Abstract
High-throughput screening and better understanding of small molecule’s structure–activity relationship (SAR) using computational biology techniques have greatly expanded the face of drug discovery process in better discovery of therapeutics for various disease. Small Molecule Modulators Database (SMMDB) includes >1100 small molecules that have been either approved by US Food and Drug Administration, are under investigation or were rejected in clinical trial for any kind of neurological diseases. The comprehensive information about small molecules includes the details about their molecular targets (such as protein or enzyme, DNA, RNA, antisense RNA etc.), pharmacokinetic and pharmacodynamic properties such as binding affinity to their targets (Kd, Ki, IC50 and EC50 if available), mode of action, log P-value, number of hydrogen bond donor and acceptors, their clinical trial status, their 2D and three-dimensional structures etc. To enrich the basic annotation of every small molecule entry present in SMMDB, it is hyperlinked to their description present in PubChem, DrugBank, PubMed and KEGG database. The annotation about their molecular targets was enriched by linking it with UniProt and GenBank and STRING database that can be utilized to study the interaction and relation between various targets involved in single neurological disease. All molecules present in the SMMDB are made available to download in single file and can be further used in establishing the SAR, structure-based drug designing as well as shape-based virtual screening for developing the novel therapeutics against neurological diseases. The scope of this database majorly covers the interest of scientific community and researchers who are engaged in putting their endeavor toward therapeutic development and investigating the pathogenic mechanism of various neurological diseases. The graphical user interface of the SMMDB is accessible on http://bsbe.iiti.ac.in/bsbe/smmdb.
Highlights
Neuron, the structural and functional unit of human nervous system, forms a complex circuit in the body that transmits different signals to perform the cellular activities
Browse option contains the list of small molecule modulators and provide various information such as Small Molecule Modulators Database (SMMDB) ID, their common name and synonyms, 2D structure, disease name and there OMIM identifier, respective Pubmed ID, current clinical trial status, link for the clinical trial database to avail the more information about the clinical studies, PubChem Compound, small molecule target name and mode of action
SMMDB ID is hyperlinked with another page that contains the detailed pharmacokinetic and pharmacodynamics properties of the small molecule modulators such as binding affinity of small molecule with molecular targets (DNA, RNA or Protein), target name and their UniProt, UniGene and Genbank ID, 3D structure, simplified molecular-input line-entry (SMILE) and smiles arbitrary target specification (SMARTS) notation, chemical and IUPAC name, International Chemical Identifier, LogD, molecular formula, molecular mass, molecular solubility, molecular weight, pKa, hydrogen bond acceptor count, hydrogen bond donor count, number of aromatic rings, number of chains, number of rotatable bonds, molecular polar surface area, molecular surface area, dipole magnitude, average bond length, minimized energy, radius of gyration and strain energy
Summary
The structural and functional unit of human nervous system, forms a complex circuit in the body that transmits different signals to perform the cellular activities Any defect in their function leads to various structural or biochemical abnormalities in the brain, spinal cord, and neurons that cause neurological disorders [1,2,3,4]. Modern medicine and advanced combinatorial chemistry owe much of its progress toward disease treatments and cures by developing small molecules as therapeutic candidates Owing to their low molecular weight (10 rotatable bonds are suspected for the poor bioavailability [18] Such molecules can penetrate the blood–brain barrier and provide a leap forward in therapeutic developments for the psychological and neurological disorders. Drugs that discriminately act at neuronal versus peripheral sites typically produce fewer treatment-related adverse events
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