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A Rapid Computational Screening of Millions of Molecules to Identify Sequence-Specific DNA Minor Groove Binders via Physicochemical Descriptors

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Biophysical and Computational Tools in Drug Discovery

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

Abstract

DNA has been an attractive target for anticancer, antitumor agents and antibiotics. While the growing number of DNA-drug complexes in structural repositories are yielding molecular insights on DNA-drug recognition principles, identification of distinct sequence-specific electrostatic potentials in the minor and major grooves of DNA has aroused keen interest in designing/identifying molecules which can bind to DNA in a sequence-specific manner. Computational protocols for examining such interactions by means of docking small molecules in the grooves of DNA are accessible. However, with the present compute-intensive docking and scoring protocols, it is nearly impossible to scan millions of molecules for DNA targeted drug discovery. This makes it necessary to develop a rapid screening protocol for scanning millions of molecules to identify potential binders to any DNA sequence of choice. RASDD (RApid Screening of DNA-Drug) is one such utility which utilizes physicochemical properties associated with DNA as well as groove binders to rapidly scan a large library of molecules. The methodology is developed using 30 DNA-drug complexes (R = 0.85) and, when tested on 18 DNA-drug complexes, yielded a correlation (R) of 0.83 between experimental and predicted binding free energies. With RASDD protocol, it is possible to scan a million compounds against a DNA sequence of interest (AT-rich) in ~18s! RASDD is freely accessible at http://www.scfbio-iitd.res.in/software/drugdesign/rasdd.jsp.

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Abbreviations

BMRB:

Biological magnetic resonance bank

CSD:

Cambridge structural database

DNA:

Deoxyribonucleic acid

HADDOCK:

High ambiguity driven protein–protein docking

NDB:

Nucleic acid database

NMR:

Nuclear magnetic resonance

PDBe:

Protein data bank in Europe

PSDDF:

Pathogen specific DNA drug finder

RCSB:

Research Collaboratory for Structural Bioinformatics

RNA:

Ribonucleic acid

PreDDICTA:

Predict DNA–drug interaction strength by computing ΔTm and affinity.

QSAR:

Quantitative structure–activity relationship

NCI:

National Cancer Institute

WI:

Wiener index

LWI:

Ligand Wiener index

LMR:

Ligand molar refractivity

LHD:

Ligand H-bond donor(s)

LHA:

Ligand H-bond acceptor(s)

LP:

Ligand partition coefficient

LC:

Ligand curvature

DC:

DNA minor groove curvature

DMR:

DNA minor groove molar refractivity

DP:

DNA minor groove partition coefficient

COM:

Center of mass

MD:

Molecular dynamics

RASDD:

Rapid screening of DNA-drug

RMS:

Root mean square

GAFF:

Generalized AMBER force field

NAB:

Nucleic acid builder

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Acknowledgments

We thank Ms. Vandana Shekhar for designing the RASDD web-front. We thank Mr. Shashank Shekhar for his help in the implementation of RASDD codes. The authors are also thankful to the Department of Biotechnology, Govt of India, and MEITY & CDAC for their support to the Supercomputing Facility for Bioinformatics and Computational Biology (SCFBIO).

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Authors and Affiliations

  1. Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India

    Pradeep Pant & B. Jayaram

  2. Supercomputing Facility for Bioinformatics and Computational Biology, New Delhi, India

    Pradeep Pant & B. Jayaram

  3. Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India

    B. Jayaram

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  1. Pradeep Pant
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Correspondence to B. Jayaram .

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  1. GIPER, Kashipur, India

    Anil Kumar Saxena

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Funding: The authors gratefully acknowledge funding from the Department of Biotechnology, Govt. of India and the National Supercomputing Mission, administered by MEITY and CDAC, for support to Supercomputing Facility for Bioinformatics and Computational Biology, IIT Delhi.

Ethical Approval: This manuscript presents computational work related to DNA targeted drug discovery, as such, no animal or human studies were performed.

Informed Consent: No patients were studied in this chapter.

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Pant, P., Jayaram, B. (2021). A Rapid Computational Screening of Millions of Molecules to Identify Sequence-Specific DNA Minor Groove Binders via Physicochemical Descriptors. 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_2021_122

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