Current
Computer-Aided Drug Design
ISSN: 1573-4099
OPEN ACCESS PLUS
Contents
Structure-Guided Design of Antibodies, 2010, 6, 128-138
Justin A. Caravella, Deping Wang, Scott M. Glaser
and Alexey Lugovskoy
[Abstract] [Full
Text Article]
Changing Paradigms in Drug Discovery: Scientific Business
Intelligence™ and Workflow Solutions, 2008,
4, 13-22
Shikha Varma-O’Brien, Frank K. Brown,
Andrew LeBeau and Robert D. Brown
[Abstract] [Full
Text Article]
Trends in High-Performance Computing Requirements
for Computer-Aided Drug Design, 2008, 4, 2-12
George Vacek, Dave Mullally and Knute Christensen
[Abstract] [Full
Text Article]
Discovery of Potent Anti-SARS-CoV MPro
Inhibitors, 2007, 3, 191-200
Suzanne Sirois, Rui Zhang, Weina Gao, Hui Gao, Yun Li,
Huiqin Zheng and Dong-Qing Wei
[Abstract] [Full
Text Article]
Structure-Activity Relationships and Rational Design Strategies
for Radical-Scavenging Antioxidants, 2005, 1, 257-273
Hong-Yu Zhang
[Abstract] [Full
Text Article]
Abstracts
[Back to top]
Structure-Guided Design of Antibodies
Justin A. Caravella, Deping Wang, Scott M. Glaser
and Alexey Lugovskoy
[Full
Text Article]
Monoclonal antibodies capable of recognizing antigens with
high affinity and specificity represent a wellestablished
class of biological agents. Since the development of hybridoma
technology in 1975, advances in recombinant DNA technologies
and computational and biophysical methods have allowed us
to develop a better understanding of the relationships between
antibody sequence, structure, and function. These advances
enable us to manipulate antibody sequences with the goal of
improving upon, or creating new biological or biophysical
properties. In this review we will focus on recent successes
in using structure-guided computational methods to design
antibodies and antibody-like molecules with optimized affinity
and specificity to antigen and for enhancing protein stability.
[Back to top]
Changing Paradigms in Drug Discovery: Scientific Business
Intelligence™ and Workflow Solutions
Shikha Varma-O’Brien, Frank K. Brown, Andrew LeBeau
and Robert D. Brown
[Full
Text Article]
Workflow solutions driven by data pipelining are increasingly
becoming popular for accessing, aggregating and analyzing
disparate data to make informed and intelligent decisions.
Uses of workflow technologies which facilitate business intelligence
(BI) improve productivity, decision making and research efficiency.
In order to provide BI in a scientific or clinical based organization,
it is imperative that the application or workflow technology
must be compatible with multiple data types and formats, be
able to analyze the data and make it available throughout
the organization. We term this as Scientific Business Intelligence
(SBI) and discuss how modeling, simulations and informatics
software, integrated with open and standards-based scientific
operating platform (SOP), can deliver scientifically-relevant
BI solutions. We illustrate SBI with several examples encompassing
all levels of users within an organization.
[Back to top]
Trends in High-Performance Computing Requirements
for Computer-Aided Drug Design
George Vacek, Dave Mullally and Knute Christensen
[Full
Text Article]
Computer-aided drug design (CADD) has become a mainstream
component of the drug discovery and development process. High
Performance Computing (HPC) provides the power that allows
CADD researchers to explore more designs in less time, and
some of the greatest improvements in CADD result directly
from advances in HPC. This paper examines some of the more
significant trends in HPC that influence computer-aided drug
design (CADD).
[Back to top]
Discovery of Potent Anti-SARS-CoV MPro
Inhibitors
Suzanne Sirois, Rui Zhang, Weina Gao, Hui Gao, Yun Li,
Huiqin Zheng and Dong-Qing Wei
[Full
Text Article]
SARS is a viral respiratory illness caused by a previously
unrecognized coronavirus, called SARS-associated coronavirus
(SARS-CoV). Because of the potential for a rapid spread of
the disease, it is vitally important to identify drugs that
effectively inhibit a known target of the SARS coronavirus.
Because of its essential role in proteolytic processing, the
main protease MPro, a cysteine
protease, is considered an attractive target for antiviral
drugs against SARS and other coronavirus infections. In this
review, we will present both peptidic and non-peptidic inhibitors
that have been designed against SARS MPro.
The most challenging requirement in designing cysteine inhibitors
is to obtain a selective non-covalent electrophilic isostere
that can react with the catalytic nucleophile. Emphasis will
be put on our recent results, both experimental and theoretical,
in the search for potent wide-spectrum inhibitors. The antiviral
activity of the octopeptide AVLQSGFR against SARS-associated
coronavirus will be presented as well as the recent hits obtained
from virtual high throughput screening (vHTS) based on the
identification of six hydrogen bond pharmacophore points from
KZ7088 docked into the active site of SARS MPro.
[Back to top]
Structure-Activity Relationships and Rational Design
Strategies for Radical-Scavenging Antioxidants
Hong-Yu Zhang
[Full
Text Article]
In the past two decades, there has been growing interest in
finding novel and non-toxic antioxidants to meet the requirements
in chemical, food and pharmaceutical industries. To accelerate
the antioxidant discovery process, various theoretical methods
have been employed to investigate the structure-activity relationships
of antioxidants. Accordingly, some rational-design strategies
for antioxidants have been proposed and applied in practice.
This review summarizes the current knowledge on this topic,
which will be helpful to direct the practice in related fields.
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