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Relativistic Quantum Chemical and Molecular Dynamics Techniques for Medicinal Chemistry of Bioinorganic Compounds

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Biophysical and Computational Tools in Drug Discovery

Part of the book series: Topics in Medicinal Chemistry ((TMC,volume 37))

Abstract

In this chapter we review relativistic quantum chemical and molecular dynamics techniques focused on drug discovery and predictive toxicology pertinent to bioinorganic compounds and chelates. We consider transition metal complexes of interest for therapeutic interventions of Alzheimer’s disease and several forms of cancer, especially ovarian and breast cancers. Hence transition metal complexes of curcumin, several analogs of cisplatin, and other second and third row transition metal complexes are highlighted as candidates for treating such diseases and in computer aided drug discovery. Next we have demonstrated the utility of relativistic quantum chemical tools for the studies of lanthanide complexes such as Gd(III) complexes with a number of multidentate ligands which are candidates for highly contrasting agents in MRI and Ce(III)/Eu(III)/Sm(III) complexes as a promising novel line of drugs for tuberculosis. We have also considered a variety of actinide complexes of interest in predictive toxicology and environmental bioremediation elucidating detailed mechanisms of interactions of uranyl and plutonyl ions with human serum protein transferrin and related microbial complexes of actinides exemplifying the significance of such relativistic techniques, especially in the context of medicinal chemistry and drug discovery involving the interactions of actinides with proteins and cells. We have not only reviewed relativistic quantum techniques but also hybrid computational techniques such as QM/MM ONIOM methods, quantum chemical optimization of geometries complexes, and hybrid quantum molecular dynamics methods for providing insights into protein–metal complex/chelate interactions. It is shown that one needs to consider multiple site or allosteric binding approaches to drug discovery in conjunction with relativistic quantum chemical studies even if they are carried out at relatively lower levels such as relativistic effective core potentials combined with density functional level of theory.

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Abbreviations

AC-Phos:

Acetamide phosphonate silane

AFM:

Atomic force microscopy

BBB:

Blood–brain barrier

CGDn:

Gd(III)-fullerene complex: C60-(Gd-DOTA)n (n = 4–5)

CoMFA:

Comparative molecular field analysis

CoMSIA:

Comparative molecular similarly indices analysis

COVID-19:

Corona virus disease-2019

CP2K:

Car-parrinello 2K adaptation of car-parrinello molecular dynamics

CPMD:

Car-parrinello molecular dynamics

CPMD/CMD:

Hybrid Car-parrinello molecular dynamics/classical molecular dynamics

DF:

Dirac-Fock computations

DOTA:

Dodecane tetraacetic acid

DTPA:

Diethylenetriaminepentaacetic acid

EDTA:

Ethylenediaminetetraacetic acid

FTIR:

Fourier transform infrared spectroscopy

H3L:

2,6-Diformyl-4-methylphenol-di(benzoylhydrazone)

HCV:

Hepatitis type C virus

HOMO:

Highest occupied molecular orbital

HOPO(3.4):

3-Hydroxy-4(1H)-pyridinone

LUMO:

Lowest unoccupied molecular orbital

MD:

Molecular dynamics

MEP:

Molecular electro static potentials

MM:

Molecular mechanics

MRI:

Magnetic resonance imaging

NNI:

Non-nucleotide inhibitors

NS5B:

Nonstructural protein 5B (NS5B) polymerase

QM/MM:

Quantum mechanics/molecular mechanics

QMSA:

Quantitative molecular similarity analysis

QSAR:

Quantitative structure activity relationship

QshAR:

Quantitative shape-activity relationship

RECP:

Relativistic effective potentials

SARS-COV-2:

Severe acute respiratory syndrome coronavirus 2

SO:

Spin-orbit coupling

T1:

Longitudinal relaxation time

T2:

Transverse relaxation time

TESPMA:

Triethoxysilylpropylmaleamic acid

TF:

Transferrin (apotransferrin)

UDP-GDH:

UDP-glucose dehydrogenase

UGT:

UDP-glucuronosyltransferase

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Acknowledgement

This review is dedicated to the fond memory of Professor Heino Nitsche of Lawrence Berkeley Lab and UC Berkeley, my collaborator and a pioneer in experimental actinide chemistry. The author was significantly benefited by numerous discussions and interactions with Prof Nitsche and his research group, especially with regard to actinide complexes.

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  1. School of Molecular Sciences, Arizona State University, Tempe, AZ, USA

    Krishnan Balasubramanian

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  1. Krishnan Balasubramanian
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Correspondence to Krishnan Balasubramanian .

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  1. GIPER, Kashipur, India

    Anil Kumar Saxena

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Balasubramanian, K. (2021). Relativistic Quantum Chemical and Molecular Dynamics Techniques for Medicinal Chemistry of Bioinorganic Compounds. In: Saxena, A.K. (eds) Biophysical and Computational Tools in Drug Discovery. Topics in Medicinal Chemistry, vol 37. Springer, Cham. https://doi.org/10.1007/7355_2020_109

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