctional immunoglobulin format for medical applications

Steinmetz

Vallée

Beil

et al. 2016

mAbs

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Bispecific immunoglobulins (Igs) typically contain at least two distinct variable domains (Fv) that bind to two different target proteins. They are conceived to facilitate clinical development of biotherapeutic agents for diseases where improved clinical outcome is obtained or expected by combination therapy compared to treatment by single agents. Almost all existing formats are linear in their concept and differ widely in drug-like and manufacture-related properties. To overcome their major limitations, we designed cross-over dual variable Ig-like proteins (CODV-Ig). Their design is akin to the design of circularly closed repeat architectures. Indeed, initial results showed that the traditional approach of utilizing (G4S) x linkers for biotherapeutics design does not identify functional CODV-Igs. Therefore, we applied an unprecedented molecular modeling strategy for linker design that consistently results in CODV-Igs with excellent biochemical and biophysical properties. CODV architecture results in a circular self-contained structure functioning as a self-supporting truss that maintains the parental antibody affinities for both antigens without positional effects. The format is universally suitable for therapeutic applications targeting both circulating and membrane-localized proteins. Due to the full functionality of the Fc domains, serum half-life extension as well as antibody-or complement-dependent cytotoxicity may support biological efficiency of CODV-Igs. We show that judicious choice in combination of epitopes and paratope orientations of bispecific biotherapeutics is anticipated to be critical for clinical outcome. Uniting the major advantages of alternative bispecific biotherapeutics, CODV-Igs are applicable in a wide range of disease areas for fast-track multi-parametric drug optimization.

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“…The modeled structures were prepared for simulation by keeping the crystallographic waters within 4.0 Å of any protein atom but removing the buffer salts from the coordinate file. Next, hydrogen atoms were added to the structure using Protein Preparation Tool from Schrödinger (26), and the optimal protonation states for the ionizable side chains were determined. The hydrogen bonding network of the initial structures was optimized, and by using the Impact refinement module with the OPLS2005 force field, the structures were minimized in vacuum (27).…”

Section: Methodsmentioning

confidence: 99%

Dengue Virus NS2B/NS3 Protease Inhibitors Exploiting the Prime Side

Lin

Ali

Rusere

et al. 2017

J Virol

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The mosquito-transmitted dengue virus (DENV) infects millions of people in tropical and subtropical regions. Maturation of DENV particles requires proper cleavage of the viral polyprotein, including processing of 8 of the 13 substrate cleavage sites by dengue virus NS2B/NS3 protease. With no available direct-acting antiviral targeting DENV, NS2/NS3 protease is a promising target for inhibitor design. Current design efforts focus on the nonprime side of the DENV protease active site, resulting in highly hydrophilic and nonspecific scaffolds. However, the prime side also significantly modulates DENV protease binding affinity, as revealed by engineering the binding loop of aprotinin, a small protein with high affinity for DENV protease. In this study, we designed a series of cyclic peptides interacting with both sides of the active site as inhibitors of dengue virus protease. The design was based on two aprotinin loops and aimed to leverage both key specific interactions of substrate sequences and the entropic advantage driving aprotinin's high affinity. By optimizing the cyclization linker, length, and amino acid sequence, the tightest cyclic peptide achieved a K i value of 2.9 M against DENV3 wild-type (WT) protease. These inhibitors provide proof of concept that both sides of DENV protease active site can be exploited to potentially achieve specificity and lower hydrophilicity in the design of inhibitors targeting DENV.IMPORTANCE Viruses of the flaviviral family, including DENV and Zika virus transmitted by Aedes aegypti, continue to be a threat to global health by causing major outbreaks in tropical and subtropical regions, with no available direct-acting antivirals for treatment. A better understanding of the molecular requirements for the design of potent and specific inhibitors against flaviviral proteins will contribute to the development of targeted therapies for infections by these viruses. The cyclic peptides reported here as DENV protease inhibitors provide novel scaffolds that enable exploiting the prime side of the protease active site, with the aim of achieving better specificity and lower hydrophilicity than those of current scaffolds in the design of antiflaviviral inhibitors.KEYWORDS dengue fever, Zika, antimicrobial peptides, antiviral agents, drug design, protease inhibitors, receptor-ligand interaction, structural biology, substrate D engue virus (DENV), the causative agent of the disease dengue fever, is endemic in more than 110 countries, with approximately 390 million people infected yearly, leading to about 20,000 deaths (1-3). Currently, no direct-acting antiviral drugs are available either in clinics or in development to combat dengue virus infections. Thus, a better understanding of the causative virus and potential viral drug targets is needed to develop effective therapies.DENV is a member of the family Flaviviridae and is an enveloped virus with a positive single-stranded RNA genome. There are four different serotypes (DENV1 to DENV4), and each serotype shares 65 to 70% seque...

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Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

Cited by 4,400 publications

References 77 publications

Steroid Hydroxylation by Basidiomycete Peroxygenases: a Combined Experimental and Computational Study

Steroid Hydroxylation by Basidiomycete Peroxygenases: a Combined Experimental and Computational Study

CODV-Ig, a universal bispecific tetravalent and multifunctional immunoglobulin format for medical applications

Dengue Virus NS2B/NS3 Protease Inhibitors Exploiting the Prime Side

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