Software based approaches for drug designing and development: A systematic review on commonly used software and its applications

Jamkhande, Prasad G.; Ghante, Mahavir H.; Ajgunde, Balaji R.

doi:10.1016/j.bfopcu.2017.10.001

Cited by 34 publications

(18 citation statements)

References 16 publications

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“…However, to realize the full potential of LASER ART, formulations in development must be appropriately screened based upon drug biodistribution and ease of drug penetration into tissue viral reservoirs. While computerized simulations were developed due to the inherent complexity of particle drug parameters this has not proven beneficial [49, 50]. This is based on broad differences in the drug properties, the size, shape and charge of the composed particle, the prodrug lipophilicity, composition and hydrophobicity, the drug loading, encasement and decorations and the inherent tissue and cell physicochemical properties [19, 51].…”

Section: Discussionmentioning

confidence: 99%

Bioimaging predictors of rilpivirine biodistribution and antiretroviral activities

et al. 2018

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Antiretroviral therapy (ART) has changed the outcome of human immunodeficiency virus type one (HIV-1) infection from certain death to a life free of disease co-morbidities. However, infected people must remain on life-long daily ART. ART reduces but fails to eliminate the viral reservoir. In order to improve upon current treatment regimens, our laboratory created long acting slow effective release (LASER) ART nanoformulated prodrugs from native medicines. LASER ART enables antiretroviral drugs (ARVs) to better reach target sites of HIV-1 infection while, at the same time, improve ART's half-life and potency. However, novel ARV design has been slowed by prolonged pharmacokinetic testing requirements. To such ends, tri-modal theranostic nanoparticles were created with single-photon emission computed tomography (SPECT/CT), magnetic resonance imaging (MRI) and fluorescence capabilities to predict LASER ART biodistribution. The created theranostic ARV probes were then employed to monitor drug tissue distribution and potency. Intrinsically Indium (In) radiolabeled, europium doped cobalt-ferrite particles and rilpivirine were encased in a polycaprolactone core surrounded by a lipid shell (InEuCF-RPV). Particle cell and tissue distribution, and antiretroviral activities were sustained in macrophage tissue depots. InEuCF-PCL/RPV particles injected into mice demonstrated co-registration of MRI and SPECT/CT tissue signals with RPV and cobalt. Cell and animal particle biodistribution paralleled ARV activities. We posit that particle selection can predict RPV distribution and potency facilitated by multifunctional theranostic nanoparticles.

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Section: Discussionmentioning

confidence: 99%

Bioimaging predictors of rilpivirine biodistribution and antiretroviral activities

et al. 2018

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“…have proposed a parallel molecular docking simulation based on CPU–GPU heterogeneous computing, which could enhance the simulation speed and finally speed up the drug development. More details about the molecular docking simulations can be found in some recent Reviews …”

Section: Modeling and Simulation Methodsmentioning

confidence: 99%

Multiscale Modeling and Simulation of Nano‐Carriers Delivery through Biological Barriers—A Review

Shi

Tian

2018

Advcd Theory and Sims

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The past several decades have witnessed the explosion of nanomedicine for cancer therapy, where notable research efforts have been made in synthesizing and delivering nano-carriers (NCs) to specific tumor sites. The effective treatment of cancer with nanomedicine poses the requirements of high solubility, prolonged circulation, low toxicity, strong targeting ability, specific distribution, and high tissue penetration capability of NCs, involving interdisciplinary research and posing challenges to the community. Along with experimental contributions for the development and application of NCs to treat cancer, multiscale modeling and simulation have also made considerable contributions to the understanding of the synthesis, translocation, and delivery of NCs and their payloads. Here, recent advances of modeling and simulation work are selected to elucidate some key concepts, methods, and applications of NCs during synthesis and drug delivery, such as assembly, translocation, targeting, cellular uptake, and penetration in tissue. The advantages and limitations of each method are highlighted, and the future perspectives in this field are also discussed.

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“…The types of software include, AutoDock, DOCK, GOLD, ICM, Glide, Surflex, Affinity, LigandFit, Discovery Studio and many others are well-reviewed in the literature [102,104,105]. The most recent docking programs in the last 5 years are CABS-dock, FlexAID, GalaxyPepDock, LightDock and MOLS 2.0 [106][107][108][109][110].…”

Section: Pinpointing the Biding Sies With Molecular Docking Simulationsmentioning

confidence: 99%

Molecular Functionality of Plant Proteins from Low- to High-Solid Systems with Ligand and Co-Solute

Paramita¹,

Panyoyai

Kasapis

2020

IJMS

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In the food industry, proteins are regarded as multifunctional systems whose bioactive hetero-polymeric properties are affected by physicochemical interactions with the surrounding components in formulations. Due to their nutritional value, plant proteins are increasingly considered by the new product developer to provide three-dimensional assemblies of required structure, texture, solubility and interfacial/bulk stability with physical, chemical or enzymatic treatment. This molecular flexibility allows them to form systems for the preservation of fresh food, retention of good nutrition and interaction with a range of microconstituents. While, animal- and milk-based proteins have been widely discussed in the literature, the role of plant proteins in the development of functional foods with enhanced nutritional profile and targeted physiological effects can be further explored. This review aims to look into the molecular functionality of plant proteins in relation to the transport of bioactive ingredients and interaction with other ligands and proteins. In doing so, it will consider preparations from low- to high-solids and the effect of structural transformation via gelation, phase separation and vitrification on protein functionality as a delivery vehicle or heterologous complex. Applications for the design of novel functional foods and nutraceuticals will also be discussed.

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Software based approaches for drug designing and development: A systematic review on commonly used software and its applications

Cited by 34 publications

References 16 publications

Bioimaging predictors of rilpivirine biodistribution and antiretroviral activities

Bioimaging predictors of rilpivirine biodistribution and antiretroviral activities

Multiscale Modeling and Simulation of Nano‐Carriers Delivery through Biological Barriers—A Review

Molecular Functionality of Plant Proteins from Low- to High-Solid Systems with Ligand and Co-Solute

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