Form 425

Filed by Ligand Pharmaceuticals Incorporated

Pursuant to Rule 425 under the

Securities Act of 1933

Subject Company: Ligand Pharmaceuticals Incorporated

Commission File No: 001-33093

The following slides will be presented by officers of Ligand Pharmaceuticals Incorporated on September 9, 2009 at the Thomas Weisel Partners Healthcare Conference in Boston, Massachusetts:


1
1
John L. Higgins
President and Chief Executive Officer
Syed Kazmi, Ph.D.
Business Development and Strategic Planning


2
Safe Harbor Statement
The following presentation contains forward-looking statements regarding the proposed
acquisition of Neurogen by Ligand, including projections regarding expectations for
potential research and development payments, savings in operational costs, cash burn
rates, timing of achieving positive cash flow, and potential revenue and profits of a
combined company.
The forward looking statements made in the presentation are subject to several risk
factors, including, but not limited to the reliance on collaborative partners for milestone
and royalty payments, regulatory hurdles facing product candidates, uncertain product
development costs, disputes regarding ownership of intellectual property, the commercial
success of approved products, the failure of Neurogen’s stockholders to approve the
merger, Ligand’s or Neurogen’s inability to satisfy the conditions of the merger, or that
the merger is otherwise delayed or ultimately not consummated, and a failure of the
combined businesses to be integrated successfully.  Additional risks may apply to
forward looking statements made in this presentation.
The risk factors facing Ligand and Neurogen are explained in greater detail in the
Company’s and Neurogen’s filings with the SEC, including the most recently filed annual
reports on Form 10-K and quarterly reports on Form 10-Q, as well as other public filings.


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Additional Information and Where to Find It
Ligand intends to file with the SEC a Registration Statement on Form S-4, which will include a proxy statement of
Neurogen and other relevant materials in connection with the proposed transaction. The proxy statement will be mailed
to the stockholders of Neurogen. Investors and security holders of Neurogen are urged to read the proxy statement and
the other relevant materials when they become available because they will contain important information about Ligand,
Neurogen and the proposed transaction. The proxy statement and other relevant materials (when they become
available), and any other documents filed by Ligand or Neurogen with the SEC, may be obtained free of charge at the
SEC's web site at www.sec.gov. In addition, investors and security holders may obtain free copies of the documents filed
with the SEC by Ligand by going to Ligand’s Investor Relations page on its corporate website at www.ligand.com.
Investors and security holders may obtain free copies of the documents filed with the SEC by Neurogen by going to
Neurogen’s Investor Relations page on its corporate website at www.neurogen.com. Investors and security holders of
Neurogen are urged to read the proxy statement and the other relevant materials when they become available before
making any voting or investment decision with respect to the proposed transaction.
Ligand and its respective directors and executive officers may be deemed to be participants in the solicitation of proxies
from the stockholders of Neurogen in favor of the proposed transaction. Information concerning Ligand’s directors and
executive officers is set forth in Ligand’s proxy statement for its 2008 annual meeting of shareholders, which was filed
with the SEC on April 29, 2008, and annual report on Form 10-K filed with the SEC on March 5, 2008.
Neurogen
and
its
respective
directors
and
executive
officers
may
be
deemed
to
be
participants
in
the
solicitation
of
proxies from the stockholders of Neurogen in favor of the proposed transaction. Information about Neurogen’s executive
officers and directors and their ownership of Neurogen common stock is set forth Neurogen’s amended annual report on
Form
10-K,
which
was
filed
with
the
SEC
on
April
30,
2009.
Investors
and
security
holders
may
obtain
more
detailed
information regarding the direct and indirect interests of Neurogen and its respective executive officers and directors in
the acquisition by reading the proxy statement regarding the merger, which will be filed with the SEC.


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Fundamentals of a Strong Biotech Company
Strong balance sheet
Spending discipline
Strong discovery capabilities and track record
Robust pipeline of partnerable
assets
Revenue diversity
Operating structure that has the potential to
generate substantial cash flows and profitability


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Ligand Company Overview
Company with great assets
-
Two royalty streams, plus two more royalty-bearing products recently approved
-
Ten pharma
deals with over 21 development programs and over $600 million of
potential milestones
-
Prolific drug discovery engine has produced multitudes of drug candidates
Highly successful drug discovery capabilities
-
Focus on early-stage drug discovery and development
-
Partner pipeline assets at earliest value inflection point
Leadership focused on shareholders and market credibility
-
Cost-efficient R&D business with tight spending discipline
-
Clear communication and transparency with investors
-
Clarity on how to drive a business forward in this market environment
Commitment to driving shareholder value and to transparency on the business
with goal to drive strong cash flow and earnings


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Ligand –
Recent events
Signed agreement to acquire Neurogen, public company with drug
screening assets, cash, pipeline and a drug partnership
PROMACTA
®
Phase I/II trial initiated with MDS
CONBRIZA™
approved in Europe for the treatment of osteoporosis
FABLYN®
Approved in Europe for the treatment of osteoporosis
Entered
license
agreement
with
ParinGenix
for
Phase
II
COPD
drug
Completed
lease
buyout,
substantially
reducing
contractual
lease
costs
going forward
Initiated Phase I SARM trial
Wyeth JAK 3 data presented at ACS


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Pending Neurogen Acquisition
Stock-for-Stock Acquisition
Consideration
-
Net proceeds from sale of real  
estate
-
Net proceeds from sale of Aplindore
-
$3 million for Phase III trial initiation
for Merck VR1 program
-
$4 million if license H3 program
CVRs
$11 million in Ligand Common Stock,
plus potential for Four Contingent Value
Rights (CVR)
Transaction Value
4Q 2009
Anticipated Closing Date
Ligand to acquire Neurogen (NRGN)
Deal
Actual timing of the transaction will depend on a number of factors, some of which are beyond either company’s control.


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Opportunity with Neurogen Acquisition
Acquire fully funded research partnership
Merck VR1 program
Access pipeline assets
Numerous opportunities including oral EPO and H3 antagonist
Leverage drug discovery capabilities of both companies
Accelerated Intelligent Drug Design platform
Gain estimated $7 million in net cash
Acquire substantial NOLs
before limitations


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Partnership Highlights


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Significant Value in Royalty Partnerships
Numerous deals with ten pharmaceutical companies
More than 21 different programs being pursued including the largest untapped
markets
Muscle wasting, COPD, thrombocytopenia, pain, asthma, Alzheimer’s
More than $600 million in potential R&D and milestone payments from existing
deals
Ligand has one of the strongest, most diverse royalty partnership rosters
in the small cap biotech universe 


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Pharmaceutical Partnerships


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Combined Product Pipeline


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PROMACTA approved for treatment of
thrombocytopenia in patients with chronic
immune ITP in November 2008.
Two Phase III Hepatitis trials ongoing
Phase III trial in Chronic Liver Disease
ongoing
Phase I/II MDS trial initiated Spring 2009
Phase I Sarcoma trial ongoing
Submitted MAA for the long-term treatment
of ITP in December 2008.
LGD-4665 and other Ligand TPO molecules
licensed to GSK in December 2008
&
Collaboration Highlights


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Thrombocytopenia -
Causes of Disease
Decreased production of platelets
Myelodysplastic
syndrome
Hepatitis C
Cancer in the bone marrow (leukemia)
Aplastic
anemia
Increased destruction of platelets
Autoimmune, such as ITP
Sequestration in the spleen
Drug-induced
Myelosuppression
by chemotherapy regimens
Anti-virals
in Hep
C therapies
Thrombocytopenia is a condition in which there is an abnormally low level of
platelets in the blood. 
Regardless of the underlying cause, thrombocytopenia leads to decreased platelet counts,
which puts patients at greater risk for bleeding and serious adverse events.


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Medical Significance of Thrombocytopenia (US)
(Estimated markets)
Potential
Treatable
Patients
ITP
~60,000
Hepatitis C
~120,000
Chronic Liver Disease                                           
~400,000
Myelodysplastic
syndrome
~20,000
Leukemia / lymphoma
~50,000
Chemotherapy induced thrombocytopenia
~140,000
Intensive care unit –
acquired
~500,000
Bone marrow transplants
~50,000
Lupus
~100,000
Cirrhosis
~113,000
HIV/other
~600,000
~ 2 million platelet transfusions per year


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ParinGenix
License
In June 2009, Ligand granted exclusive license rights to ParinGenix
for three issued U.S. patents relating to certain desulfated heparin
compounds
ParinGenix
lead compound, PGX-100, is an intravenous formulation
of
2-O,
3-O
desulfated
heparin
which
is
in
a
Phase
IIb
trial
for
the
treatment of acute COPD exacerbations (~700,000 patients require
hospitalization every year)
License terms
$350,000 upfront payment
3% royalty on net sales in the US
The transaction adds another potential lucrative royalty stream to
Ligand's already promising list of partnered, fully funded, royalty-
bearing programs


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SERM Collaborations
Bazedoxifene
Monotherapy:   
CONBRIZA approved in Europe in April 2009
Viviant pending approval in the U.S.
Bazedoxifene
in Combination with Premarin
CE (APRELA):
Phase III data published in Fertility and Sterility
NDA planned for in 2010
Lasofoxifene
(FABLYN) for osteoporosis
treatment
Approved in Europe in March 2009 for the
treatment of osteoporosis
NDA pending approval in U.S.; FDA issued
Complete Response Letter in January 2009


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Collaboration Highlights
&
Collaboration began in November 1997
Partnership resulted in lead and back-up
p38 kinase
inhibitor compounds
Anti-inflammatory therapeutics
Ongoing Clinical Trials:
Phase II in rheumatoid arthritis
Phase II in psoriasis
Phase II in atherosclerosis
The Opportunity:
Large, established target markets
If successfully developed, Ligand estimates
product could be on market in 2014  
p38 Kinase
Inhibitors


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&
Collaboration began in October 1998
Collaboration produced multiple drug          
candidates
Completed Clinical Trials:
Phase II in COPD
Phase II in asthma
Phase II in psoriasis
The Opportunity:
Large, established target markets
If successfully developed, Ligand estimates
product could be on market in 2014
Chemokine
Receptor
CXCR2
Program
Collaboration Highlights


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Collaboration Highlights
&
Other Research Program
Ongoing Clinical Trials:
Enzyme inhibitor in Phase II for oncology
Candidate for inflammatory diseases in Phase I
Candidate for respiratory diseases in Phase I
Recent Event:
BACE inhibitor for Alzheimer’s in development,
resulting in a milestone payment of $1 million


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Collaboration Highlights
&
Collaboration began March 2006
Identify and advance molecules in chosen
therapeutic programs to development  
stage
Milestone and Royalty:
7 compounds identified to date
Success-based milestone payments and
up to double-digit royalties upon
commercialization
Seventh lead compound identified resulting in
a milestone payment of $500,000
Broad Discovery Program


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Collaboration Highlights
&
Collaboration began in December 2006
$3 million per year in research funding
Alliance based on development of JAK3
kinase
inhibitors for systemic administration
for immunological and inflammatory
diseases
Success-based milestone payments and
up to double-digit royalties upon
commercialization
JAK-3 Kinase


23
SARM Program Overview


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Selective Androgen Receptor Modulator Program
LGD-4033 is a selective androgen receptor modulator (SARM),
designed to provide the benefits of androgen receptor stimulation on
skeletal muscle and bone without the side effects of the currently
marketed androgens
LGD-4033 has demonstrated increased skeletal muscle mass and
bone mineral density while sparing the prostate in males and
masculinizing
effects in females in preclinical models
A Phase I study was initiated in summer 2009 to evaluate the safety,
tolerability and pharmacokinetic profile of LGD-4033 (expected
completion 1H2010)
Target
Indications:
Sarcopenia
&
frailty,
cachexia,
osteoporosis,
hypogonadism, sexual dysfunction
Market Need:
Convenient, prostate-sparing androgen receptor modulator with
activity in bone, muscle and CNS


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Research Engine


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Ligand Research Platform
Technology
-
Gene reporter assays for nuclear receptors and JAK/STAT-coupled receptors
-
Ultra high-throughput screening platform combined with the world’s largest
proprietary
compound
collection
(5
+
million
compounds)
Highly flexible screening platform: cell-free and cell-based assays; functional and
binding assays
Consistently high rate of success across all classes of targets
Preclinical Development
-
Extensive track record both independently and with partners
-
Total of 48 clinical candidates discovered and 24 INDs
filed
Solid track record for publications
-
Quality journals: Science, Cell, Endocrinology, Journal of Medicinal Chemistry
-
First reports for many important discoveries:
Hematopoietic receptor-targeted small molecule drugs
Non-steroidal selective androgen receptor modulators
Non-steroidal selective progesterone receptor modulators
RXR-selective retinoid


27
Ligand Development & Partnerships
Clinical strategy to run Phase I-II programs through proof-of-concept
13 NDAs
and MAAs
submitted for Ligand discovered drugs
5 approved products from Ligand technology: Targretin, Panretin,
Promacta, Fablyn, Conbriza
Established track record for partnering with over 40 collaborations
with more than 30 different companies
Experience in multiple therapeutic areas
More than 21 different programs being pursued including the largest
untapped markets
Muscle wasting, COPD, thrombocytopenia, pain, asthma, osteoporosis,
Alzheimer’s


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Pro Forma Financial Forecast
* Assumes Neurogen Acquisition closes in Q4 2009
Projected to have approximately $50 million in cash at year-end 2009
Given our current outlook on the combined businesses, 2010 pro forma operating
business projected to be approximately cash-flow neutral with expenses in line with
revenue
Potential for additional revenue and cash infusion from new license agreements
More than $500 million in potential Net Operating Loss carry-forwards before
limitations
Robustly capitalized company that
has sufficient cash
to make it to profitability without additional financings


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Potential Near-Term Milestone and Events
Completion of Schering Plough CXCR2 Trial in COPD
Compound nomination from JAK-3 program by Wyeth for pre-clinical
development
Compound nomination by GSK from drug discovery collaboration
Nomination of Oral EPO drug candidate
VIVIANT FDA Action
Potential for over $10 million in milestone payments from existing
collaborations
Milestone or Event
SARM Phase I trial completion
PROMACTA EU NDA Action
PROMACTA data at ASH